Query 045384
Match_columns 194
No_of_seqs 209 out of 1470
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 12:41:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045384.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045384hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03091 hypothetical protein; 100.0 1.5E-38 3.2E-43 278.2 15.2 120 1-121 1-120 (459)
2 PLN03212 Transcription repress 100.0 4.3E-38 9.2E-43 258.4 15.2 119 3-122 14-132 (249)
3 KOG0048 Transcription factor, 100.0 9.7E-37 2.1E-41 254.0 12.3 112 10-121 4-115 (238)
4 KOG0049 Transcription factor, 99.8 2.8E-21 6E-26 175.3 10.2 117 2-120 348-465 (939)
5 KOG0049 Transcription factor, 99.8 5.8E-20 1.3E-24 166.8 9.6 113 7-119 245-412 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 6.8E-18 1.5E-22 111.7 6.8 60 18-79 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 2.7E-16 5.9E-21 142.1 7.1 107 11-118 16-122 (512)
8 KOG0050 mRNA splicing protein 99.6 2.6E-16 5.7E-21 140.1 6.5 106 13-120 5-110 (617)
9 PF00249 Myb_DNA-binding: Myb- 99.6 2E-15 4.4E-20 95.7 4.8 48 15-62 1-48 (48)
10 KOG0051 RNA polymerase I termi 99.5 1.9E-14 4.2E-19 131.4 8.9 108 8-120 379-514 (607)
11 PF00249 Myb_DNA-binding: Myb- 99.5 5.2E-14 1.1E-18 89.2 5.4 46 68-113 1-48 (48)
12 PLN03212 Transcription repress 99.3 3.1E-13 6.6E-18 111.7 2.3 58 7-66 70-127 (249)
13 PF13921 Myb_DNA-bind_6: Myb-l 99.3 7.7E-13 1.7E-17 87.3 3.6 46 71-116 1-46 (60)
14 smart00717 SANT SANT SWI3, AD 99.3 3.5E-12 7.6E-17 79.4 5.3 47 68-114 1-48 (49)
15 smart00717 SANT SANT SWI3, AD 99.3 5.7E-12 1.2E-16 78.4 5.2 48 15-63 1-48 (49)
16 PLN03091 hypothetical protein; 99.3 1.7E-12 3.7E-17 114.8 3.4 56 7-64 59-114 (459)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 3.5E-11 7.6E-16 73.6 5.7 43 70-112 1-44 (45)
18 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 4.6E-11 1E-15 73.1 4.8 45 17-62 1-45 (45)
19 KOG0048 Transcription factor, 99.1 3.8E-11 8.1E-16 100.2 4.7 56 6-63 53-108 (238)
20 KOG0051 RNA polymerase I termi 99.0 8.1E-10 1.8E-14 101.4 7.7 102 13-116 306-431 (607)
21 COG5147 REB1 Myb superfamily p 98.5 8.1E-08 1.8E-12 87.5 4.5 104 7-113 64-167 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.3 1.2E-06 2.5E-11 57.5 5.0 48 15-62 3-54 (57)
23 KOG0457 Histone acetyltransfer 98.1 2.5E-06 5.5E-11 75.7 4.8 50 12-62 69-118 (438)
24 PF13325 MCRS_N: N-terminal re 97.9 9.5E-05 2.1E-09 60.1 9.9 100 17-118 1-131 (199)
25 TIGR01557 myb_SHAQKYF myb-like 97.8 7.1E-05 1.5E-09 49.0 5.7 46 68-113 3-54 (57)
26 KOG0050 mRNA splicing protein 97.8 2.6E-05 5.6E-10 70.7 4.1 57 66-122 5-62 (617)
27 COG5259 RSC8 RSC chromatin rem 97.7 3.5E-05 7.6E-10 69.1 4.1 46 14-61 278-323 (531)
28 KOG0457 Histone acetyltransfer 97.6 8.3E-05 1.8E-09 66.2 5.6 48 66-113 70-118 (438)
29 TIGR02894 DNA_bind_RsfA transc 97.6 9.5E-05 2.1E-09 57.9 5.2 53 67-120 3-62 (161)
30 KOG1279 Chromatin remodeling f 97.5 0.0001 2.2E-09 67.5 4.4 47 13-61 251-297 (506)
31 TIGR02894 DNA_bind_RsfA transc 97.5 8.2E-05 1.8E-09 58.2 2.9 71 13-85 2-94 (161)
32 PF08914 Myb_DNA-bind_2: Rap1 97.4 0.0002 4.3E-09 48.1 3.7 52 15-66 2-61 (65)
33 PF08914 Myb_DNA-bind_2: Rap1 97.4 0.00028 6.1E-09 47.4 4.3 50 68-117 2-61 (65)
34 COG5259 RSC8 RSC chromatin rem 97.4 0.00023 4.9E-09 64.0 4.8 44 68-111 279-322 (531)
35 KOG1279 Chromatin remodeling f 97.3 0.00042 9E-09 63.6 5.3 45 67-111 252-296 (506)
36 PF13837 Myb_DNA-bind_4: Myb/S 97.2 0.00064 1.4E-08 47.6 4.4 49 69-117 2-68 (90)
37 COG5114 Histone acetyltransfer 97.1 0.0004 8.6E-09 59.9 3.2 48 15-63 63-110 (432)
38 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.00041 8.9E-09 48.6 2.5 47 16-62 2-64 (90)
39 PF13873 Myb_DNA-bind_5: Myb/S 96.8 0.0017 3.6E-08 44.6 3.9 49 14-62 1-69 (78)
40 PRK13923 putative spore coat p 96.7 0.0029 6.2E-08 50.2 5.1 53 66-119 3-62 (170)
41 PRK13923 putative spore coat p 96.7 0.0011 2.5E-08 52.5 2.7 50 12-63 2-57 (170)
42 PF13873 Myb_DNA-bind_5: Myb/S 96.5 0.011 2.5E-07 40.4 6.0 49 68-116 2-72 (78)
43 PLN03142 Probable chromatin-re 96.3 0.034 7.3E-07 55.4 10.2 103 17-120 826-991 (1033)
44 COG5114 Histone acetyltransfer 96.2 0.0064 1.4E-07 52.6 4.2 46 68-113 63-109 (432)
45 PF09111 SLIDE: SLIDE; InterP 94.5 0.095 2.1E-06 39.3 5.2 53 65-117 46-114 (118)
46 KOG2656 DNA methyltransferase 94.4 0.047 1E-06 48.4 3.8 54 68-121 130-189 (445)
47 COG5118 BDP1 Transcription ini 94.0 0.1 2.2E-06 46.3 5.0 43 69-111 366-408 (507)
48 PF09111 SLIDE: SLIDE; InterP 93.9 0.092 2E-06 39.3 4.0 49 12-60 46-108 (118)
49 PF12776 Myb_DNA-bind_3: Myb/S 93.4 0.28 6E-06 34.5 5.8 47 70-116 1-65 (96)
50 KOG4282 Transcription factor G 93.2 0.32 6.9E-06 42.5 7.0 53 68-120 54-120 (345)
51 KOG1194 Predicted DNA-binding 93.0 0.26 5.5E-06 44.7 6.0 48 67-114 186-233 (534)
52 PF08281 Sigma70_r4_2: Sigma-7 92.5 0.5 1.1E-05 29.6 5.4 41 73-114 12-52 (54)
53 COG5118 BDP1 Transcription ini 92.5 0.16 3.5E-06 45.0 4.0 45 15-61 365-409 (507)
54 KOG4282 Transcription factor G 91.5 0.25 5.4E-06 43.2 4.1 48 16-63 55-114 (345)
55 PF12776 Myb_DNA-bind_3: Myb/S 89.7 0.77 1.7E-05 32.1 4.7 44 17-60 1-60 (96)
56 PF11626 Rap1_C: TRF2-interact 89.4 0.48 1E-05 33.3 3.3 30 11-43 43-80 (87)
57 KOG4167 Predicted DNA-binding 89.2 1.4 3E-05 42.4 7.0 46 68-113 619-664 (907)
58 PF13404 HTH_AsnC-type: AsnC-t 86.2 1.5 3.2E-05 26.6 3.7 38 21-60 3-40 (42)
59 PF13404 HTH_AsnC-type: AsnC-t 86.1 2.1 4.6E-05 25.9 4.3 38 74-112 3-41 (42)
60 PF04545 Sigma70_r4: Sigma-70, 85.9 3 6.4E-05 25.7 5.1 41 74-115 7-47 (50)
61 KOG4167 Predicted DNA-binding 83.9 1.4 3E-05 42.4 4.1 44 15-60 619-662 (907)
62 smart00595 MADF subfamily of S 83.9 2.7 5.9E-05 28.9 4.7 28 89-117 29-56 (89)
63 KOG4468 Polycomb-group transcr 82.7 2.6 5.6E-05 39.7 5.2 49 68-116 88-146 (782)
64 PRK11179 DNA-binding transcrip 80.7 4.4 9.5E-05 31.2 5.3 43 74-117 9-52 (153)
65 PRK11179 DNA-binding transcrip 78.0 3.5 7.6E-05 31.7 4.0 44 21-66 9-52 (153)
66 PRK11169 leucine-responsive tr 77.0 5.6 0.00012 31.0 4.9 45 73-118 13-58 (164)
67 PF07750 GcrA: GcrA cell cycle 75.1 4.3 9.3E-05 32.0 3.7 41 70-111 2-42 (162)
68 PF04504 DUF573: Protein of un 74.8 8.5 0.00018 27.7 5.0 52 69-120 5-69 (98)
69 TIGR02985 Sig70_bacteroi1 RNA 73.4 9 0.00019 28.5 5.1 30 85-115 127-156 (161)
70 PRK11169 leucine-responsive tr 73.2 4.6 9.9E-05 31.5 3.5 45 20-66 13-57 (164)
71 KOG4329 DNA-binding protein [G 72.8 7.6 0.00016 34.7 5.0 44 69-112 278-322 (445)
72 PF11035 SnAPC_2_like: Small n 72.5 20 0.00043 31.4 7.4 49 68-116 21-73 (344)
73 PLN03142 Probable chromatin-re 70.8 6.4 0.00014 39.7 4.7 47 13-59 924-981 (1033)
74 KOG2656 DNA methyltransferase 70.3 3.7 7.9E-05 36.8 2.5 49 13-62 128-181 (445)
75 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 69.6 12 0.00027 23.6 4.2 34 75-109 8-41 (50)
76 smart00501 BRIGHT BRIGHT, ARID 68.2 5.8 0.00013 27.8 2.8 41 24-64 35-86 (93)
77 PF01388 ARID: ARID/BRIGHT DNA 67.9 3.9 8.4E-05 28.5 1.9 41 24-64 39-90 (92)
78 PF13325 MCRS_N: N-terminal re 67.1 13 0.00028 30.3 5.0 44 70-114 1-47 (199)
79 cd08319 Death_RAIDD Death doma 65.8 11 0.00023 26.4 3.7 30 76-106 2-31 (83)
80 smart00595 MADF subfamily of S 65.5 4.2 9.1E-05 27.9 1.6 22 38-61 30-51 (89)
81 KOG1194 Predicted DNA-binding 65.4 11 0.00024 34.5 4.6 48 70-117 371-418 (534)
82 TIGR02937 sigma70-ECF RNA poly 65.4 18 0.00039 26.1 5.2 34 81-115 120-153 (158)
83 PF11035 SnAPC_2_like: Small n 64.5 82 0.0018 27.7 9.5 95 5-113 11-126 (344)
84 cd08311 Death_p75NR Death doma 63.5 10 0.00022 26.1 3.2 34 73-108 2-35 (77)
85 KOG2009 Transcription initiati 63.4 7.9 0.00017 36.5 3.4 44 68-111 409-452 (584)
86 PF11626 Rap1_C: TRF2-interact 62.7 7.8 0.00017 27.1 2.6 17 64-80 43-59 (87)
87 COG2197 CitB Response regulato 62.5 15 0.00033 29.8 4.6 45 69-116 147-191 (211)
88 PF10545 MADF_DNA_bdg: Alcohol 62.4 13 0.00027 24.8 3.6 29 89-117 28-57 (85)
89 cd08803 Death_ank3 Death domai 62.0 15 0.00033 25.6 3.9 31 76-107 4-34 (84)
90 PF00196 GerE: Bacterial regul 61.5 15 0.00033 23.1 3.6 44 70-116 3-46 (58)
91 PRK04217 hypothetical protein; 60.6 24 0.00053 26.0 5.0 45 70-116 42-86 (110)
92 PF01388 ARID: ARID/BRIGHT DNA 59.8 28 0.0006 24.0 5.1 38 78-115 40-90 (92)
93 PF07638 Sigma70_ECF: ECF sigm 59.2 28 0.00061 27.4 5.6 35 78-113 142-176 (185)
94 PF10545 MADF_DNA_bdg: Alcohol 59.1 6.3 0.00014 26.4 1.5 25 38-62 29-53 (85)
95 PRK09643 RNA polymerase sigma 58.8 38 0.00083 26.6 6.3 29 85-114 148-176 (192)
96 cd06171 Sigma70_r4 Sigma70, re 58.7 34 0.00073 19.9 4.8 40 71-112 11-50 (55)
97 cd08317 Death_ank Death domain 58.7 13 0.00029 25.6 3.2 30 76-106 4-33 (84)
98 smart00501 BRIGHT BRIGHT, ARID 58.5 29 0.00062 24.2 5.0 39 78-116 36-87 (93)
99 smart00344 HTH_ASNC helix_turn 57.5 19 0.00042 25.4 4.0 44 21-66 3-46 (108)
100 PF13936 HTH_38: Helix-turn-he 57.4 16 0.00034 22.0 3.0 36 70-107 4-39 (44)
101 PRK09652 RNA polymerase sigma 57.2 32 0.00069 26.1 5.5 30 85-115 142-171 (182)
102 smart00344 HTH_ASNC helix_turn 56.2 36 0.00078 24.0 5.3 43 74-117 3-46 (108)
103 PF08281 Sigma70_r4_2: Sigma-7 55.7 19 0.00041 22.2 3.3 38 20-60 12-49 (54)
104 PRK11924 RNA polymerase sigma 54.9 28 0.00061 26.3 4.8 29 86-115 140-168 (179)
105 cd08318 Death_NMPP84 Death dom 53.6 23 0.00049 24.7 3.7 32 71-106 5-36 (86)
106 PF04504 DUF573: Protein of un 53.5 42 0.00091 24.0 5.1 69 17-85 6-94 (98)
107 PF09197 Rap1-DNA-bind: Rap1, 52.9 25 0.00055 25.7 3.9 46 17-63 1-76 (105)
108 PRK12529 RNA polymerase sigma 52.8 43 0.00094 25.9 5.6 34 85-119 141-174 (178)
109 KOG2009 Transcription initiati 51.5 15 0.00032 34.7 3.1 50 9-60 403-452 (584)
110 cd08804 Death_ank2 Death domai 50.8 26 0.00056 24.3 3.6 31 76-107 4-34 (84)
111 PRK09641 RNA polymerase sigma 50.4 36 0.00078 26.2 4.8 29 86-115 151-179 (187)
112 PF02954 HTH_8: Bacterial regu 50.3 44 0.00096 19.7 4.1 33 75-108 6-38 (42)
113 cd08777 Death_RIP1 Death Domai 48.6 27 0.00058 24.4 3.4 28 79-107 5-32 (86)
114 PRK12524 RNA polymerase sigma 48.6 62 0.0013 25.4 6.0 29 86-115 151-179 (196)
115 PRK09047 RNA polymerase factor 48.6 47 0.001 24.8 5.1 29 86-115 121-149 (161)
116 COG1522 Lrp Transcriptional re 48.0 25 0.00055 26.3 3.5 44 21-66 8-51 (154)
117 PRK09637 RNA polymerase sigma 47.9 44 0.00094 26.1 4.9 30 85-115 120-149 (181)
118 PRK12523 RNA polymerase sigma 47.6 48 0.001 25.3 5.1 31 85-116 133-163 (172)
119 PF07750 GcrA: GcrA cell cycle 47.4 26 0.00056 27.5 3.5 33 17-51 2-35 (162)
120 TIGR02939 RpoE_Sigma70 RNA pol 47.3 34 0.00074 26.4 4.2 28 87-115 154-181 (190)
121 smart00005 DEATH DEATH domain, 47.2 34 0.00073 23.2 3.7 29 76-105 5-34 (88)
122 PRK09642 RNA polymerase sigma 47.0 63 0.0014 24.2 5.6 28 86-114 121-148 (160)
123 KOG3841 TEF-1 and related tran 47.0 99 0.0022 27.9 7.3 53 67-119 75-148 (455)
124 PRK12530 RNA polymerase sigma 46.1 49 0.0011 25.9 5.0 27 86-113 149-175 (189)
125 PRK09648 RNA polymerase sigma 46.1 63 0.0014 25.0 5.6 29 86-115 154-182 (189)
126 KOG4468 Polycomb-group transcr 45.7 23 0.00049 33.7 3.3 47 15-62 88-143 (782)
127 cd08805 Death_ank1 Death domai 45.6 32 0.00069 24.1 3.4 26 76-102 4-29 (84)
128 PF09905 DUF2132: Uncharacteri 45.2 28 0.00062 23.1 2.8 44 23-79 12-62 (64)
129 PRK12531 RNA polymerase sigma 44.9 73 0.0016 24.9 5.8 29 86-115 156-184 (194)
130 TIGR02948 SigW_bacill RNA poly 44.6 46 0.001 25.6 4.6 28 87-115 152-179 (187)
131 TIGR02954 Sig70_famx3 RNA poly 44.5 52 0.0011 25.0 4.8 29 86-115 134-162 (169)
132 cd08779 Death_PIDD Death Domai 44.4 29 0.00062 24.2 3.0 32 77-109 3-37 (86)
133 PF09420 Nop16: Ribosome bioge 44.2 44 0.00095 26.1 4.4 48 13-61 112-162 (164)
134 TIGR02943 Sig70_famx1 RNA poly 43.9 58 0.0013 25.5 5.1 28 86-114 146-173 (188)
135 PRK09645 RNA polymerase sigma 43.7 59 0.0013 24.7 5.0 29 86-115 133-161 (173)
136 PRK00118 putative DNA-binding 43.5 83 0.0018 22.9 5.4 39 74-113 20-58 (104)
137 PRK12512 RNA polymerase sigma 43.3 59 0.0013 25.0 5.1 30 86-116 146-175 (184)
138 COG1522 Lrp Transcriptional re 43.3 64 0.0014 24.1 5.1 45 74-119 8-53 (154)
139 PRK12515 RNA polymerase sigma 42.4 78 0.0017 24.5 5.6 29 86-115 146-174 (189)
140 PRK11923 algU RNA polymerase s 42.0 56 0.0012 25.4 4.7 27 87-114 154-180 (193)
141 PRK12536 RNA polymerase sigma 41.9 80 0.0017 24.4 5.6 31 85-116 143-173 (181)
142 KOG3554 Histone deacetylase co 41.8 34 0.00073 31.7 3.7 42 69-110 286-328 (693)
143 TIGR02952 Sig70_famx2 RNA poly 41.5 66 0.0014 24.2 5.0 28 87-115 138-165 (170)
144 TIGR02999 Sig-70_X6 RNA polyme 41.3 68 0.0015 24.6 5.1 29 86-115 149-177 (183)
145 COG4628 Uncharacterized conser 41.2 32 0.00069 25.7 2.9 44 23-79 21-71 (136)
146 PRK09651 RNA polymerase sigma 41.0 67 0.0014 24.6 5.0 30 87-117 135-164 (172)
147 PRK09649 RNA polymerase sigma 40.4 75 0.0016 24.7 5.2 30 86-116 145-174 (185)
148 PRK06759 RNA polymerase factor 40.0 76 0.0017 23.5 5.1 28 87-115 122-149 (154)
149 PRK12514 RNA polymerase sigma 39.9 70 0.0015 24.5 4.9 28 87-115 145-172 (179)
150 PRK12546 RNA polymerase sigma 39.5 1.1E+02 0.0025 23.9 6.2 30 85-115 127-156 (188)
151 PRK05602 RNA polymerase sigma 39.5 92 0.002 24.0 5.6 29 86-115 143-171 (186)
152 PRK12528 RNA polymerase sigma 39.2 80 0.0017 23.7 5.1 29 86-115 128-156 (161)
153 PRK12527 RNA polymerase sigma 39.1 1.2E+02 0.0025 22.7 6.0 28 87-115 121-148 (159)
154 PF01710 HTH_Tnp_IS630: Transp 38.5 95 0.0021 22.7 5.2 66 8-78 46-111 (119)
155 PF09420 Nop16: Ribosome bioge 37.9 76 0.0017 24.7 4.9 45 68-112 114-162 (164)
156 PRK12547 RNA polymerase sigma 37.5 88 0.0019 23.7 5.1 29 86-115 127-155 (164)
157 TIGR02950 SigM_subfam RNA poly 37.3 27 0.00058 26.0 2.1 28 87-115 121-148 (154)
158 PRK12516 RNA polymerase sigma 37.2 82 0.0018 24.7 5.0 29 85-114 130-158 (187)
159 PRK15201 fimbriae regulatory p 36.5 1.3E+02 0.0027 24.5 5.8 45 69-116 132-176 (198)
160 PRK12532 RNA polymerase sigma 35.7 1.2E+02 0.0027 23.6 5.8 27 86-113 151-177 (195)
161 TIGR02983 SigE-fam_strep RNA p 35.4 89 0.0019 23.4 4.8 37 79-116 118-154 (162)
162 COG2963 Transposase and inacti 35.3 1.3E+02 0.0029 21.5 5.5 46 68-115 5-51 (116)
163 PRK12542 RNA polymerase sigma 35.2 93 0.002 24.0 5.0 29 86-115 137-165 (185)
164 PRK13919 putative RNA polymera 34.6 97 0.0021 23.8 5.0 28 87-115 151-178 (186)
165 PRK15411 rcsA colanic acid cap 34.4 82 0.0018 25.2 4.7 44 70-116 137-180 (207)
166 PRK12520 RNA polymerase sigma 34.4 98 0.0021 24.0 5.1 27 87-114 147-173 (191)
167 cd08306 Death_FADD Fas-associa 34.0 70 0.0015 22.2 3.7 25 81-106 7-31 (86)
168 PRK10100 DNA-binding transcrip 34.0 1.1E+02 0.0025 24.7 5.5 44 70-116 155-198 (216)
169 PRK12545 RNA polymerase sigma 33.9 97 0.0021 24.5 5.0 25 87-112 155-179 (201)
170 PRK09647 RNA polymerase sigma 33.9 1.4E+02 0.003 23.8 5.9 29 87-116 154-182 (203)
171 PRK11922 RNA polymerase sigma 33.8 49 0.0011 26.9 3.3 28 87-115 165-192 (231)
172 KOG0384 Chromodomain-helicase 33.5 27 0.00058 35.9 1.9 74 15-95 1133-1207(1373)
173 PRK09646 RNA polymerase sigma 33.4 1.4E+02 0.003 23.3 5.8 28 87-115 158-185 (194)
174 PRK06811 RNA polymerase factor 33.2 1.5E+02 0.0033 23.0 6.0 28 87-115 147-174 (189)
175 PRK12537 RNA polymerase sigma 33.0 1E+02 0.0022 23.7 4.9 29 86-115 148-176 (182)
176 smart00351 PAX Paired Box doma 33.0 2E+02 0.0043 21.2 7.5 73 13-87 13-92 (125)
177 COG5352 Uncharacterized protei 32.1 67 0.0015 24.9 3.5 39 70-109 2-40 (169)
178 PF13384 HTH_23: Homeodomain-l 31.2 66 0.0014 19.2 2.9 28 78-107 9-36 (50)
179 PRK09639 RNA polymerase sigma 30.6 1.2E+02 0.0027 22.6 4.9 29 86-115 126-154 (166)
180 TIGR02984 Sig-70_plancto1 RNA 30.4 1.5E+02 0.0032 22.6 5.4 29 86-115 155-183 (189)
181 PHA01083 hypothetical protein 30.2 77 0.0017 24.7 3.6 67 25-99 5-90 (149)
182 PF13340 DUF4096: Putative tra 30.1 26 0.00056 23.5 0.9 59 37-114 5-66 (75)
183 PF01466 Skp1: Skp1 family, di 30.1 81 0.0018 21.3 3.4 36 38-81 36-71 (78)
184 PRK01905 DNA-binding protein F 30.1 1.6E+02 0.0034 19.9 4.8 35 73-108 36-70 (77)
185 PF01527 HTH_Tnp_1: Transposas 29.7 1.6E+02 0.0034 19.1 4.7 45 68-114 4-48 (76)
186 TIGR02960 SigX5 RNA polymerase 29.6 1E+02 0.0023 26.1 4.8 28 86-114 157-184 (324)
187 PRK06930 positive control sigm 28.4 1.4E+02 0.0031 23.4 5.0 31 84-115 127-157 (170)
188 PRK12519 RNA polymerase sigma 28.2 1.1E+02 0.0024 23.7 4.4 28 87-115 157-184 (194)
189 PF10440 WIYLD: Ubiquitin-bind 28.2 42 0.0009 22.5 1.6 18 78-95 31-48 (65)
190 PRK13858 type IV secretion sys 28.1 1.9E+02 0.0042 22.4 5.5 76 8-97 21-96 (147)
191 PRK06986 fliA flagellar biosyn 28.0 1.7E+02 0.0038 23.7 5.7 30 86-116 199-228 (236)
192 PRK09638 RNA polymerase sigma 27.8 73 0.0016 24.2 3.2 29 86-115 141-169 (176)
193 PRK10360 DNA-binding transcrip 27.8 2E+02 0.0043 21.5 5.7 44 69-115 136-179 (196)
194 PRK09483 response regulator; P 27.5 1.2E+02 0.0027 23.1 4.6 45 69-116 147-191 (217)
195 PRK12525 RNA polymerase sigma 27.5 1.6E+02 0.0035 22.3 5.1 29 87-116 134-162 (168)
196 cd01670 Death Death Domain: a 27.4 82 0.0018 20.6 3.1 25 80-105 3-27 (79)
197 PRK02866 cyanate hydratase; Va 27.4 86 0.0019 24.4 3.5 33 77-110 8-40 (147)
198 PTZ00155 40S ribosomal protein 26.7 3.4E+02 0.0073 21.8 7.0 84 1-88 1-85 (181)
199 PRK12511 RNA polymerase sigma 26.7 1.6E+02 0.0034 23.0 5.0 29 86-115 126-154 (182)
200 TIGR00673 cynS cyanate hydrata 26.4 90 0.002 24.3 3.4 32 77-109 11-42 (150)
201 PRK12541 RNA polymerase sigma 26.4 1.7E+02 0.0038 21.8 5.1 28 87-115 128-155 (161)
202 PRK09636 RNA polymerase sigma 26.4 1.5E+02 0.0031 25.0 5.1 29 86-115 130-158 (293)
203 PRK12544 RNA polymerase sigma 26.2 2E+02 0.0044 22.9 5.7 28 86-114 163-190 (206)
204 PRK12538 RNA polymerase sigma 26.1 1.2E+02 0.0027 24.7 4.5 28 87-115 187-214 (233)
205 TIGR02989 Sig-70_gvs1 RNA poly 26.0 1.8E+02 0.0039 21.5 5.1 25 87-112 127-151 (159)
206 PRK09415 RNA polymerase factor 25.7 1.5E+02 0.0032 22.8 4.6 28 87-115 143-170 (179)
207 COG1168 MalY Bifunctional PLP- 25.7 80 0.0017 28.4 3.4 30 5-36 164-193 (388)
208 PRK00430 fis global DNA-bindin 25.3 2.3E+02 0.0051 20.0 5.2 33 74-107 55-87 (95)
209 TIGR03001 Sig-70_gmx1 RNA poly 25.3 2E+02 0.0043 23.8 5.6 27 87-114 177-203 (244)
210 PF09862 DUF2089: Protein of u 25.2 2.3E+02 0.0051 21.0 5.3 43 72-116 35-77 (113)
211 PF00531 Death: Death domain; 25.0 1.4E+02 0.0031 19.5 3.9 27 79-106 3-30 (83)
212 cd00569 HTH_Hin_like Helix-tur 24.9 1.1E+02 0.0023 15.5 5.0 35 71-107 6-40 (42)
213 PRK07670 RNA polymerase sigma 24.9 1.6E+02 0.0035 24.1 5.0 30 85-115 215-244 (251)
214 PF11084 DUF2621: Protein of u 24.9 96 0.0021 23.7 3.2 54 38-95 29-83 (141)
215 PRK10840 transcriptional regul 24.8 1.4E+02 0.0031 23.3 4.5 45 69-116 149-193 (216)
216 PRK08295 RNA polymerase factor 24.8 1.7E+02 0.0036 22.9 4.9 28 86-114 169-196 (208)
217 TIGR02957 SigX4 RNA polymerase 24.7 1.6E+02 0.0035 24.7 5.0 29 86-115 123-151 (281)
218 PRK12526 RNA polymerase sigma 24.7 1.8E+02 0.0039 23.0 5.1 28 87-115 169-196 (206)
219 KOG4329 DNA-binding protein [G 24.6 1.1E+02 0.0023 27.6 3.9 42 16-59 278-320 (445)
220 TIGR02959 SigZ RNA polymerase 24.3 2E+02 0.0043 21.9 5.1 28 86-114 115-142 (170)
221 cd08312 Death_MyD88 Death doma 24.0 66 0.0014 22.0 2.1 23 84-107 13-35 (79)
222 PRK11475 DNA-binding transcrip 24.0 1.6E+02 0.0034 23.7 4.7 45 69-116 133-177 (207)
223 PRK08241 RNA polymerase factor 23.8 1.4E+02 0.003 25.6 4.5 29 86-115 168-196 (339)
224 TIGR02980 SigBFG RNA polymeras 23.7 1.8E+02 0.0039 23.3 5.0 29 86-115 193-221 (227)
225 PRK13719 conjugal transfer tra 23.7 2.6E+02 0.0057 23.1 5.8 45 69-116 142-186 (217)
226 PRK09644 RNA polymerase sigma 23.5 2.7E+02 0.0059 20.8 5.7 28 86-114 123-150 (165)
227 PRK08301 sporulation sigma fac 23.5 1.8E+02 0.0038 23.5 4.9 27 87-114 198-224 (234)
228 PF00046 Homeobox: Homeobox do 23.3 1.9E+02 0.004 17.6 6.5 45 68-113 4-52 (57)
229 PRK12535 RNA polymerase sigma 23.1 1.8E+02 0.004 22.9 4.8 28 87-115 149-176 (196)
230 PRK12522 RNA polymerase sigma 22.7 2E+02 0.0044 21.7 4.9 27 87-114 135-161 (173)
231 TIGR01018 rpsD_arch ribosomal 21.6 3.6E+02 0.0077 21.3 6.0 81 1-87 1-81 (162)
232 PRK12543 RNA polymerase sigma 21.6 2.2E+02 0.0049 21.7 5.0 26 87-113 133-158 (179)
233 PRK12518 RNA polymerase sigma 21.5 82 0.0018 23.9 2.4 28 87-115 136-163 (175)
234 PRK12540 RNA polymerase sigma 21.4 2.8E+02 0.006 21.5 5.5 27 86-113 126-152 (182)
235 PRK12534 RNA polymerase sigma 21.2 2.2E+02 0.0049 21.8 4.9 28 86-114 152-179 (187)
236 PRK12533 RNA polymerase sigma 20.8 2.7E+02 0.0058 22.5 5.4 28 87-115 150-177 (216)
237 cd00131 PAX Paired Box domain 20.5 3.6E+02 0.0079 19.9 7.2 71 15-87 15-92 (128)
238 PRK12513 RNA polymerase sigma 20.5 1E+02 0.0022 24.0 2.8 27 87-114 155-181 (194)
239 PF05263 DUF722: Protein of un 20.4 2.8E+02 0.0061 21.0 5.0 39 75-115 85-125 (130)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=1.5e-38 Score=278.20 Aligned_cols=120 Identities=54% Similarity=1.028 Sum_probs=116.4
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHH
Q 045384 1 MDKTPCNSQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIM 80 (194)
Q Consensus 1 m~r~~~n~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll 80 (194)
|||++| |.++.++||+||+|||++|+++|++||..+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|+
T Consensus 1 mgr~~C-c~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLL 79 (459)
T PLN03091 1 MGRHSC-CYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLII 79 (459)
T ss_pred CCCCcc-CcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHH
Confidence 999999 9999999999999999999999999999999999999977899999999999999999999999999999999
Q ss_pred HHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHHHHhhh
Q 045384 81 ELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQIKQAE 121 (194)
Q Consensus 81 ~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~~~ 121 (194)
+++..||++|++||++|||||+++|||||+.+++++++...
T Consensus 80 eL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~ 120 (459)
T PLN03091 80 ELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRG 120 (459)
T ss_pred HHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999999999999887643
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=4.3e-38 Score=258.38 Aligned_cols=119 Identities=57% Similarity=1.090 Sum_probs=113.8
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHHH
Q 045384 3 KTPCNSQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIMEL 82 (194)
Q Consensus 3 r~~~n~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~~ 82 (194)
++|| |.++.+++++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.++|+|.+++++||+|||++|+++
T Consensus 14 ~~pc-c~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel 92 (249)
T PLN03212 14 TTPC-CTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRL 92 (249)
T ss_pred CCCC-cccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHH
Confidence 5789 999999999999999999999999999889999999996689999999999999999999999999999999999
Q ss_pred HHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHHHHhhhc
Q 045384 83 HAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQIKQAET 122 (194)
Q Consensus 83 ~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~~~~ 122 (194)
+..||++|+.||+.|||||+++|||||+.++++++.....
T Consensus 93 ~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i 132 (249)
T PLN03212 93 HRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGI 132 (249)
T ss_pred HHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCC
Confidence 9999999999999999999999999999999998776543
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=9.7e-37 Score=253.96 Aligned_cols=112 Identities=57% Similarity=0.972 Sum_probs=107.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHHHHHhhcCc
Q 045384 10 EAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIMELHAKWGNR 89 (194)
Q Consensus 10 ~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~~~~~~G~~ 89 (194)
++.+.||+||+|||++|+++|++||.++|..||+.+|++|++++||.||.|||+|+++++.||+|||.+|++++..+|++
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 34456899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHHHHHHHHhhh
Q 045384 90 WSKIAKHLPGRTDNEIKNFWRTRIQKQIKQAE 121 (194)
Q Consensus 90 W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~~~ 121 (194)
|+.||++|||||+++|||+|++.+++++.+..
T Consensus 84 Ws~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 84 WSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999987765
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.85 E-value=2.8e-21 Score=175.28 Aligned_cols=117 Identities=24% Similarity=0.436 Sum_probs=105.0
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHH
Q 045384 2 DKTPCNSQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIME 81 (194)
Q Consensus 2 ~r~~~n~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~ 81 (194)
+|... +|+|++++|+||++||.+|+.+|++||.+.|.+|-..+| +|+..|||+||.+.|....+.+.||-.||+.||.
T Consensus 348 ~R~~~-~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 348 TRFSH-TLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhee-ccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 56666 899999999999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred HHHhhc-CcHHHHhhhCCCCCHHHHHHHHHHHHHHHHHhh
Q 045384 82 LHAKWG-NRWSKIAKHLPGRTDNEIKNFWRTRIQKQIKQA 120 (194)
Q Consensus 82 ~~~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~~ 120 (194)
+|.+|| ++|.+||..||.||..|...|=..++..++.-.
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k~rl~ 465 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAKLRLA 465 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHHHHHHHHHHHh
Confidence 999999 679999999999999776655544455444433
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.81 E-value=5.8e-20 Score=166.79 Aligned_cols=113 Identities=24% Similarity=0.448 Sum_probs=104.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhh--------------------------------
Q 045384 7 NSQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSC-------------------------------- 54 (194)
Q Consensus 7 n~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc-------------------------------- 54 (194)
|+++|+++|..||.|||++|..+...++..+|..||..+|.+|+.-||
T Consensus 245 n~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~ 324 (939)
T KOG0049|consen 245 NELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITS 324 (939)
T ss_pred hhcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhh
Confidence 789999999999999999999999999999999999999977999999
Q ss_pred ----------------------hhhhhhhcCCCccCCCCCHHHHHHHHHHHHhhcCc-HHHHhhhCCCCCHHHHHHHHHH
Q 045384 55 ----------------------RLRWLNYLRPDVKRGNITPEEQLLIMELHAKWGNR-WSKIAKHLPGRTDNEIKNFWRT 111 (194)
Q Consensus 55 ----------------------r~R~~~~L~p~~~~~~WT~eEd~~Ll~~~~~~G~~-W~~Ia~~l~gRt~~~~knrw~~ 111 (194)
.-||.+.|+|.+++++||.+||.+|+.+|.+||.+ |.+|-..+|||++.||+.||.+
T Consensus 325 ~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~n 404 (939)
T KOG0049|consen 325 INSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTN 404 (939)
T ss_pred ccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHH
Confidence 35777778899999999999999999999999965 9999999999999999999999
Q ss_pred HHHHHHHh
Q 045384 112 RIQKQIKQ 119 (194)
Q Consensus 112 ~l~~~~~~ 119 (194)
.|....+.
T Consensus 405 vL~~s~K~ 412 (939)
T KOG0049|consen 405 VLNRSAKV 412 (939)
T ss_pred HHHHhhcc
Confidence 88766544
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.74 E-value=6.8e-18 Score=111.67 Aligned_cols=60 Identities=43% Similarity=0.810 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHH
Q 045384 18 WTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLI 79 (194)
Q Consensus 18 WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~L 79 (194)
||+|||++|+.+|..||. +|..||+.|| .|++.+|+.||.++|.+.+.+++||++||+.|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999995 6999999997 89999999999999999999999999999986
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=99.64 E-value=2.7e-16 Score=142.08 Aligned_cols=107 Identities=26% Similarity=0.445 Sum_probs=101.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHHHHHhhcCcH
Q 045384 11 AEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIMELHAKWGNRW 90 (194)
Q Consensus 11 p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~~~~~~G~~W 90 (194)
-.++.|.|+..||+.|..+|+.+|+.+|..||..++ .|+++||+.||.++++|.+++..|+.|||..|+.+...+|.+|
T Consensus 16 ~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~w 94 (512)
T COG5147 16 TKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQW 94 (512)
T ss_pred ceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchh
Confidence 356789999999999999999999999999999998 7999999999999999999999999999999999999999999
Q ss_pred HHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q 045384 91 SKIAKHLPGRTDNEIKNFWRTRIQKQIK 118 (194)
Q Consensus 91 ~~Ia~~l~gRt~~~~knrw~~~l~~~~~ 118 (194)
+.||..++|||..+|.+||..++.....
T Consensus 95 stia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 95 STIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhccccCccchHHHHHHHHHHhhhhhc
Confidence 9999999999999999999988887654
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.64 E-value=2.6e-16 Score=140.15 Aligned_cols=106 Identities=23% Similarity=0.509 Sum_probs=100.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHHHHHhhcCcHHH
Q 045384 13 VRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIMELHAKWGNRWSK 92 (194)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~~~~~~G~~W~~ 92 (194)
++.|.|+--||+.|..+|.+||...|+.|++.+. ..+++||+.||..+|+|.+++..|+.|||+.||.+...+...|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 5778999999999999999999999999999998 899999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHHHHHHHHhh
Q 045384 93 IAKHLPGRTDNEIKNFWRTRIQKQIKQA 120 (194)
Q Consensus 93 Ia~~l~gRt~~~~knrw~~~l~~~~~~~ 120 (194)
||..+ |||.++|-.||..++-..+...
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~ 110 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYH 110 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhh
Confidence 99999 9999999999999988776544
No 9
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.58 E-value=2e-15 Score=95.68 Aligned_cols=48 Identities=42% Similarity=0.739 Sum_probs=43.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhc
Q 045384 15 KGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYL 62 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L 62 (194)
|++||+|||++|+++|.+||..+|..||..||.+||+.||+.||.++|
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 689999999999999999998889999999987999999999999875
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.54 E-value=1.9e-14 Score=131.39 Aligned_cols=108 Identities=25% Similarity=0.471 Sum_probs=94.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCC--ccCCCCCHHHHHHHHHHHH-
Q 045384 8 SQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPD--VKRGNITPEEQLLIMELHA- 84 (194)
Q Consensus 8 ~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~--~~~~~WT~eEd~~Ll~~~~- 84 (194)
-+++ .+|+||+||++.|..+|..+|. .|..|++.|| |.+..|++||++|.... .+++.||.||.++|+++|.
T Consensus 379 ~FE~--~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~ 453 (607)
T KOG0051|consen 379 PFEN--KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNE 453 (607)
T ss_pred cccc--ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHH
Confidence 4455 8999999999999999999995 5999999996 99999999999999887 4899999999999999995
Q ss_pred ------hh-------------------cCcHHHHhhhCCCCCHHHHHHHHHHHHHHHHHhh
Q 045384 85 ------KW-------------------GNRWSKIAKHLPGRTDNEIKNFWRTRIQKQIKQA 120 (194)
Q Consensus 85 ------~~-------------------G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~~ 120 (194)
.+ +-.|+.|++.+..|+..+|+.+|..++.......
T Consensus 454 ~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~ 514 (607)
T KOG0051|consen 454 MIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNK 514 (607)
T ss_pred HHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhc
Confidence 23 1269999999999999999999999887665433
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=99.49 E-value=5.2e-14 Score=89.15 Aligned_cols=46 Identities=37% Similarity=0.681 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHhhcCc-HHHHhhhCC-CCCHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGNR-WSKIAKHLP-GRTDNEIKNFWRTRI 113 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~~-W~~Ia~~l~-gRt~~~~knrw~~~l 113 (194)
+++||+|||++|++++.+||.. |..||..|| |||..||++||+.++
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 5789999999999999999988 999999999 999999999998764
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.35 E-value=3.1e-13 Score=111.75 Aligned_cols=58 Identities=22% Similarity=0.374 Sum_probs=53.9
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCc
Q 045384 7 NSQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDV 66 (194)
Q Consensus 7 n~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~ 66 (194)
|+|+|.+++|+||+|||++|++++..||.+ |..||+.|+ +||..+|+.||..+|+..+
T Consensus 70 N~L~P~I~kgpWT~EED~lLlel~~~~GnK-Ws~IAk~Lp-GRTDnqIKNRWns~LrK~l 127 (249)
T PLN03212 70 NYLRPSVKRGGITSDEEDLILRLHRLLGNR-WSLIAGRIP-GRTDNEIKNYWNTHLRKKL 127 (249)
T ss_pred HhhchhcccCCCChHHHHHHHHHHHhcccc-HHHHHhhcC-CCCHHHHHHHHHHHHhHHH
Confidence 579999999999999999999999999965 999999998 9999999999998887543
No 13
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.34 E-value=7.7e-13 Score=87.31 Aligned_cols=46 Identities=43% Similarity=0.782 Sum_probs=39.4
Q ss_pred CCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 71 ITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 71 WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
||+|||++|+++|..||.+|..||+.|+.||+.+|++||...|++.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~ 46 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPK 46 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTT
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCccc
Confidence 9999999999999999999999999996699999999999866543
No 14
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.31 E-value=3.5e-12 Score=79.37 Aligned_cols=47 Identities=45% Similarity=0.850 Sum_probs=43.9
Q ss_pred CCCCCHHHHHHHHHHHHhhc-CcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWG-NRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
+++||++||.+|+.++..|| .+|..||..|++||+.+|++||..+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999988653
No 15
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.29 E-value=5.7e-12 Score=78.39 Aligned_cols=48 Identities=44% Similarity=0.838 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcC
Q 045384 15 KGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLR 63 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~ 63 (194)
+++||++||.+|+.++..||..+|..||..|+ +|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 47899999999999999999667999999998 9999999999998764
No 16
>PLN03091 hypothetical protein; Provisional
Probab=99.28 E-value=1.7e-12 Score=114.78 Aligned_cols=56 Identities=21% Similarity=0.466 Sum_probs=52.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCC
Q 045384 7 NSQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRP 64 (194)
Q Consensus 7 n~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p 64 (194)
|+|+|.++||+||+|||++|++++..||.+ |..||+.|+ ||++.+|+.||...|+.
T Consensus 59 NyLdP~IkKgpWT~EED~lLLeL~k~~GnK-WskIAk~LP-GRTDnqIKNRWnslLKK 114 (459)
T PLN03091 59 NYLRPDLKRGTFSQQEENLIIELHAVLGNR-WSQIAAQLP-GRTDNEIKNLWNSCLKK 114 (459)
T ss_pred hccCCcccCCCCCHHHHHHHHHHHHHhCcc-hHHHHHhcC-CCCHHHHHHHHHHHHHH
Confidence 579999999999999999999999999965 999999998 99999999999987754
No 17
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.21 E-value=3.5e-11 Score=73.64 Aligned_cols=43 Identities=47% Similarity=0.802 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHhhc-CcHHHHhhhCCCCCHHHHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWG-NRWSKIAKHLPGRTDNEIKNFWRTR 112 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~ 112 (194)
+||++|+..|+.++..+| .+|..||..+++||..+|++||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 8999999999999999999999765
No 18
>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=99.17 E-value=4.6e-11 Score=73.10 Aligned_cols=45 Identities=44% Similarity=0.841 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhc
Q 045384 17 PWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYL 62 (194)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L 62 (194)
+||++||.+|+.++..+|..+|..||..++ +|++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHhC
Confidence 599999999999999999667999999998 899999999998764
No 19
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.14 E-value=3.8e-11 Score=100.20 Aligned_cols=56 Identities=23% Similarity=0.440 Sum_probs=52.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcC
Q 045384 6 CNSQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLR 63 (194)
Q Consensus 6 ~n~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~ 63 (194)
+|+|+|+++||.||+|||.+|+++...+|.+ |+.||++|| |||...++..|...|+
T Consensus 53 ~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr-Ws~IA~~LP-GRTDNeIKN~Wnt~lk 108 (238)
T KOG0048|consen 53 TNYLRPDLKRGNFSDEEEDLIIKLHALLGNR-WSLIAGRLP-GRTDNEVKNHWNTHLK 108 (238)
T ss_pred hcccCCCccCCCCCHHHHHHHHHHHHHHCcH-HHHHHhhCC-CcCHHHHHHHHHHHHH
Confidence 5899999999999999999999999999976 999999999 9999999999977764
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.01 E-value=8.1e-10 Score=101.42 Aligned_cols=102 Identities=30% Similarity=0.445 Sum_probs=84.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHh----CCc-------------------chhhhhhhhCCCcchhhhhhhhhhhcCCCc-cC
Q 045384 13 VRKGPWTMEEDLILINYIANH----GEG-------------------VWNSLAKAAGLKRTGKSCRLRWLNYLRPDV-KR 68 (194)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~----g~~-------------------~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~-~~ 68 (194)
++-+.|+.+||+.|-..|..| |-. -|+.|...|| -|+...+...-++.-.|.- .+
T Consensus 306 ~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 306 INLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCcccccc
Confidence 445899999999999999877 110 1788899998 5999888764334444433 89
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
|.||+||++.|..+|.++|+.|..|++.| ||.+.+|+.||+.+.+..
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 99999999999999999999999999999 999999999999887654
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=98.53 E-value=8.1e-08 Score=87.48 Aligned_cols=104 Identities=17% Similarity=0.217 Sum_probs=89.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHHHHHhh
Q 045384 7 NSQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIMELHAKW 86 (194)
Q Consensus 7 n~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~~~~~~ 86 (194)
|.++|.++++.|+.|||+.|+.+...+|.. |..||..++ +|+..+|.+||.+.+.+... .+||..+....+..+..|
T Consensus 64 ~~lnp~lk~~~~~~eed~~li~l~~~~~~~-wstia~~~d-~rt~~~~~ery~~~~~~~~s-~~~s~~~~~~~f~k~d~f 140 (512)
T COG5147 64 NHLNPQLKKKNWSEEEDEQLIDLDKELGTQ-WSTIADYKD-RRTAQQCVERYVNTLEDLSS-THDSKLQRRNEFDKIDPF 140 (512)
T ss_pred hhhchhcccccccHHHHHHHHHHHHhcCch-hhhhccccC-ccchHHHHHHHHHHhhhhhc-cccccccchhhccccCch
Confidence 579999999999999999999999999987 999999998 99999999999999987655 788888888888888888
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
+..|.++....-.+-...+.|++.++.
T Consensus 141 ~~~~~~~~~~~~~~~~~~~~N~~~~~~ 167 (512)
T COG5147 141 NENSARRPDIYEDELLEREVNREASYR 167 (512)
T ss_pred hhhhhhhhhhhhcccchhhhhHHHHHH
Confidence 888888776665666667777775544
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.33 E-value=1.2e-06 Score=57.49 Aligned_cols=48 Identities=13% Similarity=0.214 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcch---hhhhhhhCCCc-chhhhhhhhhhhc
Q 045384 15 KGPWTMEEDLILINYIANHGEGVW---NSLAKAAGLKR-TGKSCRLRWLNYL 62 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W---~~Ia~~~~~~R-t~~qcr~R~~~~L 62 (194)
+-.||+||..+++++|+.+|.++| ..|++.|+..| |..||+.+++.|.
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 456999999999999999998789 99999997667 9999999998875
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.15 E-value=2.5e-06 Score=75.66 Aligned_cols=50 Identities=24% Similarity=0.619 Sum_probs=46.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhc
Q 045384 12 EVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYL 62 (194)
Q Consensus 12 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L 62 (194)
.+-..-||.+|+-+|+++++.||-+||..||.++| .|+..+|+++|.+++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 45567899999999999999999999999999999 999999999999865
No 24
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.95 E-value=9.5e-05 Score=60.06 Aligned_cols=100 Identities=23% Similarity=0.414 Sum_probs=75.5
Q ss_pred CCCHHHHHHHHHHHHHhCCcchhhhhhhh--CCCcchhhhhhhhhhhcC-CCc--------------------cCCCCCH
Q 045384 17 PWTMEEDLILINYIANHGEGVWNSLAKAA--GLKRTGKSCRLRWLNYLR-PDV--------------------KRGNITP 73 (194)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~--~~~Rt~~qcr~R~~~~L~-p~~--------------------~~~~WT~ 73 (194)
+|++++|-+|+.+|..-.. -..|+.-+ ....|...+.+||...|- |.+ .+.+||.
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 RWKPEDDLLLINAVEQTND--LESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhcC--HHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 5999999999999998653 66666543 346788889999998873 332 3568999
Q ss_pred HHHHHHHHHHHhhcC---cHHHHhh-----hCCCCCHHHHHHHHHHHHHHHHH
Q 045384 74 EEQLLIMELHAKWGN---RWSKIAK-----HLPGRTDNEIKNFWRTRIQKQIK 118 (194)
Q Consensus 74 eEd~~Ll~~~~~~G~---~W~~Ia~-----~l~gRt~~~~knrw~~~l~~~~~ 118 (194)
+|+++|......... .+.+|-. +.++||+.++.++|+.+.+..+.
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchh
Confidence 999999997766543 4777733 33789999999999976655544
No 25
>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=97.80 E-value=7.1e-05 Score=49.01 Aligned_cols=46 Identities=15% Similarity=0.227 Sum_probs=40.1
Q ss_pred CCCCCHHHHHHHHHHHHhhcC-cH---HHHhhhCC-CC-CHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGN-RW---SKIAKHLP-GR-TDNEIKNFWRTRI 113 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~-~W---~~Ia~~l~-gR-t~~~~knrw~~~l 113 (194)
+-.||+||...+++++..+|. .| ..|+..+. .| |..+|+.+...++
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 457999999999999999996 89 99999874 35 9999999987654
No 26
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.76 E-value=2.6e-05 Score=70.66 Aligned_cols=57 Identities=30% Similarity=0.489 Sum_probs=51.5
Q ss_pred ccCCCCCHHHHHHHHHHHHhhc-CcHHHHhhhCCCCCHHHHHHHHHHHHHHHHHhhhc
Q 045384 66 VKRGNITPEEQLLIMELHAKWG-NRWSKIAKHLPGRTDNEIKNFWRTRIQKQIKQAET 122 (194)
Q Consensus 66 ~~~~~WT~eEd~~Ll~~~~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~~~~ 122 (194)
++.+.|+.-||+.|-.+|.+|| +.|+.||+.|+-.|..||++||...+.+.+++...
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tew 62 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEW 62 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhh
Confidence 4678999999999999999999 56999999999999999999999999988876543
No 27
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.70 E-value=3.5e-05 Score=69.05 Aligned_cols=46 Identities=30% Similarity=0.666 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhh
Q 045384 14 RKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNY 61 (194)
Q Consensus 14 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~ 61 (194)
....||.+|..+|++.|+.||. +|.+||.++| +|+..||..|+.++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 4568999999999999999996 5999999999 99999999998754
No 28
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.65 E-value=8.3e-05 Score=66.19 Aligned_cols=48 Identities=25% Similarity=0.550 Sum_probs=43.3
Q ss_pred ccCCCCCHHHHHHHHHHHHhhc-CcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 66 VKRGNITPEEQLLIMELHAKWG-NRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 66 ~~~~~WT~eEd~~Ll~~~~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
+-...||.+|+.+|++++..|| ++|..||.++..||..+|+.+|.+.+
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 89999999998899999999997644
No 29
>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=97.64 E-value=9.5e-05 Score=57.86 Aligned_cols=53 Identities=26% Similarity=0.448 Sum_probs=46.1
Q ss_pred cCCCCCHHHHHHHHHHHHhh---cC----cHHHHhhhCCCCCHHHHHHHHHHHHHHHHHhh
Q 045384 67 KRGNITPEEQLLIMELHAKW---GN----RWSKIAKHLPGRTDNEIKNFWRTRIQKQIKQA 120 (194)
Q Consensus 67 ~~~~WT~eEd~~Ll~~~~~~---G~----~W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~~ 120 (194)
+.+.||.|||.+|.+.|..| |+ -+..+|+.| +||...|.=||+..+|+.+...
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 56789999999999999877 43 388899999 9999999999999999887554
No 30
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.51 E-value=0.0001 Score=67.50 Aligned_cols=47 Identities=30% Similarity=0.667 Sum_probs=42.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhh
Q 045384 13 VRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNY 61 (194)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~ 61 (194)
--++.||.+|+.+|+++|+.||. +|.+||.++| +|+..||..++.++
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 44677999999999999999996 5999999999 99999999988753
No 31
>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=97.48 E-value=8.2e-05 Score=58.21 Aligned_cols=71 Identities=28% Similarity=0.586 Sum_probs=53.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCc------chhhhhhhhCCCcchhhhhhhhhhhcCCCc--------------c--CCC
Q 045384 13 VRKGPWTMEEDLILINYIANHGEG------VWNSLAKAAGLKRTGKSCRLRWLNYLRPDV--------------K--RGN 70 (194)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~------~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~--------------~--~~~ 70 (194)
++...||.|||.+|.+.|-.|-.. .+..|++.++ ||+..|.-||+.++...- + .+.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRkqY~~~i~~AKkqRk~~~~~~~~ 79 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRKQYEEAIELAKKQRKELKREAGS 79 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHHHHHHHHHHHHHHHhccccCccc
Confidence 567889999999999999988321 4889999985 999999999999886321 1 244
Q ss_pred CCHHHHHHHHHHHHh
Q 045384 71 ITPEEQLLIMELHAK 85 (194)
Q Consensus 71 WT~eEd~~Ll~~~~~ 85 (194)
-|-++....|+.+..
T Consensus 80 ltl~~vI~fLq~l~~ 94 (161)
T TIGR02894 80 LTLQDVISFLQNLKT 94 (161)
T ss_pred CCHHHHHHHHHHHHh
Confidence 666666666655543
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=97.41 E-value=0.0002 Score=48.14 Aligned_cols=52 Identities=29% Similarity=0.539 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------CcchhhhhhhhCCCcchhhhhhhhhhhcCCCc
Q 045384 15 KGPWTMEEDLILINYIANHG--------EGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDV 66 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g--------~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~ 66 (194)
+-+||.|||++|+.+|..+. ..-|..+++.-+..+|-.+-|+||...|.+..
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 45799999999999996552 22499999988767888888999999987653
No 33
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.40 E-value=0.00028 Score=47.40 Aligned_cols=50 Identities=16% Similarity=0.370 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHhh--------cCc-HHHHhhhCC-CCCHHHHHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKW--------GNR-WSKIAKHLP-GRTDNEIKNFWRTRIQKQI 117 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~--------G~~-W~~Ia~~l~-gRt~~~~knrw~~~l~~~~ 117 (194)
+.+||.|||..|+..|..+ |+. |.+++..-+ .+|-.+.|+||...|+.+.
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 4589999999999999643 223 999999877 9999999999988777654
No 34
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.38 E-value=0.00023 Score=64.00 Aligned_cols=44 Identities=25% Similarity=0.465 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRT 111 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~ 111 (194)
...||.+|..+|++.+..||..|.+||+++..||..||--||..
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHc
Confidence 45899999999999999999999999999999999999999965
No 35
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.27 E-value=0.00042 Score=63.59 Aligned_cols=45 Identities=27% Similarity=0.488 Sum_probs=42.1
Q ss_pred cCCCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHH
Q 045384 67 KRGNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRT 111 (194)
Q Consensus 67 ~~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~ 111 (194)
.+..||.+|..+|++++..||..|.+||.++.+||..+|--+|..
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~ 296 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLR 296 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHh
Confidence 356899999999999999999999999999999999999999865
No 36
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.18 E-value=0.00064 Score=47.62 Aligned_cols=49 Identities=33% Similarity=0.524 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHh------hc--C------cHHHHhhhC----CCCCHHHHHHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAK------WG--N------RWSKIAKHL----PGRTDNEIKNFWRTRIQKQI 117 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~------~G--~------~W~~Ia~~l----~gRt~~~~knrw~~~l~~~~ 117 (194)
..||.+|...||+++.. ++ . -|..||..| ..||+.||+++|.++.+...
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 57999999999999876 21 1 499999977 36999999999999766553
No 37
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.10 E-value=0.0004 Score=59.88 Aligned_cols=48 Identities=25% Similarity=0.583 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcC
Q 045384 15 KGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLR 63 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~ 63 (194)
---|+..|+.+|++.....|-+||..||..+| .|+...|+++|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 34599999999999999999999999999999 9999999999988765
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.06 E-value=0.00041 Score=48.62 Aligned_cols=47 Identities=34% Similarity=0.668 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHHH--h----C---C----cchhhhhhhh---CCCcchhhhhhhhhhhc
Q 045384 16 GPWTMEEDLILINYIAN--H----G---E----GVWNSLAKAA---GLKRTGKSCRLRWLNYL 62 (194)
Q Consensus 16 g~WT~eED~~L~~~v~~--~----g---~----~~W~~Ia~~~---~~~Rt~~qcr~R~~~~L 62 (194)
-.||.+|...|+.++.. + + . .-|..||..| |..|++.||+.+|.++.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 47999999999999887 2 1 1 1499999987 45799999999998754
No 39
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.82 E-value=0.0017 Score=44.58 Aligned_cols=49 Identities=29% Similarity=0.510 Sum_probs=39.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------cchhhhhhhh----CCCcchhhhhhhhhhhc
Q 045384 14 RKGPWTMEEDLILINYIANHGE----------------GVWNSLAKAA----GLKRTGKSCRLRWLNYL 62 (194)
Q Consensus 14 ~kg~WT~eED~~L~~~v~~~g~----------------~~W~~Ia~~~----~~~Rt~~qcr~R~~~~L 62 (194)
++..||++|..+|+++|+.|.. .-|..|+..| |..|+..||+.+|.++.
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 4567999999999999998721 0299999887 22699999999998865
No 40
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.74 E-value=0.0029 Score=50.22 Aligned_cols=53 Identities=19% Similarity=0.309 Sum_probs=43.7
Q ss_pred ccCCCCCHHHHHHHHHHHHhhcC----c---HHHHhhhCCCCCHHHHHHHHHHHHHHHHHh
Q 045384 66 VKRGNITPEEQLLIMELHAKWGN----R---WSKIAKHLPGRTDNEIKNFWRTRIQKQIKQ 119 (194)
Q Consensus 66 ~~~~~WT~eEd~~Ll~~~~~~G~----~---W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~ 119 (194)
.+.+.||.|||.+|.+.|..|+. + ...++..| +||..+|.-||+..++++...
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 35678999999999999888863 2 56667788 999999999999999976543
No 41
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.72 E-value=0.0011 Score=52.48 Aligned_cols=50 Identities=30% Similarity=0.614 Sum_probs=41.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCc------chhhhhhhhCCCcchhhhhhhhhhhcC
Q 045384 12 EVRKGPWTMEEDLILINYIANHGEG------VWNSLAKAAGLKRTGKSCRLRWLNYLR 63 (194)
Q Consensus 12 ~~~kg~WT~eED~~L~~~v~~~g~~------~W~~Ia~~~~~~Rt~~qcr~R~~~~L~ 63 (194)
.+++..||.|||.+|.+.|-.|+.. -...++..+ +|++.+|..||+.++.
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHH
Confidence 3577889999999999999888533 267777777 5999999999987775
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.46 E-value=0.011 Score=40.38 Aligned_cols=49 Identities=29% Similarity=0.523 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHhhcC-----------------cHHHHhhhC-----CCCCHHHHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGN-----------------RWSKIAKHL-----PGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~-----------------~W~~Ia~~l-----~gRt~~~~knrw~~~l~~~ 116 (194)
...||.+|...|++++.+|.. -|..|+..| +.||..+++.+|..+...-
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 457999999999999987621 499999876 2599999999998876543
No 43
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=96.26 E-value=0.034 Score=55.43 Aligned_cols=103 Identities=17% Similarity=0.245 Sum_probs=78.4
Q ss_pred CCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhh-------hhhhh------cC--------------------
Q 045384 17 PWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRL-------RWLNY------LR-------------------- 63 (194)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~-------R~~~~------L~-------------------- 63 (194)
.||.-+=..++.+.++||..+-..||..|. +++...++. ||..+ +.
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 377777777888999999889999999997 899988852 22110 00
Q ss_pred -----------------CCccCCCCCHHHHHHHHHHHHhhc-CcHHHHhhh------------CCCCCHHHHHHHHHHHH
Q 045384 64 -----------------PDVKRGNITPEEQLLIMELHAKWG-NRWSKIAKH------------LPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 64 -----------------p~~~~~~WT~eEd~~Ll~~~~~~G-~~W~~Ia~~------------l~gRt~~~~knrw~~~l 113 (194)
+.-++..+|+|||..|+-.+.+|| .+|..|-.. |..||+..|..|-.+++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 112345699999999999999999 679999332 24899999999999998
Q ss_pred HHHHHhh
Q 045384 114 QKQIKQA 120 (194)
Q Consensus 114 ~~~~~~~ 120 (194)
+-..+..
T Consensus 985 ~~~~~e~ 991 (1033)
T PLN03142 985 RLIEKEN 991 (1033)
T ss_pred HHHHHHH
Confidence 8765443
No 44
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.17 E-value=0.0064 Score=52.60 Aligned_cols=46 Identities=26% Similarity=0.468 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHhhc-CcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWG-NRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
-..|+.+|+.+|+++....| ++|..||.++..|+..+||.+|....
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 34799999999999999999 78999999998899999999996543
No 45
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=94.50 E-value=0.095 Score=39.25 Aligned_cols=53 Identities=25% Similarity=0.386 Sum_probs=41.5
Q ss_pred CccCCCCCHHHHHHHHHHHHhhcC----cHHHHhhhC------------CCCCHHHHHHHHHHHHHHHH
Q 045384 65 DVKRGNITPEEQLLIMELHAKWGN----RWSKIAKHL------------PGRTDNEIKNFWRTRIQKQI 117 (194)
Q Consensus 65 ~~~~~~WT~eEd~~Ll~~~~~~G~----~W~~Ia~~l------------~gRt~~~~knrw~~~l~~~~ 117 (194)
.-++..+|++||..|+-.+.+||- .|..|...+ ..||+..|..|-.++++-..
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~ 114 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIE 114 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHH
Confidence 445678999999999999999996 699885532 38999999999999987654
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=94.36 E-value=0.047 Score=48.41 Aligned_cols=54 Identities=20% Similarity=0.287 Sum_probs=47.0
Q ss_pred CCCCCHHHHHHHHHHHHhhcCcHHHHhhh-----CCC-CCHHHHHHHHHHHHHHHHHhhh
Q 045384 68 RGNITPEEQLLIMELHAKWGNRWSKIAKH-----LPG-RTDNEIKNFWRTRIQKQIKQAE 121 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~-----l~g-Rt~~~~knrw~~~l~~~~~~~~ 121 (194)
...||.+|-.-|+++++.|.-+|.-||.. ++. ||-.++|.||+..-++.++...
T Consensus 130 dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred cccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 46799999999999999999999999997 555 9999999999988777665543
No 47
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=93.97 E-value=0.1 Score=46.34 Aligned_cols=43 Identities=21% Similarity=0.316 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRT 111 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~ 111 (194)
.+||.+|-++...++..+|..++.||..||.|...|||.+|..
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHH
Confidence 4799999999999999999999999999999999999999964
No 48
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=93.86 E-value=0.092 Score=39.34 Aligned_cols=49 Identities=22% Similarity=0.341 Sum_probs=36.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---cchhhhhhhhC-----------CCcchhhhhhhhhh
Q 045384 12 EVRKGPWTMEEDLILINYIANHGE---GVWNSLAKAAG-----------LKRTGKSCRLRWLN 60 (194)
Q Consensus 12 ~~~kg~WT~eED~~L~~~v~~~g~---~~W~~Ia~~~~-----------~~Rt~~qcr~R~~~ 60 (194)
..++..||.+||.-|+-++.+||. +.|..|-..+- ..||+..+..|-..
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 556778999999999999999998 78999987752 25676666666543
No 49
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=93.43 E-value=0.28 Score=34.48 Aligned_cols=47 Identities=32% Similarity=0.613 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHhh---cC----------cHHHHhhhC---CC--CCHHHHHHHHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKW---GN----------RWSKIAKHL---PG--RTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~---G~----------~W~~Ia~~l---~g--Rt~~~~knrw~~~l~~~ 116 (194)
.||++++..|++++.+. |+ .|..|+..| +| .|..+|+|||..+.+..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y 65 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDY 65 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHH
Confidence 49999999999987542 21 399998876 33 67899999997765543
No 50
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=93.24 E-value=0.32 Score=42.55 Aligned_cols=53 Identities=21% Similarity=0.340 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHhh----------cCcHHHHhhhC----CCCCHHHHHHHHHHHHHHHHHhh
Q 045384 68 RGNITPEEQLLIMELHAKW----------GNRWSKIAKHL----PGRTDNEIKNFWRTRIQKQIKQA 120 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~----------G~~W~~Ia~~l----~gRt~~~~knrw~~~l~~~~~~~ 120 (194)
...|+.+|-..||++.... +..|..||+.+ .-||+.+||++|.++.++..+..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k 120 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEK 120 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 3689999999999988643 23599999955 24999999999999877654443
No 51
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=93.02 E-value=0.26 Score=44.73 Aligned_cols=48 Identities=19% Similarity=0.322 Sum_probs=43.4
Q ss_pred cCCCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 67 KRGNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 67 ~~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
..+.||.||-.++-+++..||.++.+|-+.||.|+-.++..+|....+
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK 233 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKK 233 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHH
Confidence 456899999999999999999999999999999999999998876544
No 52
>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=92.53 E-value=0.5 Score=29.62 Aligned_cols=41 Identities=29% Similarity=0.354 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 73 PEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 73 ~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
++++..++.++...|-.+.+||..+ |.|...|+.+....++
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 4677778888889999999999999 9999999998876554
No 53
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=92.47 E-value=0.16 Score=45.04 Aligned_cols=45 Identities=11% Similarity=0.211 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhh
Q 045384 15 KGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNY 61 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~ 61 (194)
--+||.+|-+++.+++...|+. ++.|+..+| +|..+|++.+|.+-
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGtd-F~LIs~lfP-~R~RkqIKaKfi~E 409 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGTD-FSLISSLFP-NRERKQIKAKFIKE 409 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcch-HHHHHHhcC-chhHHHHHHHHHHH
Confidence 3469999999999999999975 999999999 99999999988763
No 54
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.50 E-value=0.25 Score=43.21 Aligned_cols=48 Identities=27% Similarity=0.533 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHHh---------CCcchhhhhhhh---CCCcchhhhhhhhhhhcC
Q 045384 16 GPWTMEEDLILINYIANH---------GEGVWNSLAKAA---GLKRTGKSCRLRWLNYLR 63 (194)
Q Consensus 16 g~WT~eED~~L~~~v~~~---------g~~~W~~Ia~~~---~~~Rt~~qcr~R~~~~L~ 63 (194)
..|+.+|-..|+.+.... ....|..||+.+ |..|++.||+.+|.+...
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 579999999999988643 112499999854 456999999999987653
No 55
>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=89.72 E-value=0.77 Score=32.13 Aligned_cols=44 Identities=27% Similarity=0.577 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHHh---CCc---------chhhhhhhhC----CCcchhhhhhhhhh
Q 045384 17 PWTMEEDLILINYIANH---GEG---------VWNSLAKAAG----LKRTGKSCRLRWLN 60 (194)
Q Consensus 17 ~WT~eED~~L~~~v~~~---g~~---------~W~~Ia~~~~----~~Rt~~qcr~R~~~ 60 (194)
.||+++++.|++++... |.. .|..|+..|. ...+..||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999988543 211 3888888763 35677888888764
No 56
>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=89.40 E-value=0.48 Score=33.32 Aligned_cols=30 Identities=30% Similarity=0.534 Sum_probs=16.1
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCCcchhhhhh
Q 045384 11 AEVRKGPWTMEEDLIL--------INYIANHGEGVWNSLAK 43 (194)
Q Consensus 11 p~~~kg~WT~eED~~L--------~~~v~~~g~~~W~~Ia~ 43 (194)
|.-..|-||+|+|+.| ..++++|| +..|+.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~ 80 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIER 80 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHH
Confidence 5566899999999998 34556666 345543
No 57
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=89.16 E-value=1.4 Score=42.40 Aligned_cols=46 Identities=15% Similarity=0.190 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
...||+.|-.++-+++..|.+.+..|++.++++|-.+|-.+|++..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWK 664 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWK 664 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHH
Confidence 3579999999999999999999999999999999999999887653
No 58
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=86.23 E-value=1.5 Score=26.61 Aligned_cols=38 Identities=21% Similarity=0.323 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhh
Q 045384 21 EEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLN 60 (194)
Q Consensus 21 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~ 60 (194)
+=|..|+.++...+...+..||+.+| =++..|..|...
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 34788999999999888999999997 688888888764
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=86.06 E-value=2.1 Score=25.89 Aligned_cols=38 Identities=21% Similarity=0.345 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhhcC-cHHHHhhhCCCCCHHHHHHHHHHH
Q 045384 74 EEQLLIMELHAKWGN-RWSKIAKHLPGRTDNEIKNFWRTR 112 (194)
Q Consensus 74 eEd~~Ll~~~~~~G~-~W~~Ia~~l~gRt~~~~knrw~~~ 112 (194)
+=|..|+.++..-|. .+..||+.+ |=|...|..|.+.+
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 447788888888884 599999999 99999999998654
No 60
>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=85.92 E-value=3 Score=25.67 Aligned_cols=41 Identities=17% Similarity=0.292 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 74 EEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 74 eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
+++..++.++--.|..+..||..+ |-|...|+.+-...+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 445556666666677899999999 99999999988777665
No 61
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=83.95 E-value=1.4 Score=42.40 Aligned_cols=44 Identities=14% Similarity=0.158 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhh
Q 045384 15 KGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLN 60 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~ 60 (194)
-.+||+-|-.++.+++..|. +++..|++.++ ++|..||-+-|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhc-cccHHHHHHHHHH
Confidence 35799999999999999998 56999999998 9999999986653
No 62
>smart00595 MADF subfamily of SANT domain.
Probab=83.85 E-value=2.7 Score=28.94 Aligned_cols=28 Identities=29% Similarity=0.554 Sum_probs=23.2
Q ss_pred cHHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 045384 89 RWSKIAKHLPGRTDNEIKNFWRTRIQKQI 117 (194)
Q Consensus 89 ~W~~Ia~~l~gRt~~~~knrw~~~l~~~~ 117 (194)
-|..||..| |-|..+|+.+|+++.....
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR~~y~ 56 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLRDRYR 56 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 399999999 5599999999998765443
No 63
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=82.69 E-value=2.6 Score=39.74 Aligned_cols=49 Identities=10% Similarity=0.354 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHhhcCcHHHH----------hhhCCCCCHHHHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGNRWSKI----------AKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~~W~~I----------a~~l~gRt~~~~knrw~~~l~~~ 116 (194)
+..||..|..-...+++++|+.+..| -....-+|..+++.+|+.++++.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m 146 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRM 146 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHH
Confidence 56899999999999999999999998 22334578889999888777654
No 64
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=80.74 E-value=4.4 Score=31.17 Aligned_cols=43 Identities=19% Similarity=0.149 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHhhc-CcHHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 045384 74 EEQLLIMELHAKWG-NRWSKIAKHLPGRTDNEIKNFWRTRIQKQI 117 (194)
Q Consensus 74 eEd~~Ll~~~~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~ 117 (194)
+-|..|+.+...-| ..|+.||+.+ |-+...|..|++.+....+
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 56888999888888 4699999999 9999999999987766554
No 65
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=77.98 E-value=3.5 Score=31.69 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCc
Q 045384 21 EEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDV 66 (194)
Q Consensus 21 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~ 66 (194)
+-|..|+.+++..|...|..||+.+| -+...|+.|+.+.....+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 57899999999999889999999996 899999999998876553
No 66
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=77.03 E-value=5.6 Score=30.97 Aligned_cols=45 Identities=13% Similarity=0.009 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHhhc-CcHHHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q 045384 73 PEEQLLIMELHAKWG-NRWSKIAKHLPGRTDNEIKNFWRTRIQKQIK 118 (194)
Q Consensus 73 ~eEd~~Ll~~~~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~~ 118 (194)
.+-|.+|+.+...-| ..|+.||+.+ |-+...|..|++.+.+..+-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 456888999888888 4699999999 99999999999887766543
No 67
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=75.09 E-value=4.3 Score=31.98 Aligned_cols=41 Identities=24% Similarity=0.164 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRT 111 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~ 111 (194)
.||+|+.+.|.++. .-|..=++||+.|.|.|.+.|.-+.+.
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 59999999888876 558888999999977999999876643
No 68
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=74.85 E-value=8.5 Score=27.65 Aligned_cols=52 Identities=13% Similarity=0.185 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHhh----cC----cHHHH----hhhCC-CCCHHHHHHHHHHHHHHHHHhh
Q 045384 69 GNITPEEQLLIMELHAKW----GN----RWSKI----AKHLP-GRTDNEIKNFWRTRIQKQIKQA 120 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~----G~----~W~~I----a~~l~-gRt~~~~knrw~~~l~~~~~~~ 120 (194)
.-||+|++..||+.+..| |. .+..+ ...+. .=+..|+..+-+.+.++.....
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~ 69 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAV 69 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHh
Confidence 369999999999998776 52 35444 33332 2477888888877766654433
No 69
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=73.38 E-value=9 Score=28.52 Aligned_cols=30 Identities=17% Similarity=0.294 Sum_probs=24.7
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
..|-.+..||+.+ |.+...|+++....+++
T Consensus 127 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 127 FEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467899999999 99999999998775444
No 70
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=73.16 E-value=4.6 Score=31.47 Aligned_cols=45 Identities=20% Similarity=0.165 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCc
Q 045384 20 MEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDV 66 (194)
Q Consensus 20 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~ 66 (194)
.+-|.+|+.+++..|.-.|..||+.+| =+...|+.|++++....+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 566889999999999889999999996 788889999998877654
No 71
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=72.78 E-value=7.6 Score=34.65 Aligned_cols=44 Identities=16% Similarity=0.180 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhh-hCCCCCHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAK-HLPGRTDNEIKNFWRTR 112 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~-~l~gRt~~~~knrw~~~ 112 (194)
..|+++|-...-+.++.||+.+..|.. +++.|+--.|-.+|+..
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 479999999999999999999999955 89999999999888654
No 72
>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=72.47 E-value=20 Score=31.41 Aligned_cols=49 Identities=24% Similarity=0.439 Sum_probs=38.2
Q ss_pred CCCCCHHHHHHHHHHHHhh-cC---cHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKW-GN---RWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~-G~---~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
-..||.-|...|+.+.... |. .-..|++.++||+..+|++.-..+..+.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rv 73 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRV 73 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHH
Confidence 4579999999888887654 43 3578999999999999999776554443
No 73
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=70.82 E-value=6.4 Score=39.71 Aligned_cols=47 Identities=21% Similarity=0.253 Sum_probs=35.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhC-----------CCcchhhhhhhhh
Q 045384 13 VRKGPWTMEEDLILINYIANHGEGVWNSLAKAAG-----------LKRTGKSCRLRWL 59 (194)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~-----------~~Rt~~qcr~R~~ 59 (194)
.++..||.|||..|+-++.+||.++|..|-..+- ..||+..+..|-.
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~ 981 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCD 981 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHH
Confidence 3444599999999999999999999999976652 2455555555543
No 74
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=70.31 E-value=3.7 Score=36.80 Aligned_cols=49 Identities=16% Similarity=0.225 Sum_probs=42.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCcchhhhhhh-----hCCCcchhhhhhhhhhhc
Q 045384 13 VRKGPWTMEEDLILINYIANHGEGVWNSLAKA-----AGLKRTGKSCRLRWLNYL 62 (194)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~-----~~~~Rt~~qcr~R~~~~L 62 (194)
++-..||.+|-.-|..+...|.-. |-.||.. ++..||....++||....
T Consensus 128 l~dn~WskeETD~LF~lck~fDLR-f~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFDLR-FFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred hccccccHHHHHHHHHHHHhcCee-EEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 445789999999999999999964 9999988 675699999999997653
No 75
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=69.60 E-value=12 Score=23.61 Aligned_cols=34 Identities=15% Similarity=0.391 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHH
Q 045384 75 EQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFW 109 (194)
Q Consensus 75 Ed~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw 109 (194)
.|+..+.++...|-.=.+||+.+ ||+.+.|+++-
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 44556688889999999999999 99999888754
No 76
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=68.17 E-value=5.8 Score=27.82 Aligned_cols=41 Identities=24% Similarity=0.512 Sum_probs=29.1
Q ss_pred HHHHHHHHHhCC-------cchhhhhhhhCCCc----chhhhhhhhhhhcCC
Q 045384 24 LILINYIANHGE-------GVWNSLAKAAGLKR----TGKSCRLRWLNYLRP 64 (194)
Q Consensus 24 ~~L~~~v~~~g~-------~~W~~Ia~~~~~~R----t~~qcr~R~~~~L~p 64 (194)
-.|..+|.+.|. +.|..||..++..- .+.+.+..|.++|.|
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 457778877763 35999999998432 245677888887764
No 77
>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=67.85 E-value=3.9 Score=28.49 Aligned_cols=41 Identities=22% Similarity=0.480 Sum_probs=28.5
Q ss_pred HHHHHHHHHhCC-------cchhhhhhhhCCCcc----hhhhhhhhhhhcCC
Q 045384 24 LILINYIANHGE-------GVWNSLAKAAGLKRT----GKSCRLRWLNYLRP 64 (194)
Q Consensus 24 ~~L~~~v~~~g~-------~~W~~Ia~~~~~~Rt----~~qcr~R~~~~L~p 64 (194)
-.|..+|...|. +.|..||..+|...+ +.+++..|.++|.|
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 357777877763 249999999975432 36688888888753
No 78
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=67.08 E-value=13 Score=30.34 Aligned_cols=44 Identities=20% Similarity=0.291 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhhcCcHHHHhhh--CC-CCCHHHHHHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWGNRWSKIAKH--LP-GRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G~~W~~Ia~~--l~-gRt~~~~knrw~~~l~ 114 (194)
.|++++|.+|+.+|. .|+.-..|++- |. .-|-..|..||..++-
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 499999999999985 45666677664 32 4688999999998874
No 79
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=65.76 E-value=11 Score=26.36 Aligned_cols=30 Identities=20% Similarity=0.460 Sum_probs=23.9
Q ss_pred HHHHHHHHHhhcCcHHHHhhhCCCCCHHHHH
Q 045384 76 QLLIMELHAKWGNRWSKIAKHLPGRTDNEIK 106 (194)
Q Consensus 76 d~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~k 106 (194)
|+.|..+....|..|..+|.+| |=|..+|.
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~ 31 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIY 31 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 4557788899999999999999 76666553
No 80
>smart00595 MADF subfamily of SANT domain.
Probab=65.53 E-value=4.2 Score=27.94 Aligned_cols=22 Identities=32% Similarity=0.866 Sum_probs=19.5
Q ss_pred hhhhhhhhCCCcchhhhhhhhhhh
Q 045384 38 WNSLAKAAGLKRTGKSCRLRWLNY 61 (194)
Q Consensus 38 W~~Ia~~~~~~Rt~~qcr~R~~~~ 61 (194)
|..||..|+ -++..|+.+|.++
T Consensus 30 W~~Ia~~l~--~~~~~~~~kw~~L 51 (89)
T smart00595 30 WEEIAEELG--LSVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHC--cCHHHHHHHHHHH
Confidence 999999997 4999999999864
No 81
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=65.45 E-value=11 Score=34.47 Aligned_cols=48 Identities=6% Similarity=0.039 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQI 117 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~ 117 (194)
.|+.++-.++++.++++|....-|+-.+...+-.++++.+...-|++.
T Consensus 371 ~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~m 418 (534)
T KOG1194|consen 371 CFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQM 418 (534)
T ss_pred ccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHHH
Confidence 388899999999999999888888888877888888888877666654
No 82
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=65.36 E-value=18 Score=26.08 Aligned_cols=34 Identities=24% Similarity=0.221 Sum_probs=26.2
Q ss_pred HHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 81 ELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 81 ~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.++-..|..+..||+.+ |-+...|+++....+++
T Consensus 120 ~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 120 VLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33334577899999999 88999999988776554
No 83
>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=64.55 E-value=82 Score=27.69 Aligned_cols=95 Identities=18% Similarity=0.274 Sum_probs=65.1
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCc---chhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHH
Q 045384 5 PCNSQEAEVRKGPWTMEEDLILINYIANHGEG---VWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIME 81 (194)
Q Consensus 5 ~~n~~~p~~~kg~WT~eED~~L~~~v~~~g~~---~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~ 81 (194)
|+.++-....--.||.-|...|+.++...... +-..|++.++ +|+..++++ |.+.|+- ..+.+
T Consensus 11 PaRy~g~~~gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~-fl~~LK~------------rvare 76 (344)
T PF11035_consen 11 PARYLGEVTGPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRD-FLQQLKG------------RVARE 76 (344)
T ss_pred CccccCCCCCcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHH-HHHHHHH------------HHHHH
Confidence 44455444445579999999999999876323 4567888898 999998876 3344432 22333
Q ss_pred HHHh-h-----cC------------cHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 82 LHAK-W-----GN------------RWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 82 ~~~~-~-----G~------------~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
++.+ | |. -|..+|..+.|.-...+-.-|...|
T Consensus 77 aiqkv~~~g~~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l 126 (344)
T PF11035_consen 77 AIQKVHPGGLKGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVL 126 (344)
T ss_pred HHHHhcccccccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHH
Confidence 3333 1 11 3999999999999998888886554
No 84
>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=63.52 E-value=10 Score=26.05 Aligned_cols=34 Identities=32% Similarity=0.563 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHH
Q 045384 73 PEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNF 108 (194)
Q Consensus 73 ~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knr 108 (194)
.||.++|+.. -..|..|..+|..| |=+...|.+.
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHHH
Confidence 5788888743 25788999999999 8788777653
No 85
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=63.40 E-value=7.9 Score=36.47 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=41.2
Q ss_pred CCCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRT 111 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~ 111 (194)
.+.|+.+|-++.-.+....|...+.|+..+|+|+..+||-+|..
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 86
>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=62.71 E-value=7.8 Score=27.08 Aligned_cols=17 Identities=35% Similarity=0.554 Sum_probs=9.7
Q ss_pred CCccCCCCCHHHHHHHH
Q 045384 64 PDVKRGNITPEEQLLIM 80 (194)
Q Consensus 64 p~~~~~~WT~eEd~~Ll 80 (194)
|.-..|-||+|+|..|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 44567889999999983
No 87
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=62.49 E-value=15 Score=29.76 Aligned_cols=45 Identities=20% Similarity=0.234 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
...|+.|-+.|.-+..-+. =.+||..| +.+...||++..++++|-
T Consensus 147 ~~LT~RE~eVL~lla~G~s--nkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAEGLS--NKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHCCCC--HHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 3689988887766554444 45999999 999999999999998874
No 88
>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=62.43 E-value=13 Score=24.81 Aligned_cols=29 Identities=21% Similarity=0.439 Sum_probs=22.8
Q ss_pred cHHHHhhhCCC-CCHHHHHHHHHHHHHHHH
Q 045384 89 RWSKIAKHLPG-RTDNEIKNFWRTRIQKQI 117 (194)
Q Consensus 89 ~W~~Ia~~l~g-Rt~~~~knrw~~~l~~~~ 117 (194)
-|..||..|.. -+..+|+.+|..+.....
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~ 57 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRYR 57 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHHH
Confidence 39999999953 678899999998765443
No 89
>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=62.03 E-value=15 Score=25.62 Aligned_cols=31 Identities=19% Similarity=0.441 Sum_probs=24.4
Q ss_pred HHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHH
Q 045384 76 QLLIMELHAKWGNRWSKIAKHLPGRTDNEIKN 107 (194)
Q Consensus 76 d~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~kn 107 (194)
|..|.......|..|.++|..| |=+..+|.+
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 5567778889999999999999 766655543
No 90
>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=61.52 E-value=15 Score=23.14 Aligned_cols=44 Identities=25% Similarity=0.339 Sum_probs=31.4
Q ss_pred CCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
..|+.|-+.|.-+.. |..=.+||..+ |.+...|+.+...++++-
T Consensus 3 ~LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHHh
Confidence 456777776555443 45556999999 999999999888877663
No 91
>PRK04217 hypothetical protein; Provisional
Probab=60.62 E-value=24 Score=25.98 Aligned_cols=45 Identities=18% Similarity=0.119 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
..|.+| ..++.++...|-.-.+||+.+ |.+...|+.++....++-
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 456666 567777777788999999999 999999999998755443
No 92
>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=59.75 E-value=28 Score=24.04 Aligned_cols=38 Identities=16% Similarity=0.389 Sum_probs=26.5
Q ss_pred HHHHHHHhhcC--------cHHHHhhhCCC---CC--HHHHHHHHHHHHHH
Q 045384 78 LIMELHAKWGN--------RWSKIAKHLPG---RT--DNEIKNFWRTRIQK 115 (194)
Q Consensus 78 ~Ll~~~~~~G~--------~W~~Ia~~l~g---Rt--~~~~knrw~~~l~~ 115 (194)
.|..+|...|+ .|..||..|.- -+ ..+++..|..+|.+
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 36677777774 59999998822 22 36788888877654
No 93
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=59.18 E-value=28 Score=27.39 Aligned_cols=35 Identities=23% Similarity=0.264 Sum_probs=27.6
Q ss_pred HHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 78 LIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 78 ~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
.++.+..-.|-.+..||..+ |-+...|+.+|....
T Consensus 142 ~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 142 RVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 34444444577899999999 999999999998764
No 94
>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=59.10 E-value=6.3 Score=26.36 Aligned_cols=25 Identities=28% Similarity=0.720 Sum_probs=20.2
Q ss_pred hhhhhhhhCCCcchhhhhhhhhhhc
Q 045384 38 WNSLAKAAGLKRTGKSCRLRWLNYL 62 (194)
Q Consensus 38 W~~Ia~~~~~~Rt~~qcr~R~~~~L 62 (194)
|..||..++..-++..|+.||.++-
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr 53 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLR 53 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHH
Confidence 9999999985567888998887643
No 95
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=58.76 E-value=38 Score=26.60 Aligned_cols=29 Identities=17% Similarity=0.159 Sum_probs=23.4
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
-.|....+||..+ |-+...|++|....++
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar~ 176 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGRA 176 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3466799999999 9999999999855433
No 96
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=58.73 E-value=34 Score=19.92 Aligned_cols=40 Identities=15% Similarity=0.219 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHH
Q 045384 71 ITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTR 112 (194)
Q Consensus 71 WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~ 112 (194)
.+++ +..++.++-..|..+..||+.+ |-+...|+.+....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3444 3445555555677899999998 88888887665443
No 97
>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=58.73 E-value=13 Score=25.56 Aligned_cols=30 Identities=20% Similarity=0.644 Sum_probs=23.2
Q ss_pred HHHHHHHHHhhcCcHHHHhhhCCCCCHHHHH
Q 045384 76 QLLIMELHAKWGNRWSKIAKHLPGRTDNEIK 106 (194)
Q Consensus 76 d~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~k 106 (194)
|..|.......|..|.++|..| |=+..+|.
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 4457777888999999999999 66665543
No 98
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=58.53 E-value=29 Score=24.21 Aligned_cols=39 Identities=15% Similarity=0.366 Sum_probs=27.8
Q ss_pred HHHHHHHhhcC--------cHHHHhhhCCC-----CCHHHHHHHHHHHHHHH
Q 045384 78 LIMELHAKWGN--------RWSKIAKHLPG-----RTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 78 ~Ll~~~~~~G~--------~W~~Ia~~l~g-----Rt~~~~knrw~~~l~~~ 116 (194)
.|..+|.+.|+ .|..||..|.- ....+++..|..+|.+-
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 36666777664 69999998832 23567899888877654
No 99
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=57.49 E-value=19 Score=25.44 Aligned_cols=44 Identities=18% Similarity=0.132 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCc
Q 045384 21 EEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDV 66 (194)
Q Consensus 21 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~ 66 (194)
+.|..|+.++...+...+..||+.++ -+...|+.|........+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 56888999999888778999999996 788889998887766543
No 100
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=57.40 E-value=16 Score=22.05 Aligned_cols=36 Identities=36% Similarity=0.518 Sum_probs=18.1
Q ss_pred CCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKN 107 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~kn 107 (194)
.+|.+|=..|..+ ..-|..=..||+.| ||+...|.+
T Consensus 4 ~Lt~~eR~~I~~l-~~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEAL-LEQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHH-HCS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHH-HHcCCCHHHHHHHH-CcCcHHHHH
Confidence 4566666666555 46788889999999 999988865
No 101
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=57.15 E-value=32 Score=26.09 Aligned_cols=30 Identities=13% Similarity=0.095 Sum_probs=23.7
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
..|-....||..| |.+...|+++....+++
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466899999999 99999999887654433
No 102
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=56.23 E-value=36 Score=23.97 Aligned_cols=43 Identities=19% Similarity=0.166 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhhc-CcHHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 045384 74 EEQLLIMELHAKWG-NRWSKIAKHLPGRTDNEIKNFWRTRIQKQI 117 (194)
Q Consensus 74 eEd~~Ll~~~~~~G-~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~ 117 (194)
+.|..|+.++...| ..++.||+.+ |-+...|..+...+....+
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 46788888888877 4699999999 9999999999988776554
No 103
>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=55.67 E-value=19 Score=22.16 Aligned_cols=38 Identities=13% Similarity=0.116 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhh
Q 045384 20 MEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLN 60 (194)
Q Consensus 20 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~ 60 (194)
++++..++.+....|- .+.+||..+| .+...++.+...
T Consensus 12 ~~~~r~i~~l~~~~g~-s~~eIa~~l~--~s~~~v~~~l~r 49 (54)
T PF08281_consen 12 PERQREIFLLRYFQGM-SYAEIAEILG--ISESTVKRRLRR 49 (54)
T ss_dssp -HHHHHHHHHHHTS----HHHHHHHCT--S-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCc-CHHHHHHHHC--cCHHHHHHHHHH
Confidence 4566667777666674 4999999996 888888776654
No 104
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=54.86 E-value=28 Score=26.33 Aligned_cols=29 Identities=28% Similarity=0.244 Sum_probs=23.2
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|.....||..| |-|...|+++....+++
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466799999999 99999999987664443
No 105
>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=53.61 E-value=23 Score=24.66 Aligned_cols=32 Identities=34% Similarity=0.635 Sum_probs=23.2
Q ss_pred CCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHH
Q 045384 71 ITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIK 106 (194)
Q Consensus 71 WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~k 106 (194)
-|.++-.. +....|..|..+|..| |=+..+|.
T Consensus 5 ~t~~~l~~---ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 5 VTGEQITV---FANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred CCHHHHHH---HHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 34444443 4577899999999999 87777764
No 106
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=53.53 E-value=42 Score=24.03 Aligned_cols=69 Identities=12% Similarity=0.302 Sum_probs=39.8
Q ss_pred CCCHHHHHHHHHHHHHh----CCc---chhhhhhhh----CCCcchhhh-------hhhhhhhcCCCccC--CCCCHHHH
Q 045384 17 PWTMEEDLILINYIANH----GEG---VWNSLAKAA----GLKRTGKSC-------RLRWLNYLRPDVKR--GNITPEEQ 76 (194)
Q Consensus 17 ~WT~eED~~L~~~v~~~----g~~---~W~~Ia~~~----~~~Rt~~qc-------r~R~~~~L~p~~~~--~~WT~eEd 76 (194)
.||++++-.|++++..| |.. ++..+...+ ...=+..|+ +.||.+........ -.++..-|
T Consensus 6 ~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k~~~g~~~~~~~~hd 85 (98)
T PF04504_consen 6 LWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKKSKNGKDPSFSKPHD 85 (98)
T ss_pred CCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhhcccCcCCCCCCHhH
Confidence 59999999999988766 522 354444443 212233333 45666655541111 25677777
Q ss_pred HHHHHHHHh
Q 045384 77 LLIMELHAK 85 (194)
Q Consensus 77 ~~Ll~~~~~ 85 (194)
..+.++-+.
T Consensus 86 ~~~f~Lsk~ 94 (98)
T PF04504_consen 86 RRLFELSKK 94 (98)
T ss_pred HHHHHHHHH
Confidence 777776543
No 107
>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=52.88 E-value=25 Score=25.74 Aligned_cols=46 Identities=22% Similarity=0.344 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHHhCC------------------------------cchhhhhhhhCCCcchhhhhhhhhhhcC
Q 045384 17 PWTMEEDLILINYIANHGE------------------------------GVWNSLAKAAGLKRTGKSCRLRWLNYLR 63 (194)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~------------------------------~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~ 63 (194)
+||++||-.|-..|.++-. .-...++...| ..|...=|+||++++.
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p-~HT~~sWRDR~RKfv~ 76 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNP-RHTENSWRDRYRKFVS 76 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTT-TS-HHHHHHHHHHTHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCC-ccchhHHHHHHHHHHH
Confidence 5899999999998876610 01445555555 6777777888887664
No 108
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=52.79 E-value=43 Score=25.89 Aligned_cols=34 Identities=15% Similarity=0.094 Sum_probs=27.7
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHHHHh
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQIKQ 119 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~ 119 (194)
..|-...+||..| |-+...|+.|....+.+-...
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHh
Confidence 3466899999999 999999999998777766543
No 109
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=51.48 E-value=15 Score=34.73 Aligned_cols=50 Identities=10% Similarity=0.288 Sum_probs=43.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhh
Q 045384 9 QEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLN 60 (194)
Q Consensus 9 ~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~ 60 (194)
.-+....++||.+|-++...+....|.. .+.|+..++ .|..+|++..+..
T Consensus 403 ~sk~~~~~~w~~se~e~fyka~~~~gs~-~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 403 YSKKLETDKWDASETELFYKALSERGSD-FSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred ccCccccCcccchhhHHhhhHHhhhccc-ccccccccc-cccHHHHHHHHhh
Confidence 3445567899999999999999999965 999999998 9999999998754
No 110
>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=50.83 E-value=26 Score=24.34 Aligned_cols=31 Identities=19% Similarity=0.442 Sum_probs=24.4
Q ss_pred HHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHH
Q 045384 76 QLLIMELHAKWGNRWSKIAKHLPGRTDNEIKN 107 (194)
Q Consensus 76 d~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~kn 107 (194)
+..|.......|..|..+|..| |=+..+|.+
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 3456667788999999999999 777776654
No 111
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=50.37 E-value=36 Score=26.15 Aligned_cols=29 Identities=10% Similarity=-0.034 Sum_probs=22.9
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|....+||..| |-|...|+++.....++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999999 99999999987655443
No 112
>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=50.26 E-value=44 Score=19.73 Aligned_cols=33 Identities=27% Similarity=0.304 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHH
Q 045384 75 EQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNF 108 (194)
Q Consensus 75 Ed~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knr 108 (194)
|-..|.+++..+|++-+..|+.| |=+...+..+
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~k 38 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHH
Confidence 66788889999999999999999 7777666544
No 113
>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=48.64 E-value=27 Score=24.40 Aligned_cols=28 Identities=32% Similarity=0.674 Sum_probs=22.3
Q ss_pred HHHHHHhhcCcHHHHhhhCCCCCHHHHHH
Q 045384 79 IMELHAKWGNRWSKIAKHLPGRTDNEIKN 107 (194)
Q Consensus 79 Ll~~~~~~G~~W~~Ia~~l~gRt~~~~kn 107 (194)
|-.+....|..|..+|..| |=+..+|..
T Consensus 5 l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 5 LDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 4445577899999999999 888877765
No 114
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=48.63 E-value=62 Score=25.40 Aligned_cols=29 Identities=10% Similarity=0.004 Sum_probs=23.1
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.+.+||..| |-+...|+++....+++
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456799999999 99999999887665444
No 115
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=48.57 E-value=47 Score=24.78 Aligned_cols=29 Identities=10% Similarity=0.123 Sum_probs=23.3
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.-..||..| |-+...|+++....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355789999999 99999999988765443
No 116
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=48.00 E-value=25 Score=26.35 Aligned_cols=44 Identities=14% Similarity=0.092 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCc
Q 045384 21 EEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDV 66 (194)
Q Consensus 21 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~ 66 (194)
+-|.+++++++..+...+..||+.+| -++..|+.|-.++.+..+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCc
Confidence 55888999999998888999999996 788889998887766553
No 117
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=47.86 E-value=44 Score=26.08 Aligned_cols=30 Identities=23% Similarity=0.079 Sum_probs=23.9
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
-.|-....||..| |-+...|+++....+++
T Consensus 120 ~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 120 LEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3466889999999 99999999988755443
No 118
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=47.64 E-value=48 Score=25.34 Aligned_cols=31 Identities=16% Similarity=0.292 Sum_probs=25.2
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
-.|-...+||..+ |.+...|+.+-..-+++-
T Consensus 133 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 133 LDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3466899999999 999999999887665554
No 119
>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=47.37 E-value=26 Score=27.54 Aligned_cols=33 Identities=27% Similarity=0.354 Sum_probs=26.0
Q ss_pred CCCHHHHHHHHHHHHHhCCcchhhhhhhhC-CCcch
Q 045384 17 PWTMEEDLILINYIANHGEGVWNSLAKAAG-LKRTG 51 (194)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~-~~Rt~ 51 (194)
.||.|+.++|.++... |. .=.+||..|| ..|++
T Consensus 2 ~Wtde~~~~L~~lw~~-G~-SasqIA~~lg~vsRnA 35 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GL-SASQIARQLGGVSRNA 35 (162)
T ss_pred CCCHHHHHHHHHHHHc-CC-CHHHHHHHhCCcchhh
Confidence 5999999999999966 42 2789999999 44544
No 120
>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=47.32 E-value=34 Score=26.39 Aligned_cols=28 Identities=11% Similarity=0.120 Sum_probs=22.5
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|.....||..+ |-|...|+++....+++
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45789999999 89999999988665443
No 121
>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=47.22 E-value=34 Score=23.19 Aligned_cols=29 Identities=24% Similarity=0.548 Sum_probs=20.4
Q ss_pred HHHHHHHHHh-hcCcHHHHhhhCCCCCHHHH
Q 045384 76 QLLIMELHAK-WGNRWSKIAKHLPGRTDNEI 105 (194)
Q Consensus 76 d~~Ll~~~~~-~G~~W~~Ia~~l~gRt~~~~ 105 (194)
.+.|..++.. .|..|..+|..| |=+..+|
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 3455566666 899999999999 5455544
No 122
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=47.05 E-value=63 Score=24.21 Aligned_cols=28 Identities=7% Similarity=-0.086 Sum_probs=22.4
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
.|-.-..||..+ |-+...|+++....++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 455788999999 9999999998765443
No 123
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=46.98 E-value=99 Score=27.89 Aligned_cols=53 Identities=17% Similarity=0.268 Sum_probs=40.1
Q ss_pred cCCCCCHHHHHHHHHHHHhhcC----------------cHHHHhhhC-----CCCCHHHHHHHHHHHHHHHHHh
Q 045384 67 KRGNITPEEQLLIMELHAKWGN----------------RWSKIAKHL-----PGRTDNEIKNFWRTRIQKQIKQ 119 (194)
Q Consensus 67 ~~~~WT~eEd~~Ll~~~~~~G~----------------~W~~Ia~~l-----~gRt~~~~knrw~~~l~~~~~~ 119 (194)
.-|.|+++=|+...++...|.. +=..||.++ ..||..||-.+-..+-|+++++
T Consensus 75 aegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 75 AEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred cccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999987642 457888865 2488899988877776666544
No 124
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=46.15 E-value=49 Score=25.90 Aligned_cols=27 Identities=4% Similarity=-0.033 Sum_probs=22.4
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
.|-....||..| |.+...|+.|....+
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr 175 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRAR 175 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 356799999999 999999999876543
No 125
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=46.09 E-value=63 Score=25.05 Aligned_cols=29 Identities=14% Similarity=0.173 Sum_probs=23.4
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|....+||..+ |-+...|+.+....+++
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456799999999 99999999988665444
No 126
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=45.74 E-value=23 Score=33.74 Aligned_cols=47 Identities=17% Similarity=0.297 Sum_probs=35.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCC---------Ccchhhhhhhhhhhc
Q 045384 15 KGPWTMEEDLILINYIANHGEGVWNSLAKAAGL---------KRTGKSCRLRWLNYL 62 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~---------~Rt~~qcr~R~~~~L 62 (194)
|-.||-.|..-+..++..+| +++..|-+.+-. -+|-.|+|..|...+
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 56799999999999999999 569988333311 356678888776654
No 127
>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=45.65 E-value=32 Score=24.06 Aligned_cols=26 Identities=15% Similarity=0.414 Sum_probs=20.2
Q ss_pred HHHHHHHHHhhcCcHHHHhhhCCCCCH
Q 045384 76 QLLIMELHAKWGNRWSKIAKHLPGRTD 102 (194)
Q Consensus 76 d~~Ll~~~~~~G~~W~~Ia~~l~gRt~ 102 (194)
|..|.......|..|.++|..| |=+.
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 4456677888999999999988 4444
No 128
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=45.21 E-value=28 Score=23.11 Aligned_cols=44 Identities=18% Similarity=0.392 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCC-------ccCCCCCHHHHHHH
Q 045384 23 DLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPD-------VKRGNITPEEQLLI 79 (194)
Q Consensus 23 D~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~-------~~~~~WT~eEd~~L 79 (194)
+.+|.++|+.|| |..+++.+. -| |.. -+|. +++.+|..+..+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~-i~----CF~-----~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERIN-IN----CFK-----NNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTT-SS----STT-----SS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcc-cc----cCC-----CCCchHHHHHHHhcCHhHHHHHHHh
Confidence 568899999998 999999886 22 221 2333 35678877766654
No 129
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=44.87 E-value=73 Score=24.94 Aligned_cols=29 Identities=14% Similarity=0.089 Sum_probs=22.9
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-...+||..| |-+...|+.|....+++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 356788999999 99999999987665444
No 130
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=44.57 E-value=46 Score=25.55 Aligned_cols=28 Identities=11% Similarity=0.016 Sum_probs=22.1
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|..-.+||..+ |.+...|+++....+++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45788999999 89999999988655443
No 131
>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=44.49 E-value=52 Score=24.98 Aligned_cols=29 Identities=14% Similarity=0.331 Sum_probs=22.4
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-....||..+ |-|...|+++....+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355788889988 88999999988765544
No 132
>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=44.42 E-value=29 Score=24.19 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=23.2
Q ss_pred HHHHHHHHhhcCcHHHHhhhCCCCCHH---HHHHHH
Q 045384 77 LLIMELHAKWGNRWSKIAKHLPGRTDN---EIKNFW 109 (194)
Q Consensus 77 ~~Ll~~~~~~G~~W~~Ia~~l~gRt~~---~~knrw 109 (194)
..|..+....|..|..+|.+| |=+.. .|+.+|
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 347788899999999999998 54443 344444
No 133
>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=44.19 E-value=44 Score=26.10 Aligned_cols=48 Identities=19% Similarity=0.253 Sum_probs=34.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCC---Ccchhhhhhhhhhh
Q 045384 13 VRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGL---KRTGKSCRLRWLNY 61 (194)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~---~Rt~~qcr~R~~~~ 61 (194)
...-.-|..|..-|..+|++||. +...+|.-..+ ..|+.||+.+...|
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 34556789999999999999995 58887754321 36777777666554
No 134
>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=43.93 E-value=58 Score=25.48 Aligned_cols=28 Identities=11% Similarity=0.051 Sum_probs=22.8
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
.|.....||..| |-+...|+.|....++
T Consensus 146 ~g~s~~EIA~~l-gis~~tvk~rl~Rar~ 173 (188)
T TIGR02943 146 LGFESDEICQEL-EISTSNCHVLLYRARL 173 (188)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 456789999999 9999999998765543
No 135
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=43.66 E-value=59 Score=24.74 Aligned_cols=29 Identities=21% Similarity=0.270 Sum_probs=22.6
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.-.+||..| |.+...|+.+....+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355678999999 99999999988765443
No 136
>PRK00118 putative DNA-binding protein; Validated
Probab=43.46 E-value=83 Score=22.88 Aligned_cols=39 Identities=18% Similarity=0.083 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 74 EEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 74 eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
+.+..++.+....|-....||+.+ |-|...|+.+-....
T Consensus 20 ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RAr 58 (104)
T PRK00118 20 EKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTE 58 (104)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 455566677777788999999999 999999988766543
No 137
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=43.34 E-value=59 Score=25.04 Aligned_cols=30 Identities=10% Similarity=0.127 Sum_probs=23.5
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
.|....+||..| |-+...|+.+....+++-
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAAL 175 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 355789999999 999999999887655443
No 138
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=43.30 E-value=64 Score=24.09 Aligned_cols=45 Identities=9% Similarity=0.106 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHhhcC-cHHHHhhhCCCCCHHHHHHHHHHHHHHHHHh
Q 045384 74 EEQLLIMELHAKWGN-RWSKIAKHLPGRTDNEIKNFWRTRIQKQIKQ 119 (194)
Q Consensus 74 eEd~~Ll~~~~~~G~-~W~~Ia~~l~gRt~~~~knrw~~~l~~~~~~ 119 (194)
+-|..|+...+.-+. .+..||+.+ |-+...|.+|-+.+.+..+-+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCcee
Confidence 557788888887774 699999999 999999999998777665433
No 139
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=42.39 E-value=78 Score=24.55 Aligned_cols=29 Identities=10% Similarity=0.108 Sum_probs=23.1
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-....||..| |-|...|+++....+++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 455789999999 88999999988764443
No 140
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=41.96 E-value=56 Score=25.40 Aligned_cols=27 Identities=11% Similarity=0.086 Sum_probs=21.3
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
|-....||..+ |-+...|+++....++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~ 180 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRARE 180 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45688999999 8899999998765443
No 141
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=41.87 E-value=80 Score=24.36 Aligned_cols=31 Identities=13% Similarity=0.057 Sum_probs=24.5
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
..|-...+||+.| |.+...|+++-...+++-
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~L 173 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKAL 173 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3456789999999 999999999887655443
No 142
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=41.76 E-value=34 Score=31.67 Aligned_cols=42 Identities=21% Similarity=0.378 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhh-hCCCCCHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAK-HLPGRTDNEIKNFWR 110 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~-~l~gRt~~~~knrw~ 110 (194)
..|+..|-.+.-+++.+||+.+..|.. +||-++-.+|-.+|.
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 379999999999999999999999966 779999999988775
No 143
>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=41.46 E-value=66 Score=24.15 Aligned_cols=28 Identities=25% Similarity=0.351 Sum_probs=21.8
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-.+||+.| |.+...|+++-...+++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55778999999 99999999887655443
No 144
>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=41.31 E-value=68 Score=24.57 Aligned_cols=29 Identities=24% Similarity=0.252 Sum_probs=23.1
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-....||..+ |-+...|+++....+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355789999999 99999999988765443
No 145
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=41.16 E-value=32 Score=25.70 Aligned_cols=44 Identities=18% Similarity=0.370 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCC-------ccCCCCCHHHHHHH
Q 045384 23 DLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPD-------VKRGNITPEEQLLI 79 (194)
Q Consensus 23 D~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~-------~~~~~WT~eEd~~L 79 (194)
+.+|.++|+.|| |..++..++ ..|.. -+|. +++.+|..|..+.+
T Consensus 21 E~llt~Lvd~YG---Wd~L~~ri~-----inCF~-----ndPSi~SSlKfLrkT~WARekvEa~ 71 (136)
T COG4628 21 ETLLTELVDFYG---WDGLATRIR-----INCFH-----NDPSIKSSLKFLRKTPWAREKVEAL 71 (136)
T ss_pred HHHHHHHHHHhC---hHHHHhhce-----ecccc-----CCccHHHHHHHHhcCHhHHHHHHHH
Confidence 568889999999 999997765 34432 1222 35677777665544
No 146
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=40.97 E-value=67 Score=24.61 Aligned_cols=30 Identities=23% Similarity=0.417 Sum_probs=24.6
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQKQI 117 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~~ 117 (194)
|-.-.+||+.+ |-+...|+++....+++-.
T Consensus 135 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 135 GLTYSEIAHKL-GVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 45789999999 9999999999877665543
No 147
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=40.37 E-value=75 Score=24.74 Aligned_cols=30 Identities=13% Similarity=0.057 Sum_probs=24.2
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
.|-.-.+||..+ |-+...|+.+....+++-
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDAL 174 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 345789999999 999999999987665544
No 148
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=40.04 E-value=76 Score=23.47 Aligned_cols=28 Identities=21% Similarity=0.332 Sum_probs=21.4
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|..-..||..+ |.+..+|+++-...+++
T Consensus 122 ~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 122 GKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45678899998 99999999877654443
No 149
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=39.88 E-value=70 Score=24.51 Aligned_cols=28 Identities=18% Similarity=0.348 Sum_probs=22.3
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-..||..| |.+...|+++....+++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 55788999999 99999999987655433
No 150
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=39.53 E-value=1.1e+02 Score=23.94 Aligned_cols=30 Identities=13% Similarity=0.088 Sum_probs=23.7
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
-.|-....||..| |-+...|+++....+++
T Consensus 127 ~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~ 156 (188)
T PRK12546 127 ASGFSYEEAAEMC-GVAVGTVKSRANRARAR 156 (188)
T ss_pred hcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 99999999988765443
No 151
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=39.46 E-value=92 Score=24.03 Aligned_cols=29 Identities=7% Similarity=0.004 Sum_probs=22.2
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|..-..||+.+ |-+...|+++....+++
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRA 171 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 455788999998 99999999887654433
No 152
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=39.21 E-value=80 Score=23.69 Aligned_cols=29 Identities=21% Similarity=0.312 Sum_probs=23.2
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.-..||..+ |-+...|+.|....+++
T Consensus 128 ~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 128 DGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 99999999988665443
No 153
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=39.07 E-value=1.2e+02 Score=22.73 Aligned_cols=28 Identities=21% Similarity=0.372 Sum_probs=22.1
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-..||..| |-+...|+++....++.
T Consensus 121 ~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 121 GLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 44678999999 99999999987654443
No 154
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=38.46 E-value=95 Score=22.68 Aligned_cols=66 Identities=18% Similarity=0.144 Sum_probs=45.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHH
Q 045384 8 SQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLL 78 (194)
Q Consensus 8 ~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~ 78 (194)
.+.|..+.++ .-+.+.|..+|+.++..--.+||+.++. ..+...++...|.-..++..+..+++..
T Consensus 46 ~~~~k~r~~~--Kid~~~L~~~v~~~pd~tl~Ela~~l~V---s~~ti~~~Lkrlg~t~KK~~~~~~~~~~ 111 (119)
T PF01710_consen 46 DLEPKPRGRK--KIDRDELKALVEENPDATLRELAERLGV---SPSTIWRALKRLGITRKKKTLHSEKDRE 111 (119)
T ss_pred cccccccccc--cccHHHHHHHHHHCCCcCHHHHHHHcCC---CHHHHHHHHHHcCchhccCcccchhHHH
Confidence 3445555554 3356679999999998777899999973 4445556667777777777776655543
No 155
>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=37.90 E-value=76 Score=24.71 Aligned_cols=45 Identities=18% Similarity=0.222 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHHHhhcCcHHHHhhhCC----CCCHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGNRWSKIAKHLP----GRTDNEIKNFWRTR 112 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~----gRt~~~~knrw~~~ 112 (194)
...-|+.|..-|..++.+||..+..+|.-.. -.|..+|+.+...+
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 4467899999999999999999999988432 48999998876544
No 156
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=37.46 E-value=88 Score=23.68 Aligned_cols=29 Identities=17% Similarity=0.083 Sum_probs=22.9
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.-..||..+ |-+...|+++-...+++
T Consensus 127 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 127 SGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 455789999999 99999999988665444
No 157
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=37.33 E-value=27 Score=25.97 Aligned_cols=28 Identities=14% Similarity=0.089 Sum_probs=23.0
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.+.+||..| |-+...|+++.....++
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKE 148 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44799999999 99999999988765444
No 158
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=37.22 E-value=82 Score=24.67 Aligned_cols=29 Identities=21% Similarity=0.098 Sum_probs=23.0
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
..|-...+||..| |-+...|+++-...++
T Consensus 130 ~~g~s~~EIA~~L-gis~~tVk~~l~Rar~ 158 (187)
T PRK12516 130 ASGFAYEEAAEIC-GCAVGTIKSRVNRARQ 158 (187)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3466789999999 9999999998765443
No 159
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=36.51 E-value=1.3e+02 Score=24.54 Aligned_cols=45 Identities=20% Similarity=0.298 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
...|+-|-+.|.-+.+ |....+||..| +-+...|+++-..+++|-
T Consensus 132 ~~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkKL 176 (198)
T PRK15201 132 RHFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRKL 176 (198)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 3588888876654443 77788999999 999999999887777663
No 160
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=35.73 E-value=1.2e+02 Score=23.55 Aligned_cols=27 Identities=11% Similarity=0.111 Sum_probs=21.7
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
.|-.-..||..| |-+...|+.+....+
T Consensus 151 ~g~s~~EIA~~l-gis~~tVk~~l~Rar 177 (195)
T PRK12532 151 LGFSSDEIQQMC-GISTSNYHTIMHRAR 177 (195)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 456789999999 999999998876543
No 161
>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=35.39 E-value=89 Score=23.37 Aligned_cols=37 Identities=14% Similarity=0.119 Sum_probs=26.2
Q ss_pred HHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 79 IMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 79 Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
++.+.--.|-.-..||..+ |-+...|+++....+++-
T Consensus 118 i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 118 VVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARL 154 (162)
T ss_pred HhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 3333334456778999999 999999999887655443
No 162
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.26 E-value=1.3e+02 Score=21.46 Aligned_cols=46 Identities=28% Similarity=0.504 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCC-CHHHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGNRWSKIAKHLPGR-TDNEIKNFWRTRIQK 115 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gR-t~~~~knrw~~~l~~ 115 (194)
+..||+|.-..+++++..-|..=+.||+.+ |- ..+++ .+|...+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l-~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQL-YKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHH-HHHHHHHHH
Confidence 457999999999999999999889999999 76 55544 456444433
No 163
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=35.15 E-value=93 Score=24.03 Aligned_cols=29 Identities=10% Similarity=0.367 Sum_probs=23.0
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.-..||..| |-+...|+++....+++
T Consensus 137 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 165 (185)
T PRK12542 137 YNLTYQEISSVM-GITEANVRKQFERARKR 165 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 455789999999 99999999987654443
No 164
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=34.56 E-value=97 Score=23.79 Aligned_cols=28 Identities=21% Similarity=0.246 Sum_probs=22.0
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-.+||..+ |-|...|+.+....+++
T Consensus 151 ~~s~~eIA~~l-gis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 151 GYTHREAAQLL-GLPLGTLKTRARRALSR 178 (186)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 44678999999 99999999887665444
No 165
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=34.37 E-value=82 Score=25.21 Aligned_cols=44 Identities=11% Similarity=0.132 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
..|+-|-+.|.-+.. |..-.+||+.| +-+...|+++-..+++|-
T Consensus 137 ~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~I~~KL 180 (207)
T PRK15411 137 SLSRTESSMLRMWMA--GQGTIQISDQM-NIKAKTVSSHKGNIKRKI 180 (207)
T ss_pred cCCHHHHHHHHHHHc--CCCHHHHHHHc-CCCHHHHHHHHHHHHHHh
Confidence 488888887655543 55567999999 999999999888777764
No 166
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=34.36 E-value=98 Score=24.01 Aligned_cols=27 Identities=11% Similarity=-0.072 Sum_probs=21.7
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
|..-.+||..+ |-+...|+++....++
T Consensus 147 g~s~~EIA~~l-gis~~tV~~~l~Rar~ 173 (191)
T PRK12520 147 ELETEEICQEL-QITATNAWVLLYRARM 173 (191)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45678999999 9999999998765443
No 167
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=34.00 E-value=70 Score=22.15 Aligned_cols=25 Identities=28% Similarity=0.662 Sum_probs=19.0
Q ss_pred HHHHhhcCcHHHHhhhCCCCCHHHHH
Q 045384 81 ELHAKWGNRWSKIAKHLPGRTDNEIK 106 (194)
Q Consensus 81 ~~~~~~G~~W~~Ia~~l~gRt~~~~k 106 (194)
-+....|..|..+|..| |=|..+|.
T Consensus 7 ~i~~~lG~~Wk~laR~L-Glse~~Id 31 (86)
T cd08306 7 VICENVGRDWRKLARKL-GLSETKIE 31 (86)
T ss_pred HHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 34466799999999999 66666654
No 168
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=33.97 E-value=1.1e+02 Score=24.71 Aligned_cols=44 Identities=20% Similarity=0.212 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
..|+-|-+.| .++.. |..-.+||+.| +-+...|+++-..+++|-
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 4787666655 55544 88889999999 999999999988877664
No 169
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=33.92 E-value=97 Score=24.47 Aligned_cols=25 Identities=16% Similarity=0.058 Sum_probs=20.7
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTR 112 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~ 112 (194)
|..-..||..+ |.+...|++|....
T Consensus 155 g~s~~EIA~~l-gis~~tVk~~l~RA 179 (201)
T PRK12545 155 DFEIDDICTEL-TLTANHCSVLLYRA 179 (201)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 45789999999 99999999887543
No 170
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=33.85 E-value=1.4e+02 Score=23.83 Aligned_cols=29 Identities=21% Similarity=0.242 Sum_probs=22.5
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
|..-..||..| |-+...|+++....+++-
T Consensus 154 g~s~~EIA~~L-gis~~tV~~~l~RArk~L 182 (203)
T PRK09647 154 GLSYEEIAATL-GVKLGTVRSRIHRGRQQL 182 (203)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45678899999 999999999887654443
No 171
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=33.80 E-value=49 Score=26.89 Aligned_cols=28 Identities=14% Similarity=0.109 Sum_probs=22.6
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-.+||..| |.+..+|+++....+++
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~k 192 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARRL 192 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45689999999 99999999988765443
No 172
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=33.50 E-value=27 Score=35.94 Aligned_cols=74 Identities=24% Similarity=0.332 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHHHHHhh-cCcHHHH
Q 045384 15 KGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIMELHAKW-GNRWSKI 93 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~~~~~~-G~~W~~I 93 (194)
-.-|..++|..|+-.|-+||.++|..|-.-=-++=+.+ ..+...+..+.+=...-..|+.++..+ +.+|...
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dK-------i~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~ 1205 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDK-------IFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKK 1205 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccccHHHhccCccccchhh-------hcccccCCchHHHHHHHHHHHHHHhhcccCCCchh
Confidence 34599999999999999999999999863211111111 111112334445555556666666665 4445554
Q ss_pred hh
Q 045384 94 AK 95 (194)
Q Consensus 94 a~ 95 (194)
.+
T Consensus 1206 ~~ 1207 (1373)
T KOG0384|consen 1206 LK 1207 (1373)
T ss_pred hh
Confidence 43
No 173
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=33.36 E-value=1.4e+02 Score=23.29 Aligned_cols=28 Identities=18% Similarity=0.294 Sum_probs=21.5
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-.+||+.| |-+...|+++-...+++
T Consensus 158 ~~s~~EIA~~L-gis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 158 GLTYREVAERL-AVPLGTVKTRMRDGLIR 185 (194)
T ss_pred CCCHHHHHHHh-CCChHhHHHHHHHHHHH
Confidence 45789999999 88999998877554433
No 174
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=33.24 E-value=1.5e+02 Score=22.96 Aligned_cols=28 Identities=36% Similarity=0.439 Sum_probs=21.7
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.=.+||..+ |.|...|+++-...+++
T Consensus 147 g~s~~EIAe~l-gis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 147 GEKIEEIAKKL-GLTRSAIDNRLSRGRKK 174 (189)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45668899999 99999999987665444
No 175
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=33.04 E-value=1e+02 Score=23.75 Aligned_cols=29 Identities=21% Similarity=0.344 Sum_probs=22.7
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.-..||..+ |-+...|+++....+++
T Consensus 148 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 148 DGCSHAEIAQRL-GAPLGTVKAWIKRSLKA 176 (182)
T ss_pred cCCCHHHHHHHH-CCChhhHHHHHHHHHHH
Confidence 355678899999 99999999988766544
No 176
>smart00351 PAX Paired Box domain.
Probab=32.99 E-value=2e+02 Score=21.19 Aligned_cols=73 Identities=15% Similarity=0.132 Sum_probs=46.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCc-chhhhhhhhhh--hcCCCcc----CCCCCHHHHHHHHHHHHh
Q 045384 13 VRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKR-TGKSCRLRWLN--YLRPDVK----RGNITPEEQLLIMELHAK 85 (194)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~R-t~~qcr~R~~~--~L~p~~~----~~~WT~eEd~~Ll~~~~~ 85 (194)
+...+.+.++-+.++.++. -|. .-..||+.++..| |...+..||.. .+.|... ...-+++++..|++++..
T Consensus 13 ~~~~~~s~~~R~riv~~~~-~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~ 90 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQ-NGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQE 90 (125)
T ss_pred cCCCCCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHH
Confidence 3455689999999998886 453 4789999998543 35555666654 2444322 223456666667766655
Q ss_pred hc
Q 045384 86 WG 87 (194)
Q Consensus 86 ~G 87 (194)
.+
T Consensus 91 ~p 92 (125)
T smart00351 91 NP 92 (125)
T ss_pred CC
Confidence 54
No 177
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.09 E-value=67 Score=24.91 Aligned_cols=39 Identities=28% Similarity=0.199 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHH
Q 045384 70 NITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFW 109 (194)
Q Consensus 70 ~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw 109 (194)
.||+|-.+.|.++-. -|-.=++||..|.|=+.+.|--+-
T Consensus 2 nWtdERve~LkKLWs-eGLSASQIAaQLGGVsRnAVIGKV 40 (169)
T COG5352 2 NWTDERVETLKKLWS-EGLSASQIAAQLGGVSRNAVIGKV 40 (169)
T ss_pred CchHHHHHHHHHHHH-cccCHHHHHHHhcCcchhhhheee
Confidence 599999888877654 366778999999998888775433
No 178
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=31.25 E-value=66 Score=19.22 Aligned_cols=28 Identities=29% Similarity=0.383 Sum_probs=19.2
Q ss_pred HHHHHHHhhcCcHHHHhhhCCCCCHHHHHH
Q 045384 78 LIMELHAKWGNRWSKIAKHLPGRTDNEIKN 107 (194)
Q Consensus 78 ~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~kn 107 (194)
.++.++.. |.....||+.| |-+...|.+
T Consensus 9 ~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~ 36 (50)
T PF13384_consen 9 QIIRLLRE-GWSIREIAKRL-GVSRSTVYR 36 (50)
T ss_dssp -HHHHHHH-T--HHHHHHHH-TS-HHHHHH
T ss_pred HHHHHHHC-CCCHHHHHHHH-CcCHHHHHH
Confidence 45566666 88999999999 888888765
No 179
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=30.56 E-value=1.2e+02 Score=22.60 Aligned_cols=29 Identities=21% Similarity=0.310 Sum_probs=22.3
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.=..||..| |-+...|+++....+++
T Consensus 126 ~g~s~~eIA~~l-gis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 126 SGYSYKEIAEAL-GIKESSVGTTLARAKKK 154 (166)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 556678899999 99999999887654443
No 180
>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=30.43 E-value=1.5e+02 Score=22.62 Aligned_cols=29 Identities=14% Similarity=0.504 Sum_probs=22.2
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.-.+||..+ |-|...|+.+....+++
T Consensus 155 ~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 155 EGLSFAEVAERM-DRSEGAVSMLWVRGLAR 183 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 455778899988 99999998887655444
No 181
>PHA01083 hypothetical protein
Probab=30.22 E-value=77 Score=24.70 Aligned_cols=67 Identities=19% Similarity=0.233 Sum_probs=36.7
Q ss_pred HHHHHH-HHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHHHHHhhcC---------------
Q 045384 25 ILINYI-ANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIMELHAKWGN--------------- 88 (194)
Q Consensus 25 ~L~~~v-~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~~~~~~G~--------------- 88 (194)
.|++++ +.....+-..||+.+|..|.. ...|++-+ +.+.++++-..|-++...-+.
T Consensus 5 kLLda~K~a~~~~sdkqLA~~LGVs~q~---IS~~R~G~-----r~~i~de~A~~LAe~aGiDp~eall~i~aDraetp~ 76 (149)
T PHA01083 5 KLLDAYKKAKNYVQYKQIAHDLGVSPQK---ISKMRTGV-----RTYISDEEAIFLAESAGIDPEIALLGCHADRNENPR 76 (149)
T ss_pred HHHHHHHHHHhhccHHHHHHHhCCCHHH---HHHHHcCC-----CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhcCCHH
Confidence 344444 445555688999999854443 34454321 224566555554444322111
Q ss_pred ---cHHHHhhhCCC
Q 045384 89 ---RWSKIAKHLPG 99 (194)
Q Consensus 89 ---~W~~Ia~~l~g 99 (194)
=|..|++++.|
T Consensus 77 ~kalWesIaKKlng 90 (149)
T PHA01083 77 AKAIWESIAKKQNG 90 (149)
T ss_pred HHHHHHHHHHHHhc
Confidence 28888887755
No 182
>PF13340 DUF4096: Putative transposase of IS4/5 family (DUF4096)
Probab=30.14 E-value=26 Score=23.50 Aligned_cols=59 Identities=10% Similarity=0.194 Sum_probs=35.4
Q ss_pred chhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHHHH---HhhcCcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 37 VWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIMELH---AKWGNRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 37 ~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~~~---~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
.|..|+..|+ .+...--+ ..-++..+++++ ...|..|..+...|+ ....|.++|+...
T Consensus 5 ~W~~i~p~lp-~~~~~~~~----------------~~~~~R~v~~ail~~lrtG~~Wr~LP~~fg--~~~tv~~~f~rW~ 65 (75)
T PF13340_consen 5 EWALIEPLLP-PRKPRGGR----------------PRIDLREVLNAILYVLRTGCPWRDLPEDFG--PWSTVYRRFRRWS 65 (75)
T ss_pred HHHHHHhhCC-CCCCCCCC----------------CccchHHHHhcccccceecceecccchhcc--CcCcHHHHHHHHH
Confidence 5999999998 33321100 111333444543 466889999999996 4446677776544
Q ss_pred H
Q 045384 114 Q 114 (194)
Q Consensus 114 ~ 114 (194)
+
T Consensus 66 ~ 66 (75)
T PF13340_consen 66 R 66 (75)
T ss_pred H
Confidence 3
No 183
>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=30.14 E-value=81 Score=21.28 Aligned_cols=36 Identities=19% Similarity=0.277 Sum_probs=25.2
Q ss_pred hhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHH
Q 045384 38 WNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIME 81 (194)
Q Consensus 38 W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~ 81 (194)
-..||..+. |+|+.++|..+. +. ..+|+||...|.+
T Consensus 36 ~~~iA~~i~-gks~eeir~~fg------i~-~d~t~eee~~i~~ 71 (78)
T PF01466_consen 36 CKYIANMIK-GKSPEEIRKYFG------IE-NDLTPEEEEEIRK 71 (78)
T ss_dssp HHHHHHHHT-TS-HHHHHHHHT----------TSSHHHHHHHHH
T ss_pred HHHHHHHhc-CCCHHHHHHHcC------CC-CCCCHHHHHHHHH
Confidence 568888887 999999998662 22 3689988877543
No 184
>PRK01905 DNA-binding protein Fis; Provisional
Probab=30.11 E-value=1.6e+02 Score=19.86 Aligned_cols=35 Identities=23% Similarity=0.188 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHH
Q 045384 73 PEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNF 108 (194)
Q Consensus 73 ~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knr 108 (194)
.-|...+..++...|...++.|+.+ |-+...++.+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 3466678889999999999999998 6666555443
No 185
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=29.69 E-value=1.6e+02 Score=19.09 Aligned_cols=45 Identities=24% Similarity=0.425 Sum_probs=31.4
Q ss_pred CCCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
+..||+|+-..++..+..-|..-..||+.+ |=+..++.+ |...++
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~-gi~~~~l~~-W~~~~~ 48 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREY-GISPSTLYN-WRKQYR 48 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHH-TS-HHHHHH-HHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeeccc-ccccccccH-HHHHHh
Confidence 457999999999999988899999999988 556666554 655443
No 186
>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=29.57 E-value=1e+02 Score=26.08 Aligned_cols=28 Identities=18% Similarity=0.222 Sum_probs=22.5
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
.|-.-.+||..| |.+...|+++....++
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 184 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARA 184 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355789999999 9999999998765443
No 187
>PRK06930 positive control sigma-like factor; Validated
Probab=28.41 E-value=1.4e+02 Score=23.42 Aligned_cols=31 Identities=19% Similarity=0.306 Sum_probs=24.2
Q ss_pred HhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 84 AKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 84 ~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
...|..-..||..| |-+...|+.+....+++
T Consensus 127 ~~eg~s~~EIA~~l-giS~~tVk~~l~Ra~~k 157 (170)
T PRK06930 127 RGYGLSYSEIADYL-NIKKSTVQSMIERAEKK 157 (170)
T ss_pred HHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 34567789999999 99999999887665444
No 188
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.24 E-value=1.1e+02 Score=23.71 Aligned_cols=28 Identities=36% Similarity=0.313 Sum_probs=21.1
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.=..||..+ |-+...|+.+....+++
T Consensus 157 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 184 (194)
T PRK12519 157 GLSQSEIAKRL-GIPLGTVKARARQGLLK 184 (194)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 45678899999 88999999877654443
No 189
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=28.21 E-value=42 Score=22.45 Aligned_cols=18 Identities=17% Similarity=0.484 Sum_probs=14.4
Q ss_pred HHHHHHHhhcCcHHHHhh
Q 045384 78 LIMELHAKWGNRWSKIAK 95 (194)
Q Consensus 78 ~Ll~~~~~~G~~W~~Ia~ 95 (194)
.|.++++.||++|.-|-.
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 466788889999999864
No 190
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=28.11 E-value=1.9e+02 Score=22.43 Aligned_cols=76 Identities=12% Similarity=-0.022 Sum_probs=55.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHHHHHHhhc
Q 045384 8 SQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIMELHAKWG 87 (194)
Q Consensus 8 ~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll~~~~~~G 87 (194)
...|.+..-+.|++|=..|..-.+..|.. ..++-..+= .+.. +.+.-..-|.|+-..|+..+...|
T Consensus 21 ~~~~kvVsvRLTe~Ey~~L~~rA~~aGlS-~SEfIRqAi-~~~~------------g~V~v~r~T~e~~~~lir~l~gia 86 (147)
T PRK13858 21 VEGFKVVSTRLRSAEYESFSAQARLLGLS-DSMAIRVAV-RRIG------------GFLEIDAETREKMEAILQSIGTLS 86 (147)
T ss_pred ccCCeEEEEecCHHHHHHHHHHHHHcCCC-HHHHHHHHH-HhcC------------CeEeecccCHHHHHHHHHHHHHHH
Confidence 66777888899999999999999999964 443332221 1111 222235678888888999999999
Q ss_pred CcHHHHhhhC
Q 045384 88 NRWSKIAKHL 97 (194)
Q Consensus 88 ~~W~~Ia~~l 97 (194)
++-.+||+++
T Consensus 87 nNLNQLAr~a 96 (147)
T PRK13858 87 SNIAALLSAY 96 (147)
T ss_pred HHHHHHHHHH
Confidence 9999999987
No 191
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=28.03 E-value=1.7e+02 Score=23.66 Aligned_cols=30 Identities=13% Similarity=0.212 Sum_probs=23.5
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
.|-....||..+ |-+...|+.+....+++-
T Consensus 199 ~g~s~~EIA~~l-gis~~tV~~~~~ra~~~L 228 (236)
T PRK06986 199 EELNLKEIGAVL-GVSESRVSQIHSQAIKRL 228 (236)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 455789999999 999999998876655443
No 192
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=27.78 E-value=73 Score=24.23 Aligned_cols=29 Identities=24% Similarity=0.411 Sum_probs=22.6
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-....||..| |-+...|+.+....+++
T Consensus 141 ~g~s~~eIA~~l-~is~~~V~~~l~ra~~~ 169 (176)
T PRK09638 141 YGYTYEEIAKML-NIPEGTVKSRVHHGIKQ 169 (176)
T ss_pred cCCCHHHHHHHH-CCChhHHHHHHHHHHHH
Confidence 355789999999 88999998887655444
No 193
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=27.75 E-value=2e+02 Score=21.51 Aligned_cols=44 Identities=20% Similarity=0.265 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
...|+.|-+.|.-+.. |-.-.+||..+ +-+...|+++.+++++|
T Consensus 136 ~~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHRANLMEK 179 (196)
T ss_pred cCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3688888776655443 55778999999 78999999988777665
No 194
>PRK09483 response regulator; Provisional
Probab=27.51 E-value=1.2e+02 Score=23.13 Aligned_cols=45 Identities=11% Similarity=0.295 Sum_probs=33.9
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
...|+-|-+.|.-+ ..|..=.+||..| +-+...|+++-+.+++|-
T Consensus 147 ~~Lt~rE~~vl~~~--~~G~~~~~Ia~~l-~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMI--TKGQKVNEISEQL-NLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHH--HCCCCHHHHHHHh-CCCHHHHHHHHHHHHHHc
Confidence 35888888877443 3565566999999 789999999887777663
No 195
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=27.50 E-value=1.6e+02 Score=22.29 Aligned_cols=29 Identities=17% Similarity=0.294 Sum_probs=23.0
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
|-...+||..| |-+...|+++-...++.-
T Consensus 134 g~s~~EIA~~l-~is~~tV~~~l~ra~~~~ 162 (168)
T PRK12525 134 GLTYVEIGERL-GVSLSRIHQYMVEAFKCC 162 (168)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45789999999 999999998876655543
No 196
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=27.42 E-value=82 Score=20.64 Aligned_cols=25 Identities=44% Similarity=0.789 Sum_probs=17.7
Q ss_pred HHHHHhhcCcHHHHhhhCCCCCHHHH
Q 045384 80 MELHAKWGNRWSKIAKHLPGRTDNEI 105 (194)
Q Consensus 80 l~~~~~~G~~W~~Ia~~l~gRt~~~~ 105 (194)
..+....|..|..+|..| |=+..+|
T Consensus 3 ~~ia~~lg~~W~~la~~L-gl~~~~I 27 (79)
T cd01670 3 DKLAKKLGKDWKKLARKL-GLSDGEI 27 (79)
T ss_pred HHHHHHHhhHHHHHHHHh-CCCHHHH
Confidence 345567789999999998 4444444
No 197
>PRK02866 cyanate hydratase; Validated
Probab=27.41 E-value=86 Score=24.36 Aligned_cols=33 Identities=18% Similarity=0.277 Sum_probs=26.8
Q ss_pred HHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHH
Q 045384 77 LLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWR 110 (194)
Q Consensus 77 ~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~ 110 (194)
+.|+++-.+-|-.|..||+.+ |++...+-.-..
T Consensus 8 e~Ll~AK~~kGLTw~~IA~~i-G~S~v~vaaa~l 40 (147)
T PRK02866 8 EKILAAKKEKGLTWADIAEAI-GLSEVWVTAALL 40 (147)
T ss_pred HHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHh
Confidence 357777788899999999999 999987766443
No 198
>PTZ00155 40S ribosomal protein S9; Provisional
Probab=26.72 E-value=3.4e+02 Score=21.80 Aligned_cols=84 Identities=14% Similarity=0.054 Sum_probs=49.3
Q ss_pred CCCCCCC-CCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHH
Q 045384 1 MDKTPCN-SQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLI 79 (194)
Q Consensus 1 m~r~~~n-~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~L 79 (194)
||+.|-+ +..-...+.||-.+--..=.+++.+||-.+=.++-+. .+-...+|..-..++.-. ..+++-..+.+.|
T Consensus 1 ~~~~~~~~~k~y~~P~~P~~k~rl~~E~~li~kYgLknk~E~wk~---~~~~~kiR~~Ar~L~~l~-~~d~~r~~~~~~L 76 (181)
T PTZ00155 1 MGRNYRNHSKTYKTPRRPFEKERLDAELKLCGEYGLKNKREIWRV---QYTLAKIRKAARELLTLD-EKDPKRLFEGEAL 76 (181)
T ss_pred CCCCCCCCCcccCCCCCchhHHHHHHHHHHHHHHCCCCHHHHHHH---HHHHHHHHHHHHHHHhcC-CCCcHHHHHHHHH
Confidence 6666654 4555667888988776666778889997763333222 122223333333333211 2356666666778
Q ss_pred HHHHHhhcC
Q 045384 80 MELHAKWGN 88 (194)
Q Consensus 80 l~~~~~~G~ 88 (194)
+.-...||-
T Consensus 77 L~kL~~~Gi 85 (181)
T PTZ00155 77 LRRMHRLGL 85 (181)
T ss_pred HHHHHHhCC
Confidence 888888884
No 199
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=26.66 E-value=1.6e+02 Score=22.98 Aligned_cols=29 Identities=14% Similarity=0.015 Sum_probs=22.3
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|..-.+||..| |-+...|+++....+++
T Consensus 126 eg~s~~EIA~~l-gis~~tV~~~l~Rar~~ 154 (182)
T PRK12511 126 EGLSYQEAAAVL-GIPIGTLMSRIGRARAA 154 (182)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 355788999999 99999999987654443
No 200
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=26.40 E-value=90 Score=24.34 Aligned_cols=32 Identities=22% Similarity=0.220 Sum_probs=25.4
Q ss_pred HHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHH
Q 045384 77 LLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFW 109 (194)
Q Consensus 77 ~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw 109 (194)
+.|+++-..-|-.|..||+.+ |++...+-.-.
T Consensus 11 ~~Ll~AK~~KGLTwe~IAe~i-G~sevwvaaa~ 42 (150)
T TIGR00673 11 DALLESKKKKGLTFADIADGL-GLAEVFVAAAL 42 (150)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 457777788899999999999 89987665433
No 201
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=26.37 E-value=1.7e+02 Score=21.80 Aligned_cols=28 Identities=18% Similarity=0.182 Sum_probs=21.2
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-.+||..| |-+...|+.+-...+++
T Consensus 128 ~~s~~eIA~~l-gis~~tv~~~l~Rar~~ 155 (161)
T PRK12541 128 GFSYKEIAEMT-GLSLAKVKIELHRGRKE 155 (161)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44678999999 88899998887655443
No 202
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=26.36 E-value=1.5e+02 Score=25.04 Aligned_cols=29 Identities=21% Similarity=0.390 Sum_probs=22.9
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.-.+||..+ |.+...|+++.....++
T Consensus 130 ~g~s~~EIA~~l-g~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 130 FGVPFDEIASTL-GRSPAACRQLASRARKH 158 (293)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355678999999 99999999988654433
No 203
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=26.25 E-value=2e+02 Score=22.89 Aligned_cols=28 Identities=4% Similarity=-0.070 Sum_probs=21.9
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
.|-.-.+||..+ |-|...|++|....++
T Consensus 163 ~g~s~~EIAe~l-gis~~tV~~~l~RAr~ 190 (206)
T PRK12544 163 IELETNEICHAV-DLSVSNLNVLLYRARL 190 (206)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 345678999999 9999999998765443
No 204
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=26.11 E-value=1.2e+02 Score=24.74 Aligned_cols=28 Identities=14% Similarity=0.162 Sum_probs=22.0
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-.+||..| |.+...|+++....+++
T Consensus 187 g~s~~EIA~~L-gis~~tVk~~l~RAr~k 214 (233)
T PRK12538 187 NMSNGEIAEVM-DTTVAAVESLLKRGRQQ 214 (233)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45678999999 99999999887654443
No 205
>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=25.96 E-value=1.8e+02 Score=21.48 Aligned_cols=25 Identities=28% Similarity=0.363 Sum_probs=18.3
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTR 112 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~ 112 (194)
|-.=..||..+ |-|...|+.+....
T Consensus 127 g~~~~eIA~~l-~is~~tv~~~l~Ra 151 (159)
T TIGR02989 127 GVSLTALAEQL-GRTVNAVYKALSRL 151 (159)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHH
Confidence 44667888888 88888888776544
No 206
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=25.68 E-value=1.5e+02 Score=22.81 Aligned_cols=28 Identities=18% Similarity=0.168 Sum_probs=20.9
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-..||..+ |-+...|+++....+++
T Consensus 143 g~s~~EIA~~l-~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 143 ELSIKEIAEVT-GVNENTVKTRLKKAKEL 170 (179)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44567888888 77889998888665543
No 207
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=25.68 E-value=80 Score=28.43 Aligned_cols=30 Identities=27% Similarity=0.408 Sum_probs=22.5
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCc
Q 045384 5 PCNSQEAEVRKGPWTMEEDLILINYIANHGEG 36 (194)
Q Consensus 5 ~~n~~~p~~~kg~WT~eED~~L~~~v~~~g~~ 36 (194)
.||..+|. .--||.||-.+|.+++++||..
T Consensus 164 LCnPHNP~--Grvwt~eeL~~i~elc~kh~v~ 193 (388)
T COG1168 164 LCNPHNPT--GRVWTKEELRKIAELCLRHGVR 193 (388)
T ss_pred EeCCCCCC--CccccHHHHHHHHHHHHHcCCE
Confidence 36555543 2249999999999999999853
No 208
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=25.28 E-value=2.3e+02 Score=20.00 Aligned_cols=33 Identities=15% Similarity=0.104 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHH
Q 045384 74 EEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKN 107 (194)
Q Consensus 74 eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~kn 107 (194)
-|...|..++..+|.+.++.|+.| |=+...++.
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~r 87 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRK 87 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHH
Confidence 466778889999999999999999 766665443
No 209
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=25.26 E-value=2e+02 Score=23.81 Aligned_cols=27 Identities=7% Similarity=0.103 Sum_probs=22.0
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
|-...+||..+ |-+...|+.+....++
T Consensus 177 g~S~~EIA~~L-gis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 177 GLSMDRIGAMY-QVHRSTVSRWVAQARE 203 (244)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 55789999999 9999999998865433
No 210
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=25.18 E-value=2.3e+02 Score=20.95 Aligned_cols=43 Identities=23% Similarity=0.312 Sum_probs=32.0
Q ss_pred CHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 72 TPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 72 T~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
++|+-+ .+...-...++-..+++.+ |=+--.+|+|...++++-
T Consensus 35 ~~E~~~-Fi~~Fi~~rGnlKe~e~~l-giSYPTvR~rLd~ii~~l 77 (113)
T PF09862_consen 35 SPEQLE-FIKLFIKNRGNLKEMEKEL-GISYPTVRNRLDKIIEKL 77 (113)
T ss_pred CHHHHH-HHHHHHHhcCCHHHHHHHH-CCCcHHHHHHHHHHHHHh
Confidence 445444 4455555555678999999 889999999998888775
No 211
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=24.99 E-value=1.4e+02 Score=19.51 Aligned_cols=27 Identities=30% Similarity=0.790 Sum_probs=18.2
Q ss_pred HHHHH-HhhcCcHHHHhhhCCCCCHHHHH
Q 045384 79 IMELH-AKWGNRWSKIAKHLPGRTDNEIK 106 (194)
Q Consensus 79 Ll~~~-~~~G~~W~~Ia~~l~gRt~~~~k 106 (194)
|..++ ...|..|..+|..| |=+..+|.
T Consensus 3 l~~~l~~~~~~~Wk~La~~L-g~~~~~i~ 30 (83)
T PF00531_consen 3 LFDLLAEDLGSDWKRLARKL-GLSESEIE 30 (83)
T ss_dssp HHHHHHHSHSTCHHHHHHHT-TS-HHHHH
T ss_pred HHHHHhhcchhhHHHHHHHh-CcCHHHHH
Confidence 33433 45678899999999 76666554
No 212
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=24.90 E-value=1.1e+02 Score=15.49 Aligned_cols=35 Identities=26% Similarity=0.335 Sum_probs=21.9
Q ss_pred CCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHH
Q 045384 71 ITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKN 107 (194)
Q Consensus 71 WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~kn 107 (194)
.+.++-..++..+ .-|.....||+.+ |.+...+.+
T Consensus 6 ~~~~~~~~i~~~~-~~~~s~~~ia~~~-~is~~tv~~ 40 (42)
T cd00569 6 LTPEQIEEARRLL-AAGESVAEIARRL-GVSRSTLYR 40 (42)
T ss_pred CCHHHHHHHHHHH-HcCCCHHHHHHHH-CCCHHHHHH
Confidence 4554444454444 3456788999888 777766654
No 213
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=24.88 E-value=1.6e+02 Score=24.15 Aligned_cols=30 Identities=17% Similarity=0.153 Sum_probs=23.0
Q ss_pred hhcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 85 KWGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 85 ~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
..|..-..||..+ |-|...|+.+....+++
T Consensus 215 ~~~~s~~EIA~~l-gis~~tV~~~~~ra~~~ 244 (251)
T PRK07670 215 KEELTLTEIGQVL-NLSTSRISQIHSKALFK 244 (251)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3455789999999 99999999887665443
No 214
>PF11084 DUF2621: Protein of unknown function (DUF2621); InterPro: IPR020203 This entry represents a group of uncharacterised proteins.
Probab=24.87 E-value=96 Score=23.71 Aligned_cols=54 Identities=28% Similarity=0.370 Sum_probs=35.6
Q ss_pred hhhhhhhhCCCcchhhhhhhhhhh-cCCCccCCCCCHHHHHHHHHHHHhhcCcHHHHhh
Q 045384 38 WNSLAKAAGLKRTGKSCRLRWLNY-LRPDVKRGNITPEEQLLIMELHAKWGNRWSKIAK 95 (194)
Q Consensus 38 W~~Ia~~~~~~Rt~~qcr~R~~~~-L~p~~~~~~WT~eEd~~Ll~~~~~~G~~W~~Ia~ 95 (194)
..+.-+.|| ...+++.-+ |++| +. ..+.-||+|+-++|-++|.-...-...||+
T Consensus 29 FRKFLK~lP-KeDGkS~LD-Wq~~yi~--~trhlW~de~K~lL~eLV~PVPelFRdvAk 83 (141)
T PF11084_consen 29 FRKFLKRLP-KEDGKSILD-WQEYYIE--KTRHLWTDEQKALLEELVSPVPELFRDVAK 83 (141)
T ss_pred HHHHHHhCC-cccCccccc-HHHHHHH--HhHhhcCHHHHHHHHHHhhcCcHHHHHHHH
Confidence 566667777 455554433 4433 33 245689999999999999877765655555
No 215
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=24.85 E-value=1.4e+02 Score=23.30 Aligned_cols=45 Identities=22% Similarity=0.261 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
...|+-|-+.|.-+. -|..=.+||+.| +-+...|+++-..+++|-
T Consensus 149 ~~Lt~rE~evl~~~~--~G~s~~eIA~~l-~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 149 KRLSPKESEVLRLFA--EGFLVTEIAKKL-NRSIKTISSQKKSAMMKL 193 (216)
T ss_pred ccCCHHHHHHHHHHH--CCCCHHHHHHHH-CCCHHHHHHHHHHHHHHc
Confidence 358888876654443 466667999999 999999999888877764
No 216
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.76 E-value=1.7e+02 Score=22.85 Aligned_cols=28 Identities=25% Similarity=0.316 Sum_probs=21.9
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
.|-.-..||..+ |-+...|+++-....+
T Consensus 169 e~~s~~EIA~~l-gis~~tV~~~l~rar~ 196 (208)
T PRK08295 169 DGKSYQEIAEEL-NRHVKSIDNALQRVKR 196 (208)
T ss_pred ccCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355788999999 9999999987765443
No 217
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=24.69 E-value=1.6e+02 Score=24.67 Aligned_cols=29 Identities=10% Similarity=0.318 Sum_probs=23.2
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
+|-.-.+||..| |.|...|+.+....+++
T Consensus 123 ~g~s~~EIA~~l-g~s~~tVr~~l~RAr~~ 151 (281)
T TIGR02957 123 FDYPYEEIASIV-GKSEANCRQLVSRARRH 151 (281)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 455779999999 89999999988665443
No 218
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=24.65 E-value=1.8e+02 Score=23.01 Aligned_cols=28 Identities=18% Similarity=0.164 Sum_probs=21.7
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-..||..+ |.+...|+++....+++
T Consensus 169 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 196 (206)
T PRK12526 169 ELSQEQLAQQL-NVPLGTVKSRLRLALAK 196 (206)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44678999999 99999999887654443
No 219
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=24.60 E-value=1.1e+02 Score=27.64 Aligned_cols=42 Identities=12% Similarity=0.076 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCcchhhhhhh-hCCCcchhhhhhhhh
Q 045384 16 GPWTMEEDLILINYIANHGEGVWNSLAKA-AGLKRTGKSCRLRWL 59 (194)
Q Consensus 16 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~-~~~~Rt~~qcr~R~~ 59 (194)
.-||.+|=..+-+.++.|| +++..|... ++ .|+...|.+-|.
T Consensus 278 ~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvr-tRsvgElVeyYY 320 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYG-KDFHLIRANKVR-TRSVGELVEYYY 320 (445)
T ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHhcccc-cchHHHHHHHHH
Confidence 3599999999999999999 569888755 65 899999987553
No 220
>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=24.33 E-value=2e+02 Score=21.90 Aligned_cols=28 Identities=21% Similarity=0.108 Sum_probs=21.2
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
.|-.=.+||..| |-+...|+++....++
T Consensus 115 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~ 142 (170)
T TIGR02959 115 EGLSQQEIAEKL-GLSLSGAKSRVQRGRK 142 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 345678899999 8999999988765443
No 221
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and
Probab=24.04 E-value=66 Score=21.95 Aligned_cols=23 Identities=26% Similarity=0.458 Sum_probs=17.6
Q ss_pred HhhcCcHHHHhhhCCCCCHHHHHH
Q 045384 84 AKWGNRWSKIAKHLPGRTDNEIKN 107 (194)
Q Consensus 84 ~~~G~~W~~Ia~~l~gRt~~~~kn 107 (194)
...|+.|..+|.+| |-+...|++
T Consensus 13 ~~~g~DWr~LA~~L-g~~~~~I~~ 35 (79)
T cd08312 13 RVVAADWTALAEEM-GFEYLEIRN 35 (79)
T ss_pred CCcccCHHHHHHHc-CCCHHHHHH
Confidence 44789999999999 666656553
No 222
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=23.96 E-value=1.6e+02 Score=23.72 Aligned_cols=45 Identities=20% Similarity=0.263 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
...|+-|-+.|.-+.. |..=.+||..| +-+...|+.+-.++++|-
T Consensus 133 ~~LT~RE~eVL~ll~~--G~snkeIA~~L-~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 133 RMLSPTEREILRFMSR--GYSMPQIAEQL-ERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHHHHHHHHHHHHHHc
Confidence 3588888887665554 55566999999 999999999888887763
No 223
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=23.81 E-value=1.4e+02 Score=25.60 Aligned_cols=29 Identities=10% Similarity=0.092 Sum_probs=22.9
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|-.-.+||..| |.+...|+.+....+++
T Consensus 168 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 196 (339)
T PRK08241 168 LGWSAAEVAELL-DTSVAAVNSALQRARAT 196 (339)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 345678999999 99999999988665443
No 224
>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=23.73 E-value=1.8e+02 Score=23.29 Aligned_cols=29 Identities=24% Similarity=0.350 Sum_probs=22.1
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
.|..-.+||+.+ |-+...|+.+....+++
T Consensus 193 ~~~s~~eIA~~l-gis~~~v~~~~~ra~~~ 221 (227)
T TIGR02980 193 EDKTQSEIAERL-GISQMHVSRLLRRALKK 221 (227)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355788999999 88999988876655444
No 225
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=23.69 E-value=2.6e+02 Score=23.13 Aligned_cols=45 Identities=18% Similarity=0.051 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHhhcCcHHHHhhhCCCCCHHHHHHHHHHHHHHH
Q 045384 69 GNITPEEQLLIMELHAKWGNRWSKIAKHLPGRTDNEIKNFWRTRIQKQ 116 (194)
Q Consensus 69 ~~WT~eEd~~Ll~~~~~~G~~W~~Ia~~l~gRt~~~~knrw~~~l~~~ 116 (194)
.+-|+-|-+.|.-+.. |..-..||+.| +-+...|+++-..+++|-
T Consensus 142 ~~LS~RE~eVL~Lia~--G~SnkEIA~~L-~IS~~TVk~hvs~I~~KL 186 (217)
T PRK13719 142 NKVTKYQNDVFILYSF--GFSHEYIAQLL-NITVGSSKNKISEILKFF 186 (217)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 4678888876654443 77788999999 999999999887776653
No 226
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=23.54 E-value=2.7e+02 Score=20.83 Aligned_cols=28 Identities=14% Similarity=-0.005 Sum_probs=20.4
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
.|-.-.+||..| |-+...|+.+-....+
T Consensus 123 ~g~s~~eIA~~l-gis~~tv~~~l~Rar~ 150 (165)
T PRK09644 123 HELTYEEAASVL-DLKLNTYKSHLFRGRK 150 (165)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 345678889988 8899999887654433
No 227
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=23.50 E-value=1.8e+02 Score=23.51 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=21.5
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
|-....||..+ |-+...|+++-...++
T Consensus 198 g~s~~EIA~~l-gis~~tVk~~~~rA~~ 224 (234)
T PRK08301 198 EKTQKEVADML-GISQSYISRLEKRIIK 224 (234)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56789999999 9999999887655443
No 228
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=23.27 E-value=1.9e+02 Score=17.63 Aligned_cols=45 Identities=27% Similarity=0.409 Sum_probs=35.0
Q ss_pred CCCCCHHHHHHHHHHHHhhcC----cHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 68 RGNITPEEQLLIMELHAKWGN----RWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 68 ~~~WT~eEd~~Ll~~~~~~G~----~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
+..+|.++-..|.+.+..... .-..||..+ |-+..+|++-|....
T Consensus 4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~nrR 52 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQNRR 52 (57)
T ss_dssp SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHHhH
Confidence 457898998988888877432 367888888 999999999776543
No 229
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=23.08 E-value=1.8e+02 Score=22.85 Aligned_cols=28 Identities=14% Similarity=0.068 Sum_probs=22.0
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|..-..||..| |.+...|+++....++.
T Consensus 149 g~s~~EIAe~l-gis~~tV~~~l~Rar~~ 176 (196)
T PRK12535 149 GYTYEEAAKIA-DVRVGTIRSRVARARAD 176 (196)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 44678999999 99999999988655443
No 230
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.72 E-value=2e+02 Score=21.74 Aligned_cols=27 Identities=7% Similarity=0.030 Sum_probs=20.2
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
|..-.+||..+ |.+...|+.+-...++
T Consensus 135 ~~s~~EIA~~l-gis~~tV~~~l~Ra~~ 161 (173)
T PRK12522 135 QYSYKEMSEIL-NIPIGTVKYRLNYAKK 161 (173)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 44568888888 8889999887655433
No 231
>TIGR01018 rpsD_arch ribosomal protein S4(archaeal type)/S9(eukaryote cytosolic type). This model finds eukaryotic ribosomal protein S9 as well as archaeal ribosomal protein S4.
Probab=21.60 E-value=3.6e+02 Score=21.25 Aligned_cols=81 Identities=17% Similarity=0.118 Sum_probs=46.9
Q ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcchhhhhhhhhhhcCCCccCCCCCHHHHHHHH
Q 045384 1 MDKTPCNSQEAEVRKGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRTGKSCRLRWLNYLRPDVKRGNITPEEQLLIM 80 (194)
Q Consensus 1 m~r~~~n~~~p~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R~~~~L~p~~~~~~WT~eEd~~Ll 80 (194)
||.+--++..-...+.+|-.+--..=.+++.+||-.+=.++-+. +.-...+|..-..++.-. +++-..+-..|+
T Consensus 1 mg~p~~~~k~~~~P~~pw~ker~~~E~~l~~kYgLknk~E~wk~---~~~~~kiR~~Ar~L~~l~---d~~r~~~~~~LL 74 (162)
T TIGR01018 1 MGDPRKPRKKYETPRHPWIKERLDRELKLVGKYGLRNKKEVWKA---ETTLRKYRRAARELLGLD---DEQRLFEGNQLL 74 (162)
T ss_pred CCCCCCCCcccCCCCCChhhhhCHHHHHHHHHHCCCCHHHHHHH---HHHHHHHHHHHHHHHcCC---cHHHHHHHHHHH
Confidence 66542234455667888988776666778899997763333222 122233333333344222 566666667777
Q ss_pred HHHHhhc
Q 045384 81 ELHAKWG 87 (194)
Q Consensus 81 ~~~~~~G 87 (194)
.-...+|
T Consensus 75 ~kL~~~G 81 (162)
T TIGR01018 75 RRLVRLG 81 (162)
T ss_pred HHHHHcC
Confidence 7777777
No 232
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=21.57 E-value=2.2e+02 Score=21.71 Aligned_cols=26 Identities=15% Similarity=0.079 Sum_probs=19.7
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
|-.-.+||..+ |-+...|+++....+
T Consensus 133 ~~s~~EIA~~l-gis~~tV~~~l~ra~ 158 (179)
T PRK12543 133 DYSQEEIAQLL-QIPIGTVKSRIHAAL 158 (179)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 44678889988 888888888765443
No 233
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=21.52 E-value=82 Score=23.91 Aligned_cols=28 Identities=14% Similarity=-0.022 Sum_probs=22.1
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-..||..| |-|...|+++....+++
T Consensus 136 g~s~~eIA~~l-g~s~~tv~~~l~Rar~~ 163 (175)
T PRK12518 136 DLPQKEIAEIL-NIPVGTVKSRLFYARRQ 163 (175)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44678999999 99999999988665443
No 234
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.38 E-value=2.8e+02 Score=21.48 Aligned_cols=27 Identities=19% Similarity=0.053 Sum_probs=20.6
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRI 113 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l 113 (194)
.|-.-.+||..| |-+...|+.+-...+
T Consensus 126 ~g~s~~EIA~~L-gis~~tV~~~l~RAr 152 (182)
T PRK12540 126 SGFSYEDAAAIC-GCAVGTIKSRVNRAR 152 (182)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 355678999999 888999988765443
No 235
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=21.18 E-value=2.2e+02 Score=21.77 Aligned_cols=28 Identities=14% Similarity=0.246 Sum_probs=20.7
Q ss_pred hcCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 86 WGNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 86 ~G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
.|-...+||..| |=+...|+++-...++
T Consensus 152 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~ 179 (187)
T PRK12534 152 EGITYEELAART-DTPIGTVKSWIRRGLA 179 (187)
T ss_pred cCCCHHHHHHHh-CCChhHHHHHHHHHHH
Confidence 355788899988 8888888887655433
No 236
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=20.81 E-value=2.7e+02 Score=22.50 Aligned_cols=28 Identities=7% Similarity=0.004 Sum_probs=21.4
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|-.-.+||..| |-+...|+.+-...+++
T Consensus 150 g~s~~EIAe~L-giS~~tVk~~L~RAr~~ 177 (216)
T PRK12533 150 DMSYREIAAIA-DVPVGTVMSRLARARRR 177 (216)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44678899999 99999999887654443
No 237
>cd00131 PAX Paired Box domain
Probab=20.50 E-value=3.6e+02 Score=19.94 Aligned_cols=71 Identities=14% Similarity=0.086 Sum_probs=45.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCcchhhhhhhhCCCcc-hhhhhhhhhhh--cCCCccCC----CCCHHHHHHHHHHHHhhc
Q 045384 15 KGPWTMEEDLILINYIANHGEGVWNSLAKAAGLKRT-GKSCRLRWLNY--LRPDVKRG----NITPEEQLLIMELHAKWG 87 (194)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt-~~qcr~R~~~~--L~p~~~~~----~WT~eEd~~Ll~~~~~~G 87 (194)
..+.|.+.-++++.+++ .|. .-..||+.++..++ ...+..||... +.|....+ .-+++.+..|+.++...+
T Consensus 15 ~~~lS~d~R~rIv~~~~-~G~-s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p 92 (128)
T cd00131 15 GRPLPDSIRQRIVELAQ-SGI-RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENP 92 (128)
T ss_pred CCcCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCC
Confidence 34678888888888886 454 48999999985433 44455566542 44533222 246666677776776655
No 238
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=20.47 E-value=1e+02 Score=23.97 Aligned_cols=27 Identities=22% Similarity=0.271 Sum_probs=20.9
Q ss_pred cCcHHHHhhhCCCCCHHHHHHHHHHHHH
Q 045384 87 GNRWSKIAKHLPGRTDNEIKNFWRTRIQ 114 (194)
Q Consensus 87 G~~W~~Ia~~l~gRt~~~~knrw~~~l~ 114 (194)
|..-..||..+ |-+...|+++....++
T Consensus 155 g~s~~EIA~~l-gis~~tV~~~l~ra~~ 181 (194)
T PRK12513 155 DLELEEIAELT-GVPEETVKSRLRYALQ 181 (194)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45689999999 8999999987654433
No 239
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.37 E-value=2.8e+02 Score=21.00 Aligned_cols=39 Identities=26% Similarity=0.592 Sum_probs=23.0
Q ss_pred HHHHHHHHH-Hhh-cCcHHHHhhhCCCCCHHHHHHHHHHHHHH
Q 045384 75 EQLLIMELH-AKW-GNRWSKIAKHLPGRTDNEIKNFWRTRIQK 115 (194)
Q Consensus 75 Ed~~Ll~~~-~~~-G~~W~~Ia~~l~gRt~~~~knrw~~~l~~ 115 (194)
|++.++.+. ... |..|-.||..+ +-+..+|+. |+..+|.
T Consensus 85 e~k~Ii~lry~~r~~~TW~~IA~~l-~i~erta~r-~~~~fK~ 125 (130)
T PF05263_consen 85 EEKRIIKLRYDRRSRRTWYQIAQKL-HISERTARR-WRDRFKN 125 (130)
T ss_pred HHHHHHHHHHcccccchHHHHHHHh-CccHHHHHH-HHHHHHH
Confidence 344555544 333 36799999988 566666654 4444444
Done!