Query 025602
Match_columns 250
No_of_seqs 266 out of 1460
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 07:31:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025602.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025602hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03212 Transcription repress 100.0 2E-38 4.4E-43 276.1 13.7 126 3-129 11-136 (249)
2 PLN03091 hypothetical protein; 100.0 3.1E-37 6.8E-42 286.2 16.5 127 4-131 1-127 (459)
3 KOG0048 Transcription factor, 100.0 2.9E-36 6.4E-41 266.1 10.9 111 14-124 5-115 (238)
4 KOG0049 Transcription factor, 99.8 4.8E-20 1.1E-24 177.1 8.2 110 1-111 338-453 (939)
5 KOG0049 Transcription factor, 99.8 8.1E-19 1.8E-23 168.8 8.0 113 14-126 249-416 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 1.7E-17 3.8E-22 116.0 4.2 60 21-82 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 7E-16 1.5E-20 147.9 6.7 107 14-121 16-122 (512)
8 KOG0050 mRNA splicing protein 99.6 6.2E-16 1.3E-20 146.0 3.5 107 15-123 4-110 (617)
9 KOG0051 RNA polymerase I termi 99.5 2.2E-14 4.8E-19 139.0 6.7 103 17-122 383-513 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.5 7.7E-15 1.7E-19 98.4 1.5 48 18-65 1-48 (48)
11 PLN03212 Transcription repress 99.4 1.8E-14 3.9E-19 126.2 -0.1 65 2-68 57-126 (249)
12 PF00249 Myb_DNA-binding: Myb- 99.4 3E-13 6.6E-18 90.6 5.4 46 71-116 1-48 (48)
13 PLN03091 hypothetical protein; 99.4 9.2E-14 2E-18 130.1 0.9 65 2-68 46-115 (459)
14 PF13921 Myb_DNA-bind_6: Myb-l 99.3 3.7E-12 8E-17 88.9 6.0 52 74-125 1-52 (60)
15 smart00717 SANT SANT SWI3, AD 99.2 2.2E-11 4.8E-16 79.9 6.0 47 71-117 1-48 (49)
16 smart00717 SANT SANT SWI3, AD 99.2 1.4E-11 3E-16 80.9 2.8 48 18-66 1-48 (49)
17 KOG0048 Transcription factor, 99.1 9.5E-12 2.1E-16 110.0 1.2 62 3-66 42-108 (238)
18 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1.9E-10 4.1E-15 74.3 5.9 44 73-116 1-45 (45)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 1.1E-10 2.4E-15 75.4 2.4 45 20-65 1-45 (45)
20 KOG0051 RNA polymerase I termi 98.9 1.5E-09 3.3E-14 105.7 5.8 103 15-119 305-431 (607)
21 COG5147 REB1 Myb superfamily p 98.5 1.3E-08 2.7E-13 98.3 -1.2 98 16-116 289-396 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.1 2.6E-06 5.7E-11 59.2 2.8 49 17-65 2-54 (57)
23 KOG0457 Histone acetyltransfer 98.0 2.5E-06 5.4E-11 80.3 2.4 50 15-65 69-118 (438)
24 TIGR01557 myb_SHAQKYF myb-like 97.8 8.2E-05 1.8E-09 51.7 5.9 46 71-116 3-54 (57)
25 KOG0457 Histone acetyltransfer 97.6 0.00012 2.6E-09 69.1 6.1 49 68-116 69-118 (438)
26 PF13325 MCRS_N: N-terminal re 97.6 0.00013 2.8E-09 62.9 5.7 99 20-120 1-130 (199)
27 TIGR02894 DNA_bind_RsfA transc 97.4 0.00021 4.6E-09 59.4 4.4 52 70-122 3-61 (161)
28 COG5259 RSC8 RSC chromatin rem 97.4 7.6E-05 1.6E-09 71.0 2.0 46 17-64 278-323 (531)
29 KOG0050 mRNA splicing protein 97.3 0.00019 4.1E-09 69.1 4.0 59 69-127 5-64 (617)
30 KOG1279 Chromatin remodeling f 97.1 0.00021 4.6E-09 69.5 2.2 47 16-64 251-297 (506)
31 PF08914 Myb_DNA-bind_2: Rap1 96.9 0.0016 3.5E-08 46.4 4.7 50 71-120 2-61 (65)
32 PF08914 Myb_DNA-bind_2: Rap1 96.9 0.00027 5.9E-09 50.4 0.6 52 18-69 2-61 (65)
33 COG5259 RSC8 RSC chromatin rem 96.9 0.0012 2.7E-08 62.9 4.8 45 71-115 279-323 (531)
34 PF13837 Myb_DNA-bind_4: Myb/S 96.8 0.001 2.3E-08 49.3 3.1 51 71-122 1-69 (90)
35 KOG1279 Chromatin remodeling f 96.8 0.0018 3.9E-08 63.1 5.4 46 70-115 252-297 (506)
36 PF13837 Myb_DNA-bind_4: Myb/S 96.6 0.00065 1.4E-08 50.4 0.6 48 18-65 1-64 (90)
37 COG5114 Histone acetyltransfer 96.6 0.00085 1.9E-08 61.3 1.0 50 16-66 61-110 (432)
38 PRK13923 putative spore coat p 96.5 0.0029 6.3E-08 53.3 4.1 52 70-122 4-62 (170)
39 TIGR02894 DNA_bind_RsfA transc 96.2 0.0017 3.8E-08 54.0 0.7 51 16-68 2-58 (161)
40 PF13873 Myb_DNA-bind_5: Myb/S 95.6 0.0044 9.6E-08 45.0 0.8 49 17-65 1-69 (78)
41 PLN03142 Probable chromatin-re 95.5 0.065 1.4E-06 56.7 9.3 99 20-119 826-987 (1033)
42 PF13873 Myb_DNA-bind_5: Myb/S 95.5 0.026 5.6E-07 40.9 4.5 47 71-117 2-70 (78)
43 COG5114 Histone acetyltransfer 95.5 0.017 3.8E-07 53.0 4.2 47 71-117 63-110 (432)
44 PRK13923 putative spore coat p 94.6 0.011 2.3E-07 49.9 0.4 49 16-66 3-57 (170)
45 PF09111 SLIDE: SLIDE; InterP 93.5 0.19 4.1E-06 40.0 5.4 51 68-118 46-112 (118)
46 KOG2656 DNA methyltransferase 93.4 0.064 1.4E-06 50.5 3.0 85 40-125 75-190 (445)
47 COG5118 BDP1 Transcription ini 93.1 0.16 3.5E-06 47.7 5.1 47 72-118 366-412 (507)
48 KOG4282 Transcription factor G 92.4 0.23 5E-06 46.1 5.2 48 71-118 54-115 (345)
49 PF12776 Myb_DNA-bind_3: Myb/S 91.0 0.65 1.4E-05 34.5 5.5 47 73-120 1-65 (96)
50 COG5118 BDP1 Transcription ini 90.6 0.16 3.4E-06 47.8 2.1 60 17-78 364-431 (507)
51 KOG1194 Predicted DNA-binding 90.4 1.3 2.8E-05 42.8 7.9 47 71-117 187-233 (534)
52 PF09111 SLIDE: SLIDE; InterP 88.1 0.5 1.1E-05 37.6 3.0 35 14-48 45-82 (118)
53 PF08281 Sigma70_r4_2: Sigma-7 87.6 1.5 3.2E-05 29.1 4.7 41 76-117 12-52 (54)
54 KOG4282 Transcription factor G 83.7 0.61 1.3E-05 43.3 1.7 48 18-65 54-113 (345)
55 KOG4167 Predicted DNA-binding 81.8 4.5 9.7E-05 41.4 6.9 44 71-114 619-662 (907)
56 PF12776 Myb_DNA-bind_3: Myb/S 81.1 1.2 2.6E-05 33.1 2.1 44 20-63 1-60 (96)
57 PF11626 Rap1_C: TRF2-interact 78.9 2.1 4.5E-05 31.9 2.8 30 14-46 43-80 (87)
58 PF11035 SnAPC_2_like: Small n 78.6 57 0.0012 30.4 13.9 98 5-116 8-126 (344)
59 KOG4468 Polycomb-group transcr 77.4 3.7 7.9E-05 41.1 4.7 49 71-119 88-146 (782)
60 PF13404 HTH_AsnC-type: AsnC-t 75.7 6.9 0.00015 25.1 4.2 38 77-115 3-41 (42)
61 PF04545 Sigma70_r4: Sigma-70, 74.7 7.6 0.00016 25.3 4.4 41 77-118 7-47 (50)
62 KOG4167 Predicted DNA-binding 73.0 5.2 0.00011 40.9 4.6 44 18-63 619-662 (907)
63 PRK11179 DNA-binding transcrip 71.6 8 0.00017 31.5 4.7 43 77-120 9-52 (153)
64 PF13404 HTH_AsnC-type: AsnC-t 69.5 2.5 5.4E-05 27.2 1.1 37 24-62 3-39 (42)
65 PRK11169 leucine-responsive tr 66.0 9.9 0.00021 31.4 4.2 44 76-120 13-57 (164)
66 smart00595 MADF subfamily of S 65.0 6.5 0.00014 28.6 2.7 23 93-116 30-52 (89)
67 KOG4329 DNA-binding protein [G 64.8 12 0.00026 35.4 4.9 42 72-113 278-320 (445)
68 KOG2656 DNA methyltransferase 62.6 3.6 7.8E-05 39.1 1.1 49 15-64 127-180 (445)
69 TIGR02985 Sig70_bacteroi1 RNA 61.9 19 0.00042 28.3 5.2 36 80-116 119-154 (161)
70 cd08319 Death_RAIDD Death doma 59.6 15 0.00032 27.3 3.7 30 79-109 2-31 (83)
71 PF07750 GcrA: GcrA cell cycle 59.2 13 0.00029 31.0 3.8 41 73-114 2-42 (162)
72 PRK11179 DNA-binding transcrip 59.1 5 0.00011 32.8 1.2 46 23-70 8-53 (153)
73 PF01388 ARID: ARID/BRIGHT DNA 57.8 3.4 7.4E-05 30.6 0.0 40 27-66 39-89 (92)
74 KOG2009 Transcription initiati 57.1 12 0.00026 37.4 3.7 44 71-114 409-452 (584)
75 PRK11169 leucine-responsive tr 55.7 4.7 0.0001 33.3 0.6 46 23-70 13-58 (164)
76 cd08803 Death_ank3 Death domai 55.0 22 0.00047 26.4 4.0 31 79-110 4-34 (84)
77 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 54.8 31 0.00066 23.2 4.3 37 76-113 6-42 (50)
78 PF11035 SnAPC_2_like: Small n 54.5 48 0.001 30.8 6.8 49 71-120 21-73 (344)
79 KOG1194 Predicted DNA-binding 54.5 8.2 0.00018 37.4 2.0 46 16-63 185-230 (534)
80 PF13325 MCRS_N: N-terminal re 54.0 30 0.00065 30.0 5.2 45 73-118 1-48 (199)
81 PLN03142 Probable chromatin-re 51.9 8.3 0.00018 41.3 1.7 34 15-48 923-956 (1033)
82 cd08317 Death_ank Death domain 49.5 21 0.00045 26.1 3.1 30 79-109 4-33 (84)
83 smart00344 HTH_ASNC helix_turn 49.5 39 0.00084 25.3 4.8 43 77-120 3-46 (108)
84 PF07750 GcrA: GcrA cell cycle 49.3 14 0.00031 30.8 2.5 34 20-56 2-35 (162)
85 PF04504 DUF573: Protein of un 49.3 32 0.00069 26.2 4.2 49 72-121 5-66 (98)
86 PF11626 Rap1_C: TRF2-interact 46.8 10 0.00022 28.2 1.0 17 67-83 43-59 (87)
87 TIGR02937 sigma70-ECF RNA poly 46.2 44 0.00095 25.4 4.7 34 83-117 119-152 (158)
88 PRK04217 hypothetical protein; 46.2 51 0.0011 25.8 5.0 42 73-116 42-83 (110)
89 PF01388 ARID: ARID/BRIGHT DNA 45.3 59 0.0013 23.8 5.1 37 81-117 40-89 (92)
90 cd08318 Death_NMPP84 Death dom 44.9 33 0.00072 25.3 3.6 26 83-109 11-36 (86)
91 cd08804 Death_ank2 Death domai 44.1 34 0.00073 25.3 3.5 31 79-110 4-34 (84)
92 PRK09652 RNA polymerase sigma 42.8 53 0.0011 26.3 4.9 27 88-115 142-168 (182)
93 PRK11924 RNA polymerase sigma 41.8 54 0.0012 26.2 4.8 28 88-116 139-166 (179)
94 PF10545 MADF_DNA_bdg: Alcohol 41.5 27 0.00058 24.6 2.6 25 92-116 28-53 (85)
95 smart00501 BRIGHT BRIGHT, ARID 40.5 69 0.0015 23.6 4.8 38 81-118 36-86 (93)
96 PF07638 Sigma70_ECF: ECF sigm 39.8 58 0.0013 27.2 4.8 36 80-116 141-176 (185)
97 KOG2009 Transcription initiati 39.7 18 0.00039 36.2 1.9 48 14-63 405-452 (584)
98 cd06171 Sigma70_r4 Sigma70, re 39.6 89 0.0019 19.1 4.8 36 78-114 14-49 (55)
99 smart00351 PAX Paired Box doma 39.5 1.1E+02 0.0023 24.1 6.0 75 14-90 11-92 (125)
100 PRK09413 IS2 repressor TnpA; R 39.4 52 0.0011 25.7 4.2 46 17-66 9-54 (121)
101 PRK13858 type IV secretion sys 39.3 48 0.001 27.4 4.0 83 3-100 14-96 (147)
102 PRK09643 RNA polymerase sigma 38.6 67 0.0015 26.7 5.0 26 88-114 148-173 (192)
103 KOG4468 Polycomb-group transcr 38.6 12 0.00026 37.5 0.5 49 17-66 87-144 (782)
104 cd08777 Death_RIP1 Death Domai 37.7 43 0.00093 24.9 3.2 29 81-110 4-32 (86)
105 cd08805 Death_ank1 Death domai 36.6 50 0.0011 24.5 3.4 27 79-106 4-30 (84)
106 cd08311 Death_p75NR Death doma 35.9 42 0.00091 24.5 2.9 33 76-110 2-34 (77)
107 PRK09641 RNA polymerase sigma 35.6 77 0.0017 25.8 4.8 26 90-116 152-177 (187)
108 PRK12532 RNA polymerase sigma 34.9 1E+02 0.0022 25.5 5.5 34 89-123 151-187 (195)
109 KOG4329 DNA-binding protein [G 34.7 26 0.00057 33.2 2.0 43 19-63 278-321 (445)
110 KOG0384 Chromodomain-helicase 33.4 22 0.00047 38.7 1.4 82 9-97 1124-1206(1373)
111 PRK09047 RNA polymerase factor 33.2 1.1E+02 0.0023 24.2 5.2 27 89-116 121-147 (161)
112 smart00005 DEATH DEATH domain, 33.1 56 0.0012 23.4 3.2 29 79-108 5-34 (88)
113 cd08779 Death_PIDD Death Domai 32.8 50 0.0011 24.4 2.9 21 80-100 3-23 (86)
114 COG2197 CitB Response regulato 32.1 55 0.0012 28.1 3.5 44 72-118 147-190 (211)
115 PRK12523 RNA polymerase sigma 32.0 1.1E+02 0.0023 24.8 5.1 31 87-118 132-162 (172)
116 PRK09648 RNA polymerase sigma 31.5 1.1E+02 0.0023 25.2 5.1 28 88-116 153-180 (189)
117 TIGR02939 RpoE_Sigma70 RNA pol 31.5 77 0.0017 25.8 4.2 26 90-116 154-179 (190)
118 TIGR02954 Sig70_famx3 RNA poly 31.4 1E+02 0.0022 24.8 4.9 27 90-117 135-161 (169)
119 PRK09645 RNA polymerase sigma 31.2 1.1E+02 0.0024 24.6 5.1 26 90-116 134-159 (173)
120 PRK12529 RNA polymerase sigma 31.1 1.1E+02 0.0025 24.9 5.2 32 88-120 141-172 (178)
121 PF02954 HTH_8: Bacterial regu 30.7 1.3E+02 0.0027 18.9 4.2 34 77-111 5-38 (42)
122 PRK09637 RNA polymerase sigma 30.7 1.1E+02 0.0023 25.3 4.9 27 89-116 121-147 (181)
123 PRK12512 RNA polymerase sigma 30.5 1.1E+02 0.0025 24.8 5.1 26 90-116 147-172 (184)
124 PF09420 Nop16: Ribosome bioge 30.0 1.3E+02 0.0028 24.8 5.3 45 71-115 114-162 (164)
125 KOG3841 TEF-1 and related tran 29.6 1E+02 0.0022 29.5 4.9 54 69-122 74-148 (455)
126 PRK12530 RNA polymerase sigma 29.2 1.2E+02 0.0026 25.1 5.0 25 90-115 150-174 (189)
127 PRK11923 algU RNA polymerase s 29.2 1.1E+02 0.0023 25.2 4.7 26 90-116 154-179 (193)
128 TIGR02943 Sig70_famx1 RNA poly 29.1 1.3E+02 0.0028 25.0 5.2 26 89-115 146-171 (188)
129 PRK09642 RNA polymerase sigma 29.0 1.3E+02 0.0028 23.8 5.1 26 89-115 121-146 (160)
130 PRK12515 RNA polymerase sigma 28.9 1.3E+02 0.0028 24.8 5.1 27 89-116 146-172 (189)
131 PRK12531 RNA polymerase sigma 28.8 1.3E+02 0.0028 25.0 5.1 26 90-116 157-182 (194)
132 TIGR02948 SigW_bacill RNA poly 28.6 1.1E+02 0.0023 24.9 4.6 26 90-116 152-177 (187)
133 COG1522 Lrp Transcriptional re 27.3 1.4E+02 0.0029 23.6 4.9 44 77-121 8-52 (154)
134 KOG3554 Histone deacetylase co 27.1 78 0.0017 31.1 3.8 42 72-113 286-328 (693)
135 PRK12524 RNA polymerase sigma 26.8 1.4E+02 0.003 24.8 5.0 26 89-115 151-176 (196)
136 smart00344 HTH_ASNC helix_turn 26.6 40 0.00086 25.2 1.5 43 24-68 3-45 (108)
137 cd08306 Death_FADD Fas-associa 26.6 1E+02 0.0022 22.7 3.7 28 81-109 4-31 (86)
138 PRK06759 RNA polymerase factor 26.5 1.6E+02 0.0034 23.1 5.1 26 90-116 122-147 (154)
139 PF13936 HTH_38: Helix-turn-he 26.5 72 0.0016 20.3 2.5 36 73-110 4-39 (44)
140 PF09905 DUF2132: Uncharacteri 26.3 62 0.0013 22.9 2.2 44 26-82 12-62 (64)
141 PF00196 GerE: Bacterial regul 26.3 54 0.0012 21.8 2.0 43 73-118 3-45 (58)
142 COG1522 Lrp Transcriptional re 26.2 33 0.00071 27.3 1.0 44 23-68 7-50 (154)
143 PRK12514 RNA polymerase sigma 25.4 1.6E+02 0.0034 23.9 5.0 26 90-116 145-170 (179)
144 PRK12527 RNA polymerase sigma 25.1 1.8E+02 0.0038 23.0 5.2 26 90-116 121-146 (159)
145 PRK12536 RNA polymerase sigma 24.9 1.6E+02 0.0035 24.0 5.1 27 89-116 144-170 (181)
146 TIGR02999 Sig-70_X6 RNA polyme 24.3 1.8E+02 0.0038 23.6 5.1 26 90-116 150-175 (183)
147 PRK12528 RNA polymerase sigma 24.3 1.8E+02 0.004 23.0 5.1 28 89-117 128-155 (161)
148 TIGR02952 Sig70_famx2 RNA poly 24.1 1.7E+02 0.0038 23.1 5.0 26 90-116 138-163 (170)
149 PRK05602 RNA polymerase sigma 23.8 1.6E+02 0.0035 24.1 4.8 26 89-115 143-168 (186)
150 PRK12547 RNA polymerase sigma 23.8 1.9E+02 0.0041 23.2 5.1 27 89-116 127-153 (164)
151 PRK00118 putative DNA-binding 23.6 2.1E+02 0.0045 22.1 5.0 38 76-114 19-56 (104)
152 PRK09649 RNA polymerase sigma 23.6 1.6E+02 0.0036 24.2 4.8 27 90-117 146-172 (185)
153 PRK12516 RNA polymerase sigma 23.3 1.8E+02 0.0039 24.1 5.0 27 88-115 130-156 (187)
154 TIGR02950 SigM_subfam RNA poly 23.2 61 0.0013 25.4 2.1 26 90-116 121-146 (154)
155 TIGR02983 SigE-fam_strep RNA p 23.0 1.8E+02 0.0039 23.0 4.8 35 82-117 118-152 (162)
156 PRK09651 RNA polymerase sigma 22.9 1.5E+02 0.0032 24.0 4.4 28 90-118 135-162 (172)
157 PRK13919 putative RNA polymera 22.5 1.9E+02 0.0042 23.4 5.1 26 90-116 151-176 (186)
158 cd01670 Death Death Domain: a 22.2 1E+02 0.0022 21.4 2.9 26 82-108 2-27 (79)
159 PRK12542 RNA polymerase sigma 21.7 2E+02 0.0044 23.4 5.0 27 89-116 137-163 (185)
160 PRK15201 fimbriae regulatory p 21.5 2.4E+02 0.0052 24.4 5.3 43 73-118 133-175 (198)
161 PF06163 DUF977: Bacterial pro 21.5 2.8E+02 0.0061 22.4 5.4 45 73-118 4-53 (127)
162 KOG0385 Chromatin remodeling c 21.3 1E+02 0.0022 32.3 3.6 96 20-117 797-957 (971)
163 TIGR02984 Sig-70_plancto1 RNA 21.1 2.1E+02 0.0046 23.1 5.0 28 89-117 155-182 (189)
164 PF10440 WIYLD: Ubiquitin-bind 21.0 73 0.0016 22.7 1.8 19 80-98 30-48 (65)
165 PRK10100 DNA-binding transcrip 20.4 2.2E+02 0.0047 24.5 5.1 43 73-118 155-197 (216)
166 PRK01905 DNA-binding protein F 20.4 2.8E+02 0.0061 19.8 4.9 35 76-111 36-70 (77)
167 PRK12520 RNA polymerase sigma 20.1 2.3E+02 0.005 23.2 5.1 25 90-115 147-171 (191)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=2e-38 Score=276.08 Aligned_cols=126 Identities=63% Similarity=1.248 Sum_probs=118.9
Q ss_pred CCCCCcccccCCCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCccCCCCCHHHHHHH
Q 025602 3 GKRKTPCCSKGEGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLV 82 (250)
Q Consensus 3 g~~~~~c~~k~~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT~eEd~~L 82 (250)
+..+.|||.| ++++|++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.++|+|.+++++||.|||++|
T Consensus 11 ~~~~~pcc~K-~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lL 89 (249)
T PLN03212 11 SKKTTPCCTK-MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLI 89 (249)
T ss_pred CCCCCCCccc-CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHH
Confidence 4567899999 999999999999999999999999989999999996699999999999999999999999999999999
Q ss_pred HHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhhhhhcCCCCCCC
Q 025602 83 IRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRVDANHHHHQN 129 (250)
Q Consensus 83 l~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k~~~~~~~~~~~ 129 (250)
++++.+||++|+.||++|||||+++|||||+.++++++...+..+..
T Consensus 90 lel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~ 136 (249)
T PLN03212 90 LRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQT 136 (249)
T ss_pred HHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCC
Confidence 99999999999999999999999999999999999998876665543
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=3.1e-37 Score=286.25 Aligned_cols=127 Identities=53% Similarity=1.052 Sum_probs=120.3
Q ss_pred CCCCcccccCCCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCccCCCCCHHHHHHHH
Q 025602 4 KRKTPCCSKGEGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLVI 83 (250)
Q Consensus 4 ~~~~~c~~k~~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT~eEd~~Ll 83 (250)
|||++||.| .+++||+||+|||++|+++|.+||.++|..||+.++.+|+++|||+||.++|+|.+++++||.|||++|+
T Consensus 1 mgr~~Cc~K-qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLL 79 (459)
T PLN03091 1 MGRHSCCYK-QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLII 79 (459)
T ss_pred CCCCccCcC-CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHH
Confidence 699999999 9999999999999999999999999999999999977999999999999999999999999999999999
Q ss_pred HHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhhhhhcCCCCCCCCc
Q 025602 84 RLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRVDANHHHHQNRS 131 (250)
Q Consensus 84 ~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k~~~~~~~~~~~~s 131 (250)
+++++||++|.+||++|||||+++|||||+.+|+++++..+..+....
T Consensus 80 eL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~k 127 (459)
T PLN03091 80 ELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHK 127 (459)
T ss_pred HHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCC
Confidence 999999999999999999999999999999999999987766554333
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=2.9e-36 Score=266.06 Aligned_cols=111 Identities=60% Similarity=1.094 Sum_probs=107.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCccCCCCCHHHHHHHHHHHHHhCCCH
Q 025602 14 EGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLVIRLHKLLGNRW 93 (250)
Q Consensus 14 ~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT~eEd~~Ll~~~~~~g~~W 93 (250)
+.+.||+||+|||++|+++|.+||.++|..||+.+|++|++++||+||.|||+|++++|.||+|||.+|++|++.+|++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 34567999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhhhhhhhcCC
Q 025602 94 ALIAGRLPGRTDNDIKNYWNTKLSKRVDANH 124 (250)
Q Consensus 94 ~~Ia~~lpgRT~~~~knrw~~~l~k~~~~~~ 124 (250)
+.||++|||||+++|||+|++.|++|+....
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999999999998766
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.81 E-value=4.8e-20 Score=177.14 Aligned_cols=110 Identities=25% Similarity=0.510 Sum_probs=102.5
Q ss_pred CCCCCCCccccc-----CCCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCccCCCCC
Q 025602 1 MAGKRKTPCCSK-----GEGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFS 75 (250)
Q Consensus 1 m~g~~~~~c~~k-----~~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT 75 (250)
|+||.+++=-.+ +|++++|+||++||.+|+.+|.+||.+.|.+|-+.+| +|+..|||+||.|.|+...+.+.||
T Consensus 338 mpgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~ 416 (939)
T KOG0049|consen 338 MPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWT 416 (939)
T ss_pred cCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCcee
Confidence 889988876555 3999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHH
Q 025602 76 KDEEDLVIRLHKLLGN-RWALIAGRLPGRTDNDIKNY 111 (250)
Q Consensus 76 ~eEd~~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knr 111 (250)
-.||+.|+.+|+.||. +|.+||..||.||..|...|
T Consensus 417 l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rr 453 (939)
T KOG0049|consen 417 LVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRR 453 (939)
T ss_pred ecchHHHHHHHHHHccchHHHHHHHccccchhHHHHH
Confidence 9999999999999996 89999999999999665444
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.76 E-value=8.1e-19 Score=168.78 Aligned_cols=113 Identities=21% Similarity=0.414 Sum_probs=105.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccccc-----------------------------------
Q 025602 14 EGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCR----------------------------------- 58 (250)
Q Consensus 14 ~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr----------------------------------- 58 (250)
|.++|..|+.|||+.|+.+...++..+|..||..||++|+..||.
T Consensus 249 P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~nSh 328 (939)
T KOG0049|consen 249 PKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSINSH 328 (939)
T ss_pred CccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhccCc
Confidence 899999999999999999999999999999999999779999997
Q ss_pred -------------------ccccccccCCccCCCCCHHHHHHHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 59 -------------------LRWMNYLRPDIKRGNFSKDEEDLVIRLHKLLGN-RWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 59 -------------------~Rw~~~L~p~l~~~~WT~eEd~~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
-||...|+|++++|+||.+||.+|+.+|.+||. .|-+|-..+|||++.||+.||...|..
T Consensus 329 I~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~ 408 (939)
T KOG0049|consen 329 IQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNR 408 (939)
T ss_pred cchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHH
Confidence 788999999999999999999999999999996 799999999999999999999999988
Q ss_pred hhhcCCCC
Q 025602 119 RVDANHHH 126 (250)
Q Consensus 119 ~~~~~~~~ 126 (250)
+.+...+.
T Consensus 409 s~K~~rW~ 416 (939)
T KOG0049|consen 409 SAKVERWT 416 (939)
T ss_pred hhccCcee
Confidence 77655543
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=99.69 E-value=1.7e-17 Score=116.04 Aligned_cols=60 Identities=42% Similarity=0.927 Sum_probs=55.4
Q ss_pred CCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCccCCCCCHHHHHHH
Q 025602 21 WKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLV 82 (250)
Q Consensus 21 WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT~eEd~~L 82 (250)
||+|||++|+.+|..||. +|..||+.|| .|++.+|+.||.++|++.+++++||.+||++|
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 999999999999999997 8999999997 89999999999999999999999999999987
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=99.61 E-value=7e-16 Score=147.94 Aligned_cols=107 Identities=29% Similarity=0.524 Sum_probs=102.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCccCCCCCHHHHHHHHHHHHHhCCCH
Q 025602 14 EGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLVIRLHKLLGNRW 93 (250)
Q Consensus 14 ~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT~eEd~~Ll~~~~~~g~~W 93 (250)
-.++.|.|+..||+.|..+|..+|..+|+.||..+. .|++++|+.||.++++|.++++.|+.+||..|+.+..++|..|
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 467889999999999999999999999999999998 7999999999999999999999999999999999999999999
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhhhhhhh
Q 025602 94 ALIAGRLPGRTDNDIKNYWNTKLSKRVD 121 (250)
Q Consensus 94 ~~Ia~~lpgRT~~~~knrw~~~l~k~~~ 121 (250)
+.||..+++||..+|.+||...+.....
T Consensus 95 stia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 95 STIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhccccCccchHHHHHHHHHHhhhhhc
Confidence 9999999999999999999988876655
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.58 E-value=6.2e-16 Score=146.01 Aligned_cols=107 Identities=28% Similarity=0.659 Sum_probs=101.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCccCCCCCHHHHHHHHHHHHHhCCCHH
Q 025602 15 GLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLVIRLHKLLGNRWA 94 (250)
Q Consensus 15 ~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT~eEd~~Ll~~~~~~g~~W~ 94 (250)
-++.|.|+.-||+.|..+|.+||...|+.|++.+. ..+++||+.||..+|+|.|++..|+.+||..|+.+.+.+...|.
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwr 82 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWR 82 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccc
Confidence 35789999999999999999999999999999998 88999999999999999999999999999999999999999999
Q ss_pred HHhhhCCCCCHHHHHHHHHHhhhhhhhcC
Q 025602 95 LIAGRLPGRTDNDIKNYWNTKLSKRVDAN 123 (250)
Q Consensus 95 ~Ia~~lpgRT~~~~knrw~~~l~k~~~~~ 123 (250)
.|+..| |||.+||-.||+.+|-......
T Consensus 83 tIa~i~-gr~~~qc~eRy~~ll~~~~s~~ 110 (617)
T KOG0050|consen 83 TIADIM-GRTSQQCLERYNNLLDVYVSYH 110 (617)
T ss_pred hHHHHh-hhhHHHHHHHHHHHHHHHHhhh
Confidence 999999 9999999999999997776543
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.50 E-value=2.2e-14 Score=139.02 Aligned_cols=103 Identities=26% Similarity=0.528 Sum_probs=93.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCC--ccCCCCCHHHHHHHHHHHH-------
Q 025602 17 NRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPD--IKRGNFSKDEEDLVIRLHK------- 87 (250)
Q Consensus 17 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~--l~~~~WT~eEd~~Ll~~~~------- 87 (250)
.+|.||+||++.|..+|..+|. .|.+|+..|+ |.+..|++||+++..++ .+++.||.+|++.|+.+|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 8999999999999999999998 9999999996 99999999999999887 5899999999999999995
Q ss_pred Hh-------------------CCCHHHHhhhCCCCCHHHHHHHHHHhhhhhhhc
Q 025602 88 LL-------------------GNRWALIAGRLPGRTDNDIKNYWNTKLSKRVDA 122 (250)
Q Consensus 88 ~~-------------------g~~W~~Ia~~lpgRT~~~~knrw~~~l~k~~~~ 122 (250)
++ +..|..|++.+.+|+..+|+-+|+.++......
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n 513 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFN 513 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhh
Confidence 22 236999999999999999999999998776544
No 10
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.49 E-value=7.7e-15 Score=98.43 Aligned_cols=48 Identities=40% Similarity=0.774 Sum_probs=43.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccc
Q 025602 18 RGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYL 65 (250)
Q Consensus 18 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L 65 (250)
|++||+|||++|+++|.+||.++|..||..||.+||+.||+.||.++|
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 689999999999999999999669999999988999999999999875
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.43 E-value=1.8e-14 Score=126.24 Aligned_cols=65 Identities=17% Similarity=0.327 Sum_probs=60.9
Q ss_pred CCCCCCcccccC-----CCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCC
Q 025602 2 AGKRKTPCCSKG-----EGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPD 68 (250)
Q Consensus 2 ~g~~~~~c~~k~-----~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~ 68 (250)
+||+..+|+.+| |.+++++||+|||++|++++..||. +|..||+.|+ +||..+|+.||..+|++.
T Consensus 57 ~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~Gn-KWs~IAk~Lp-GRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 57 LLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGN-RWSLIAGRIP-GRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred cCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhccc-cHHHHHhhcC-CCCHHHHHHHHHHHHhHH
Confidence 489999999986 8999999999999999999999998 8999999999 999999999999987754
No 12
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.42 E-value=3e-13 Score=90.62 Aligned_cols=46 Identities=30% Similarity=0.663 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-HHHHhhhCC-CCCHHHHHHHHHHhh
Q 025602 71 RGNFSKDEEDLVIRLHKLLGNR-WALIAGRLP-GRTDNDIKNYWNTKL 116 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~~-W~~Ia~~lp-gRT~~~~knrw~~~l 116 (250)
+++||++||++|++++.+||.+ |..||..|| +||..||++||+.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999998 999999999 999999999998764
No 13
>PLN03091 hypothetical protein; Provisional
Probab=99.37 E-value=9.2e-14 Score=130.13 Aligned_cols=65 Identities=17% Similarity=0.412 Sum_probs=60.5
Q ss_pred CCCCCCcccccC-----CCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCC
Q 025602 2 AGKRKTPCCSKG-----EGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPD 68 (250)
Q Consensus 2 ~g~~~~~c~~k~-----~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~ 68 (250)
+||...+|+.+| |.|+||+||+|||++|++++.+||. +|..||+.|+ +|++.+|+.||+..|+..
T Consensus 46 ~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~Gn-KWskIAk~LP-GRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 46 LQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGN-RWSQIAAQLP-GRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred cCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCc-chHHHHHhcC-CCCHHHHHHHHHHHHHHH
Confidence 388999999986 9999999999999999999999998 8999999998 999999999999877654
No 14
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.31 E-value=3.7e-12 Score=88.92 Aligned_cols=52 Identities=31% Similarity=0.627 Sum_probs=43.1
Q ss_pred CCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhhhhhcCCC
Q 025602 74 FSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRVDANHH 125 (250)
Q Consensus 74 WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k~~~~~~~ 125 (250)
||++||++|+++|..||.+|..||+.|+.||..+|++||+..|++.+.....
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~w 52 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPW 52 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSS
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCc
Confidence 9999999999999999999999999997799999999999977665544433
No 15
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.23 E-value=2.2e-11 Score=79.91 Aligned_cols=47 Identities=40% Similarity=0.837 Sum_probs=44.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 71 RGNFSKDEEDLVIRLHKLLG-NRWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g-~~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
+++||++||.+|+.++.+|| .+|..||..||+||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 899999999999999999999988764
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.17 E-value=1.4e-11 Score=80.89 Aligned_cols=48 Identities=38% Similarity=0.891 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccccccccccccc
Q 025602 18 RGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLR 66 (250)
Q Consensus 18 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 66 (250)
+++||++||++|+.++..||..+|..||..++ +|++.+|+.||.+++.
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 46899999999999999999559999999999 9999999999998764
No 17
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.14 E-value=9.5e-12 Score=110.02 Aligned_cols=62 Identities=18% Similarity=0.398 Sum_probs=57.6
Q ss_pred CCCCCcccccC-----CCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccccccccccccc
Q 025602 3 GKRKTPCCSKG-----EGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLR 66 (250)
Q Consensus 3 g~~~~~c~~k~-----~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 66 (250)
||-..+|+.+| |.|+||.||+|||++|++++..+|. +|+.||+.|| |||+..++.+|..+|+
T Consensus 42 ~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GN-rWs~IA~~LP-GRTDNeIKN~Wnt~lk 108 (238)
T KOG0048|consen 42 RRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGN-RWSLIAGRLP-GRTDNEVKNHWNTHLK 108 (238)
T ss_pred CccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCc-HHHHHHhhCC-CcCHHHHHHHHHHHHH
Confidence 77788999986 9999999999999999999999999 7999999999 9999999999877663
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=99.11 E-value=1.9e-10 Score=74.26 Aligned_cols=44 Identities=34% Similarity=0.731 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHHHhC-CCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 73 NFSKDEEDLVIRLHKLLG-NRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 73 ~WT~eEd~~Ll~~~~~~g-~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
+||.+|+.+|+.++.++| .+|..||..|++||..+|++||+.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999997753
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.04 E-value=1.1e-10 Score=75.40 Aligned_cols=45 Identities=40% Similarity=0.845 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccc
Q 025602 20 AWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYL 65 (250)
Q Consensus 20 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L 65 (250)
+||++||++|+.++..||.++|..||..++ +|++.+|+.||.+++
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 599999999999999999669999999999 899999999998753
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.90 E-value=1.5e-09 Score=105.67 Aligned_cols=103 Identities=25% Similarity=0.372 Sum_probs=86.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHh----CC-------------------CCccchhhhcCCccccccccccccccccCCc-c
Q 025602 15 GLNRGAWKAVEDKILTDYIKAY----GE-------------------GKWRHIPKAAGLKRCGKSCRLRWMNYLRPDI-K 70 (250)
Q Consensus 15 ~i~kg~WT~eED~~L~~~v~~~----g~-------------------~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l-~ 70 (250)
.++-+.|+.+||+.|...|+.| |- +-|..|...|| .|+...++.+-++...|-- .
T Consensus 305 e~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~~ 383 (607)
T KOG0051|consen 305 EINLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFENK 383 (607)
T ss_pred hhhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCccccc
Confidence 3455999999999999999987 11 12678888999 6999999884444444432 8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhhh
Q 025602 71 RGNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSKR 119 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k~ 119 (250)
+|.||++|++.|..+|.++|+.|..|++.| ||.+.+|+.||..+++..
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 999999999999999999999999999999 999999999999888655
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=98.51 E-value=1.3e-08 Score=98.33 Aligned_cols=98 Identities=28% Similarity=0.577 Sum_probs=85.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccC--CccCCCCCHHHHHHHHHHHHHhC---
Q 025602 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRP--DIKRGNFSKDEEDLVIRLHKLLG--- 90 (250)
Q Consensus 16 i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p--~l~~~~WT~eEd~~Ll~~~~~~g--- 90 (250)
-.+|.||+||+..|..++..+|. .|..|...++ |-+..||+||++|... .+++++|+.+|+.+|...+.+.-
T Consensus 289 ~~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~ 365 (512)
T COG5147 289 EQRGKWTKEEEQELAKLVVEHGG-SWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEA 365 (512)
T ss_pred hhhccCccccccccccccccccc-hhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHH
Confidence 35799999999999999999997 9999998875 9999999999999988 68889999999999998887432
Q ss_pred -----CCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 91 -----NRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 91 -----~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
..|..|+..+++|....|+.++..+.
T Consensus 366 ~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 366 QQSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred hhhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 26999999999999888888775544
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=98.08 E-value=2.6e-06 Score=59.23 Aligned_cols=49 Identities=12% Similarity=0.235 Sum_probs=43.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCc---cchhhhcCCcc-ccccccccccccc
Q 025602 17 NRGAWKAVEDKILTDYIKAYGEGKW---RHIPKAAGLKR-CGKSCRLRWMNYL 65 (250)
Q Consensus 17 ~kg~WT~eED~~L~~~v~~~g~~~W---~~Ia~~l~~~R-t~~qcr~Rw~~~L 65 (250)
++-.||+||..+++++|+.+|.++| ..|++.|+..| |..||+.+++.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3567999999999999999999999 99999987667 9999999887764
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.02 E-value=2.5e-06 Score=80.28 Aligned_cols=50 Identities=22% Similarity=0.589 Sum_probs=46.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccc
Q 025602 15 GLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYL 65 (250)
Q Consensus 15 ~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L 65 (250)
.+-...||++|+-+|++++..||.|||..||.++| .|++.+|+++|.+++
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 999999999999875
No 24
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.77 E-value=8.2e-05 Score=51.71 Aligned_cols=46 Identities=17% Similarity=0.260 Sum_probs=40.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-CH---HHHhhhCC-CC-CHHHHHHHHHHhh
Q 025602 71 RGNFSKDEEDLVIRLHKLLGN-RW---ALIAGRLP-GR-TDNDIKNYWNTKL 116 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~-~W---~~Ia~~lp-gR-T~~~~knrw~~~l 116 (250)
+-.||+||...+++++..+|. +| ..|+..|. .| |..||+.+...+.
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 457999999999999999998 99 99999984 45 9999999987654
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.59 E-value=0.00012 Score=69.10 Aligned_cols=49 Identities=22% Similarity=0.398 Sum_probs=43.9
Q ss_pred CccCCCCCHHHHHHHHHHHHHhC-CCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 68 DIKRGNFSKDEEDLVIRLHKLLG-NRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 68 ~l~~~~WT~eEd~~Ll~~~~~~g-~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
.+-...||.+||.+||+++..|| .+|..||.++..||..+|+.+|.+++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 34466899999999999999999 49999999999999999999997654
No 26
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.58 E-value=0.00013 Score=62.95 Aligned_cols=99 Identities=20% Similarity=0.345 Sum_probs=71.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccchhhhcCC--ccccccccccccccc-cCCcc--------------------CCCCCH
Q 025602 20 AWKAVEDKILTDYIKAYGEGKWRHIPKAAGL--KRCGKSCRLRWMNYL-RPDIK--------------------RGNFSK 76 (250)
Q Consensus 20 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~--~Rt~~qcr~Rw~~~L-~p~l~--------------------~~~WT~ 76 (250)
+|+++.|-+|+.+|..-. +-..|+.-+.. .-|-..+.+||+..| +|.+. +.+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 599999999999998765 36666655443 336677789999876 44332 468999
Q ss_pred HHHHHHHHHHHHhCC---CHHHHhh-----hCCCCCHHHHHHHHHHhhhhhh
Q 025602 77 DEEDLVIRLHKLLGN---RWALIAG-----RLPGRTDNDIKNYWNTKLSKRV 120 (250)
Q Consensus 77 eEd~~Ll~~~~~~g~---~W~~Ia~-----~lpgRT~~~~knrw~~~l~k~~ 120 (250)
+||++|......... .+.+|=. +.++||+.++.++|..+.+-.+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999997765543 4666622 2379999999999985444433
No 27
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.39 E-value=0.00021 Score=59.38 Aligned_cols=52 Identities=15% Similarity=0.236 Sum_probs=45.7
Q ss_pred cCCCCCHHHHHHHHHHHHHhCC-------CHHHHhhhCCCCCHHHHHHHHHHhhhhhhhc
Q 025602 70 KRGNFSKDEEDLVIRLHKLLGN-------RWALIAGRLPGRTDNDIKNYWNTKLSKRVDA 122 (250)
Q Consensus 70 ~~~~WT~eEd~~Ll~~~~~~g~-------~W~~Ia~~lpgRT~~~~knrw~~~l~k~~~~ 122 (250)
+...||.|||.+|.+.|-.|-. -...++..| +||..+|--|||+.|++++..
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 3568999999999999998832 388899999 999999999999999998764
No 28
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.39 E-value=7.6e-05 Score=70.99 Aligned_cols=46 Identities=22% Similarity=0.613 Sum_probs=43.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccccccccccc
Q 025602 17 NRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNY 64 (250)
Q Consensus 17 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~ 64 (250)
....||.+|..+|++.|++||. +|.+||.++| +|+..||..|+.+.
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 6679999999999999999998 9999999999 99999999999874
No 29
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.33 E-value=0.00019 Score=69.09 Aligned_cols=59 Identities=22% Similarity=0.404 Sum_probs=53.5
Q ss_pred ccCCCCCHHHHHHHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHHHHHhhhhhhhcCCCCC
Q 025602 69 IKRGNFSKDEEDLVIRLHKLLGN-RWALIAGRLPGRTDNDIKNYWNTKLSKRVDANHHHH 127 (250)
Q Consensus 69 l~~~~WT~eEd~~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knrw~~~l~k~~~~~~~~~ 127 (250)
++.|-|+.-||++|-.+|..||. .|+.|++.++-.|..||++||...+.+.++...+..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~ 64 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSR 64 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhh
Confidence 56789999999999999999996 799999999999999999999999999888766543
No 30
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.14 E-value=0.00021 Score=69.48 Aligned_cols=47 Identities=23% Similarity=0.663 Sum_probs=43.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccccccccccc
Q 025602 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNY 64 (250)
Q Consensus 16 i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~ 64 (250)
--++.||.+|..+|+++|++||. +|.+||.+++ +|+..||..++.+.
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 35788999999999999999998 9999999999 99999999998774
No 31
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.95 E-value=0.0016 Score=46.43 Aligned_cols=50 Identities=18% Similarity=0.318 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------C-CHHHHhhhCC-CCCHHHHHHHHHHhhhhhh
Q 025602 71 RGNFSKDEEDLVIRLHKLLG--------N-RWALIAGRLP-GRTDNDIKNYWNTKLSKRV 120 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g--------~-~W~~Ia~~lp-gRT~~~~knrw~~~l~k~~ 120 (250)
+.+||.+||.+|++.|+++. + =|.++++.-| .+|-.+.++||...|+.+.
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 45899999999999997653 2 2999999987 8999999999988877654
No 32
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.93 E-value=0.00027 Score=50.43 Aligned_cols=52 Identities=25% Similarity=0.446 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------C--CccchhhhcCCccccccccccccccccCCc
Q 025602 18 RGAWKAVEDKILTDYIKAYGE------G--KWRHIPKAAGLKRCGKSCRLRWMNYLRPDI 69 (250)
Q Consensus 18 kg~WT~eED~~L~~~v~~~g~------~--~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l 69 (250)
|-+||+|||++|+..|..+.. | =|..+++.-+..+|-.+-|+||...|.+..
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 457999999999999976521 2 299999888768899999999999987643
No 33
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.89 E-value=0.0012 Score=62.91 Aligned_cols=45 Identities=18% Similarity=0.276 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 71 RGNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
...||.+|..+|++.+..||..|.+||.++.+||..||--||-++
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 348999999999999999999999999999999999999999653
No 34
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.83 E-value=0.001 Score=49.25 Aligned_cols=51 Identities=31% Similarity=0.539 Sum_probs=35.1
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--C------CHHHHhhhC----CCCCHHHHHHHHHHhhhhhhhc
Q 025602 71 RGNFSKDEEDLVIRLHKL------LG--N------RWALIAGRL----PGRTDNDIKNYWNTKLSKRVDA 122 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~------~g--~------~W~~Ia~~l----pgRT~~~~knrw~~~l~k~~~~ 122 (250)
+..||.+|...||+++.+ ++ . -|..||..| ..||..||+++|+++ +++++.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L-~~~Yk~ 69 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL-KKKYKK 69 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH-HHHHHC
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HHHHHH
Confidence 357999999999999887 21 1 399999987 369999999999774 455544
No 35
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.82 E-value=0.0018 Score=63.14 Aligned_cols=46 Identities=15% Similarity=0.330 Sum_probs=42.5
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 70 KRGNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 70 ~~~~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
.+..||.+|.-+|++++..||-+|.+||.++.+||..||-.|+-.+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 3568999999999999999999999999999999999999998543
No 36
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.61 E-value=0.00065 Score=50.38 Aligned_cols=48 Identities=29% Similarity=0.655 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C---C----CCccchhhhc---CCccccccccccccccc
Q 025602 18 RGAWKAVEDKILTDYIKA--Y----G---E----GKWRHIPKAA---GLKRCGKSCRLRWMNYL 65 (250)
Q Consensus 18 kg~WT~eED~~L~~~v~~--~----g---~----~~W~~Ia~~l---~~~Rt~~qcr~Rw~~~L 65 (250)
|-.||.+|...|+.++.. + + . .-|..||..| |..|++.||+.+|.+..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 347999999999999987 2 1 1 1399999887 56899999999998853
No 37
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.55 E-value=0.00085 Score=61.33 Aligned_cols=50 Identities=20% Similarity=0.533 Sum_probs=45.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccccccccccccc
Q 025602 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLR 66 (250)
Q Consensus 16 i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 66 (250)
|----|+..|+-+|++.....|-|||..||..+| .|+...|+.+|..++.
T Consensus 61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 3345699999999999999999999999999999 9999999999988765
No 38
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.55 E-value=0.0029 Score=53.29 Aligned_cols=52 Identities=13% Similarity=0.268 Sum_probs=44.0
Q ss_pred cCCCCCHHHHHHHHHHHHHhCCC-------HHHHhhhCCCCCHHHHHHHHHHhhhhhhhc
Q 025602 70 KRGNFSKDEEDLVIRLHKLLGNR-------WALIAGRLPGRTDNDIKNYWNTKLSKRVDA 122 (250)
Q Consensus 70 ~~~~WT~eEd~~Ll~~~~~~g~~-------W~~Ia~~lpgRT~~~~knrw~~~l~k~~~~ 122 (250)
+...||.|+|.+|.+.|-.|+.. ...++..| +||..+|..|||+.++++...
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 46789999999999998888642 66677788 999999999999999987653
No 39
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.17 E-value=0.0017 Score=53.98 Aligned_cols=51 Identities=24% Similarity=0.541 Sum_probs=43.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC------CCccchhhhcCCccccccccccccccccCC
Q 025602 16 LNRGAWKAVEDKILTDYIKAYGE------GKWRHIPKAAGLKRCGKSCRLRWMNYLRPD 68 (250)
Q Consensus 16 i~kg~WT~eED~~L~~~v~~~g~------~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~ 68 (250)
.+.-.||.|||.+|-+.|-+|-. ..+..|+..| +||+.-|.-||..+++..
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L--~RTsAACGFRWNs~VRkq 58 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL--NRTAAACGFRWNAYVRKQ 58 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH--cccHHHhcchHHHHHHHH
Confidence 45678999999999999999932 2488999998 499999999999998753
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.60 E-value=0.0044 Score=45.00 Aligned_cols=49 Identities=20% Similarity=0.394 Sum_probs=39.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------CCccchhhhc----CCccccccccccccccc
Q 025602 17 NRGAWKAVEDKILTDYIKAYGE----------------GKWRHIPKAA----GLKRCGKSCRLRWMNYL 65 (250)
Q Consensus 17 ~kg~WT~eED~~L~~~v~~~g~----------------~~W~~Ia~~l----~~~Rt~~qcr~Rw~~~L 65 (250)
++..||.+|.+.|+++|.+|.. .-|..|+..| |..|+..+++..|.+..
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 3568999999999999999821 2499999887 22689999999998764
No 41
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.54 E-value=0.065 Score=56.72 Aligned_cols=99 Identities=12% Similarity=0.277 Sum_probs=75.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccc-------ccccc----------------------------
Q 025602 20 AWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRL-------RWMNY---------------------------- 64 (250)
Q Consensus 20 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~-------Rw~~~---------------------------- 64 (250)
.||.-+=..++.+..+||..+-..||..+. +++...++. ||...
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 488888888888999999988999999997 788877761 11110
Q ss_pred --------------c-cCCccCCCCCHHHHHHHHHHHHHhC-CCHHHHhhh------------CCCCCHHHHHHHHHHhh
Q 025602 65 --------------L-RPDIKRGNFSKDEEDLVIRLHKLLG-NRWALIAGR------------LPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 65 --------------L-~p~l~~~~WT~eEd~~Ll~~~~~~g-~~W~~Ia~~------------lpgRT~~~~knrw~~~l 116 (250)
+ .+..++..+|++||..|+-++.+|| .+|..|-.. +..||+..|..|.+++|
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 0 0122234699999999999999999 479998432 34899999999999888
Q ss_pred hhh
Q 025602 117 SKR 119 (250)
Q Consensus 117 ~k~ 119 (250)
+--
T Consensus 985 ~~~ 987 (1033)
T PLN03142 985 RLI 987 (1033)
T ss_pred HHH
Confidence 654
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.49 E-value=0.026 Score=40.91 Aligned_cols=47 Identities=28% Similarity=0.508 Sum_probs=38.5
Q ss_pred CCCCCHHHHHHHHHHHHHhC-----------------CCHHHHhhhC-----CCCCHHHHHHHHHHhhh
Q 025602 71 RGNFSKDEEDLVIRLHKLLG-----------------NRWALIAGRL-----PGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g-----------------~~W~~Ia~~l-----pgRT~~~~knrw~~~l~ 117 (250)
...||.+|..+|++++.++. .-|..|+..| +.||..+++.+|..+..
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~ 70 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKS 70 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Confidence 35799999999999998872 1299998876 36999999999977653
No 43
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.46 E-value=0.017 Score=52.97 Aligned_cols=47 Identities=28% Similarity=0.409 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 71 RGNFSKDEEDLVIRLHKLLGN-RWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
-..|+.+||.+|++....+|- +|..||.++..|+..+||.+|....-
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 457999999999999999995 99999999999999999999876543
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.61 E-value=0.011 Score=49.86 Aligned_cols=49 Identities=22% Similarity=0.496 Sum_probs=39.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC------CccchhhhcCCcccccccccccccccc
Q 025602 16 LNRGAWKAVEDKILTDYIKAYGEG------KWRHIPKAAGLKRCGKSCRLRWMNYLR 66 (250)
Q Consensus 16 i~kg~WT~eED~~L~~~v~~~g~~------~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 66 (250)
.++..||.|||.+|-+.|..|+.. -...++..| +|+...|..||.-+++
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHH
Confidence 467889999999999999998642 266677777 5999999999977665
No 45
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=93.49 E-value=0.19 Score=39.99 Aligned_cols=51 Identities=20% Similarity=0.389 Sum_probs=40.4
Q ss_pred CccCCCCCHHHHHHHHHHHHHhCC----CHHHHhhh------------CCCCCHHHHHHHHHHhhhh
Q 025602 68 DIKRGNFSKDEEDLVIRLHKLLGN----RWALIAGR------------LPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 68 ~l~~~~WT~eEd~~Ll~~~~~~g~----~W~~Ia~~------------lpgRT~~~~knrw~~~l~k 118 (250)
.-++..||++||..|+-++.+||- .|..|-.. +..||+..|..|.+++|+-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 456779999999999999999997 79888553 2479999999999998864
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=93.43 E-value=0.064 Score=50.48 Aligned_cols=85 Identities=24% Similarity=0.391 Sum_probs=65.0
Q ss_pred CccchhhhcCCccccccccccccccccCC-------------------------ccCCCCCHHHHHHHHHHHHHhCCCHH
Q 025602 40 KWRHIPKAAGLKRCGKSCRLRWMNYLRPD-------------------------IKRGNFSKDEEDLVIRLHKLLGNRWA 94 (250)
Q Consensus 40 ~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~-------------------------l~~~~WT~eEd~~Ll~~~~~~g~~W~ 94 (250)
.|.-++=..+ .|...-...+|.....+. +....||.+|-+-|+++++.|.-+|-
T Consensus 75 ~W~w~pFtn~-aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~ 153 (445)
T KOG2656|consen 75 PWKWVPFTNS-ARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCCc-cccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 5776665555 676766777777763221 11346999999999999999999999
Q ss_pred HHhhh-----CCC-CCHHHHHHHHHHhhhhhhhcCCC
Q 025602 95 LIAGR-----LPG-RTDNDIKNYWNTKLSKRVDANHH 125 (250)
Q Consensus 95 ~Ia~~-----lpg-RT~~~~knrw~~~l~k~~~~~~~ 125 (250)
.|+.. ++. ||-.++|.||+...++-++++..
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~ 190 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAP 190 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccCC
Confidence 99987 655 99999999999988877765443
No 47
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=93.07 E-value=0.16 Score=47.73 Aligned_cols=47 Identities=21% Similarity=0.323 Sum_probs=42.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 72 GNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 72 ~~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
.+||.+|-++...+...+|..++.|+..+|.|...|||.+|...-++
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 37999999999999999999999999999999999999999765443
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.41 E-value=0.23 Score=46.11 Aligned_cols=48 Identities=19% Similarity=0.288 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCCHHHHhhhC----CCCCHHHHHHHHHHhhhh
Q 025602 71 RGNFSKDEEDLVIRLHKLL----------GNRWALIAGRL----PGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~----------g~~W~~Ia~~l----pgRT~~~~knrw~~~l~k 118 (250)
...|+.+|-..||++..++ +..|..||+.+ --||+.+|+++|.++.++
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~ 115 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKK 115 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 4689999999999998765 23599999965 359999999999776544
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=90.99 E-value=0.65 Score=34.49 Aligned_cols=47 Identities=28% Similarity=0.500 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------CHHHHhhhC---C--CCCHHHHHHHHHHhhhhhh
Q 025602 73 NFSKDEEDLVIRLHKLL---GN----------RWALIAGRL---P--GRTDNDIKNYWNTKLSKRV 120 (250)
Q Consensus 73 ~WT~eEd~~Ll~~~~~~---g~----------~W~~Ia~~l---p--gRT~~~~knrw~~~l~k~~ 120 (250)
.||+++++.|++++.+. |+ .|..|+..| + ..|..||++||.. |++..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~-lk~~y 65 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT-LKKDY 65 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH-HHHHH
Confidence 49999999999998654 21 299998887 2 3578999999965 44443
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.64 E-value=0.16 Score=47.83 Aligned_cols=60 Identities=15% Similarity=0.292 Sum_probs=48.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccccccccccc--ccCCc------cCCCCCHHH
Q 025602 17 NRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNY--LRPDI------KRGNFSKDE 78 (250)
Q Consensus 17 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~--L~p~l------~~~~WT~eE 78 (250)
.--+||.+|-+++.+++...|+ ++..|+..+| +|..+|++..|.+- .+|.. .+.|+..+|
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP-~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~e 431 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGT-DFSLISSLFP-NRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVE 431 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcc-hHHHHHHhcC-chhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHH
Confidence 3457999999999999999999 9999999999 99999999998773 23311 145676666
No 51
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=90.36 E-value=1.3 Score=42.78 Aligned_cols=47 Identities=15% Similarity=0.301 Sum_probs=42.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 71 RGNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
...||.||-.++-.+...||+++.+|-+.||.|+-..+..+|+..-+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK 233 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKK 233 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHH
Confidence 45799999999999999999999999999999999999998865443
No 52
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=88.08 E-value=0.5 Score=37.55 Aligned_cols=35 Identities=23% Similarity=0.493 Sum_probs=29.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCC---CCccchhhhc
Q 025602 14 EGLNRGAWKAVEDKILTDYIKAYGE---GKWRHIPKAA 48 (250)
Q Consensus 14 ~~i~kg~WT~eED~~L~~~v~~~g~---~~W~~Ia~~l 48 (250)
|.-++..||.+||.-|+-.+.+||- +.|..|-..+
T Consensus 45 ~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 45 PNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp STSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 3667889999999999999999998 8999998776
No 53
>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=87.57 E-value=1.5 Score=29.08 Aligned_cols=41 Identities=20% Similarity=0.262 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 76 KDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 76 ~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
++++..++.++...|-.|.+||..+ |.|...|+.+....++
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 4677888888888899999999999 9999999998766544
No 54
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=83.66 E-value=0.61 Score=43.28 Aligned_cols=48 Identities=21% Similarity=0.441 Sum_probs=38.0
Q ss_pred CCCCCHHHHHHHHHHHHHh----CCC-----Cccchhhhc---CCccccccccccccccc
Q 025602 18 RGAWKAVEDKILTDYIKAY----GEG-----KWRHIPKAA---GLKRCGKSCRLRWMNYL 65 (250)
Q Consensus 18 kg~WT~eED~~L~~~v~~~----g~~-----~W~~Ia~~l---~~~Rt~~qcr~Rw~~~L 65 (250)
...|+.+|-..|+.+.... ..+ -|..||..+ |..|++.||+.+|.+..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 3689999999999988753 222 499999844 56899999999998753
No 55
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=81.83 E-value=4.5 Score=41.35 Aligned_cols=44 Identities=11% Similarity=0.188 Sum_probs=40.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHH
Q 025602 71 RGNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNT 114 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~ 114 (250)
...||+.|-.+.-+++..|.+++-.|++.++++|-.+|-.+|++
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 35799999999999999999999999999999999999888653
No 56
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=81.07 E-value=1.2 Score=33.06 Aligned_cols=44 Identities=20% Similarity=0.498 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------CccchhhhcC----Cccccccccccccc
Q 025602 20 AWKAVEDKILTDYIKAY---GEG---------KWRHIPKAAG----LKRCGKSCRLRWMN 63 (250)
Q Consensus 20 ~WT~eED~~L~~~v~~~---g~~---------~W~~Ia~~l~----~~Rt~~qcr~Rw~~ 63 (250)
.||+++++.|++++... |.. .|..|+..|. ...+..||+.||..
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 59999999999988654 221 2888887774 23445566666543
No 57
>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=78.86 E-value=2.1 Score=31.90 Aligned_cols=30 Identities=27% Similarity=0.454 Sum_probs=16.5
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCCCCccchhh
Q 025602 14 EGLNRGAWKAVEDKIL--------TDYIKAYGEGKWRHIPK 46 (250)
Q Consensus 14 ~~i~kg~WT~eED~~L--------~~~v~~~g~~~W~~Ia~ 46 (250)
|.-..|-||+|+|+.| ..++++|| +..|+.
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 4455889999999999 44666777 345544
No 58
>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=78.59 E-value=57 Score=30.37 Aligned_cols=98 Identities=19% Similarity=0.259 Sum_probs=68.1
Q ss_pred CCCcccccCCCCCCCCCCHHHHHHHHHHHHHhCCCC---ccchhhhcCCccccccccccccccccCCccCCCCCHHHHHH
Q 025602 5 RKTPCCSKGEGLNRGAWKAVEDKILTDYIKAYGEGK---WRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDL 81 (250)
Q Consensus 5 ~~~~c~~k~~~i~kg~WT~eED~~L~~~v~~~g~~~---W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT~eEd~~ 81 (250)
...|.+..++...-..||.-|-..|+.+........ -.+|++.++ +|+..++++. .+.|+ +..
T Consensus 8 R~~PaRy~g~~~gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~f-l~~LK------------~rv 73 (344)
T PF11035_consen 8 RAAPARYLGEVTGPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRDF-LQQLK------------GRV 73 (344)
T ss_pred CCCCccccCCCCCcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHHH-HHHHH------------HHH
Confidence 445666665555567899999999999988763223 457788888 9999888764 33332 334
Q ss_pred HHHHHHH-h-----CC------------CHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 82 VIRLHKL-L-----GN------------RWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 82 Ll~~~~~-~-----g~------------~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
+.+++++ | |. -|..+|+.+.|.-...+-.-|...|
T Consensus 74 areaiqkv~~~g~~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l 126 (344)
T PF11035_consen 74 AREAIQKVHPGGLKGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVL 126 (344)
T ss_pred HHHHHHHhcccccccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHH
Confidence 5555554 2 11 1999999999998888888887665
No 59
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=77.38 E-value=3.7 Score=41.06 Aligned_cols=49 Identities=12% Similarity=0.415 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHhh----------hCCCCCHHHHHHHHHHhhhhh
Q 025602 71 RGNFSKDEEDLVIRLHKLLGNRWALIAG----------RLPGRTDNDIKNYWNTKLSKR 119 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~~W~~Ia~----------~lpgRT~~~~knrw~~~l~k~ 119 (250)
+..||-+|+.-...+++++|+++..|-. ...-+|..|++.+|+..+++-
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 5689999999999999999999999822 233468889999988777653
No 60
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=75.70 E-value=6.9 Score=25.14 Aligned_cols=38 Identities=18% Similarity=0.324 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 77 DEEDLVIRLHKLLGN-RWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 77 eEd~~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
+=|..|+.+...-+. .|.+||+.+ |=|...|..|+..+
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 447888888888886 799999999 88999999998653
No 61
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=74.73 E-value=7.6 Score=25.28 Aligned_cols=41 Identities=32% Similarity=0.381 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 77 DEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 77 eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
+++..++.++--.|..+.+||..| |-|...|+.+....+++
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 456666666666667899999999 88999999988776653
No 62
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=73.03 E-value=5.2 Score=40.91 Aligned_cols=44 Identities=14% Similarity=0.386 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccc
Q 025602 18 RGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMN 63 (250)
Q Consensus 18 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~ 63 (250)
.-.||+.|-.++.+++-.|.. ++-.|++.++ ++|..||-+-|+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K-DF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK-DFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc-cHHHHHHHhc-cccHHHHHHHHHH
Confidence 357999999999999999997 9999999999 9999999988765
No 63
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=71.56 E-value=8 Score=31.53 Aligned_cols=43 Identities=9% Similarity=0.063 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHHHHHhhhhhh
Q 025602 77 DEEDLVIRLHKLLGN-RWALIAGRLPGRTDNDIKNYWNTKLSKRV 120 (250)
Q Consensus 77 eEd~~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knrw~~~l~k~~ 120 (250)
+-|..|+++.++-|. .|++||+.+ |-|...|+.|++.+....+
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 568889999888886 899999999 9999999999987766554
No 64
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=69.55 E-value=2.5 Score=27.22 Aligned_cols=37 Identities=14% Similarity=0.231 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhCCCCccchhhhcCCcccccccccccc
Q 025602 24 VEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWM 62 (250)
Q Consensus 24 eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~ 62 (250)
+=|..|+.++...+...|..||+.+| =+...|..|+.
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~ 39 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIR 39 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHH
Confidence 45889999999999889999999997 67777877764
No 65
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=66.03 E-value=9.9 Score=31.39 Aligned_cols=44 Identities=7% Similarity=-0.017 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHHHHHhhhhhh
Q 025602 76 KDEEDLVIRLHKLLGN-RWALIAGRLPGRTDNDIKNYWNTKLSKRV 120 (250)
Q Consensus 76 ~eEd~~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knrw~~~l~k~~ 120 (250)
.+-|.+|+.+.++-|+ .|++||+.+ |=|...|..|++.+....+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 4568889988888887 899999999 9999999999988776554
No 66
>smart00595 MADF subfamily of SANT domain.
Probab=65.04 E-value=6.5 Score=28.65 Aligned_cols=23 Identities=30% Similarity=0.585 Sum_probs=20.1
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 93 WALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 93 W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|..||..| |-|..+|+.+|+++-
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR 52 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHH
Confidence 99999999 449999999997754
No 67
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=64.79 E-value=12 Score=35.44 Aligned_cols=42 Identities=19% Similarity=0.348 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHhh-hCCCCCHHHHHHHHH
Q 025602 72 GNFSKDEEDLVIRLHKLLGNRWALIAG-RLPGRTDNDIKNYWN 113 (250)
Q Consensus 72 ~~WT~eEd~~Ll~~~~~~g~~W~~Ia~-~lpgRT~~~~knrw~ 113 (250)
..|+++|-...-+-++.||+++..|.. .++.|+--.|-.+|+
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYY 320 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYY 320 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHH
Confidence 479999999999999999999999955 589999999988764
No 68
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=62.62 E-value=3.6 Score=39.05 Aligned_cols=49 Identities=20% Similarity=0.293 Sum_probs=42.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccchhhh-----cCCcccccccccccccc
Q 025602 15 GLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKA-----AGLKRCGKSCRLRWMNY 64 (250)
Q Consensus 15 ~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~-----l~~~Rt~~qcr~Rw~~~ 64 (250)
.++-..||.+|-+-|.++..+|-- +|-.||.. ++..||....++||+.+
T Consensus 127 ~l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 455678999999999999999998 89999988 67569999999999875
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=61.93 E-value=19 Score=28.27 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 80 DLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 80 ~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
..++.+.-..|-.+.+||..+ |.|...|+.+.+..+
T Consensus 119 r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~ 154 (161)
T TIGR02985 119 RKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKAL 154 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 333344334467899999999 899999999987654
No 70
>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=59.61 E-value=15 Score=27.30 Aligned_cols=30 Identities=27% Similarity=0.450 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhCCCHHHHhhhCCCCCHHHHH
Q 025602 79 EDLVIRLHKLLGNRWALIAGRLPGRTDNDIK 109 (250)
Q Consensus 79 d~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~k 109 (250)
|+.|..+...+|..|..+|.+| |=|..+|.
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 5678889999999999999999 65665543
No 71
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=59.24 E-value=13 Score=31.00 Aligned_cols=41 Identities=17% Similarity=0.198 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHH
Q 025602 73 NFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNT 114 (250)
Q Consensus 73 ~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~ 114 (250)
.||+|+.+.|.+|. .-|..=++||..|.+.|.+.|--+-+.
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 59999999999887 447778999999987999999876643
No 72
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=59.13 E-value=5 Score=32.75 Aligned_cols=46 Identities=11% Similarity=0.101 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCcc
Q 025602 23 AVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIK 70 (250)
Q Consensus 23 ~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~ 70 (250)
.+-|.+|+.+..+.|.-.|+.||+.+| -+...|+.|+.+....++-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 357999999999999989999999996 7888999998876655443
No 73
>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=57.81 E-value=3.4 Score=30.58 Aligned_cols=40 Identities=23% Similarity=0.430 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCC-------CCccchhhhcCCccc----ccccccccccccc
Q 025602 27 KILTDYIKAYGE-------GKWRHIPKAAGLKRC----GKSCRLRWMNYLR 66 (250)
Q Consensus 27 ~~L~~~v~~~g~-------~~W~~Ia~~l~~~Rt----~~qcr~Rw~~~L~ 66 (250)
-.|..+|.+.|- +.|..||..++.... +.+++..|.++|.
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 357777777762 469999999985442 2456666766654
No 74
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=57.11 E-value=12 Score=37.40 Aligned_cols=44 Identities=20% Similarity=0.373 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHH
Q 025602 71 RGNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNT 114 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~ 114 (250)
.++|+..|-++...+..+.|.+.+.|+..+|+|+..+||.+|..
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 46899999999999999999999999999999999999999854
No 75
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=55.70 E-value=4.7 Score=33.31 Aligned_cols=46 Identities=15% Similarity=0.120 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCcc
Q 025602 23 AVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIK 70 (250)
Q Consensus 23 ~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~ 70 (250)
.+-|.+|+.+..+.|.-.|..||+.+| -+...|+.|+.+....++-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 567999999999999989999999996 7778899888877655543
No 76
>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=54.99 E-value=22 Score=26.41 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHH
Q 025602 79 EDLVIRLHKLLGNRWALIAGRLPGRTDNDIKN 110 (250)
Q Consensus 79 d~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~kn 110 (250)
|..|..+...+|..|.++|..| |=+..+|.+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 5678888899999999999999 666665544
No 77
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=54.78 E-value=31 Score=23.24 Aligned_cols=37 Identities=30% Similarity=0.453 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHH
Q 025602 76 KDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWN 113 (250)
Q Consensus 76 ~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~ 113 (250)
.++|+..+.++.+.|-.-.+||+.+ ||+.+.|+++-+
T Consensus 6 t~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 6 TDAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYLK 42 (50)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHHH
T ss_pred CHHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHhc
Confidence 4567777888899999999999999 999998888643
No 78
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=54.54 E-value=48 Score=30.84 Aligned_cols=49 Identities=31% Similarity=0.548 Sum_probs=37.8
Q ss_pred CCCCCHHHHHHHHHHHHHh-CC---CHHHHhhhCCCCCHHHHHHHHHHhhhhhh
Q 025602 71 RGNFSKDEEDLVIRLHKLL-GN---RWALIAGRLPGRTDNDIKNYWNTKLSKRV 120 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~-g~---~W~~Ia~~lpgRT~~~~knrw~~~l~k~~ 120 (250)
-..||.-|...|+.+.+.. |. .-.+|++.++||+..+|++.-. .||.|+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~-~LK~rv 73 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQ-QLKGRV 73 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHH-HHHHHH
Confidence 3579999999999888765 43 4678999999999999998654 344443
No 79
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=54.52 E-value=8.2 Score=37.44 Aligned_cols=46 Identities=15% Similarity=0.234 Sum_probs=39.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccc
Q 025602 16 LNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMN 63 (250)
Q Consensus 16 i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~ 63 (250)
-....||.||--++.++...||. ++.+|-+.|| .|+-.+++.-|+.
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~LP-~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFGK-DFHKIRQALP-HRSLASLVQYYYS 230 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhcc-cHHHHHHHcc-CccHHHHHHHHHH
Confidence 34567999999999999999998 9999999999 9998888766554
No 80
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=53.96 E-value=30 Score=30.01 Aligned_cols=45 Identities=16% Similarity=0.187 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHhhhC---CCCCHHHHHHHHHHhhhh
Q 025602 73 NFSKDEEDLVIRLHKLLGNRWALIAGRL---PGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 73 ~WT~eEd~~Ll~~~~~~g~~W~~Ia~~l---pgRT~~~~knrw~~~l~k 118 (250)
.|++.+|-+|+.+|.. ++.-..|+.-+ -.-|-.+|..||+.+|--
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd 48 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYD 48 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcC
Confidence 4999999999999865 44455555543 245889999999998854
No 81
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=51.88 E-value=8.3 Score=41.29 Aligned_cols=34 Identities=15% Similarity=0.303 Sum_probs=29.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhc
Q 025602 15 GLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAA 48 (250)
Q Consensus 15 ~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l 48 (250)
.-++..||.|||..|+-.+.+||-++|..|-..+
T Consensus 923 ~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 923 QNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 3445569999999999999999999999997766
No 82
>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=49.47 E-value=21 Score=26.12 Aligned_cols=30 Identities=30% Similarity=0.623 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhCCCHHHHhhhCCCCCHHHHH
Q 025602 79 EDLVIRLHKLLGNRWALIAGRLPGRTDNDIK 109 (250)
Q Consensus 79 d~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~k 109 (250)
|..|..+.+.+|..|.++|..| |=+..+|.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~ 33 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDID 33 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHH
Confidence 4567788889999999999999 66655543
No 83
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=49.46 E-value=39 Score=25.30 Aligned_cols=43 Identities=12% Similarity=0.112 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHHHHHhhhhhh
Q 025602 77 DEEDLVIRLHKLLGN-RWALIAGRLPGRTDNDIKNYWNTKLSKRV 120 (250)
Q Consensus 77 eEd~~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knrw~~~l~k~~ 120 (250)
+.|..|+.+..+.+. .+..||+.+ |-+...|..+.+.+....+
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 567888888888775 899999999 9999999999988776654
No 84
>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=49.33 E-value=14 Score=30.79 Aligned_cols=34 Identities=12% Similarity=0.108 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccc
Q 025602 20 AWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKS 56 (250)
Q Consensus 20 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~q 56 (250)
.||+|+.++|.++...-- .=.+||..|| +.+...
T Consensus 2 ~Wtde~~~~L~~lw~~G~--SasqIA~~lg-~vsRnA 35 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL--SASQIARQLG-GVSRNA 35 (162)
T ss_pred CCCHHHHHHHHHHHHcCC--CHHHHHHHhC-Ccchhh
Confidence 499999999999996533 4689999998 444433
No 85
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=49.27 E-value=32 Score=26.23 Aligned_cols=49 Identities=14% Similarity=0.167 Sum_probs=31.9
Q ss_pred CCCCHHHHHHHHHHHHHh----CC----CHHHHhhh----CC-CCCHHHHHHHHHHhhhhhhh
Q 025602 72 GNFSKDEEDLVIRLHKLL----GN----RWALIAGR----LP-GRTDNDIKNYWNTKLSKRVD 121 (250)
Q Consensus 72 ~~WT~eEd~~Ll~~~~~~----g~----~W~~Ia~~----lp-gRT~~~~knrw~~~l~k~~~ 121 (250)
.-||+++|..||+.+..| |. .|..+-.. |. .=|..|+..+-.. |++|+.
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Kirr-LK~Ky~ 66 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRR-LKKKYR 66 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHH-HHHHHH
Confidence 369999999999998777 52 45444333 32 2377888877755 344443
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=46.81 E-value=10 Score=28.20 Aligned_cols=17 Identities=18% Similarity=0.559 Sum_probs=10.1
Q ss_pred CCccCCCCCHHHHHHHH
Q 025602 67 PDIKRGNFSKDEEDLVI 83 (250)
Q Consensus 67 p~l~~~~WT~eEd~~Ll 83 (250)
|.-..|-||+++|..|.
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 55668899999999994
No 87
>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=46.22 E-value=44 Score=25.42 Aligned_cols=34 Identities=24% Similarity=0.212 Sum_probs=25.2
Q ss_pred HHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 83 IRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 83 l~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
+.++-..|..+.+||+.+ |=|...|+++.+..++
T Consensus 119 i~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 119 LVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARK 152 (158)
T ss_pred HhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334434577899999999 6799999988876543
No 88
>PRK04217 hypothetical protein; Provisional
Probab=46.16 E-value=51 Score=25.79 Aligned_cols=42 Identities=14% Similarity=0.088 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 73 NFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 73 ~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
.-|.+| ..++.+....|-...+||+.+ |-|...|+.+++...
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RAr 83 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSAR 83 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 355555 677777777788999999999 999999999987543
No 89
>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=45.27 E-value=59 Score=23.77 Aligned_cols=37 Identities=16% Similarity=0.277 Sum_probs=26.1
Q ss_pred HHHHHHHHhC--------CCHHHHhhhCCC---CC--HHHHHHHHHHhhh
Q 025602 81 LVIRLHKLLG--------NRWALIAGRLPG---RT--DNDIKNYWNTKLS 117 (250)
Q Consensus 81 ~Ll~~~~~~g--------~~W~~Ia~~lpg---RT--~~~~knrw~~~l~ 117 (250)
.|..+|...| ..|..|+..|.- -+ ..+++..|..+|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 4666777776 369999999822 22 3678998988774
No 90
>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=44.85 E-value=33 Score=25.33 Aligned_cols=26 Identities=27% Similarity=0.535 Sum_probs=20.6
Q ss_pred HHHHHHhCCCHHHHhhhCCCCCHHHHH
Q 025602 83 IRLHKLLGNRWALIAGRLPGRTDNDIK 109 (250)
Q Consensus 83 l~~~~~~g~~W~~Ia~~lpgRT~~~~k 109 (250)
..+....|..|..+|..| |=+..+|.
T Consensus 11 ~~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 11 TVFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 335678899999999999 77777664
No 91
>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=44.09 E-value=34 Score=25.26 Aligned_cols=31 Identities=26% Similarity=0.440 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHH
Q 025602 79 EDLVIRLHKLLGNRWALIAGRLPGRTDNDIKN 110 (250)
Q Consensus 79 d~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~kn 110 (250)
|..|..+...+|.+|..+|+.| |=+..+|.+
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 4567778889999999999999 677776655
No 92
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=42.77 E-value=53 Score=26.33 Aligned_cols=27 Identities=15% Similarity=0.140 Sum_probs=22.0
Q ss_pred HhCCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 88 LLGNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 88 ~~g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
..|-.+..||..| |-+...|+.+....
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra 168 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRA 168 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 3467899999999 88999998887643
No 93
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=41.81 E-value=54 Score=26.20 Aligned_cols=28 Identities=21% Similarity=0.177 Sum_probs=22.3
Q ss_pred HhCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 88 LLGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 88 ~~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
..|....+||..| |-|...|+++....+
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~ 166 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRAR 166 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3466899999999 889999998876533
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=41.48 E-value=27 Score=24.57 Aligned_cols=25 Identities=28% Similarity=0.432 Sum_probs=20.0
Q ss_pred CHHHHhhhCCC-CCHHHHHHHHHHhh
Q 025602 92 RWALIAGRLPG-RTDNDIKNYWNTKL 116 (250)
Q Consensus 92 ~W~~Ia~~lpg-RT~~~~knrw~~~l 116 (250)
-|..||..|.. -+..+|+.+|+++.
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr 53 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLR 53 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHH
Confidence 39999999953 57788999997754
No 95
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=40.51 E-value=69 Score=23.63 Aligned_cols=38 Identities=21% Similarity=0.322 Sum_probs=26.8
Q ss_pred HHHHHHHHhC--------CCHHHHhhhCCC-----CCHHHHHHHHHHhhhh
Q 025602 81 LVIRLHKLLG--------NRWALIAGRLPG-----RTDNDIKNYWNTKLSK 118 (250)
Q Consensus 81 ~Ll~~~~~~g--------~~W~~Ia~~lpg-----RT~~~~knrw~~~l~k 118 (250)
.|..+|.+.| +.|..|+..|.- ....+++..|...|.+
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 4666677766 369999999832 2356788888887754
No 96
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=39.78 E-value=58 Score=27.16 Aligned_cols=36 Identities=22% Similarity=0.252 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 80 DLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 80 ~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
..++++..-.|-.+.+||..| |-|...|+.+|...-
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 334444444577899999999 999999999996543
No 97
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=39.68 E-value=18 Score=36.19 Aligned_cols=48 Identities=17% Similarity=0.311 Sum_probs=43.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccc
Q 025602 14 EGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMN 63 (250)
Q Consensus 14 ~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~ 63 (250)
.....++||.+|-++........|. +.+.|+..++ .|..+|++..+..
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERGS-DFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhcc-cccccccccc-cccHHHHHHHHhh
Confidence 5677899999999999999999999 8999999999 9999998876654
No 98
>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=39.61 E-value=89 Score=19.09 Aligned_cols=36 Identities=25% Similarity=0.218 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHH
Q 025602 78 EEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNT 114 (250)
Q Consensus 78 Ed~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~ 114 (250)
++..++.++-..|..+..||..+ |=+...|+.+.+.
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~ 49 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHR 49 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 34555555556677899999998 7777777776544
No 99
>smart00351 PAX Paired Box domain.
Probab=39.48 E-value=1.1e+02 Score=24.10 Aligned_cols=75 Identities=11% Similarity=0.065 Sum_probs=48.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCcc-ccccccccccc--cccCCcc----CCCCCHHHHHHHHHHH
Q 025602 14 EGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKR-CGKSCRLRWMN--YLRPDIK----RGNFSKDEEDLVIRLH 86 (250)
Q Consensus 14 ~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R-t~~qcr~Rw~~--~L~p~l~----~~~WT~eEd~~Ll~~~ 86 (250)
.-+...+.+.++=+.++.++. -|. .-..||+.++..| |...+..||.. .+.|.-. ...-+..++..|++++
T Consensus 11 ~~~~~~~~s~~~R~riv~~~~-~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~ 88 (125)
T smart00351 11 VFVNGRPLPDEERQRIVELAQ-NGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYK 88 (125)
T ss_pred eecCCCCCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHH
Confidence 344556799999999998886 454 6899999998665 35555666653 3444221 2234556666677666
Q ss_pred HHhC
Q 025602 87 KLLG 90 (250)
Q Consensus 87 ~~~g 90 (250)
.+.+
T Consensus 89 ~~~p 92 (125)
T smart00351 89 QENP 92 (125)
T ss_pred HHCC
Confidence 5543
No 100
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=39.37 E-value=52 Score=25.67 Aligned_cols=46 Identities=13% Similarity=0.158 Sum_probs=33.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccccccccccccc
Q 025602 17 NRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLR 66 (250)
Q Consensus 17 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 66 (250)
++..||.|+=..++..+...|. .=..||..++. +. +-..+|.+.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~-sv~evA~e~gI--s~-~tl~~W~r~y~ 54 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM-TVSLVARQHGV--AA-SQLFLWRKQYQ 54 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC-CHHHHHHHHCc--CH-HHHHHHHHHHh
Confidence 4578999998877777777776 67899999984 33 33456776553
No 101
>PRK13858 type IV secretion system T-DNA border endonuclease VirD1; Provisional
Probab=39.32 E-value=48 Score=27.40 Aligned_cols=83 Identities=10% Similarity=0.082 Sum_probs=61.2
Q ss_pred CCCCCcccccCCCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCccCCCCCHHHHHHH
Q 025602 3 GKRKTPCCSKGEGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLV 82 (250)
Q Consensus 3 g~~~~~c~~k~~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT~eEd~~L 82 (250)
|+.+.|+... +.+..-+.|++|-..|..-....|. ...++-..+- .+.+ +.+.-..-|.++-..|
T Consensus 14 ~~~~~~~~~~-~kvVsvRLTe~Ey~~L~~rA~~aGl-S~SEfIRqAi-~~~~------------g~V~v~r~T~e~~~~l 78 (147)
T PRK13858 14 DRRESAKVEG-FKVVSTRLRSAEYESFSAQARLLGL-SDSMAIRVAV-RRIG------------GFLEIDAETREKMEAI 78 (147)
T ss_pred ccccCccccC-CeEEEEecCHHHHHHHHHHHHHcCC-CHHHHHHHHH-HhcC------------CeEeecccCHHHHHHH
Confidence 5666676665 8888999999999999999999998 5554443332 1111 1121246788888788
Q ss_pred HHHHHHhCCCHHHHhhhC
Q 025602 83 IRLHKLLGNRWALIAGRL 100 (250)
Q Consensus 83 l~~~~~~g~~W~~Ia~~l 100 (250)
+.-+..+|++-.+||+++
T Consensus 79 ir~l~gianNLNQLAr~a 96 (147)
T PRK13858 79 LQSIGTLSSNIAALLSAY 96 (147)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 888899999999999987
No 102
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=38.63 E-value=67 Score=26.72 Aligned_cols=26 Identities=23% Similarity=0.221 Sum_probs=21.9
Q ss_pred HhCCCHHHHhhhCCCCCHHHHHHHHHH
Q 025602 88 LLGNRWALIAGRLPGRTDNDIKNYWNT 114 (250)
Q Consensus 88 ~~g~~W~~Ia~~lpgRT~~~~knrw~~ 114 (250)
..|....+||..| |-|...|++|...
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~r 173 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCAR 173 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 3467899999999 8999999999854
No 103
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=38.57 E-value=12 Score=37.52 Aligned_cols=49 Identities=16% Similarity=0.350 Sum_probs=36.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCC---------cccccccccccccccc
Q 025602 17 NRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGL---------KRCGKSCRLRWMNYLR 66 (250)
Q Consensus 17 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~---------~Rt~~qcr~Rw~~~L~ 66 (250)
.|..||-.|.+.+..+++.+|. ++..|-..+-. -++-.|+|..|++.+.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred cccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 4778999999999999999998 89888322211 3445577777776543
No 104
>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=37.71 E-value=43 Score=24.87 Aligned_cols=29 Identities=31% Similarity=0.549 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCCHHHHhhhCCCCCHHHHHH
Q 025602 81 LVIRLHKLLGNRWALIAGRLPGRTDNDIKN 110 (250)
Q Consensus 81 ~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~kn 110 (250)
-|-.+....|.+|..+|+.| |=+..+|..
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 45555678899999999999 777777765
No 105
>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=36.56 E-value=50 Score=24.55 Aligned_cols=27 Identities=26% Similarity=0.311 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhCCCHHHHhhhCCCCCHH
Q 025602 79 EDLVIRLHKLLGNRWALIAGRLPGRTDN 106 (250)
Q Consensus 79 d~~Ll~~~~~~g~~W~~Ia~~lpgRT~~ 106 (250)
|..|..+...+|..|.++|..| |=+..
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~ 30 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVE 30 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHH
Confidence 5567788889999999999998 44443
No 106
>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=35.92 E-value=42 Score=24.47 Aligned_cols=33 Identities=27% Similarity=0.537 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHH
Q 025602 76 KDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKN 110 (250)
Q Consensus 76 ~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~kn 110 (250)
.||-++|+.. -..|.+|..+|..| |=+...|.+
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5677777732 25688999999999 777777765
No 107
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=35.56 E-value=77 Score=25.76 Aligned_cols=26 Identities=12% Similarity=-0.057 Sum_probs=21.4
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|..+.+||..| |-|...|+++.+...
T Consensus 152 ~~s~~eIA~~l-gis~~~v~~~l~Rar 177 (187)
T PRK09641 152 DLSLKEISEIL-DLPVGTVKTRIHRGR 177 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 56799999999 889999998875443
No 108
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=34.90 E-value=1e+02 Score=25.53 Aligned_cols=34 Identities=15% Similarity=0.148 Sum_probs=24.8
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHH---hhhhhhhcC
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNT---KLSKRVDAN 123 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~---~l~k~~~~~ 123 (250)
.|..-.+||..| |-|...|+.+... .|++.+...
T Consensus 151 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~~l~~~ 187 (195)
T PRK12532 151 LGFSSDEIQQMC-GISTSNYHTIMHRARESLRQCLQIK 187 (195)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 366789999999 8899999988764 444455433
No 109
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=34.68 E-value=26 Score=33.25 Aligned_cols=43 Identities=14% Similarity=0.246 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccchh-hhcCCccccccccccccc
Q 025602 19 GAWKAVEDKILTDYIKAYGEGKWRHIP-KAAGLKRCGKSCRLRWMN 63 (250)
Q Consensus 19 g~WT~eED~~L~~~v~~~g~~~W~~Ia-~~l~~~Rt~~qcr~Rw~~ 63 (250)
-.||.+|-..+.+.++.||. ++..|- .++. +|+...|.+-|+-
T Consensus 278 ~~wsEeEcr~FEegl~~yGK-DF~lIr~nkvr-tRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGK-DFHLIRANKVR-TRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcc-cHHHHHhcccc-cchHHHHHHHHHH
Confidence 35999999999999999998 899995 4565 9999999887654
No 110
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=33.39 E-value=22 Score=38.67 Aligned_cols=82 Identities=17% Similarity=0.181 Sum_probs=47.7
Q ss_pred ccccCCCCCCCCCCHHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCccCCCCCHHHHHHHHHHHHH
Q 025602 9 CCSKGEGLNRGAWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIKRGNFSKDEEDLVIRLHKL 88 (250)
Q Consensus 9 c~~k~~~i~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~~~~WT~eEd~~Ll~~~~~ 88 (250)
|..+.+...---|..+||..|+-.|-+||-|+|..|-.-=-++=+.+ ..+...+-.+.+=..+-..|+.+...
T Consensus 1124 ~~~~~~~~~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dK-------i~~~e~~P~a~~L~~R~~yLls~~~~ 1196 (1373)
T KOG0384|consen 1124 YLPKSVHSWDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDK-------IFLVETVPQAKHLQRRADYLLSLLRK 1196 (1373)
T ss_pred CCCccccCcccCCCchhhhhHhhhhhhcccccHHHhccCccccchhh-------hcccccCCchHHHHHHHHHHHHHHhh
Confidence 33333333556799999999999999999999999842211111111 11111133445555666667766666
Q ss_pred h-CCCHHHHh
Q 025602 89 L-GNRWALIA 97 (250)
Q Consensus 89 ~-g~~W~~Ia 97 (250)
+ +.+|....
T Consensus 1197 ~~~~~~~~~~ 1206 (1373)
T KOG0384|consen 1197 HDKGNTPKKL 1206 (1373)
T ss_pred cccCCCchhh
Confidence 5 33444433
No 111
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=33.15 E-value=1.1e+02 Score=24.24 Aligned_cols=27 Identities=15% Similarity=0.106 Sum_probs=21.9
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
.|-.-.+||..| |-|...|+.+....+
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~ 147 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRAT 147 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 366789999999 889999999876443
No 112
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=33.07 E-value=56 Score=23.42 Aligned_cols=29 Identities=31% Similarity=0.591 Sum_probs=21.0
Q ss_pred HHHHHHHHHH-hCCCHHHHhhhCCCCCHHHH
Q 025602 79 EDLVIRLHKL-LGNRWALIAGRLPGRTDNDI 108 (250)
Q Consensus 79 d~~Ll~~~~~-~g~~W~~Ia~~lpgRT~~~~ 108 (250)
...|..++.. .|..|..+|+.| |=+..+|
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 4556666666 899999999999 4445544
No 113
>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=32.79 E-value=50 Score=24.43 Aligned_cols=21 Identities=24% Similarity=0.404 Sum_probs=18.8
Q ss_pred HHHHHHHHHhCCCHHHHhhhC
Q 025602 80 DLVIRLHKLLGNRWALIAGRL 100 (250)
Q Consensus 80 ~~Ll~~~~~~g~~W~~Ia~~l 100 (250)
+-|..+...+|..|..++..|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L 23 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL 23 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc
Confidence 457888899999999999998
No 114
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=32.10 E-value=55 Score=28.09 Aligned_cols=44 Identities=20% Similarity=0.182 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 72 GNFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 72 ~~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
...|+.|-+.|.-+.+ |..=.+||..| +.|...||+|..++++|
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHH
Confidence 3688888777665544 44557999999 99999999999888865
No 115
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=32.01 E-value=1.1e+02 Score=24.78 Aligned_cols=31 Identities=32% Similarity=0.437 Sum_probs=24.4
Q ss_pred HHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 87 KLLGNRWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 87 ~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
...|-...+||..| |-+...|+.+-...+++
T Consensus 132 ~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 132 RLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33466899999999 99999999987665543
No 116
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=31.52 E-value=1.1e+02 Score=25.17 Aligned_cols=28 Identities=18% Similarity=0.173 Sum_probs=22.3
Q ss_pred HhCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 88 LLGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 88 ~~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
..|....+||..| |-+...|+.+.+..+
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~ 180 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRAL 180 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3367899999999 888999998876544
No 117
>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=31.47 E-value=77 Score=25.83 Aligned_cols=26 Identities=12% Similarity=0.028 Sum_probs=21.0
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|....+||..| |=|...|+++.+..+
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar 179 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAR 179 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 55789999999 888999999875543
No 118
>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=31.41 E-value=1e+02 Score=24.77 Aligned_cols=27 Identities=19% Similarity=0.288 Sum_probs=21.4
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
|-...+||..| |-|...|+++....++
T Consensus 135 g~s~~eiA~~l-gis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 135 DLTIKEIAEVM-NKPEGTVKTYLHRALK 161 (169)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 55788999998 7799999998865543
No 119
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=31.16 E-value=1.1e+02 Score=24.59 Aligned_cols=26 Identities=31% Similarity=0.331 Sum_probs=21.3
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|..-.+||..| |.+...|+.+.+..+
T Consensus 134 g~s~~EIA~~l-gis~~tV~~~l~ra~ 159 (173)
T PRK09645 134 GWSTAQIAADL-GIPEGTVKSRLHYAL 159 (173)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 56789999999 899999999876544
No 120
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=31.09 E-value=1.1e+02 Score=24.94 Aligned_cols=32 Identities=22% Similarity=0.156 Sum_probs=25.8
Q ss_pred HhCCCHHHHhhhCCCCCHHHHHHHHHHhhhhhh
Q 025602 88 LLGNRWALIAGRLPGRTDNDIKNYWNTKLSKRV 120 (250)
Q Consensus 88 ~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k~~ 120 (250)
..|-...+||..| |-+...|+.|....+.+-.
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3366899999999 9999999999877665543
No 121
>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=30.72 E-value=1.3e+02 Score=18.89 Aligned_cols=34 Identities=18% Similarity=0.125 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHH
Q 025602 77 DEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNY 111 (250)
Q Consensus 77 eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knr 111 (250)
=|...|.++...++.+-+..|+.| |=+...+..+
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~k 38 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHH
Confidence 367788899999999999999998 5555555443
No 122
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=30.67 E-value=1.1e+02 Score=25.31 Aligned_cols=27 Identities=22% Similarity=0.076 Sum_probs=22.0
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
.|-...+||..| |-|...|+.+....+
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar 147 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGR 147 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 366899999999 899999999875443
No 123
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=30.45 E-value=1.1e+02 Score=24.83 Aligned_cols=26 Identities=15% Similarity=0.229 Sum_probs=21.5
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|....+||..| |-|...|+.+....+
T Consensus 147 g~s~~eIA~~l-~is~~tV~~~l~ra~ 172 (184)
T PRK12512 147 GASIKETAAKL-SMSEGAVRVALHRGL 172 (184)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 66789999999 889999999876544
No 124
>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=30.03 E-value=1.3e+02 Score=24.83 Aligned_cols=45 Identities=13% Similarity=0.146 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHhhhCC----CCCHHHHHHHHHHh
Q 025602 71 RGNFSKDEEDLVIRLHKLLGNRWALIAGRLP----GRTDNDIKNYWNTK 115 (250)
Q Consensus 71 ~~~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lp----gRT~~~~knrw~~~ 115 (250)
...-|+.|...|..|+.+||.++...+.-.. -.|..||+.+....
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 4568999999999999999999999987643 37999998877543
No 125
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=29.58 E-value=1e+02 Score=29.47 Aligned_cols=54 Identities=19% Similarity=0.184 Sum_probs=42.9
Q ss_pred ccCCCCCHHHHHHHHHHHHHhC----------------CCHHHHhhhC-----CCCCHHHHHHHHHHhhhhhhhc
Q 025602 69 IKRGNFSKDEEDLVIRLHKLLG----------------NRWALIAGRL-----PGRTDNDIKNYWNTKLSKRVDA 122 (250)
Q Consensus 69 l~~~~WT~eEd~~Ll~~~~~~g----------------~~W~~Ia~~l-----pgRT~~~~knrw~~~l~k~~~~ 122 (250)
.-.|.|+++=|+...++.+.|. .+=..||+++ ..||..||-.|-..+-|++.+.
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999873 1357889886 3689999999987777777664
No 126
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=29.20 E-value=1.2e+02 Score=25.09 Aligned_cols=25 Identities=4% Similarity=-0.073 Sum_probs=21.3
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
|-...+||..| |-|...|+.|....
T Consensus 150 g~s~~EIA~~l-gis~~tVk~~l~RA 174 (189)
T PRK12530 150 ELSSEQICQEC-DISTSNLHVLLYRA 174 (189)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 66799999999 99999999986543
No 127
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=29.18 E-value=1.1e+02 Score=25.22 Aligned_cols=26 Identities=12% Similarity=0.037 Sum_probs=20.7
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|-...+||..| |-|...|+++....+
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar 179 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAR 179 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 55689999999 888999999876543
No 128
>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=29.08 E-value=1.3e+02 Score=24.97 Aligned_cols=26 Identities=15% Similarity=0.072 Sum_probs=21.6
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
.|....+||..| |-|...|+.|....
T Consensus 146 ~g~s~~EIA~~l-gis~~tvk~rl~Ra 171 (188)
T TIGR02943 146 LGFESDEICQEL-EISTSNCHVLLYRA 171 (188)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHH
Confidence 366789999999 99999999987544
No 129
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.04 E-value=1.3e+02 Score=23.80 Aligned_cols=26 Identities=8% Similarity=-0.120 Sum_probs=21.1
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
.|-.-.+||..| |-+...|+++....
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Ra 146 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRA 146 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 356789999999 99999999986543
No 130
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=28.88 E-value=1.3e+02 Score=24.76 Aligned_cols=27 Identities=7% Similarity=-0.010 Sum_probs=21.7
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
.|-...+||..| |-|...|+++....+
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar 172 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYAR 172 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 356789999999 889999999876533
No 131
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=28.77 E-value=1.3e+02 Score=24.97 Aligned_cols=26 Identities=8% Similarity=-0.036 Sum_probs=21.2
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|....+||..| |-|...|+.|.+..+
T Consensus 157 g~s~~EIA~~l-gis~~tVk~rl~ra~ 182 (194)
T PRK12531 157 ELPHQQVAEMF-DIPLGTVKSRLRLAV 182 (194)
T ss_pred CCCHHHHHHHh-CcCHHHHHHHHHHHH
Confidence 56789999999 899999998875544
No 132
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=28.59 E-value=1.1e+02 Score=24.86 Aligned_cols=26 Identities=12% Similarity=-0.057 Sum_probs=20.7
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|..-.+||..| |-|...|+++.+...
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar 177 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGR 177 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 55789999999 889999998875443
No 133
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=27.27 E-value=1.4e+02 Score=23.63 Aligned_cols=44 Identities=18% Similarity=0.128 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHHHHHhhhhhhh
Q 025602 77 DEEDLVIRLHKLLGN-RWALIAGRLPGRTDNDIKNYWNTKLSKRVD 121 (250)
Q Consensus 77 eEd~~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knrw~~~l~k~~~ 121 (250)
+-|.+|+++.++-+. .+..||+.+ |-|...|..|-+.+.+.-+-
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI 52 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVI 52 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCce
Confidence 457788888887776 799999999 89999999999777766543
No 134
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=27.13 E-value=78 Score=31.13 Aligned_cols=42 Identities=21% Similarity=0.309 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHh-hhCCCCCHHHHHHHHH
Q 025602 72 GNFSKDEEDLVIRLHKLLGNRWALIA-GRLPGRTDNDIKNYWN 113 (250)
Q Consensus 72 ~~WT~eEd~~Ll~~~~~~g~~W~~Ia-~~lpgRT~~~~knrw~ 113 (250)
..||..|-.+..++..+||+++..|. .+||=++-..|-.+|+
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 36999999999999999999999995 4569999999887764
No 135
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.75 E-value=1.4e+02 Score=24.75 Aligned_cols=26 Identities=12% Similarity=-0.069 Sum_probs=20.9
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
.|-.+.+||..| |=+...|+++....
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra 176 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARG 176 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 366899999999 88888888886543
No 136
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=26.63 E-value=40 Score=25.24 Aligned_cols=43 Identities=9% Similarity=0.043 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCC
Q 025602 24 VEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPD 68 (250)
Q Consensus 24 eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~ 68 (250)
+.|..|+.++...+.-.+..||+.++ -+...|+.|.......+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 57889999999998878999999986 67777877766654443
No 137
>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=26.62 E-value=1e+02 Score=22.72 Aligned_cols=28 Identities=21% Similarity=0.458 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCCHHHHhhhCCCCCHHHHH
Q 025602 81 LVIRLHKLLGNRWALIAGRLPGRTDNDIK 109 (250)
Q Consensus 81 ~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~k 109 (250)
.+--+....|..|..+|+.| |=|..+|.
T Consensus 4 ~f~~i~~~lG~~Wk~laR~L-Glse~~Id 31 (86)
T cd08306 4 AFDVICENVGRDWRKLARKL-GLSETKIE 31 (86)
T ss_pred HHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 34445567799999999999 66666554
No 138
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=26.51 E-value=1.6e+02 Score=23.09 Aligned_cols=26 Identities=19% Similarity=0.146 Sum_probs=20.4
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|....+||..| |-+...|+.+-...+
T Consensus 122 ~~s~~EIA~~l-~is~~tV~~~~~ra~ 147 (154)
T PRK06759 122 GKTMGEIALET-EMTYYQVRWIYRQAL 147 (154)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 55688999988 889999988865543
No 139
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=26.49 E-value=72 Score=20.33 Aligned_cols=36 Identities=25% Similarity=0.359 Sum_probs=17.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHH
Q 025602 73 NFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKN 110 (250)
Q Consensus 73 ~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~kn 110 (250)
.+|.+|-..|..+ ..-|..=.+||+.| ||+...|.+
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 4666666666655 45677789999999 999988765
No 140
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=26.30 E-value=62 Score=22.93 Aligned_cols=44 Identities=23% Similarity=0.598 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCCcc-------CCCCCHHHHHHH
Q 025602 26 DKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPDIK-------RGNFSKDEEDLV 82 (250)
Q Consensus 26 D~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~l~-------~~~WT~eEd~~L 82 (250)
+.+|.++|..|| |...++.+. -| |.. -+|+++ +.+|..+.-+.|
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 578899999998 999998887 33 322 245543 678887766554
No 141
>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=26.27 E-value=54 Score=21.83 Aligned_cols=43 Identities=21% Similarity=0.261 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 73 NFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 73 ~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
..|+.|-+.|.-+. -|..=.+||..+ +.+...|+.+...+++|
T Consensus 3 ~LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 35666666555443 355667999999 99999999988776654
No 142
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=26.22 E-value=33 Score=27.30 Aligned_cols=44 Identities=7% Similarity=-0.017 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHhCCCCccchhhhcCCccccccccccccccccCC
Q 025602 23 AVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCRLRWMNYLRPD 68 (250)
Q Consensus 23 ~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~ 68 (250)
.+-|.+++++.+..+...+..||+.++ -+...|+.|-.+..+.+
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEG 50 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCC
Confidence 356889999999999889999999996 77788887766654444
No 143
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=25.35 E-value=1.6e+02 Score=23.88 Aligned_cols=26 Identities=19% Similarity=0.294 Sum_probs=21.1
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|-.-.+||..| |.|...|+.+....+
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar 170 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSL 170 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHH
Confidence 55788999999 999999999875433
No 144
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=25.11 E-value=1.8e+02 Score=23.03 Aligned_cols=26 Identities=19% Similarity=0.195 Sum_probs=20.9
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|-.-.+||..| |-+...|+.|....+
T Consensus 121 ~~s~~eIA~~l-gis~~tv~~~l~ra~ 146 (159)
T PRK12527 121 GLSHQQIAEHL-GISRSLVEKHIVNAM 146 (159)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 55678999999 889999999876443
No 145
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=24.93 E-value=1.6e+02 Score=23.95 Aligned_cols=27 Identities=22% Similarity=0.080 Sum_probs=22.3
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
.|-...+||..| |-+...|+++-...+
T Consensus 144 ~g~s~~EIA~~l-~is~~tV~~~l~rar 170 (181)
T PRK12536 144 EGLSVAETAQLT-GLSESAVKVGIHRGL 170 (181)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 366799999999 999999999876544
No 146
>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=24.29 E-value=1.8e+02 Score=23.57 Aligned_cols=26 Identities=23% Similarity=0.263 Sum_probs=21.3
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|-...+||..| |-+...|+.+....+
T Consensus 150 g~s~~EIA~~l-gis~~tVk~~l~Rar 175 (183)
T TIGR02999 150 GLTVEEIAELL-GVSVRTVERDWRFAR 175 (183)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 56789999999 899999999876543
No 147
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=24.27 E-value=1.8e+02 Score=22.99 Aligned_cols=28 Identities=29% Similarity=0.312 Sum_probs=22.3
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
.|-...+||..+ |-+...|+.|....++
T Consensus 128 ~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 128 DGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 366789999999 8899999998765543
No 148
>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=24.09 E-value=1.7e+02 Score=23.13 Aligned_cols=26 Identities=23% Similarity=0.193 Sum_probs=20.4
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|-.-.+||+.| |-+...|+.+-...+
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~ 163 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAI 163 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 56788999999 888999988875433
No 149
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=23.82 E-value=1.6e+02 Score=24.05 Aligned_cols=26 Identities=8% Similarity=-0.019 Sum_probs=20.2
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
.|..-.+||+.| |-|...|+.+.+..
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Ra 168 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARG 168 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHH
Confidence 356788999998 88888888886543
No 150
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=23.80 E-value=1.9e+02 Score=23.16 Aligned_cols=27 Identities=19% Similarity=0.049 Sum_probs=21.5
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
.|-.-.+||..| |-+...|+++-...+
T Consensus 127 ~g~s~~eIA~~l-gis~~tV~~~l~Rar 153 (164)
T PRK12547 127 SGFSYEDAAAIC-GCAVGTIKSRVSRAR 153 (164)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 356789999999 888999998875544
No 151
>PRK00118 putative DNA-binding protein; Validated
Probab=23.59 E-value=2.1e+02 Score=22.14 Aligned_cols=38 Identities=11% Similarity=0.073 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHH
Q 025602 76 KDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNT 114 (250)
Q Consensus 76 ~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~ 114 (250)
++.+..++.+....|....+||+.+ |-|...|+.+-..
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~R 56 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKR 56 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 4556677777777888999999999 9999999887654
No 152
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=23.57 E-value=1.6e+02 Score=24.17 Aligned_cols=27 Identities=19% Similarity=0.090 Sum_probs=22.1
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
|-.-.+||..| |-|...|+.+....++
T Consensus 146 g~s~~EIA~~l-gis~~tVk~~l~Rar~ 172 (185)
T PRK09649 146 GLSYADAAAVC-GCPVGTIRSRVARARD 172 (185)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 55689999999 9999999999865443
No 153
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=23.35 E-value=1.8e+02 Score=24.12 Aligned_cols=27 Identities=22% Similarity=0.091 Sum_probs=21.7
Q ss_pred HhCCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 88 LLGNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 88 ~~g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
..|-...+||..| |-|...|+.|-...
T Consensus 130 ~~g~s~~EIA~~L-gis~~tVk~~l~Ra 156 (187)
T PRK12516 130 ASGFAYEEAAEIC-GCAVGTIKSRVNRA 156 (187)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 3466799999999 88999999886543
No 154
>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=23.24 E-value=61 Score=25.44 Aligned_cols=26 Identities=15% Similarity=-0.006 Sum_probs=21.5
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|-.+.+||..| |-|...|+++.....
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~ 146 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRAR 146 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 45799999999 889999999986544
No 155
>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=23.02 E-value=1.8e+02 Score=23.01 Aligned_cols=35 Identities=23% Similarity=0.183 Sum_probs=24.8
Q ss_pred HHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 82 VIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 82 Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
++.+.-..|-.=.+||..| |-+...|+.+....++
T Consensus 118 i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~ 152 (162)
T TIGR02983 118 VVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALA 152 (162)
T ss_pred HhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3333334466778999999 8899999998765443
No 156
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=22.90 E-value=1.5e+02 Score=24.01 Aligned_cols=28 Identities=25% Similarity=0.398 Sum_probs=22.8
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
|....+||+.| |-+...|+++....+++
T Consensus 135 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 135 GLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 55789999999 99999999998765543
No 157
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=22.53 E-value=1.9e+02 Score=23.43 Aligned_cols=26 Identities=23% Similarity=0.116 Sum_probs=20.8
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
|..-.+||..| |-|...|+.+.+..+
T Consensus 151 ~~s~~eIA~~l-gis~~~V~~~l~ra~ 176 (186)
T PRK13919 151 GYTHREAAQLL-GLPLGTLKTRARRAL 176 (186)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 45678999999 889999998876544
No 158
>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=22.17 E-value=1e+02 Score=21.43 Aligned_cols=26 Identities=38% Similarity=0.723 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCHHHHhhhCCCCCHHHH
Q 025602 82 VIRLHKLLGNRWALIAGRLPGRTDNDI 108 (250)
Q Consensus 82 Ll~~~~~~g~~W~~Ia~~lpgRT~~~~ 108 (250)
+..+...+|..|..+|..| |=+..+|
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I 27 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEI 27 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHH
Confidence 4456778899999999998 3344443
No 159
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=21.75 E-value=2e+02 Score=23.44 Aligned_cols=27 Identities=11% Similarity=0.279 Sum_probs=21.6
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHhh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTKL 116 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~l 116 (250)
.|-.-.+||..| |-|...|+.+....+
T Consensus 137 ~g~s~~EIA~~l-gis~~tVk~~l~Rar 163 (185)
T PRK12542 137 YNLTYQEISSVM-GITEANVRKQFERAR 163 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 356789999999 899999999875443
No 160
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=21.46 E-value=2.4e+02 Score=24.36 Aligned_cols=43 Identities=21% Similarity=0.279 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 73 NFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 73 ~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
..|+.|-+.|.-+.+ |....+||..| +-|...|+++-..+++|
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkK 175 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 477777766655543 77899999999 89999999988776654
No 161
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.46 E-value=2.8e+02 Score=22.36 Aligned_cols=45 Identities=18% Similarity=0.413 Sum_probs=32.8
Q ss_pred CCCHHHHH----HHHHHHHHhCC-CHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 73 NFSKDEED----LVIRLHKLLGN-RWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 73 ~WT~eEd~----~Ll~~~~~~g~-~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
++|+||-+ .|+++++++|. .-.++.... |=+.+.|+.+.+.++..
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~T-GasR~Tvk~~lreLVa~ 53 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRITIKQLVAKT-GASRNTVKRYLRELVAR 53 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHH-CCCHHHHHHHHHHHHHc
Confidence 68888854 45788888897 455566555 77888899888777643
No 162
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=21.26 E-value=1e+02 Score=32.35 Aligned_cols=96 Identities=16% Similarity=0.247 Sum_probs=59.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccchhhhcCCcccccccc-----------------------------------------
Q 025602 20 AWKAVEDKILTDYIKAYGEGKWRHIPKAAGLKRCGKSCR----------------------------------------- 58 (250)
Q Consensus 20 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr----------------------------------------- 58 (250)
.||+-+=...+.+..+||.++-..||+.+. + |...+.
T Consensus 797 ~w~k~df~~fi~a~eKygr~di~~ia~~~e-~-~~eev~~y~rvfwer~~el~d~ek~~~~ie~~e~~i~r~~~~~~~ld 874 (971)
T KOG0385|consen 797 NWTKRDFNQFIKANEKYGRDDIENIAAEVE-G-TPEEVGEYARVFWERLEELSDIEKIIYQIERGEKRIQRGDSIKKALD 874 (971)
T ss_pred chhhhhHHHHHHHhhccCcchhhhhHHhhc-C-CHHHHHHHHHHHHHHHHHhhhhHHHHHHHhhhHhhhhHHHHHHHHHh
Confidence 478888888888888888766666666654 2 222211
Q ss_pred ---ccccc----cc-cCCccCCCCCHHHHHHHHHHHHHhCC----CHHHHhhh------------CCCCCHHHHHHHHHH
Q 025602 59 ---LRWMN----YL-RPDIKRGNFSKDEEDLVIRLHKLLGN----RWALIAGR------------LPGRTDNDIKNYWNT 114 (250)
Q Consensus 59 ---~Rw~~----~L-~p~l~~~~WT~eEd~~Ll~~~~~~g~----~W~~Ia~~------------lpgRT~~~~knrw~~ 114 (250)
.||.+ .| .+..++...|.+||..|+..+.++|- .|..+-.. +..||...+..|+++
T Consensus 875 ~k~~~~k~p~~l~i~~~~nk~~~ys~~edrfL~~~l~K~g~~~~~~~e~lr~~~~~~~~frfdw~~~sRt~~el~Rr~nt 954 (971)
T KOG0385|consen 875 DKIARYKAPHQLRIQYGTNKGKNYSEEEDRFLECMLHKLGFDAENVYEELRQPIRNSPQFRFDWFIKSRTAMELQRRCNT 954 (971)
T ss_pred hhHhhhcCchheeeeeccccCCCCchhhHHHHHHHHHHhccCchhHHHHHHHHHhcCcccccceeeehhhHHHHHhcCCe
Confidence 23333 11 11124568999999999999999984 25444322 234677666666666
Q ss_pred hhh
Q 025602 115 KLS 117 (250)
Q Consensus 115 ~l~ 117 (250)
++.
T Consensus 955 li~ 957 (971)
T KOG0385|consen 955 LIT 957 (971)
T ss_pred eEE
Confidence 553
No 163
>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=21.11 E-value=2.1e+02 Score=23.07 Aligned_cols=28 Identities=25% Similarity=0.500 Sum_probs=21.6
Q ss_pred hCCCHHHHhhhCCCCCHHHHHHHHHHhhh
Q 025602 89 LGNRWALIAGRLPGRTDNDIKNYWNTKLS 117 (250)
Q Consensus 89 ~g~~W~~Ia~~lpgRT~~~~knrw~~~l~ 117 (250)
.|-.-.+||..| |-|...|+.+....++
T Consensus 155 ~g~s~~eIA~~l-gis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 155 EGLSFAEVAERM-DRSEGAVSMLWVRGLA 182 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 356788999988 8899999888765443
No 164
>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=20.97 E-value=73 Score=22.67 Aligned_cols=19 Identities=32% Similarity=0.573 Sum_probs=15.2
Q ss_pred HHHHHHHHHhCCCHHHHhh
Q 025602 80 DLVIRLHKLLGNRWALIAG 98 (250)
Q Consensus 80 ~~Ll~~~~~~g~~W~~Ia~ 98 (250)
..|.+|.+.||++|.-|-.
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3577888899999999864
No 165
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=20.37 E-value=2.2e+02 Score=24.52 Aligned_cols=43 Identities=21% Similarity=0.292 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHHHHHhhhh
Q 025602 73 NFSKDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNYWNTKLSK 118 (250)
Q Consensus 73 ~WT~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knrw~~~l~k 118 (250)
..|+.|-+.|.-+ .. |..-.+||+.| +-+...|+++...+++|
T Consensus 155 ~Lt~rE~~Vl~l~-~~-G~s~~eIA~~L-~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 155 LLTHREKEILNKL-RI-GASNNEIARSL-FISENTVKTHLYNLFKK 197 (216)
T ss_pred CCCHHHHHHHHHH-Hc-CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 4677665555444 44 88899999999 89999999988776654
No 166
>PRK01905 DNA-binding protein Fis; Provisional
Probab=20.37 E-value=2.8e+02 Score=19.78 Aligned_cols=35 Identities=23% Similarity=0.226 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHhCCCHHHHhhhCCCCCHHHHHHH
Q 025602 76 KDEEDLVIRLHKLLGNRWALIAGRLPGRTDNDIKNY 111 (250)
Q Consensus 76 ~eEd~~Ll~~~~~~g~~W~~Ia~~lpgRT~~~~knr 111 (250)
.-|...|.+++...+.++++.|+.+ |=+...+..+
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 3467788899999999999999998 5555554443
No 167
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=20.11 E-value=2.3e+02 Score=23.22 Aligned_cols=25 Identities=12% Similarity=-0.124 Sum_probs=20.6
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHh
Q 025602 90 GNRWALIAGRLPGRTDNDIKNYWNTK 115 (250)
Q Consensus 90 g~~W~~Ia~~lpgRT~~~~knrw~~~ 115 (250)
|..-.+||..| |-|...|+.|....
T Consensus 147 g~s~~EIA~~l-gis~~tV~~~l~Ra 171 (191)
T PRK12520 147 ELETEEICQEL-QITATNAWVLLYRA 171 (191)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 55678999999 99999999997543
Done!