Query 028922
Match_columns 202
No_of_seqs 255 out of 1419
Neff 7.0
Searched_HMMs 46136
Date Fri Mar 29 04:40:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028922.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028922hhsearch_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 2.9E-37 6.3E-42 257.3 14.2 122 4-125 14-135 (249)
2 PLN03091 hypothetical protein; 100.0 2.8E-36 6.1E-41 267.8 14.7 122 2-123 1-122 (459)
3 KOG0048 Transcription factor, 100.0 2.4E-35 5.1E-40 249.0 11.1 112 10-121 4-115 (238)
4 KOG0049 Transcription factor, 99.9 1.1E-21 2.3E-26 180.6 8.0 114 2-116 347-461 (939)
5 KOG0049 Transcription factor, 99.8 5.4E-21 1.2E-25 176.0 9.1 113 8-120 246-413 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 3E-18 6.5E-23 114.9 5.4 60 18-79 1-60 (60)
7 KOG0050 mRNA splicing protein 99.7 1.2E-16 2.6E-21 144.4 7.0 108 13-122 5-112 (617)
8 COG5147 REB1 Myb superfamily p 99.6 2.8E-16 6.1E-21 144.0 7.6 108 10-118 15-122 (512)
9 KOG0051 RNA polymerase I termi 99.6 7.2E-15 1.6E-19 136.2 7.8 106 14-122 383-516 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.6 5.6E-15 1.2E-19 94.9 5.0 46 68-113 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.5 3.6E-15 7.7E-20 95.9 3.1 48 15-62 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.4 9.5E-14 2.1E-18 92.9 4.7 47 71-117 1-47 (60)
13 PLN03212 Transcription repress 99.4 1.3E-13 2.8E-18 115.7 6.1 69 45-121 10-80 (249)
14 smart00717 SANT SANT SWI3, AD 99.4 1.5E-12 3.2E-17 82.1 5.7 47 68-114 1-48 (49)
15 KOG0048 Transcription factor, 99.3 1.2E-12 2.7E-17 110.6 4.4 59 64-122 5-65 (238)
16 PLN03091 hypothetical protein; 99.3 2.8E-12 6.1E-17 115.0 5.0 59 63-121 9-69 (459)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.3 1.2E-11 2.6E-16 76.7 5.6 44 70-113 1-45 (45)
18 smart00717 SANT SANT SWI3, AD 99.2 8.9E-12 1.9E-16 78.5 4.0 48 15-63 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 9E-11 2E-15 72.7 3.6 44 17-61 1-44 (45)
20 KOG0051 RNA polymerase I termi 99.0 8E-10 1.7E-14 102.9 6.9 103 13-117 306-432 (607)
21 COG5147 REB1 Myb superfamily p 98.5 1.2E-08 2.6E-13 94.2 -1.3 100 11-113 287-396 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.3 1.2E-06 2.6E-11 58.3 5.5 47 68-114 3-55 (57)
23 TIGR01557 myb_SHAQKYF myb-like 98.2 2.1E-06 4.6E-11 57.1 3.7 49 14-62 2-54 (57)
24 KOG0050 mRNA splicing protein 98.0 3.3E-06 7.1E-11 77.4 3.7 59 66-124 5-64 (617)
25 KOG0457 Histone acetyltransfer 98.0 6E-06 1.3E-10 74.4 3.8 51 12-63 69-119 (438)
26 PF13325 MCRS_N: N-terminal re 97.9 4.9E-05 1.1E-09 62.6 8.1 99 17-117 1-130 (199)
27 KOG0457 Histone acetyltransfer 97.9 1.9E-05 4.1E-10 71.3 5.6 50 65-114 69-119 (438)
28 COG5259 RSC8 RSC chromatin rem 97.6 4.3E-05 9.4E-10 69.5 3.1 46 14-61 278-323 (531)
29 TIGR02894 DNA_bind_RsfA transc 97.6 9.4E-05 2E-09 58.8 4.3 52 67-119 3-61 (161)
30 COG5259 RSC8 RSC chromatin rem 97.5 0.0001 2.2E-09 67.1 4.3 46 68-113 279-324 (531)
31 KOG1279 Chromatin remodeling f 97.5 0.00018 3.8E-09 66.9 5.3 48 66-113 251-298 (506)
32 PF08914 Myb_DNA-bind_2: Rap1 97.4 0.00018 3.9E-09 49.1 3.9 50 68-117 2-61 (65)
33 KOG1279 Chromatin remodeling f 97.4 0.00017 3.6E-09 67.1 4.2 49 11-61 249-297 (506)
34 PF13837 Myb_DNA-bind_4: Myb/S 97.3 0.00019 4.2E-09 51.0 2.6 52 68-120 1-70 (90)
35 PF08914 Myb_DNA-bind_2: Rap1 97.1 0.00033 7.2E-09 47.8 1.8 51 15-65 2-60 (65)
36 PF13837 Myb_DNA-bind_4: Myb/S 96.9 0.00053 1.2E-08 48.7 2.1 47 15-61 1-63 (90)
37 TIGR02894 DNA_bind_RsfA transc 96.9 0.00061 1.3E-08 54.2 2.6 50 13-64 2-57 (161)
38 PRK13923 putative spore coat p 96.6 0.0023 5.1E-08 51.5 3.8 50 67-117 4-60 (170)
39 PLN03142 Probable chromatin-re 96.5 0.012 2.5E-07 59.4 9.0 99 17-116 826-987 (1033)
40 COG5114 Histone acetyltransfer 96.2 0.0027 6E-08 55.6 2.3 48 15-63 63-110 (432)
41 PF13873 Myb_DNA-bind_5: Myb/S 96.2 0.0081 1.8E-07 41.7 4.3 48 68-115 2-71 (78)
42 COG5114 Histone acetyltransfer 96.0 0.0082 1.8E-07 52.7 3.9 47 68-114 63-110 (432)
43 PRK13923 putative spore coat p 95.9 0.0043 9.4E-08 49.9 1.7 49 13-63 3-57 (170)
44 PF13873 Myb_DNA-bind_5: Myb/S 95.8 0.014 3E-07 40.5 3.8 48 15-62 2-69 (78)
45 KOG2656 DNA methyltransferase 94.4 0.052 1.1E-06 48.9 4.2 56 68-123 130-191 (445)
46 PF09111 SLIDE: SLIDE; InterP 94.3 0.094 2E-06 39.9 4.8 52 65-116 46-113 (118)
47 COG5118 BDP1 Transcription ini 93.8 0.096 2.1E-06 47.1 4.7 44 70-113 367-410 (507)
48 KOG4282 Transcription factor G 92.3 0.33 7.1E-06 43.0 5.9 49 68-116 54-116 (345)
49 PF12776 Myb_DNA-bind_3: Myb/S 91.7 0.48 1E-05 33.7 5.2 44 70-113 1-62 (96)
50 PF09111 SLIDE: SLIDE; InterP 91.4 0.32 6.9E-06 37.0 4.1 35 12-46 46-83 (118)
51 PF11626 Rap1_C: TRF2-interact 90.8 0.38 8.3E-06 34.3 3.8 31 11-44 43-81 (87)
52 KOG4167 Predicted DNA-binding 90.7 0.2 4.4E-06 48.5 2.9 44 15-60 619-662 (907)
53 COG5118 BDP1 Transcription ini 90.4 0.26 5.6E-06 44.5 3.1 106 16-123 366-485 (507)
54 KOG1194 Predicted DNA-binding 89.6 2 4.3E-05 39.8 8.1 46 68-113 187-232 (534)
55 PF08281 Sigma70_r4_2: Sigma-7 88.7 1.2 2.5E-05 28.3 4.5 41 73-114 12-52 (54)
56 KOG4329 DNA-binding protein [G 86.7 4 8.7E-05 36.9 8.1 44 68-111 277-321 (445)
57 KOG4282 Transcription factor G 84.8 0.87 1.9E-05 40.4 3.1 47 16-62 55-113 (345)
58 PF12776 Myb_DNA-bind_3: Myb/S 84.8 1.3 2.8E-05 31.4 3.5 44 17-60 1-60 (96)
59 PF13404 HTH_AsnC-type: AsnC-t 84.2 1 2.3E-05 27.7 2.4 38 21-60 3-40 (42)
60 KOG4167 Predicted DNA-binding 83.5 9 0.0002 37.6 9.3 44 68-111 619-662 (907)
61 KOG4468 Polycomb-group transcr 81.8 2.7 5.9E-05 40.2 5.1 52 67-118 87-148 (782)
62 smart00595 MADF subfamily of S 80.2 2 4.3E-05 30.0 3.0 25 90-115 30-54 (89)
63 PF13404 HTH_AsnC-type: AsnC-t 80.0 4 8.7E-05 25.0 3.9 38 74-112 3-41 (42)
64 PRK11179 DNA-binding transcrip 75.9 2.4 5.3E-05 33.1 2.6 45 20-66 8-52 (153)
65 PRK11179 DNA-binding transcrip 74.2 6.3 0.00014 30.7 4.5 44 74-118 9-53 (153)
66 PF01388 ARID: ARID/BRIGHT DNA 74.0 7.7 0.00017 27.3 4.6 38 78-115 40-90 (92)
67 KOG1194 Predicted DNA-binding 73.9 3.6 7.8E-05 38.1 3.4 48 11-60 183-230 (534)
68 PF04545 Sigma70_r4: Sigma-70, 73.5 8.3 0.00018 23.9 4.2 41 74-115 7-47 (50)
69 PRK11169 leucine-responsive tr 71.6 2.7 5.9E-05 33.2 1.9 46 19-66 12-57 (164)
70 smart00501 BRIGHT BRIGHT, ARID 70.0 10 0.00022 27.0 4.5 38 78-115 36-86 (93)
71 KOG2009 Transcription initiati 69.4 5.9 0.00013 37.8 3.9 45 67-111 408-452 (584)
72 PRK11169 leucine-responsive tr 68.5 8.6 0.00019 30.3 4.2 45 73-118 13-58 (164)
73 PF11626 Rap1_C: TRF2-interact 66.8 6 0.00013 28.1 2.7 17 64-80 43-59 (87)
74 PF13325 MCRS_N: N-terminal re 65.6 15 0.00032 30.5 5.1 43 70-113 1-46 (199)
75 TIGR02985 Sig70_bacteroi1 RNA 65.5 14 0.00031 27.8 4.8 36 78-114 120-155 (161)
76 PF07750 GcrA: GcrA cell cycle 63.4 8.8 0.00019 30.6 3.3 41 70-111 2-42 (162)
77 PF11035 SnAPC_2_like: Small n 61.0 37 0.00079 30.2 6.9 45 68-112 21-69 (344)
78 PLN03142 Probable chromatin-re 60.5 9.1 0.0002 39.2 3.5 35 12-46 923-957 (1033)
79 cd08319 Death_RAIDD Death doma 59.8 13 0.00028 26.4 3.3 29 76-105 2-30 (83)
80 PF11035 SnAPC_2_like: Small n 56.2 39 0.00085 30.1 6.2 85 16-114 22-127 (344)
81 KOG2009 Transcription initiati 56.0 7.3 0.00016 37.2 1.9 53 6-60 400-452 (584)
82 PF09197 Rap1-DNA-bind: Rap1, 55.6 12 0.00026 27.9 2.6 46 17-63 1-76 (105)
83 KOG2656 DNA methyltransferase 53.2 4.7 0.0001 36.7 0.1 50 11-61 126-180 (445)
84 KOG3554 Histone deacetylase co 51.7 41 0.00088 31.6 5.9 42 69-110 286-328 (693)
85 COG1522 Lrp Transcriptional re 50.6 13 0.00029 28.3 2.4 45 20-66 7-51 (154)
86 PF10440 WIYLD: Ubiquitin-bind 49.0 13 0.00029 25.2 1.8 18 78-95 31-48 (65)
87 TIGR02937 sigma70-ECF RNA poly 49.0 34 0.00073 24.9 4.3 43 71-115 111-153 (158)
88 PF09420 Nop16: Ribosome bioge 48.9 48 0.001 26.3 5.3 46 67-112 113-162 (164)
89 PF04504 DUF573: Protein of un 48.8 37 0.00081 24.7 4.3 46 69-114 5-63 (98)
90 KOG4468 Polycomb-group transcr 48.7 12 0.00025 36.1 2.0 48 14-62 87-143 (782)
91 PF05263 DUF722: Protein of un 48.1 35 0.00076 26.3 4.2 42 71-115 82-125 (130)
92 PRK09652 RNA polymerase sigma 47.9 36 0.00079 26.1 4.5 28 85-113 142-169 (182)
93 cd08803 Death_ank3 Death domai 47.4 31 0.00068 24.4 3.6 30 76-106 4-33 (84)
94 PF10545 MADF_DNA_bdg: Alcohol 46.8 18 0.00038 24.4 2.3 26 90-115 29-55 (85)
95 PRK09643 RNA polymerase sigma 46.5 64 0.0014 25.6 5.8 28 85-113 148-175 (192)
96 smart00344 HTH_ASNC helix_turn 46.1 36 0.00078 24.3 3.9 43 74-117 3-46 (108)
97 PRK09413 IS2 repressor TnpA; R 45.9 93 0.002 23.1 6.3 45 14-62 9-53 (121)
98 smart00344 HTH_ASNC helix_turn 45.6 23 0.0005 25.3 2.9 44 21-66 3-46 (108)
99 cd08317 Death_ank Death domain 43.2 26 0.00057 24.4 2.7 29 76-105 4-32 (84)
100 PRK11924 RNA polymerase sigma 42.8 46 0.001 25.4 4.4 28 85-113 139-166 (179)
101 PF02954 HTH_8: Bacterial regu 42.5 55 0.0012 19.6 3.8 35 74-109 5-39 (42)
102 cd08311 Death_p75NR Death doma 41.9 29 0.00064 24.1 2.7 33 73-107 2-34 (77)
103 KOG0384 Chromodomain-helicase 41.6 37 0.00081 35.5 4.3 76 15-97 1133-1209(1373)
104 cd06171 Sigma70_r4 Sigma70, re 41.0 74 0.0016 18.6 4.3 39 71-111 11-49 (55)
105 cd08318 Death_NMPP84 Death dom 40.6 37 0.00081 23.9 3.2 24 81-105 12-35 (86)
106 PF07638 Sigma70_ECF: ECF sigm 40.0 52 0.0011 26.2 4.3 37 76-113 140-176 (185)
107 PRK04217 hypothetical protein; 38.9 71 0.0015 23.9 4.6 43 70-114 42-84 (110)
108 PRK09641 RNA polymerase sigma 38.1 60 0.0013 25.2 4.4 28 86-114 151-178 (187)
109 PF07750 GcrA: GcrA cell cycle 36.2 48 0.001 26.4 3.5 39 17-58 2-40 (162)
110 KOG4329 DNA-binding protein [G 36.2 35 0.00076 31.0 2.9 43 16-60 278-321 (445)
111 PRK12523 RNA polymerase sigma 35.8 79 0.0017 24.4 4.7 35 80-115 128-162 (172)
112 PRK09637 RNA polymerase sigma 35.6 73 0.0016 25.1 4.5 28 85-113 120-147 (181)
113 PRK09047 RNA polymerase factor 35.0 86 0.0019 23.6 4.7 28 86-114 121-148 (161)
114 TIGR02954 Sig70_famx3 RNA poly 34.5 77 0.0017 24.3 4.4 29 86-115 134-162 (169)
115 PRK12529 RNA polymerase sigma 34.4 1E+02 0.0022 24.1 5.2 33 85-118 141-173 (178)
116 PF09905 DUF2132: Uncharacteri 34.3 59 0.0013 22.0 3.1 44 23-79 12-62 (64)
117 TIGR02939 RpoE_Sigma70 RNA pol 34.3 59 0.0013 25.3 3.8 28 86-114 153-180 (190)
118 KOG0724 Zuotin and related mol 34.1 37 0.0008 29.8 2.8 64 69-132 165-235 (335)
119 PRK11923 algU RNA polymerase s 33.7 74 0.0016 25.0 4.3 27 86-113 153-179 (193)
120 PRK09645 RNA polymerase sigma 33.3 89 0.0019 24.0 4.6 28 86-114 133-160 (173)
121 PRK12531 RNA polymerase sigma 33.2 89 0.0019 24.7 4.7 28 86-114 156-183 (194)
122 PRK09648 RNA polymerase sigma 33.1 90 0.0019 24.5 4.7 29 86-115 154-182 (189)
123 TIGR02943 Sig70_famx1 RNA poly 32.9 92 0.002 24.6 4.7 28 85-113 145-172 (188)
124 PRK12512 RNA polymerase sigma 32.8 91 0.002 24.3 4.7 29 86-115 146-174 (184)
125 cd08804 Death_ank2 Death domai 32.6 58 0.0013 22.9 3.1 31 76-107 4-34 (84)
126 cd08777 Death_RIP1 Death Domai 32.4 51 0.0011 23.3 2.8 29 78-107 4-32 (86)
127 PRK12515 RNA polymerase sigma 31.8 98 0.0021 24.3 4.7 27 86-113 146-172 (189)
128 PRK09642 RNA polymerase sigma 31.7 1E+02 0.0022 23.3 4.7 28 85-113 120-147 (160)
129 TIGR02948 SigW_bacill RNA poly 31.6 82 0.0018 24.4 4.2 27 87-114 152-178 (187)
130 PRK12530 RNA polymerase sigma 31.5 96 0.0021 24.5 4.6 27 86-113 149-175 (189)
131 smart00005 DEATH DEATH domain, 31.2 59 0.0013 22.2 2.9 29 76-105 5-34 (88)
132 PLN03162 golden-2 like transcr 29.9 1.3E+02 0.0028 27.6 5.4 44 69-112 238-286 (526)
133 cd08779 Death_PIDD Death Domai 29.7 53 0.0012 23.1 2.5 21 77-97 3-23 (86)
134 PRK12524 RNA polymerase sigma 29.3 1.1E+02 0.0024 24.3 4.6 27 86-113 151-177 (196)
135 PF01466 Skp1: Skp1 family, di 29.2 52 0.0011 22.6 2.3 35 38-80 36-70 (78)
136 KOG3841 TEF-1 and related tran 29.1 1E+02 0.0022 28.3 4.6 55 66-120 74-149 (455)
137 KOG0384 Chromodomain-helicase 29.0 37 0.00079 35.5 2.0 24 70-93 1135-1159(1373)
138 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 28.9 1E+02 0.0022 19.7 3.5 36 72-109 6-41 (50)
139 COG1522 Lrp Transcriptional re 28.9 87 0.0019 23.7 3.8 44 74-118 8-52 (154)
140 PRK06759 RNA polymerase factor 28.4 1.3E+02 0.0027 22.5 4.6 28 86-114 121-148 (154)
141 PRK12527 RNA polymerase sigma 28.4 1.3E+02 0.0028 22.7 4.8 28 86-114 120-147 (159)
142 PRK05602 RNA polymerase sigma 27.9 1.4E+02 0.003 23.3 4.9 27 86-113 143-169 (186)
143 PF13936 HTH_38: Helix-turn-he 27.7 64 0.0014 19.6 2.3 36 70-107 4-39 (44)
144 PRK13919 putative RNA polymera 27.4 1.7E+02 0.0036 22.7 5.3 29 86-115 150-178 (186)
145 TIGR02952 Sig70_famx2 RNA poly 27.4 1.3E+02 0.0028 22.8 4.6 27 86-113 137-163 (170)
146 PRK01905 DNA-binding protein F 27.4 1.6E+02 0.0034 20.2 4.5 36 72-108 35-70 (77)
147 PRK09649 RNA polymerase sigma 27.3 1.2E+02 0.0025 23.9 4.4 29 86-115 145-173 (185)
148 PF04504 DUF573: Protein of un 27.3 2.4E+02 0.0052 20.3 6.4 70 15-85 4-94 (98)
149 PF09420 Nop16: Ribosome bioge 27.3 59 0.0013 25.7 2.6 46 13-59 112-160 (164)
150 KOG0385 Chromatin remodeling c 27.1 1E+02 0.0022 31.0 4.6 96 17-114 797-957 (971)
151 TIGR02999 Sig-70_X6 RNA polyme 27.0 1.3E+02 0.0029 23.2 4.7 27 86-113 149-175 (183)
152 PRK00118 putative DNA-binding 26.9 1.5E+02 0.0033 21.9 4.6 39 73-112 19-57 (104)
153 PRK12514 RNA polymerase sigma 26.8 1.3E+02 0.0028 23.2 4.6 27 87-114 145-171 (179)
154 PRK12532 RNA polymerase sigma 26.4 1.2E+02 0.0027 23.8 4.4 27 85-112 150-176 (195)
155 PRK12528 RNA polymerase sigma 26.3 1.5E+02 0.0032 22.5 4.7 29 85-114 127-155 (161)
156 cd08805 Death_ank1 Death domai 26.1 85 0.0018 22.2 3.0 22 76-97 4-25 (84)
157 PRK12536 RNA polymerase sigma 26.1 1.4E+02 0.003 23.3 4.6 29 85-114 143-171 (181)
158 COG2197 CitB Response regulato 26.0 1.2E+02 0.0026 24.8 4.4 44 69-115 147-190 (211)
159 PRK12542 RNA polymerase sigma 25.9 1.4E+02 0.003 23.3 4.6 29 85-114 136-164 (185)
160 PRK09646 RNA polymerase sigma 25.8 1.9E+02 0.004 22.9 5.4 28 86-114 157-184 (194)
161 PRK09651 RNA polymerase sigma 25.4 1.2E+02 0.0025 23.5 4.1 29 86-115 134-162 (172)
162 PRK12547 RNA polymerase sigma 25.3 1.6E+02 0.0034 22.6 4.7 29 85-114 126-154 (164)
163 PRK12516 RNA polymerase sigma 25.0 1.5E+02 0.0032 23.5 4.6 29 84-113 129-157 (187)
164 TIGR02983 SigE-fam_strep RNA p 24.8 1.9E+02 0.0042 21.8 5.1 37 78-115 117-153 (162)
165 COG4628 Uncharacterized conser 24.8 1.1E+02 0.0024 23.3 3.4 45 23-80 21-72 (136)
166 PF13384 HTH_23: Homeodomain-l 24.2 81 0.0018 19.1 2.4 29 77-107 8-36 (50)
167 cd08306 Death_FADD Fas-associa 24.1 1.1E+02 0.0024 21.5 3.3 27 79-106 5-31 (86)
168 smart00351 PAX Paired Box doma 23.7 3.1E+02 0.0068 20.4 6.7 75 11-87 11-92 (125)
169 TIGR02950 SigM_subfam RNA poly 23.6 52 0.0011 24.7 1.6 27 87-114 121-147 (154)
170 PRK12546 RNA polymerase sigma 23.5 1.4E+02 0.0031 23.7 4.3 30 84-114 126-155 (188)
171 PRK15411 rcsA colanic acid cap 22.8 1.6E+02 0.0035 23.8 4.5 43 70-115 137-179 (207)
172 PRK12545 RNA polymerase sigma 22.7 1.7E+02 0.0037 23.4 4.6 26 86-112 154-179 (201)
173 PRK15201 fimbriae regulatory p 22.7 2.2E+02 0.0047 23.5 5.1 43 70-115 133-175 (198)
174 PRK00430 fis global DNA-bindin 22.1 2.2E+02 0.0048 20.4 4.6 34 74-108 55-88 (95)
175 KOG3554 Histone deacetylase co 22.0 62 0.0013 30.5 2.0 39 17-56 287-325 (693)
176 PRK06811 RNA polymerase factor 21.9 2.2E+02 0.0048 22.3 5.1 28 87-115 147-174 (189)
177 TIGR02984 Sig-70_plancto1 RNA 21.8 1.9E+02 0.004 22.4 4.6 29 85-114 154-182 (189)
178 COG2963 Transposase and inacti 21.4 2.8E+02 0.006 20.0 5.2 44 68-113 5-49 (116)
179 PRK11922 RNA polymerase sigma 21.3 93 0.002 25.6 2.8 26 87-113 165-190 (231)
180 PF00531 Death: Death domain; 21.2 83 0.0018 21.0 2.2 23 25-47 2-24 (83)
181 PRK12520 RNA polymerase sigma 20.7 2E+02 0.0044 22.5 4.6 27 86-113 146-172 (191)
182 TIGR02960 SigX5 RNA polymerase 20.3 1.7E+02 0.0036 25.1 4.4 28 86-114 157-184 (324)
183 PRK10100 DNA-binding transcrip 20.1 2.1E+02 0.0046 23.4 4.8 43 70-115 155-197 (216)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=2.9e-37 Score=257.26 Aligned_cols=122 Identities=62% Similarity=1.147 Sum_probs=115.2
Q ss_pred CCCcccCCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHHHHHH
Q 028922 4 VSSQCTKKEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLILRLH 83 (202)
Q Consensus 4 ~~~~~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll~~v 83 (202)
++++|.|+.++|++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.++|+|.+++++||.|||++|++++
T Consensus 14 ~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~ 93 (249)
T PLN03212 14 TTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLH 93 (249)
T ss_pred CCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHH
Confidence 56789999999999999999999999999998999999999966999999999999999999999999999999999999
Q ss_pred HHhCCChHHHhccCCCCCHHHHHHHHHHhhhHHHhhcCCCCC
Q 028922 84 KLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSKKIKQNEKPSR 125 (202)
Q Consensus 84 ~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~~~~~~~~ 125 (202)
..||++|+.||+.|||||+++||+||+.++++.+.+.+....
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~ 135 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQ 135 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCC
Confidence 999999999999999999999999999999998887665443
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=2.8e-36 Score=267.82 Aligned_cols=122 Identities=57% Similarity=1.020 Sum_probs=116.8
Q ss_pred CCCCCcccCCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHHHH
Q 028922 2 VTVSSQCTKKEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLILR 81 (202)
Q Consensus 2 ~~~~~~~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll~ 81 (202)
++|+++|.|++++||+||+|||++|+++|.+||..+|..||+.++++|+++|||+||.++|+|.+++++||.|||++|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 58999999999999999999999999999999999999999998779999999999999999999999999999999999
Q ss_pred HHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhHHHhhcCCC
Q 028922 82 LHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSKKIKQNEKP 123 (202)
Q Consensus 82 ~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~~~~~~ 123 (202)
++++||++|..||..|||||+++||+||+.+++++++..+..
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~ 122 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGID 122 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence 999999999999999999999999999999999988865443
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=2.4e-35 Score=248.96 Aligned_cols=112 Identities=61% Similarity=1.074 Sum_probs=107.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHHHHHHHHhCCC
Q 028922 10 KKEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLILRLHKLLGNR 89 (202)
Q Consensus 10 ~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll~~v~~~G~~ 89 (202)
++.+.||+||+|||++|+++|++||+.+|..||+.+|++|++++||.||.+||+|.+++|.||+|||.+|++++..||++
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 45566899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHhccCCCCCHHHHHHHHHHhhhHHHhhcC
Q 028922 90 WSLIAGRLPGRTDNEIKNYWNSHLSKKIKQNE 121 (202)
Q Consensus 90 W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~~~~ 121 (202)
|+.||++|||||++.|||+|+..+++++....
T Consensus 84 Ws~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 84 WSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999999998775
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.85 E-value=1.1e-21 Score=180.58 Aligned_cols=114 Identities=27% Similarity=0.423 Sum_probs=103.4
Q ss_pred CCCCCcccCCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHHHH
Q 028922 2 VTVSSQCTKKEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLILR 81 (202)
Q Consensus 2 ~~~~~~~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll~ 81 (202)
++|...+..|++++|+||++||.+|..+|++||.++|.+|.+.+| ||+..|||+||.+.|+...+.+.||-.||+.|+.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 467778889999999999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred HHHHhC-CChHHHhccCCCCCHHHHHHHHHHhhhHH
Q 028922 82 LHKLLG-NRWSLIAGRLPGRTDNEIKNYWNSHLSKK 116 (202)
Q Consensus 82 ~v~~~G-~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~ 116 (202)
+|++|| ++|.+||..||+||..|...|-...+.-+
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k 461 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAK 461 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHHHHHHHH
Confidence 999999 67999999999999976654444434333
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.84 E-value=5.4e-21 Score=175.96 Aligned_cols=113 Identities=26% Similarity=0.469 Sum_probs=106.1
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccch-------------------------------
Q 028922 8 CTKKEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRL------------------------------- 56 (202)
Q Consensus 8 ~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~------------------------------- 56 (202)
...|+++|..|++|||++|..+...++..+|..||..++++|+..||.+
T Consensus 246 ~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~ 325 (939)
T KOG0049|consen 246 ELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSI 325 (939)
T ss_pred hcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhc
Confidence 4689999999999999999999999999999999999997799999987
Q ss_pred -----------------------hhhccccCCCCCCCCCHHHHHHHHHHHHHhCCC-hHHHhccCCCCCHHHHHHHHHHh
Q 028922 57 -----------------------RWMNYLRPHIKRGNISDQEEDLILRLHKLLGNR-WSLIAGRLPGRTDNEIKNYWNSH 112 (202)
Q Consensus 57 -----------------------Rw~~~L~p~~~k~~WT~eEd~~Ll~~v~~~G~~-W~~Ia~~l~gRT~~q~k~rw~~~ 112 (202)
||.+.|+|++++|+||.+||-+|+.+|.+||.+ |.+|...+|||++.|||.||.+.
T Consensus 326 nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nv 405 (939)
T KOG0049|consen 326 NSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNV 405 (939)
T ss_pred cCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHH
Confidence 999999999999999999999999999999965 99999999999999999999999
Q ss_pred hhHHHhhc
Q 028922 113 LSKKIKQN 120 (202)
Q Consensus 113 l~~~~~~~ 120 (202)
|....+.+
T Consensus 406 L~~s~K~~ 413 (939)
T KOG0049|consen 406 LNRSAKVE 413 (939)
T ss_pred HHHhhccC
Confidence 98876654
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.74 E-value=3e-18 Score=114.92 Aligned_cols=60 Identities=43% Similarity=0.840 Sum_probs=55.2
Q ss_pred CCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHH
Q 028922 18 WTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLI 79 (202)
Q Consensus 18 WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~L 79 (202)
||++||++|+.+|..|| .+|..||+.|| +||+.||+.||.++|.|.+++++||.+||.+|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 79999999997 89999999999999999999999999999987
No 7
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.66 E-value=1.2e-16 Score=144.39 Aligned_cols=108 Identities=28% Similarity=0.563 Sum_probs=102.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHHHHHHHHhCCChHH
Q 028922 13 ANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLILRLHKLLGNRWSL 92 (202)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll~~v~~~G~~W~~ 92 (202)
++-|.|+.-||+.|..+|.+||.+.|.+|++.+. -++++||+.||..+|+|.+++..|+.+||.+||.+.+.....|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 5678999999999999999999999999999998 899999999999999999999999999999999999999999999
Q ss_pred HhccCCCCCHHHHHHHHHHhhhHHHhhcCC
Q 028922 93 IAGRLPGRTDNEIKNYWNSHLSKKIKQNEK 122 (202)
Q Consensus 93 Ia~~l~gRT~~q~k~rw~~~l~~~~~~~~~ 122 (202)
|+..| |||++||-.||..++...+.....
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 99999 999999999999999887766544
No 8
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.64 E-value=2.8e-16 Score=144.03 Aligned_cols=108 Identities=30% Similarity=0.543 Sum_probs=102.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHHHHHHHHhCCC
Q 028922 10 KKEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLILRLHKLLGNR 89 (202)
Q Consensus 10 ~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll~~v~~~G~~ 89 (202)
..+.+.|.|+..||+.|..+|+.+|+++|..||..+. .|+++||+.||.++++|.++++.|+.+||..|+.+...+|..
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ 93 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch
Confidence 3456789999999999999999999999999999998 699999999999999999999999999999999999999999
Q ss_pred hHHHhccCCCCCHHHHHHHHHHhhhHHHh
Q 028922 90 WSLIAGRLPGRTDNEIKNYWNSHLSKKIK 118 (202)
Q Consensus 90 W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~ 118 (202)
|+.||..+++||..+|.+||...+.....
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999988877655
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.55 E-value=7.2e-15 Score=136.16 Aligned_cols=106 Identities=28% Similarity=0.570 Sum_probs=95.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCC--CCCCCCCHHHHHHHHHHHH-------
Q 028922 14 NRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPH--IKRGNISDQEEDLILRLHK------- 84 (202)
Q Consensus 14 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~--~~k~~WT~eEd~~Ll~~v~------- 84 (202)
.||.||++|++.|..+|..+| +.|.+|+..|+ |.+..|++||+++...+ .+++.||.||.+.|+.+|+
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 799999999999999999999 99999999995 99999999999999887 5999999999999999995
Q ss_pred Hh-------C------------CChHHHhccCCCCCHHHHHHHHHHhhhHHHhhcCC
Q 028922 85 LL-------G------------NRWSLIAGRLPGRTDNEIKNYWNSHLSKKIKQNEK 122 (202)
Q Consensus 85 ~~-------G------------~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~~~~~ 122 (202)
.| | -+|+.|+..+.+|+..||+.+|+.++.........
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~~ 516 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKRQ 516 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhccc
Confidence 33 1 15999999999999999999999988776555433
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=99.55 E-value=5.6e-15 Score=94.94 Aligned_cols=46 Identities=33% Similarity=0.658 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-hHHHhccCC-CCCHHHHHHHHHHhh
Q 028922 68 RGNISDQEEDLILRLHKLLGNR-WSLIAGRLP-GRTDNEIKNYWNSHL 113 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G~~-W~~Ia~~l~-gRT~~q~k~rw~~~l 113 (202)
|++||++||++|+++|.+||.+ |..||..|| |||+.||++||++++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999988 999999999 999999999999864
No 11
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.54 E-value=3.6e-15 Score=95.87 Aligned_cols=48 Identities=44% Similarity=0.809 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccc
Q 028922 15 RGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYL 62 (202)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L 62 (202)
|++||++||++|+++|.+||..+|..||..||.+||+.||+.||.++|
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 689999999999999999997779999999998999999999999875
No 12
>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=99.45 E-value=9.5e-14 Score=92.93 Aligned_cols=47 Identities=40% Similarity=0.716 Sum_probs=40.7
Q ss_pred CCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhHHH
Q 028922 71 ISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSKKI 117 (202)
Q Consensus 71 WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~ 117 (202)
||++||++|+.+|..||++|..||..|+.||+.+|++||+..|.+.+
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~ 47 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKI 47 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTS
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccc
Confidence 99999999999999999999999999966999999999999776543
No 13
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.44 E-value=1.3e-13 Score=115.67 Aligned_cols=69 Identities=20% Similarity=0.421 Sum_probs=59.2
Q ss_pred hccCcCccccchhhhccccCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhccC-CCCCHHHHHHHHHHhhhHHHhhcC
Q 028922 45 AGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLILRLHKLLG-NRWSLIAGRL-PGRTDNEIKNYWNSHLSKKIKQNE 121 (202)
Q Consensus 45 l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l-~gRT~~q~k~rw~~~l~~~~~~~~ 121 (202)
++ +|++.-|. ++++++++||+|||++|+++|++|| .+|..||+.+ ++||+.|||.||.++|++.++++.
T Consensus 10 ~~-~~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgp 80 (249)
T PLN03212 10 VS-KKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGG 80 (249)
T ss_pred CC-CCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCC
Confidence 44 55555453 3578999999999999999999999 5799999998 699999999999999999888763
No 14
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.36 E-value=1.5e-12 Score=82.11 Aligned_cols=47 Identities=38% Similarity=0.813 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 68 RGNISDQEEDLILRLHKLLG-NRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
+++||++||.+|+.++..|| .+|..||..|++||+.+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998764
No 15
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.32 E-value=1.2e-12 Score=110.57 Aligned_cols=59 Identities=17% Similarity=0.286 Sum_probs=53.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhccCC-CCCHHHHHHHHHHhhhHHHhhcCC
Q 028922 64 PHIKRGNISDQEEDLILRLHKLLG-NRWSLIAGRLP-GRTDNEIKNYWNSHLSKKIKQNEK 122 (202)
Q Consensus 64 p~~~k~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~-gRT~~q~k~rw~~~l~~~~~~~~~ 122 (202)
+.+.+||||.|||.+|+++|++|| ++|..||+.++ +|++++||-||.++|++.++++.-
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~f 65 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNF 65 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCC
Confidence 345579999999999999999999 55999999998 999999999999999999987643
No 16
>PLN03091 hypothetical protein; Provisional
Probab=99.28 E-value=2.8e-12 Score=115.05 Aligned_cols=59 Identities=20% Similarity=0.401 Sum_probs=53.4
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhccC-CCCCHHHHHHHHHHhhhHHHhhcC
Q 028922 63 RPHIKRGNISDQEEDLILRLHKLLG-NRWSLIAGRL-PGRTDNEIKNYWNSHLSKKIKQNE 121 (202)
Q Consensus 63 ~p~~~k~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l-~gRT~~q~k~rw~~~l~~~~~~~~ 121 (202)
++.+++++||+|||++|+++|.+|| .+|..||+.+ +|||++|||.||.++|++.++++.
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgp 69 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGT 69 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCC
Confidence 3578899999999999999999999 4699999988 599999999999999999887653
No 17
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.26 E-value=1.2e-11 Score=76.75 Aligned_cols=44 Identities=36% Similarity=0.723 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 70 NISDQEEDLILRLHKLLG-NRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
+||.+|+..|+.++..|| .+|..||..|++||+.+|++||..++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 699999999999999999 89999999999999999999998753
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.23 E-value=8.9e-12 Score=78.46 Aligned_cols=48 Identities=35% Similarity=0.801 Sum_probs=44.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhcccc
Q 028922 15 RGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLR 63 (202)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 63 (202)
++.||++||.+|..++..||..+|..||..++ +||+.+|+.||.+++.
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 47899999999999999999889999999999 9999999999998754
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=99.09 E-value=9e-11 Score=72.69 Aligned_cols=44 Identities=39% Similarity=0.782 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhcc
Q 028922 17 AWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNY 61 (202)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~ 61 (202)
.||++||..|..++..+|..+|..||..++ +|++.+|+.||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHh
Confidence 599999999999999999889999999999 89999999999765
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.99 E-value=8e-10 Score=102.94 Aligned_cols=103 Identities=23% Similarity=0.292 Sum_probs=86.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHh----CCC-------------------ChhHHhhhhccCcCccccchhhhccccCCC-CC
Q 028922 13 ANRGAWTAEEDQKLAQAIEVH----GPK-------------------KWKSVAAKAGLNRCGKSCRLRWMNYLRPHI-KR 68 (202)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~----g~~-------------------~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~-~k 68 (202)
++-+.|+++||+.|.+.|..| |-. -|+.|...|| -|+...++.+-++..+|-- ++
T Consensus 306 ~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 306 INLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCcccccc
Confidence 344899999999999999776 110 1788888899 6999988885555555533 99
Q ss_pred CCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhHHH
Q 028922 69 GNISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSKKI 117 (202)
Q Consensus 69 ~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~ 117 (202)
|.||++|++.|..+|.++|+.|..|+..| ||.+..|+.||+++....-
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~ 432 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGS 432 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhcccc
Confidence 99999999999999999999999999999 9999999999998876653
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=1.2e-08 Score=94.19 Aligned_cols=100 Identities=29% Similarity=0.561 Sum_probs=86.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccC--CCCCCCCCHHHHHHHHHHHHHh--
Q 028922 11 KEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRP--HIKRGNISDQEEDLILRLHKLL-- 86 (202)
Q Consensus 11 ~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p--~~~k~~WT~eEd~~Ll~~v~~~-- 86 (202)
+--.+|.||++|+..|...+..+| ..|..|...+ +|-+..||+||.++..+ .+++++|+.||+.+|...|...
T Consensus 287 ~f~~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~--~rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~ 363 (512)
T COG5147 287 IFEQRGKWTKEEEQELAKLVVEHG-GSWTEIGKLL--GRMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRL 363 (512)
T ss_pred HHhhhccCcccccccccccccccc-chhhHhhhhh--ccCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHH
Confidence 334579999999999999999999 8999999887 49999999999999988 6889999999999999988732
Q ss_pred C------CChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 87 G------NRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 87 G------~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
+ -.|..|+.++++|+..+|+.++....
T Consensus 364 ~~~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 364 EAQQSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred HHhhhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 1 24999999999999999988776544
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=98.34 E-value=1.2e-06 Score=58.30 Aligned_cols=47 Identities=17% Similarity=0.208 Sum_probs=41.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-Ch---HHHhccCC-CC-CHHHHHHHHHHhhh
Q 028922 68 RGNISDQEEDLILRLHKLLGN-RW---SLIAGRLP-GR-TDNEIKNYWNSHLS 114 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G~-~W---~~Ia~~l~-gR-T~~q~k~rw~~~l~ 114 (202)
+-.||+||+..+++++..||. .| ..|+..|. .| |..||+.|++.+..
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 558999999999999999996 89 99999883 46 99999999987754
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.17 E-value=2.1e-06 Score=57.09 Aligned_cols=49 Identities=18% Similarity=0.348 Sum_probs=43.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCh---hHHhhhhccCc-Cccccchhhhccc
Q 028922 14 NRGAWTAEEDQKLAQAIEVHGPKKW---KSVAAKAGLNR-CGKSCRLRWMNYL 62 (202)
Q Consensus 14 ~kg~WT~eED~~L~~~v~~~g~~~W---~~Ia~~l~~~R-t~~qcr~Rw~~~L 62 (202)
.|-.||+||..+++.+|..+|..+| ..|++.|...+ |..||+.+++.|.
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 3668999999999999999997799 99999887556 9999999988764
No 24
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.05 E-value=3.3e-06 Score=77.44 Aligned_cols=59 Identities=31% Similarity=0.465 Sum_probs=53.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHhhhHHHhhcCCCC
Q 028922 66 IKRGNISDQEEDLILRLHKLLG-NRWSLIAGRLPGRTDNEIKNYWNSHLSKKIKQNEKPS 124 (202)
Q Consensus 66 ~~k~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~~~~~~~ 124 (202)
++.|.|+.-||+.|..+|.+|| +.|+.|++.++-.|+.||++||...+++.+++-....
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 5678999999999999999999 4599999999999999999999999999998865443
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.97 E-value=6e-06 Score=74.38 Aligned_cols=51 Identities=24% Similarity=0.506 Sum_probs=46.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhcccc
Q 028922 12 EANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLR 63 (202)
Q Consensus 12 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 63 (202)
.+-...||.+|+-+|++++..||.+||..||.++| .|+..+|+++|.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHHh
Confidence 34567899999999999999999999999999999 9999999999998763
No 26
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.93 E-value=4.9e-05 Score=62.64 Aligned_cols=99 Identities=21% Similarity=0.343 Sum_probs=71.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHhhhhc--cCcCccccchhhhccc-cCCC--------------------CCCCCCH
Q 028922 17 AWTAEEDQKLAQAIEVHGPKKWKSVAAKAG--LNRCGKSCRLRWMNYL-RPHI--------------------KRGNISD 73 (202)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~--~~Rt~~qcr~Rw~~~L-~p~~--------------------~k~~WT~ 73 (202)
+|++++|-.|+.+|..-. +-..|+.-+. ..-|...+.+||+..| +|.+ .+.+||.
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 699999999999998775 6666665543 2335566777998865 4432 4569999
Q ss_pred HHHHHHHHHHHHhCC---ChHHH----hccC-CCCCHHHHHHHHHHhhhHHH
Q 028922 74 QEEDLILRLHKLLGN---RWSLI----AGRL-PGRTDNEIKNYWNSHLSKKI 117 (202)
Q Consensus 74 eEd~~Ll~~v~~~G~---~W~~I----a~~l-~gRT~~q~k~rw~~~l~~~~ 117 (202)
+|+++|......... .+.+| +..| ++||+.++.++|..+....+
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 999999987665543 37666 2224 89999999999996544443
No 27
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.90 E-value=1.9e-05 Score=71.26 Aligned_cols=50 Identities=26% Similarity=0.379 Sum_probs=45.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 65 HIKRGNISDQEEDLILRLHKLLG-NRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 65 ~~~k~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.+-...||.+|+-+|++++..|| ++|..||.++..||..+|+.||.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 45567899999999999999999 899999999999999999999987653
No 28
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.60 E-value=4.3e-05 Score=69.50 Aligned_cols=46 Identities=26% Similarity=0.595 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhcc
Q 028922 14 NRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNY 61 (202)
Q Consensus 14 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~ 61 (202)
....||.+|..+|++.|+.|| .+|.+||.+++ +|+..||..||.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 456899999999999999999 89999999999 99999999999874
No 29
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.57 E-value=9.4e-05 Score=58.76 Aligned_cols=52 Identities=17% Similarity=0.282 Sum_probs=45.1
Q ss_pred CCCCCCHHHHHHHHHHHHHh---CC----ChHHHhccCCCCCHHHHHHHHHHhhhHHHhh
Q 028922 67 KRGNISDQEEDLILRLHKLL---GN----RWSLIAGRLPGRTDNEIKNYWNSHLSKKIKQ 119 (202)
Q Consensus 67 ~k~~WT~eEd~~Ll~~v~~~---G~----~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~~ 119 (202)
+...||.|||.+|-+.|-.| |+ -...++..| +||+.+|.-||++++++.+..
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 45689999999999999887 43 288999999 999999999999999987644
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.51 E-value=0.0001 Score=67.13 Aligned_cols=46 Identities=22% Similarity=0.237 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 68 RGNISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
..+||.+|..+|++++..||..|.+||.++.+||..||--||-++-
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LP 324 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLP 324 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCC
Confidence 3489999999999999999999999999999999999999997653
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.46 E-value=0.00018 Score=66.94 Aligned_cols=48 Identities=19% Similarity=0.304 Sum_probs=43.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 66 IKRGNISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 66 ~~k~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
-.+..||.+|..+|++++..||-.|.+||.++.+||..||-.|+..+-
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 346689999999999999999999999999999999999999997543
No 32
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.45 E-value=0.00018 Score=49.09 Aligned_cols=50 Identities=20% Similarity=0.398 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHHHHHHHh---C-----CC-hHHHhccCC-CCCHHHHHHHHHHhhhHHH
Q 028922 68 RGNISDQEEDLILRLHKLL---G-----NR-WSLIAGRLP-GRTDNEIKNYWNSHLSKKI 117 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~---G-----~~-W~~Ia~~l~-gRT~~q~k~rw~~~l~~~~ 117 (202)
+.++|.+||..|+..|..+ | ++ |..++..-| .+|-.+.|+||...|.++.
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 5689999999999999654 2 22 999999887 9999999999998887654
No 33
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.39 E-value=0.00017 Score=67.12 Aligned_cols=49 Identities=33% Similarity=0.681 Sum_probs=45.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhcc
Q 028922 11 KEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNY 61 (202)
Q Consensus 11 ~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~ 61 (202)
..-.++.||.+|.-+|+++|..|| .+|.+||.+++ +||..||..++.+.
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccC-CCCHHHHHHHHHhc
Confidence 445678899999999999999999 89999999999 99999999998874
No 34
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.27 E-value=0.00019 Score=50.96 Aligned_cols=52 Identities=35% Similarity=0.529 Sum_probs=35.6
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--C------ChHHHhccC----CCCCHHHHHHHHHHhhhHHHhhc
Q 028922 68 RGNISDQEEDLILRLHKL------LG--N------RWSLIAGRL----PGRTDNEIKNYWNSHLSKKIKQN 120 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~------~G--~------~W~~Ia~~l----~gRT~~q~k~rw~~~l~~~~~~~ 120 (202)
+..||.+|...||.++.. ++ + -|..||..| ..||+.||+++|.++. +..++.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~-~~Yk~~ 70 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK-KKYKKI 70 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH-HHHHCS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH-HHHHHH
Confidence 358999999999999877 21 1 299999997 4799999999999854 444443
No 35
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.05 E-value=0.00033 Score=47.78 Aligned_cols=51 Identities=27% Similarity=0.403 Sum_probs=33.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCC--------CChhHHhhhhccCcCccccchhhhccccCC
Q 028922 15 RGAWTAEEDQKLAQAIEVHGP--------KKWKSVAAKAGLNRCGKSCRLRWMNYLRPH 65 (202)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~--------~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~ 65 (202)
|.+||.+||+.|+..|..+.. .=|..+++.-++.+|-.+-|+||...|.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 568999999999999976631 139999998877889999999999988764
No 36
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.93 E-value=0.00053 Score=48.65 Aligned_cols=47 Identities=36% Similarity=0.690 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C---C----CChhHHhhhh---ccCcCccccchhhhcc
Q 028922 15 RGAWTAEEDQKLAQAIEV--H----G---P----KKWKSVAAKA---GLNRCGKSCRLRWMNY 61 (202)
Q Consensus 15 kg~WT~eED~~L~~~v~~--~----g---~----~~W~~Ia~~l---~~~Rt~~qcr~Rw~~~ 61 (202)
|..||.+|...|+.++.. + + . .-|..||..| |..||+.||+.+|.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 457999999999999977 1 1 1 1499999987 4579999999999874
No 37
>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=96.93 E-value=0.00061 Score=54.18 Aligned_cols=50 Identities=34% Similarity=0.692 Sum_probs=42.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHh---CC---CChhHHhhhhccCcCccccchhhhccccC
Q 028922 13 ANRGAWTAEEDQKLAQAIEVH---GP---KKWKSVAAKAGLNRCGKSCRLRWMNYLRP 64 (202)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~---g~---~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p 64 (202)
.+...||.|||.+|.+.|-+| |. ....+|+..++ ||+..|.-||..++..
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 356789999999999999998 31 15889999984 9999999999998764
No 38
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.62 E-value=0.0023 Score=51.47 Aligned_cols=50 Identities=16% Similarity=0.239 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCC-------hHHHhccCCCCCHHHHHHHHHHhhhHHH
Q 028922 67 KRGNISDQEEDLILRLHKLLGNR-------WSLIAGRLPGRTDNEIKNYWNSHLSKKI 117 (202)
Q Consensus 67 ~k~~WT~eEd~~Ll~~v~~~G~~-------W~~Ia~~l~gRT~~q~k~rw~~~l~~~~ 117 (202)
+...||.|+|.+|-+.|-.|+.. ...++..| +||+.+|..||++++++++
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Y 60 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQY 60 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHH
Confidence 46789999999999988888732 56667777 9999999999999998654
No 39
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=96.54 E-value=0.012 Score=59.45 Aligned_cols=99 Identities=16% Similarity=0.289 Sum_probs=77.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccch-------hhhc-----------------------------
Q 028922 17 AWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRL-------RWMN----------------------------- 60 (202)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~-------Rw~~----------------------------- 60 (202)
.||.-+=..++.+..+||..+-..||..|. ++|...++. ||..
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 488888888999999999889999999998 898877764 1111
Q ss_pred --------c-----c-cCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhcc------------CCCCCHHHHHHHHHHhh
Q 028922 61 --------Y-----L-RPHIKRGNISDQEEDLILRLHKLLG-NRWSLIAGR------------LPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 61 --------~-----L-~p~~~k~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~------------l~gRT~~q~k~rw~~~l 113 (202)
- + -+..++..+|++||..|+-.+.+|| .+|..|-.. +..||+..|..|...++
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 0 1223445799999999999999999 679998332 25899999999999887
Q ss_pred hHH
Q 028922 114 SKK 116 (202)
Q Consensus 114 ~~~ 116 (202)
.-.
T Consensus 985 ~~~ 987 (1033)
T PLN03142 985 RLI 987 (1033)
T ss_pred HHH
Confidence 654
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.23 E-value=0.0027 Score=55.63 Aligned_cols=48 Identities=19% Similarity=0.504 Sum_probs=44.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhcccc
Q 028922 15 RGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLR 63 (202)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 63 (202)
---|+..|+-+|+++..-.|.+||..||.++| .|+...|+++|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 34699999999999999999999999999999 9999999999998765
No 41
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.23 E-value=0.0081 Score=41.67 Aligned_cols=48 Identities=27% Similarity=0.500 Sum_probs=39.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-----------------ChHHHhccC-----CCCCHHHHHHHHHHhhhH
Q 028922 68 RGNISDQEEDLILRLHKLLGN-----------------RWSLIAGRL-----PGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G~-----------------~W~~Ia~~l-----~gRT~~q~k~rw~~~l~~ 115 (202)
+..||.+|...|++++.+|.. -|..|+..| +.||..+|+.+|.++...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 458999999999999988721 399998886 369999999999986543
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.96 E-value=0.0082 Score=52.73 Aligned_cols=47 Identities=26% Similarity=0.376 Sum_probs=43.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 68 RGNISDQEEDLILRLHKLLG-NRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
-..|+..|+.+|+++..-.| ++|..||.++..|+...||.||..+..
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 44799999999999999999 889999999999999999999987654
No 43
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.86 E-value=0.0043 Score=49.95 Aligned_cols=49 Identities=29% Similarity=0.569 Sum_probs=39.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC------ChhHHhhhhccCcCccccchhhhcccc
Q 028922 13 ANRGAWTAEEDQKLAQAIEVHGPK------KWKSVAAKAGLNRCGKSCRLRWMNYLR 63 (202)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~------~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 63 (202)
.+...||.|+|.+|.+.|..|+.. -...++..| +||+.+|..||..++.
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 457899999999999999998532 366777777 5999999999966654
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.79 E-value=0.014 Score=40.50 Aligned_cols=48 Identities=25% Similarity=0.461 Sum_probs=39.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCC----------------CChhHHhhhh----ccCcCccccchhhhccc
Q 028922 15 RGAWTAEEDQKLAQAIEVHGP----------------KKWKSVAAKA----GLNRCGKSCRLRWMNYL 62 (202)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~----------------~~W~~Ia~~l----~~~Rt~~qcr~Rw~~~L 62 (202)
+..||++|...|+.+|.+|.. .-|..|+..+ +..|+..||+..|.+..
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 568999999999999988721 1399999987 23689999999998764
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=94.39 E-value=0.052 Score=48.88 Aligned_cols=56 Identities=27% Similarity=0.341 Sum_probs=48.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhcc-----CCC-CCHHHHHHHHHHhhhHHHhhcCCC
Q 028922 68 RGNISDQEEDLILRLHKLLGNRWSLIAGR-----LPG-RTDNEIKNYWNSHLSKKIKQNEKP 123 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~-----l~g-RT~~q~k~rw~~~l~~~~~~~~~~ 123 (202)
...||.+|-+.|+.+++.|--+|-.||.. ++. ||-..++.||+.+.+..++-....
T Consensus 130 dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred cccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 35799999999999999999999999988 655 999999999999887776655433
No 46
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=94.28 E-value=0.094 Score=39.88 Aligned_cols=52 Identities=21% Similarity=0.349 Sum_probs=40.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----ChHHHhccC------------CCCCHHHHHHHHHHhhhHH
Q 028922 65 HIKRGNISDQEEDLILRLHKLLGN----RWSLIAGRL------------PGRTDNEIKNYWNSHLSKK 116 (202)
Q Consensus 65 ~~~k~~WT~eEd~~Ll~~v~~~G~----~W~~Ia~~l------------~gRT~~q~k~rw~~~l~~~ 116 (202)
+.++..+|++||.-|+-.+.+||- .|..|-..+ ..||+..|..|...++.-.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 566789999999999999999996 598885442 4799999999999887543
No 47
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=93.84 E-value=0.096 Score=47.12 Aligned_cols=44 Identities=23% Similarity=0.357 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 70 NISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
+||.+|-+++..++..+|...+.||..||.|...||+.+|.+--
T Consensus 367 ~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Ee 410 (507)
T COG5118 367 RWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEE 410 (507)
T ss_pred cccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHh
Confidence 89999999999999999999999999999999999999997543
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.28 E-value=0.33 Score=43.03 Aligned_cols=49 Identities=16% Similarity=0.245 Sum_probs=39.6
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCChHHHhccC----CCCCHHHHHHHHHHhhhHH
Q 028922 68 RGNISDQEEDLILRLHKLL----------GNRWSLIAGRL----PGRTDNEIKNYWNSHLSKK 116 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~----------G~~W~~Ia~~l----~gRT~~q~k~rw~~~l~~~ 116 (202)
...|+.+|-..||++..+. +.-|..||..+ .-||+.||+++|.++.++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Y 116 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKY 116 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 3689999999999998653 23499999965 4599999999999877554
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=91.68 E-value=0.48 Score=33.65 Aligned_cols=44 Identities=25% Similarity=0.427 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------ChHHHhccCC-----CCCHHHHHHHHHHhh
Q 028922 70 NISDQEEDLILRLHKLL---GN----------RWSLIAGRLP-----GRTDNEIKNYWNSHL 113 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~---G~----------~W~~Ia~~l~-----gRT~~q~k~rw~~~l 113 (202)
.||++++..|++++... |+ .|..|+..|. ..|..||++||..+-
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk 62 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLK 62 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHH
Confidence 49999999999998543 21 2999988872 357889999987644
No 50
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=91.40 E-value=0.32 Score=36.96 Aligned_cols=35 Identities=17% Similarity=0.338 Sum_probs=29.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CChhHHhhhhc
Q 028922 12 EANRGAWTAEEDQKLAQAIEVHGP---KKWKSVAAKAG 46 (202)
Q Consensus 12 ~~~kg~WT~eED~~L~~~v~~~g~---~~W~~Ia~~l~ 46 (202)
..++..||.+||.-|+-++.+||. +.|..|...+.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir 83 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIR 83 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHH
Confidence 667889999999999999999998 79999998764
No 51
>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=90.78 E-value=0.38 Score=34.33 Aligned_cols=31 Identities=29% Similarity=0.593 Sum_probs=18.1
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCCCChhHHhhh
Q 028922 11 KEANRGAWTAEEDQKL--------AQAIEVHGPKKWKSVAAK 44 (202)
Q Consensus 11 ~~~~kg~WT~eED~~L--------~~~v~~~g~~~W~~Ia~~ 44 (202)
|.-..|.||+++|+.| ..++++|| +..|+..
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~R 81 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIERR 81 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHHH
Confidence 5567899999999999 44667777 5555543
No 52
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=90.73 E-value=0.2 Score=48.50 Aligned_cols=44 Identities=16% Similarity=0.244 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhc
Q 028922 15 RGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMN 60 (202)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~ 60 (202)
-..||+.|-.++.+++..|. +++..|+++++ ++|++||-+-|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhc-cccHHHHHHHHHH
Confidence 45899999999999999999 89999999999 9999999987753
No 53
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.35 E-value=0.26 Score=44.46 Aligned_cols=106 Identities=13% Similarity=0.196 Sum_probs=69.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhcc--ccCC-----C-CCCCCCHHHHHHHHHHH----
Q 028922 16 GAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNY--LRPH-----I-KRGNISDQEEDLILRLH---- 83 (202)
Q Consensus 16 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~--L~p~-----~-~k~~WT~eEd~~Ll~~v---- 83 (202)
-+||.+|-+++.+++...| .++..|+.++| +|..+|++..|.+- .+|. + .+-|+..+|-..+...+
T Consensus 366 ~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP-~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~~~~~e~l 443 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWG-TDFSLISSLFP-NRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLRSYLLEKL 443 (507)
T ss_pred CcccHHHHHHHHHHHHHhc-chHHHHHHhcC-chhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHHHHHHHHH
Confidence 4899999999999999999 79999999999 99999999988763 2221 1 24467776654332221
Q ss_pred HHhCCChHHHhccC--CCCCHHHHHHHHHHhhhHHHhhcCCC
Q 028922 84 KLLGNRWSLIAGRL--PGRTDNEIKNYWNSHLSKKIKQNEKP 123 (202)
Q Consensus 84 ~~~G~~W~~Ia~~l--~gRT~~q~k~rw~~~l~~~~~~~~~~ 123 (202)
..+.+--..|-+.+ .-||+..+..--+.+.+..+.+.+..
T Consensus 444 ~Elq~E~k~~~~~~EE~k~~A~E~~q~~Q~l~~~~L~k~~~~ 485 (507)
T COG5118 444 IELQNEHKHHMKEIEEAKNTAKEEDQTAQRLNDANLNKKGSG 485 (507)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhhhhhhccCCC
Confidence 12222222333333 24677766666666666666555443
No 54
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=89.55 E-value=2 Score=39.75 Aligned_cols=46 Identities=17% Similarity=0.294 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 68 RGNISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
...||.||--++-.+...||+...+|-..||.|+-..+..+|+..-
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~K 232 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWK 232 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHH
Confidence 5589999999999999999999999999999999999998887543
No 55
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=88.68 E-value=1.2 Score=28.29 Aligned_cols=41 Identities=20% Similarity=0.254 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 73 DQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 73 ~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
++++..++.++-..|-.+.+||..+ |.|...|+.+....++
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 3566778888888899999999999 9999999998776543
No 56
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=86.71 E-value=4 Score=36.87 Aligned_cols=44 Identities=23% Similarity=0.302 Sum_probs=39.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHH-hccCCCCCHHHHHHHHHH
Q 028922 68 RGNISDQEEDLILRLHKLLGNRWSLI-AGRLPGRTDNEIKNYWNS 111 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G~~W~~I-a~~l~gRT~~q~k~rw~~ 111 (202)
-..||++|-..+-+.++.||+....| +..++.|+-..|-..|+.
T Consensus 277 l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 277 LSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred cccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH
Confidence 34899999999999999999999999 556899999999988764
No 57
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=84.84 E-value=0.87 Score=40.35 Aligned_cols=47 Identities=28% Similarity=0.432 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHh---------CCCChhHHhhhh---ccCcCccccchhhhccc
Q 028922 16 GAWTAEEDQKLAQAIEVH---------GPKKWKSVAAKA---GLNRCGKSCRLRWMNYL 62 (202)
Q Consensus 16 g~WT~eED~~L~~~v~~~---------g~~~W~~Ia~~l---~~~Rt~~qcr~Rw~~~L 62 (202)
..|+.+|-..|+.+.... ...-|..||..+ +..||+.||+.+|.+..
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 689999999999988533 124599999854 45699999999998753
No 58
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=84.82 E-value=1.3 Score=31.40 Aligned_cols=44 Identities=25% Similarity=0.530 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------ChhHHhhhhc----cCcCccccchhhhc
Q 028922 17 AWTAEEDQKLAQAIEVH---GPK---------KWKSVAAKAG----LNRCGKSCRLRWMN 60 (202)
Q Consensus 17 ~WT~eED~~L~~~v~~~---g~~---------~W~~Ia~~l~----~~Rt~~qcr~Rw~~ 60 (202)
.||+++++.|++++... |.. .|..|+..|. ...+..||+.||..
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 59999999999988544 211 3999998874 23455778887754
No 59
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=84.22 E-value=1 Score=27.70 Aligned_cols=38 Identities=21% Similarity=0.361 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhc
Q 028922 21 EEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMN 60 (202)
Q Consensus 21 eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~ 60 (202)
+=|.+|+.+++..+...+..||+.++ =+...|..|+.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 44889999999999889999999996 888889888754
No 60
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=83.53 E-value=9 Score=37.61 Aligned_cols=44 Identities=9% Similarity=0.161 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHH
Q 028922 68 RGNISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNS 111 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~ 111 (202)
...||+.|-.++-.++-.|-+..-.|++.++++|-.||-.+|+.
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 45899999999999999999999999999999999999888763
No 61
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=81.84 E-value=2.7 Score=40.19 Aligned_cols=52 Identities=15% Similarity=0.398 Sum_probs=42.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChHHH----------hccCCCCCHHHHHHHHHHhhhHHHh
Q 028922 67 KRGNISDQEEDLILRLHKLLGNRWSLI----------AGRLPGRTDNEIKNYWNSHLSKKIK 118 (202)
Q Consensus 67 ~k~~WT~eEd~~Ll~~v~~~G~~W~~I----------a~~l~gRT~~q~k~rw~~~l~~~~~ 118 (202)
.+..||-.|..-+..+++++|+....| -....-+|-.|++.+|+..+.+.-+
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred cccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHh
Confidence 366899999999999999999999988 2233457888999999987766443
No 62
>smart00595 MADF subfamily of SANT domain.
Probab=80.22 E-value=2 Score=30.04 Aligned_cols=25 Identities=32% Similarity=0.603 Sum_probs=21.2
Q ss_pred hHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 90 WSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 90 W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
|..||..| |-|..+|+.+|.++-..
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~ 54 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 99999999 55999999999876433
No 63
>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=79.97 E-value=4 Score=25.04 Aligned_cols=38 Identities=21% Similarity=0.323 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhCC-ChHHHhccCCCCCHHHHHHHHHHh
Q 028922 74 QEEDLILRLHKLLGN-RWSLIAGRLPGRTDNEIKNYWNSH 112 (202)
Q Consensus 74 eEd~~Ll~~v~~~G~-~W~~Ia~~l~gRT~~q~k~rw~~~ 112 (202)
+=|..|+.++..-|. .+..||..+ |=|...|..|...+
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 457889999888884 599999999 99999999998753
No 64
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=75.86 E-value=2.4 Score=33.05 Aligned_cols=45 Identities=13% Similarity=0.169 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCC
Q 028922 20 AEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHI 66 (202)
Q Consensus 20 ~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~ 66 (202)
.+-|.+|+.+++..|...|..||+.++ -+...|+.|+.+....++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 357999999999999889999999995 999999999988766554
No 65
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=74.25 E-value=6.3 Score=30.71 Aligned_cols=44 Identities=14% Similarity=0.048 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHhhhHHHh
Q 028922 74 QEEDLILRLHKLLG-NRWSLIAGRLPGRTDNEIKNYWNSHLSKKIK 118 (202)
Q Consensus 74 eEd~~Ll~~v~~~G-~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~ 118 (202)
+-|.+|+.+..+-| ..|+.||+.+ |-|...|+.|++.+....+-
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 57889999998888 4699999999 99999999999987765443
No 66
>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=73.96 E-value=7.7 Score=27.33 Aligned_cols=38 Identities=16% Similarity=0.335 Sum_probs=28.3
Q ss_pred HHHHHHHHhCC--------ChHHHhccCC---CCC--HHHHHHHHHHhhhH
Q 028922 78 LILRLHKLLGN--------RWSLIAGRLP---GRT--DNEIKNYWNSHLSK 115 (202)
Q Consensus 78 ~Ll~~v~~~G~--------~W~~Ia~~l~---gRT--~~q~k~rw~~~l~~ 115 (202)
.|..+|...|+ .|..||..|. +-+ +.+++..|..+|.+
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 57788888884 6999999982 122 36789999888754
No 67
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=73.89 E-value=3.6 Score=38.11 Aligned_cols=48 Identities=21% Similarity=0.290 Sum_probs=40.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhc
Q 028922 11 KEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMN 60 (202)
Q Consensus 11 ~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~ 60 (202)
.......||.||--+|.++...|| .+..+|-++|| .|+-.++..-|..
T Consensus 183 r~~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP-~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 183 RTEFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALP-HRSLASLVQYYYS 230 (534)
T ss_pred cCCCcccchHHHHHHHHHHHHHhc-ccHHHHHHHcc-CccHHHHHHHHHH
Confidence 444567899999999999999999 89999999999 9998877765543
No 68
>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=73.51 E-value=8.3 Score=23.93 Aligned_cols=41 Identities=27% Similarity=0.370 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 74 QEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 74 eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
+++..++.++--.|..+..||..| |-|...|+.+....+.+
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 345555555555567799999999 88999999888776654
No 69
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=71.58 E-value=2.7 Score=33.20 Aligned_cols=46 Identities=13% Similarity=0.179 Sum_probs=39.6
Q ss_pred CHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCC
Q 028922 19 TAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHI 66 (202)
Q Consensus 19 T~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~ 66 (202)
-.+-|.+|+.+++..|...|..||+.++ -+...|+.|+.+....++
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 3567999999999999889999999995 889999999988766554
No 70
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=70.02 E-value=10 Score=26.98 Aligned_cols=38 Identities=21% Similarity=0.334 Sum_probs=28.8
Q ss_pred HHHHHHHHhCC--------ChHHHhccCCC-----CCHHHHHHHHHHhhhH
Q 028922 78 LILRLHKLLGN--------RWSLIAGRLPG-----RTDNEIKNYWNSHLSK 115 (202)
Q Consensus 78 ~Ll~~v~~~G~--------~W~~Ia~~l~g-----RT~~q~k~rw~~~l~~ 115 (202)
.|..+|.+.|+ .|..||..|.- ....+++..|..+|.+
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 57778888875 59999999822 2356789999888765
No 71
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=69.38 E-value=5.9 Score=37.82 Aligned_cols=45 Identities=22% Similarity=0.358 Sum_probs=41.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHH
Q 028922 67 KRGNISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNS 111 (202)
Q Consensus 67 ~k~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~ 111 (202)
..+.||.+|-.+...+....|...+.||..+|+|+..|||.+|..
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 456899999999999999999999999999999999999999864
No 72
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=68.53 E-value=8.6 Score=30.32 Aligned_cols=45 Identities=13% Similarity=0.028 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhCC-ChHHHhccCCCCCHHHHHHHHHHhhhHHHh
Q 028922 73 DQEEDLILRLHKLLGN-RWSLIAGRLPGRTDNEIKNYWNSHLSKKIK 118 (202)
Q Consensus 73 ~eEd~~Ll~~v~~~G~-~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~ 118 (202)
.+-|.+|+.+..+-|. .|+.||+.+ |=+...|+.|++.+....+-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 4568889999888884 699999999 99999999999987766543
No 73
>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=66.79 E-value=6 Score=28.07 Aligned_cols=17 Identities=12% Similarity=0.372 Sum_probs=9.9
Q ss_pred CCCCCCCCCHHHHHHHH
Q 028922 64 PHIKRGNISDQEEDLIL 80 (202)
Q Consensus 64 p~~~k~~WT~eEd~~Ll 80 (202)
|.-..|-||+++|..|.
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 55568899999999983
No 74
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=65.62 E-value=15 Score=30.48 Aligned_cols=43 Identities=16% Similarity=0.169 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccC---CCCCHHHHHHHHHHhh
Q 028922 70 NISDQEEDLILRLHKLLGNRWSLIAGRL---PGRTDNEIKNYWNSHL 113 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l---~gRT~~q~k~rw~~~l 113 (202)
.|++.+|-.|+.+|.. |+.-..|+.-+ -.-|-..|..||+.+|
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~ll 46 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALL 46 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHH
Confidence 4999999999999854 77777776554 3458899999999887
No 75
>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=65.51 E-value=14 Score=27.77 Aligned_cols=36 Identities=22% Similarity=0.302 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 78 LILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 78 ~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.++.+.-..|-.+..||..+ |.|...|+.+......
T Consensus 120 ~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 120 KIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALK 155 (161)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 33444334577899999999 9999999999887543
No 76
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=63.40 E-value=8.8 Score=30.63 Aligned_cols=41 Identities=22% Similarity=0.208 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHH
Q 028922 70 NISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNS 111 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~ 111 (202)
.||+|..+.|.++.. -|-.=++||..|.+.|-++|.-+-+.
T Consensus 2 ~Wtde~~~~L~~lw~-~G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWA-EGLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHH-cCCCHHHHHHHhCCcchhhhhhhhhc
Confidence 599999999988874 48889999999977999999877654
No 77
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=60.95 E-value=37 Score=30.24 Aligned_cols=45 Identities=29% Similarity=0.474 Sum_probs=35.8
Q ss_pred CCCCCHHHHHHHHHHHHHh-CCC---hHHHhccCCCCCHHHHHHHHHHh
Q 028922 68 RGNISDQEEDLILRLHKLL-GNR---WSLIAGRLPGRTDNEIKNYWNSH 112 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~-G~~---W~~Ia~~l~gRT~~q~k~rw~~~ 112 (202)
-..||.-|-..|+++.+-. |.. -..|++.++||+..+|++.-+.+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~L 69 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQL 69 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHH
Confidence 4589999999999988765 544 56889999999999999755443
No 78
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=60.46 E-value=9.1 Score=39.18 Aligned_cols=35 Identities=14% Similarity=0.227 Sum_probs=30.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhc
Q 028922 12 EANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAG 46 (202)
Q Consensus 12 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~ 46 (202)
..++..+|.+||..|+-++.+||..+|.+|...+.
T Consensus 923 ~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~ 957 (1033)
T PLN03142 923 QNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFR 957 (1033)
T ss_pred CCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHH
Confidence 34456699999999999999999999999987763
No 79
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=59.80 E-value=13 Score=26.36 Aligned_cols=29 Identities=24% Similarity=0.478 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHHHH
Q 028922 76 EDLILRLHKLLGNRWSLIAGRLPGRTDNEI 105 (202)
Q Consensus 76 d~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~ 105 (202)
|+.|..+....|..|..+|.+| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 4568888999999999999999 6666554
No 80
>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=56.19 E-value=39 Score=30.06 Aligned_cols=85 Identities=16% Similarity=0.292 Sum_probs=63.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCC---ChhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHHHHHHHH-h-----
Q 028922 16 GAWTAEEDQKLAQAIEVHGPK---KWKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLILRLHKL-L----- 86 (202)
Q Consensus 16 g~WT~eED~~L~~~v~~~g~~---~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll~~v~~-~----- 86 (202)
..||.-|...|+.+++..... +-.+|++.++ +|+..++++- .+.|+ +..+.+++++ |
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~f-l~~LK------------~rvareaiqkv~~~g~~ 87 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRDF-LQQLK------------GRVAREAIQKVHPGGLK 87 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHHH-HHHHH------------HHHHHHHHHHhcccccc
Confidence 589999999999999876323 5678999999 9999888773 33332 2244455544 2
Q ss_pred CC------------ChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 87 GN------------RWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 87 G~------------~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
|. -|..+|..+.|.-...+-.-|.+.|.
T Consensus 88 ~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 88 GPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred cccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 11 29999999999999999888887774
No 81
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=56.03 E-value=7.3 Score=37.23 Aligned_cols=53 Identities=15% Similarity=0.243 Sum_probs=46.8
Q ss_pred CcccCCCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhc
Q 028922 6 SQCTKKEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMN 60 (202)
Q Consensus 6 ~~~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~ 60 (202)
..+..+....++||.+|-++...++...| .+...|+...+ +|+.+|++..+..
T Consensus 400 ~~t~sk~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 400 YATYSKKLETDKWDASETELFYKALSERG-SDFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred hhhccCccccCcccchhhHHhhhHHhhhc-ccccccccccc-cccHHHHHHHHhh
Confidence 34556777889999999999999999999 79999999999 9999999998764
No 82
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=55.62 E-value=12 Score=27.87 Aligned_cols=46 Identities=28% Similarity=0.456 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHHHh--------CC----------------------CChhHHhhhhccCcCccccchhhhcccc
Q 028922 17 AWTAEEDQKLAQAIEVH--------GP----------------------KKWKSVAAKAGLNRCGKSCRLRWMNYLR 63 (202)
Q Consensus 17 ~WT~eED~~L~~~v~~~--------g~----------------------~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~ 63 (202)
++|++||-.|...|.++ ++ .-....+...| ..|..+-|+||++++.
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p-~HT~~sWRDR~RKfv~ 76 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNP-RHTENSWRDRYRKFVS 76 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTT-TS-HHHHHHHHHHTHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCC-ccchhHHHHHHHHHHH
Confidence 58999999999999766 10 01445556666 7788888888887653
No 83
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=53.20 E-value=4.7 Score=36.69 Aligned_cols=50 Identities=16% Similarity=0.250 Sum_probs=42.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhh-----hccCcCccccchhhhcc
Q 028922 11 KEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAK-----AGLNRCGKSCRLRWMNY 61 (202)
Q Consensus 11 ~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~-----l~~~Rt~~qcr~Rw~~~ 61 (202)
.+++-..||.+|-..|..+...|. -+|--||.. .+..||....++||..+
T Consensus 126 ~~l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 126 AHLNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred HhhccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 345668899999999999999998 788888876 66459999999999875
No 84
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=51.73 E-value=41 Score=31.62 Aligned_cols=42 Identities=21% Similarity=0.270 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCChHHHhc-cCCCCCHHHHHHHHH
Q 028922 69 GNISDQEEDLILRLHKLLGNRWSLIAG-RLPGRTDNEIKNYWN 110 (202)
Q Consensus 69 ~~WT~eEd~~Ll~~v~~~G~~W~~Ia~-~l~gRT~~q~k~rw~ 110 (202)
..||..|-.++-+++.+||+....|.. +||-++-..|-.+|+
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 379999999999999999999999955 559999999988776
No 85
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=50.64 E-value=13 Score=28.27 Aligned_cols=45 Identities=9% Similarity=0.113 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCC
Q 028922 20 AEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHI 66 (202)
Q Consensus 20 ~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~ 66 (202)
.+-|.+++++++..+...+..||+.++ -++..|+.|-.+....++
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCc
Confidence 356889999999999889999999996 888889988777655443
No 86
>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=49.05 E-value=13 Score=25.23 Aligned_cols=18 Identities=33% Similarity=0.639 Sum_probs=14.9
Q ss_pred HHHHHHHHhCCChHHHhc
Q 028922 78 LILRLHKLLGNRWSLIAG 95 (202)
Q Consensus 78 ~Ll~~v~~~G~~W~~Ia~ 95 (202)
.|.+|++.||++|..|-.
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 577888999999999953
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=48.98 E-value=34 Score=24.89 Aligned_cols=43 Identities=26% Similarity=0.325 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 71 ISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 71 WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
.++.+-.. +.++-..|..+..||..+ |=|...|+.+....+.+
T Consensus 111 L~~~~~~i-i~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 111 LPEREREV-LVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred CCHHHHHH-HhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44333333 333334578899999999 77999999888775543
No 88
>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=48.94 E-value=48 Score=26.25 Aligned_cols=46 Identities=17% Similarity=0.197 Sum_probs=38.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChHHHhccC----CCCCHHHHHHHHHHh
Q 028922 67 KRGNISDQEEDLILRLHKLLGNRWSLIAGRL----PGRTDNEIKNYWNSH 112 (202)
Q Consensus 67 ~k~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l----~gRT~~q~k~rw~~~ 112 (202)
....-|..|..-|..|+.+||.....+|.-. --.|+.||+.+...+
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 3457889999999999999999999998653 358999999887654
No 89
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=48.81 E-value=37 Score=24.65 Aligned_cols=46 Identities=15% Similarity=0.051 Sum_probs=30.1
Q ss_pred CCCCHHHHHHHHHHHHHh----CC----ChHHHhcc----C-CCCCHHHHHHHHHHhhh
Q 028922 69 GNISDQEEDLILRLHKLL----GN----RWSLIAGR----L-PGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 69 ~~WT~eEd~~Ll~~v~~~----G~----~W~~Ia~~----l-~gRT~~q~k~rw~~~l~ 114 (202)
.-||++++-.||+++..| |. .|..+... + ..=|.+|+.++-+.+-+
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~ 63 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKK 63 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence 369999999999999877 62 35444333 3 22366777776665433
No 90
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=48.66 E-value=12 Score=36.08 Aligned_cols=48 Identities=19% Similarity=0.362 Sum_probs=36.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhcc---------CcCccccchhhhccc
Q 028922 14 NRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGL---------NRCGKSCRLRWMNYL 62 (202)
Q Consensus 14 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~---------~Rt~~qcr~Rw~~~L 62 (202)
.|..||-.|..-+..++..+| ++...|-..+.. -+|-.|+|.+|.+.+
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred cccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 367899999999999999999 899888443321 244467888777654
No 91
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=48.09 E-value=35 Score=26.33 Aligned_cols=42 Identities=21% Similarity=0.460 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHH-HHHh-CCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 71 ISDQEEDLILRL-HKLL-GNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 71 WT~eEd~~Ll~~-v~~~-G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
++++ ++.++.+ +..+ |..|-.||..+ +-+..+|+ ||+.-++.
T Consensus 82 l~de-~k~Ii~lry~~r~~~TW~~IA~~l-~i~erta~-r~~~~fK~ 125 (130)
T PF05263_consen 82 LIDE-EKRIIKLRYDRRSRRTWYQIAQKL-HISERTAR-RWRDRFKN 125 (130)
T ss_pred hCHH-HHHHHHHHHcccccchHHHHHHHh-CccHHHHH-HHHHHHHH
Confidence 3444 4444433 2333 35699999998 56666666 44444443
No 92
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=47.89 E-value=36 Score=26.09 Aligned_cols=28 Identities=14% Similarity=0.106 Sum_probs=22.5
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
..|-....||..| |-+...|+.+....+
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~ 169 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRAR 169 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 4567899999999 889999988766543
No 93
>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=47.40 E-value=31 Score=24.39 Aligned_cols=30 Identities=23% Similarity=0.340 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHHHHH
Q 028922 76 EDLILRLHKLLGNRWSLIAGRLPGRTDNEIK 106 (202)
Q Consensus 76 d~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k 106 (202)
|..|..+....|..|..+|..| |=+...|.
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~ 33 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEIN 33 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHH
Confidence 5567778889999999999999 65655443
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=46.76 E-value=18 Score=24.39 Aligned_cols=26 Identities=23% Similarity=0.455 Sum_probs=20.9
Q ss_pred hHHHhccCC-CCCHHHHHHHHHHhhhH
Q 028922 90 WSLIAGRLP-GRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 90 W~~Ia~~l~-gRT~~q~k~rw~~~l~~ 115 (202)
|..||..|. .-+..+|+.+|.++-..
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~~ 55 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRDR 55 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHHH
Confidence 999999994 36788999999876543
No 95
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=46.51 E-value=64 Score=25.63 Aligned_cols=28 Identities=18% Similarity=0.146 Sum_probs=23.0
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
..|.....||..| |-+...|++|.....
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar 175 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGR 175 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3567899999999 999999999985443
No 96
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=46.14 E-value=36 Score=24.31 Aligned_cols=43 Identities=12% Similarity=0.084 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHhC-CChHHHhccCCCCCHHHHHHHHHHhhhHHH
Q 028922 74 QEEDLILRLHKLLG-NRWSLIAGRLPGRTDNEIKNYWNSHLSKKI 117 (202)
Q Consensus 74 eEd~~Ll~~v~~~G-~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~ 117 (202)
+.|..|+.++...| -.++.||+.+ |-+...|+.+...+....+
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 56788888888877 4699999999 9999999999988776544
No 97
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=45.88 E-value=93 Score=23.11 Aligned_cols=45 Identities=20% Similarity=0.237 Sum_probs=31.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccc
Q 028922 14 NRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYL 62 (202)
Q Consensus 14 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L 62 (202)
++..||+|+-..+...+...| ..-..||..++. +..++ .+|.+.+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI--s~~tl-~~W~r~y 53 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV--AASQL-FLWRKQY 53 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc--CHHHH-HHHHHHH
Confidence 367899999887777777766 678899999873 44333 3465544
No 98
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.63 E-value=23 Score=25.33 Aligned_cols=44 Identities=16% Similarity=0.172 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCC
Q 028922 21 EEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHI 66 (202)
Q Consensus 21 eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~ 66 (202)
+.|.+++.++...+...+..||+.++ -+...|+.|.......++
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 56889999999998889999999985 888889888877655443
No 99
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=43.24 E-value=26 Score=24.42 Aligned_cols=29 Identities=28% Similarity=0.623 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHHHH
Q 028922 76 EDLILRLHKLLGNRWSLIAGRLPGRTDNEI 105 (202)
Q Consensus 76 d~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~ 105 (202)
|..|..+.+..|..|.++|..| |=+...|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4457777888999999999999 5555444
No 100
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=42.79 E-value=46 Score=25.38 Aligned_cols=28 Identities=21% Similarity=0.176 Sum_probs=22.4
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
..|.....||..| |-|...|+++.....
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~ 166 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRAR 166 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3467899999999 889999988876543
No 101
>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=42.48 E-value=55 Score=19.61 Aligned_cols=35 Identities=23% Similarity=0.153 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHH
Q 028922 74 QEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYW 109 (202)
Q Consensus 74 eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw 109 (202)
-|-..|..++..+|++-+..|+.| |=+...+..+-
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 367788999999999999999998 66666555443
No 102
>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=41.88 E-value=29 Score=24.14 Aligned_cols=33 Identities=30% Similarity=0.550 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 028922 73 DQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKN 107 (202)
Q Consensus 73 ~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~ 107 (202)
.||.++|+.. -..|..|...|..| |=+...|.+
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 5788888742 25678899999999 767766653
No 103
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=41.64 E-value=37 Score=35.47 Aligned_cols=76 Identities=17% Similarity=0.216 Sum_probs=51.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHHHHHHHHh-CCChHHH
Q 028922 15 RGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLILRLHKLL-GNRWSLI 93 (202)
Q Consensus 15 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll~~v~~~-G~~W~~I 93 (202)
---|..++|..|+-.|-+||.++|..|-.- +.-|... ...+.-....+.+=......|+.++... +.+|...
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGygswe~Ir~D------p~L~l~d-Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~ 1205 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYGSWEAIRLD------PDLGLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKK 1205 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccccHHHhccC------ccccchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCchh
Confidence 357999999999999999999999988632 1111110 1112222456677778888888888877 6667776
Q ss_pred hccC
Q 028922 94 AGRL 97 (202)
Q Consensus 94 a~~l 97 (202)
+..-
T Consensus 1206 ~~~~ 1209 (1373)
T KOG0384|consen 1206 LKRE 1209 (1373)
T ss_pred hhcc
Confidence 6554
No 104
>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=41.02 E-value=74 Score=18.57 Aligned_cols=39 Identities=18% Similarity=0.250 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHH
Q 028922 71 ISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNS 111 (202)
Q Consensus 71 WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~ 111 (202)
.+++ +..++.++-..|..+..||..+ |=+...|+.+...
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~ 49 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHR 49 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 3444 4445555545677899999998 7777777765544
No 105
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=40.61 E-value=37 Score=23.90 Aligned_cols=24 Identities=33% Similarity=0.570 Sum_probs=19.2
Q ss_pred HHHHHhCCChHHHhccCCCCCHHHH
Q 028922 81 RLHKLLGNRWSLIAGRLPGRTDNEI 105 (202)
Q Consensus 81 ~~v~~~G~~W~~Ia~~l~gRT~~q~ 105 (202)
.+....|..|..+|..| |=+..+|
T Consensus 12 ~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 12 VFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 35577899999999999 7676665
No 106
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=40.04 E-value=52 Score=26.20 Aligned_cols=37 Identities=19% Similarity=0.243 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 76 EDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 76 d~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
...++.+..-.|-.+..||..+ |-+...|+.+|...-
T Consensus 140 ~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 140 QRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3444444445677899999999 999999999998654
No 107
>PRK04217 hypothetical protein; Provisional
Probab=38.91 E-value=71 Score=23.86 Aligned_cols=43 Identities=19% Similarity=0.086 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 70 NISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.-|.+| ..++.++...|-.-..||+.+ |-+...|+.++.....
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArk 84 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARK 84 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 456666 567777777788999999999 9999999998876443
No 108
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=38.15 E-value=60 Score=25.19 Aligned_cols=28 Identities=11% Similarity=-0.083 Sum_probs=22.4
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.|.....||..+ |-|...|+++......
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466799999999 9999999888765443
No 109
>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=36.24 E-value=48 Score=26.42 Aligned_cols=39 Identities=15% Similarity=0.171 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccchhh
Q 028922 17 AWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRW 58 (202)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw 58 (202)
.||.|..++|.++...- ..=..||..|+ +.|...+.-+-
T Consensus 2 ~Wtde~~~~L~~lw~~G--~SasqIA~~lg-~vsRnAViGk~ 40 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEG--LSASQIARQLG-GVSRNAVIGKA 40 (162)
T ss_pred CCCHHHHHHHHHHHHcC--CCHHHHHHHhC-Ccchhhhhhhh
Confidence 59999999999998543 46789999998 56655554443
No 110
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=36.15 E-value=35 Score=31.02 Aligned_cols=43 Identities=19% Similarity=0.344 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCCChhHHhhh-hccCcCccccchhhhc
Q 028922 16 GAWTAEEDQKLAQAIEVHGPKKWKSVAAK-AGLNRCGKSCRLRWMN 60 (202)
Q Consensus 16 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~-l~~~Rt~~qcr~Rw~~ 60 (202)
..|+.+|=..+.+.++.|| ++...|.+. ++ +|+...|-+-|..
T Consensus 278 ~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvr-tRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYG-KDFHLIRANKVR-TRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHhcccc-cchHHHHHHHHHH
Confidence 3699999999999999999 899888765 55 8999999886643
No 111
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=35.75 E-value=79 Score=24.43 Aligned_cols=35 Identities=26% Similarity=0.390 Sum_probs=26.4
Q ss_pred HHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 80 LRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 80 l~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
+.+....|-....||..+ |-+...|+.+-...+++
T Consensus 128 ~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 128 FLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333334567899999999 99999999987765544
No 112
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=35.65 E-value=73 Score=25.13 Aligned_cols=28 Identities=25% Similarity=0.113 Sum_probs=22.9
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
..|-....||..| |-|...|+++.....
T Consensus 120 ~~g~~~~EIA~~l-gis~~tV~~~l~Rar 147 (181)
T PRK09637 120 LEGLSQKEIAEKL-GLSLSGAKSRVQRGR 147 (181)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 3467899999999 899999998876544
No 113
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=35.01 E-value=86 Score=23.64 Aligned_cols=28 Identities=11% Similarity=0.076 Sum_probs=22.6
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.|-.-..||..| |-|...|+.|....++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~ 148 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATH 148 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466789999999 8999999988765443
No 114
>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=34.47 E-value=77 Score=24.32 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=22.8
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
.|-....||..+ |-|...|+++....+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 88999999888765543
No 115
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=34.43 E-value=1e+02 Score=24.09 Aligned_cols=33 Identities=21% Similarity=0.159 Sum_probs=26.8
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhhhHHHh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHLSKKIK 118 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~ 118 (202)
..|-....||..| |-+...|+.|....+..-+.
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 4467899999999 99999999998877665443
No 116
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=34.30 E-value=59 Score=21.99 Aligned_cols=44 Identities=16% Similarity=0.405 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCCC-------CCCCCCHHHHHHH
Q 028922 23 DQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPHI-------KRGNISDQEEDLI 79 (202)
Q Consensus 23 D~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~-------~k~~WT~eEd~~L 79 (202)
+..|.++|+.|| |..+++.+. -| |.. -+|++ ++.||-.+..+.|
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 568899999999 999998886 22 221 23443 4678877766654
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=34.27 E-value=59 Score=25.32 Aligned_cols=28 Identities=11% Similarity=-0.008 Sum_probs=22.3
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.|.....||..| |=|...|+++.....+
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~ 180 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRARE 180 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 356799999999 8889999988765543
No 118
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=34.15 E-value=37 Score=29.75 Aligned_cols=64 Identities=20% Similarity=0.278 Sum_probs=40.9
Q ss_pred CCCCHHHHHHHHHHHHHhC-CChHHHhccC-CCCCHHHHHHHHH-----HhhhHHHhhcCCCCCCCCccch
Q 028922 69 GNISDQEEDLILRLHKLLG-NRWSLIAGRL-PGRTDNEIKNYWN-----SHLSKKIKQNEKPSRGSTAKDL 132 (202)
Q Consensus 69 ~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l-~gRT~~q~k~rw~-----~~l~~~~~~~~~~~~~~~~~~~ 132 (202)
.+|+..+..+....+.++| ..|..|+..+ ..|++.++..+-. ..+...........+.+.+...
T Consensus 165 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~~~~~~~s~~~~~ 235 (335)
T KOG0724|consen 165 TPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGEEEKRRKSIEDIT 235 (335)
T ss_pred chhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhccccccchhhhhh
Confidence 3677777777777778888 4699998887 6788888877654 3333343444444444434333
No 119
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=33.74 E-value=74 Score=25.01 Aligned_cols=27 Identities=11% Similarity=-0.017 Sum_probs=21.4
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
.|-....||..+ |-|...|+++.....
T Consensus 153 ~g~s~~eIA~~l-gis~~tv~~~l~Rar 179 (193)
T PRK11923 153 DGLSYEDIASVM-QCPVGTVRSRIFRAR 179 (193)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 356789999999 888999988876544
No 120
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=33.26 E-value=89 Score=24.00 Aligned_cols=28 Identities=25% Similarity=0.258 Sum_probs=22.7
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.|-.-..||..| |.+...|+.|....++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~ 160 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALR 160 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 466789999999 9999999988775543
No 121
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=33.22 E-value=89 Score=24.75 Aligned_cols=28 Identities=7% Similarity=-0.075 Sum_probs=22.8
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.|-....||..| |-|...|+.|....++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~ 183 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVE 183 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 466789999999 9999999988765544
No 122
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=33.09 E-value=90 Score=24.47 Aligned_cols=29 Identities=17% Similarity=0.192 Sum_probs=23.1
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
.|.....||..| |-+...|+.+....+.+
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467799999999 88899999887665443
No 123
>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=32.89 E-value=92 Score=24.64 Aligned_cols=28 Identities=14% Similarity=0.051 Sum_probs=22.8
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
..|..-..||..| |-|...|+.|....+
T Consensus 145 ~~g~s~~EIA~~l-gis~~tvk~rl~Rar 172 (188)
T TIGR02943 145 VLGFESDEICQEL-EISTSNCHVLLYRAR 172 (188)
T ss_pred HhCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 3467799999999 999999998876554
No 124
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=32.82 E-value=91 Score=24.28 Aligned_cols=29 Identities=14% Similarity=0.187 Sum_probs=23.1
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
.|.....||..| |-|...|+.+....+++
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999887765543
No 125
>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=32.62 E-value=58 Score=22.88 Aligned_cols=31 Identities=26% Similarity=0.465 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 028922 76 EDLILRLHKLLGNRWSLIAGRLPGRTDNEIKN 107 (202)
Q Consensus 76 d~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~ 107 (202)
+..|-.+....|..|..+|+.| |=|...|..
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 3456667788999999999999 666666643
No 126
>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=32.44 E-value=51 Score=23.32 Aligned_cols=29 Identities=34% Similarity=0.574 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 028922 78 LILRLHKLLGNRWSLIAGRLPGRTDNEIKN 107 (202)
Q Consensus 78 ~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~ 107 (202)
.|-.+....|..|..+|+.| |=|..+|..
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 34455577899999999999 777777653
No 127
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=31.80 E-value=98 Score=24.31 Aligned_cols=27 Identities=7% Similarity=-0.013 Sum_probs=22.2
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
.|-....||..| |-|...|+++.....
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 466799999999 889999998876544
No 128
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.68 E-value=1e+02 Score=23.34 Aligned_cols=28 Identities=11% Similarity=-0.091 Sum_probs=22.3
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
..|-.-..||..| |-+...|++|.....
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar 147 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRAR 147 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3466789999999 999999998876544
No 129
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=31.59 E-value=82 Score=24.44 Aligned_cols=27 Identities=11% Similarity=-0.052 Sum_probs=21.5
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 87 GNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 87 G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
|..-..||..| |-|...|+++.....+
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56789999999 8899999988765443
No 130
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=31.50 E-value=96 Score=24.53 Aligned_cols=27 Identities=7% Similarity=-0.064 Sum_probs=22.3
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
.|-....||..| |-|...|+.|.....
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr 175 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRAR 175 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 466799999999 999999998876444
No 131
>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=31.18 E-value=59 Score=22.24 Aligned_cols=29 Identities=28% Similarity=0.580 Sum_probs=20.5
Q ss_pred HHHHHHHHHH-hCCChHHHhccCCCCCHHHH
Q 028922 76 EDLILRLHKL-LGNRWSLIAGRLPGRTDNEI 105 (202)
Q Consensus 76 d~~Ll~~v~~-~G~~W~~Ia~~l~gRT~~q~ 105 (202)
...|..++.. .|..|..+|+.| |=+..+|
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 3456666666 799999999999 4444444
No 132
>PLN03162 golden-2 like transcription factor; Provisional
Probab=29.92 E-value=1.3e+02 Score=27.61 Aligned_cols=44 Identities=14% Similarity=-0.017 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHHHhCC---ChHHHhccC--CCCCHHHHHHHHHHh
Q 028922 69 GNISDQEEDLILRLHKLLGN---RWSLIAGRL--PGRTDNEIKNYWNSH 112 (202)
Q Consensus 69 ~~WT~eEd~~Ll~~v~~~G~---~W~~Ia~~l--~gRT~~q~k~rw~~~ 112 (202)
=.||+|=+++++++|.++|. .=+.|-+.| +|=|-.+|+.|.+.+
T Consensus 238 LrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKY 286 (526)
T PLN03162 238 VDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKY 286 (526)
T ss_pred ccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 47999999999999999993 256676665 889999999887654
No 133
>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=29.70 E-value=53 Score=23.14 Aligned_cols=21 Identities=29% Similarity=0.445 Sum_probs=18.6
Q ss_pred HHHHHHHHHhCCChHHHhccC
Q 028922 77 DLILRLHKLLGNRWSLIAGRL 97 (202)
Q Consensus 77 ~~Ll~~v~~~G~~W~~Ia~~l 97 (202)
..|..+....|..|..+|.+|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L 23 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL 23 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc
Confidence 457788899999999999998
No 134
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=29.33 E-value=1.1e+02 Score=24.26 Aligned_cols=27 Identities=11% Similarity=-0.091 Sum_probs=21.0
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
.|-.+..||..| |=+...|+++....+
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~ 177 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGK 177 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 466899999999 888888887765443
No 135
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=29.18 E-value=52 Score=22.60 Aligned_cols=35 Identities=20% Similarity=0.251 Sum_probs=25.2
Q ss_pred hhHHhhhhccCcCccccchhhhccccCCCCCCCCCHHHHHHHH
Q 028922 38 WKSVAAKAGLNRCGKSCRLRWMNYLRPHIKRGNISDQEEDLIL 80 (202)
Q Consensus 38 W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~~~k~~WT~eEd~~Ll 80 (202)
-..||..+. |+|+.+.|..+. + ....|++|...|.
T Consensus 36 ~~~iA~~i~-gks~eeir~~fg------i-~~d~t~eee~~i~ 70 (78)
T PF01466_consen 36 CKYIANMIK-GKSPEEIRKYFG------I-ENDLTPEEEEEIR 70 (78)
T ss_dssp HHHHHHHHT-TS-HHHHHHHHT----------TSSHHHHHHHH
T ss_pred HHHHHHHhc-CCCHHHHHHHcC------C-CCCCCHHHHHHHH
Confidence 567888888 999999998762 2 4479999888764
No 136
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=29.10 E-value=1e+02 Score=28.26 Aligned_cols=55 Identities=18% Similarity=0.146 Sum_probs=41.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC----------------ChHHHhccC-----CCCCHHHHHHHHHHhhhHHHhhc
Q 028922 66 IKRGNISDQEEDLILRLHKLLGN----------------RWSLIAGRL-----PGRTDNEIKNYWNSHLSKKIKQN 120 (202)
Q Consensus 66 ~~k~~WT~eEd~~Ll~~v~~~G~----------------~W~~Ia~~l-----~gRT~~q~k~rw~~~l~~~~~~~ 120 (202)
.--|.|+++=|+.+.+++..|.. +=..||+.+ ..||.+||..|-+-+-+++++..
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~rei 149 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREI 149 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999988742 346777765 45899999999877666665543
No 137
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=29.00 E-value=37 Score=35.52 Aligned_cols=24 Identities=17% Similarity=0.365 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHHHHHHhC-CChHHH
Q 028922 70 NISDQEEDLILRLHKLLG-NRWSLI 93 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G-~~W~~I 93 (202)
.|..++|..||-.|-+|| ++|..|
T Consensus 1135 ~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1135 DWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred CCCchhhhhHhhhhhhcccccHHHh
Confidence 699999999999999999 789888
No 138
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=28.95 E-value=1e+02 Score=19.70 Aligned_cols=36 Identities=28% Similarity=0.460 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHH
Q 028922 72 SDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYW 109 (202)
Q Consensus 72 T~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw 109 (202)
|..| +..+.++...|-.=..||+.+ ||+-+.|+++-
T Consensus 6 t~~E-qaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 6 TDAE-QAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp -HHH-HHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred CHHH-HHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 4444 445567778899999999999 99998887643
No 139
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=28.90 E-value=87 Score=23.66 Aligned_cols=44 Identities=16% Similarity=0.116 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhCC-ChHHHhccCCCCCHHHHHHHHHHhhhHHHh
Q 028922 74 QEEDLILRLHKLLGN-RWSLIAGRLPGRTDNEIKNYWNSHLSKKIK 118 (202)
Q Consensus 74 eEd~~Ll~~v~~~G~-~W~~Ia~~l~gRT~~q~k~rw~~~l~~~~~ 118 (202)
+-|.+|+++.+.-|. .+..||+.+ |-+...|++|-..+.+..+.
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 557788888888774 599999999 99999999999877766543
No 140
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=28.44 E-value=1.3e+02 Score=22.54 Aligned_cols=28 Identities=18% Similarity=0.165 Sum_probs=21.7
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.|..-..||..+ |-+...|+.+-...++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALE 148 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355789999999 9999999987765443
No 141
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=28.43 E-value=1.3e+02 Score=22.74 Aligned_cols=28 Identities=18% Similarity=0.169 Sum_probs=21.9
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.|-.=..||..| |-+...|+.|....++
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~ 147 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMK 147 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 355679999999 9999999988765443
No 142
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=27.92 E-value=1.4e+02 Score=23.35 Aligned_cols=27 Identities=7% Similarity=-0.058 Sum_probs=21.0
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
.|-.-..||..| |-|...|+.+....+
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar 169 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGR 169 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHH
Confidence 466789999998 888888888766544
No 143
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=27.70 E-value=64 Score=19.59 Aligned_cols=36 Identities=28% Similarity=0.368 Sum_probs=18.2
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 028922 70 NISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKN 107 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~ 107 (202)
.+|.+|-..|..++ .-|..=..||..| ||+...|..
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHH
Confidence 46777777766664 5677889999999 999988865
No 144
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=27.43 E-value=1.7e+02 Score=22.74 Aligned_cols=29 Identities=24% Similarity=0.141 Sum_probs=22.6
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
.|-.=..||..+ |-|...|+.+.+..+.+
T Consensus 150 ~~~s~~eIA~~l-gis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 150 QGYTHREAAQLL-GLPLGTLKTRARRALSR 178 (186)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355689999999 99999999887765543
No 145
>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=27.39 E-value=1.3e+02 Score=22.84 Aligned_cols=27 Identities=19% Similarity=0.149 Sum_probs=21.3
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
.|-+-..||..| |-+...|+.+-....
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~ 163 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAI 163 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 356789999999 888999988776544
No 146
>PRK01905 DNA-binding protein Fis; Provisional
Probab=27.38 E-value=1.6e+02 Score=20.16 Aligned_cols=36 Identities=28% Similarity=0.266 Sum_probs=27.3
Q ss_pred CHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHH
Q 028922 72 SDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNY 108 (202)
Q Consensus 72 T~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~r 108 (202)
..-|...+.+++..+|++++..|+.+ |=+...++.+
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 34567788999999999999999998 5555555443
No 147
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=27.31 E-value=1.2e+02 Score=23.95 Aligned_cols=29 Identities=17% Similarity=0.104 Sum_probs=23.7
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
.|-.-..||..| |-|...|+.|....++.
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 173 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDA 173 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 99999999998765543
No 148
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=27.28 E-value=2.4e+02 Score=20.33 Aligned_cols=70 Identities=14% Similarity=0.276 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHHHh----CC---CChhHHhhhhc----cCcCcccc-------chhhhccccCCCCCC---CCCH
Q 028922 15 RGAWTAEEDQKLAQAIEVH----GP---KKWKSVAAKAG----LNRCGKSC-------RLRWMNYLRPHIKRG---NISD 73 (202)
Q Consensus 15 kg~WT~eED~~L~~~v~~~----g~---~~W~~Ia~~l~----~~Rt~~qc-------r~Rw~~~L~p~~~k~---~WT~ 73 (202)
...||++++-.|++++..| |. .+|..+...+. ..=+..|. +.||.+.... .+.| .++.
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k-~~~g~~~~~~~ 82 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK-SKNGKDPSFSK 82 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh-cccCcCCCCCC
Confidence 4569999999999998777 52 25555444442 11122232 2244444333 1222 5666
Q ss_pred HHHHHHHHHHHH
Q 028922 74 QEEDLILRLHKL 85 (202)
Q Consensus 74 eEd~~Ll~~v~~ 85 (202)
.-|..+.++.++
T Consensus 83 ~hd~~~f~Lsk~ 94 (98)
T PF04504_consen 83 PHDRRLFELSKK 94 (98)
T ss_pred HhHHHHHHHHHH
Confidence 777777766553
No 149
>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=27.28 E-value=59 Score=25.71 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=31.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhcc---CcCccccchhhh
Q 028922 13 ANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGL---NRCGKSCRLRWM 59 (202)
Q Consensus 13 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~---~Rt~~qcr~Rw~ 59 (202)
.....=|..|-.-|..+|++|| .|+...|.-..+ -.|+.||+.+..
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhccCCCCcccCCHHHHHHHHH
Confidence 4566789999999999999999 787766643210 134455554443
No 150
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=27.09 E-value=1e+02 Score=31.00 Aligned_cols=96 Identities=19% Similarity=0.263 Sum_probs=61.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccch----------------------------------------
Q 028922 17 AWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRL---------------------------------------- 56 (202)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~---------------------------------------- 56 (202)
.||.-+=..++.+..+||..+-..||+.+. + |+..+..
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 488888888888888888777777777665 3 3221111
Q ss_pred ----hhhc----cc-cCCCCCCCCCHHHHHHHHHHHHHhCC----ChHHHhcc------------CCCCCHHHHHHHHHH
Q 028922 57 ----RWMN----YL-RPHIKRGNISDQEEDLILRLHKLLGN----RWSLIAGR------------LPGRTDNEIKNYWNS 111 (202)
Q Consensus 57 ----Rw~~----~L-~p~~~k~~WT~eEd~~Ll~~v~~~G~----~W~~Ia~~------------l~gRT~~q~k~rw~~ 111 (202)
||++ .+ .+..++.+.|.+||.-|+-++.++|- .|..+-.. +..||...+..|+..
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 4433 11 11226679999999999999999993 25444221 245777777767666
Q ss_pred hhh
Q 028922 112 HLS 114 (202)
Q Consensus 112 ~l~ 114 (202)
++.
T Consensus 955 li~ 957 (971)
T KOG0385|consen 955 LIT 957 (971)
T ss_pred eEE
Confidence 553
No 151
>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=26.99 E-value=1.3e+02 Score=23.17 Aligned_cols=27 Identities=22% Similarity=0.228 Sum_probs=22.3
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
.|-....||..+ |-+...|+.|.....
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar 175 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFAR 175 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 456789999999 999999999877544
No 152
>PRK00118 putative DNA-binding protein; Validated
Probab=26.88 E-value=1.5e+02 Score=21.86 Aligned_cols=39 Identities=10% Similarity=0.066 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHh
Q 028922 73 DQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSH 112 (202)
Q Consensus 73 ~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~ 112 (202)
++.+..++.+.-..|-....||..+ |-|...|+.+-...
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RA 57 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRT 57 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3455666777777788999999999 99999988776543
No 153
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=26.77 E-value=1.3e+02 Score=23.24 Aligned_cols=27 Identities=19% Similarity=0.259 Sum_probs=22.2
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 87 GNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 87 G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
|-.-..||..| |.|...|+.+....++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~ 171 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLL 171 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHH
Confidence 66789999999 9999999988765443
No 154
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=26.36 E-value=1.2e+02 Score=23.84 Aligned_cols=27 Identities=15% Similarity=0.132 Sum_probs=21.6
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSH 112 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~ 112 (202)
..|-.-..||..| |-|...|+.|....
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Ra 176 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRA 176 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 3466789999999 89999998877643
No 155
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=26.28 E-value=1.5e+02 Score=22.49 Aligned_cols=29 Identities=28% Similarity=0.315 Sum_probs=23.2
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
-.|-.-..||..+ |-+...|+.|....++
T Consensus 127 ~~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 127 VDGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3467899999999 8999999988776543
No 156
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=26.14 E-value=85 Score=22.21 Aligned_cols=22 Identities=27% Similarity=0.440 Sum_probs=18.3
Q ss_pred HHHHHHHHHHhCCChHHHhccC
Q 028922 76 EDLILRLHKLLGNRWSLIAGRL 97 (202)
Q Consensus 76 d~~Ll~~v~~~G~~W~~Ia~~l 97 (202)
|-.|-...+..|..|..+|..|
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L 25 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL 25 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc
Confidence 4456677788999999999998
No 157
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=26.14 E-value=1.4e+02 Score=23.28 Aligned_cols=29 Identities=21% Similarity=0.107 Sum_probs=23.4
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
..|-....||..| |.+...|+++-...++
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~ 171 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLK 171 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3466899999999 9999999998765443
No 158
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=26.00 E-value=1.2e+02 Score=24.76 Aligned_cols=44 Identities=20% Similarity=0.185 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 69 GNISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 69 ~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
...|+.|-+.|.-+. -|-.=..||..| +.+...|++|..++++|
T Consensus 147 ~~LT~RE~eVL~lla--~G~snkeIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLA--EGLSNKEIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHH--CCCCHHHHHHHH-CCCHhHHHHHHHHHHHH
Confidence 368888887654333 366778999999 99999999999988866
No 159
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=25.93 E-value=1.4e+02 Score=23.31 Aligned_cols=29 Identities=10% Similarity=0.269 Sum_probs=23.1
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
..|-.-..||..| |-|...|++|.....+
T Consensus 136 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 164 (185)
T PRK12542 136 FYNLTYQEISSVM-GITEANVRKQFERARK 164 (185)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3466789999999 9999999998765443
No 160
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=25.84 E-value=1.9e+02 Score=22.86 Aligned_cols=28 Identities=21% Similarity=0.169 Sum_probs=21.4
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.|-.-..||..| |-+...|+.+-...+.
T Consensus 157 ~~~s~~EIA~~L-gis~~tVk~~l~ra~~ 184 (194)
T PRK09646 157 GGLTYREVAERL-AVPLGTVKTRMRDGLI 184 (194)
T ss_pred cCCCHHHHHHHh-CCChHhHHHHHHHHHH
Confidence 355789999999 7799999887665443
No 161
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=25.42 E-value=1.2e+02 Score=23.52 Aligned_cols=29 Identities=28% Similarity=0.343 Sum_probs=23.5
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
.|-.-.+||..+ |-+...|+++....+..
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355789999999 99999999988765544
No 162
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=25.27 E-value=1.6e+02 Score=22.56 Aligned_cols=29 Identities=17% Similarity=0.039 Sum_probs=22.6
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
..|-.-..||..+ |-+...|+++-....+
T Consensus 126 ~~g~s~~eIA~~l-gis~~tV~~~l~Rar~ 154 (164)
T PRK12547 126 ASGFSYEDAAAIC-GCAVGTIKSRVSRARN 154 (164)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3466789999999 8889999988765543
No 163
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=25.03 E-value=1.5e+02 Score=23.53 Aligned_cols=29 Identities=21% Similarity=0.044 Sum_probs=22.8
Q ss_pred HHhCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 84 KLLGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 84 ~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
...|-....||..| |-+...|+.|-...+
T Consensus 129 ~~~g~s~~EIA~~L-gis~~tVk~~l~Rar 157 (187)
T PRK12516 129 GASGFAYEEAAEIC-GCAVGTIKSRVNRAR 157 (187)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 34467899999999 889999998866444
No 164
>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=24.77 E-value=1.9e+02 Score=21.76 Aligned_cols=37 Identities=16% Similarity=0.156 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 78 LILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 78 ~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
.++.+.-..|-+=..||..| |-+...|+.+....+.+
T Consensus 117 ~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 117 AVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALAR 153 (162)
T ss_pred HHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 33333334466789999999 89999999888766544
No 165
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=24.76 E-value=1.1e+02 Score=23.29 Aligned_cols=45 Identities=13% Similarity=0.420 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhCCCChhHHhhhhccCcCccccchhhhccccCC-------CCCCCCCHHHHHHHH
Q 028922 23 DQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRLRWMNYLRPH-------IKRGNISDQEEDLIL 80 (202)
Q Consensus 23 D~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~Rw~~~L~p~-------~~k~~WT~eEd~~Ll 80 (202)
+.+|.++|..|| |..++..++ ..|.. -+|+ +++.+|..|-.+.|.
T Consensus 21 E~llt~Lvd~YG---Wd~L~~ri~-----inCF~-----ndPSi~SSlKfLrkT~WARekvEa~Y 72 (136)
T COG4628 21 ETLLTELVDFYG---WDGLATRIR-----INCFH-----NDPSIKSSLKFLRKTPWAREKVEALY 72 (136)
T ss_pred HHHHHHHHHHhC---hHHHHhhce-----ecccc-----CCccHHHHHHHHhcCHhHHHHHHHHH
Confidence 568889999999 999997665 33432 1233 357899988777553
No 166
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.19 E-value=81 Score=19.08 Aligned_cols=29 Identities=31% Similarity=0.363 Sum_probs=19.2
Q ss_pred HHHHHHHHHhCCChHHHhccCCCCCHHHHHH
Q 028922 77 DLILRLHKLLGNRWSLIAGRLPGRTDNEIKN 107 (202)
Q Consensus 77 ~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~ 107 (202)
..++.++.. |.....||..+ |-+...|..
T Consensus 8 ~~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~ 36 (50)
T PF13384_consen 8 AQIIRLLRE-GWSIREIAKRL-GVSRSTVYR 36 (50)
T ss_dssp --HHHHHHH-T--HHHHHHHH-TS-HHHHHH
T ss_pred HHHHHHHHC-CCCHHHHHHHH-CcCHHHHHH
Confidence 456667766 99999999999 788777763
No 167
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=24.05 E-value=1.1e+02 Score=21.49 Aligned_cols=27 Identities=22% Similarity=0.512 Sum_probs=19.4
Q ss_pred HHHHHHHhCCChHHHhccCCCCCHHHHH
Q 028922 79 ILRLHKLLGNRWSLIAGRLPGRTDNEIK 106 (202)
Q Consensus 79 Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k 106 (202)
+--+.+..|..|..+|+.| |=|..+|.
T Consensus 5 f~~i~~~lG~~Wk~laR~L-Glse~~Id 31 (86)
T cd08306 5 FDVICENVGRDWRKLARKL-GLSETKIE 31 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 3344566799999999999 66666553
No 168
>smart00351 PAX Paired Box domain.
Probab=23.69 E-value=3.1e+02 Score=20.41 Aligned_cols=75 Identities=15% Similarity=0.147 Sum_probs=47.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCChhHHhhhhccCc-Cccccchhhhc--cccCCC----CCCCCCHHHHHHHHHHH
Q 028922 11 KEANRGAWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNR-CGKSCRLRWMN--YLRPHI----KRGNISDQEEDLILRLH 83 (202)
Q Consensus 11 ~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R-t~~qcr~Rw~~--~L~p~~----~k~~WT~eEd~~Ll~~v 83 (202)
...+..+.+.++-+++..++. .| ..-..||+.++..+ |...+..||.. .+.|.- ....-+...+..|++++
T Consensus 11 ~~~~~~~~s~~~R~riv~~~~-~G-~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~ 88 (125)
T smart00351 11 VFVNGRPLPDEERQRIVELAQ-NG-VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYK 88 (125)
T ss_pred eecCCCCCCHHHHHHHHHHHH-cC-CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHH
Confidence 445566799999999988886 45 57889999997544 34556666654 244421 22234556666666665
Q ss_pred HHhC
Q 028922 84 KLLG 87 (202)
Q Consensus 84 ~~~G 87 (202)
...+
T Consensus 89 ~~~p 92 (125)
T smart00351 89 QENP 92 (125)
T ss_pred HHCC
Confidence 5443
No 169
>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=23.58 E-value=52 Score=24.68 Aligned_cols=27 Identities=15% Similarity=0.005 Sum_probs=22.1
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 87 GNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 87 G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
|-.+..||..| |=|...|+++......
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARK 147 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45799999999 8999999998876543
No 170
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.48 E-value=1.4e+02 Score=23.68 Aligned_cols=30 Identities=17% Similarity=0.048 Sum_probs=23.6
Q ss_pred HHhCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 84 KLLGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 84 ~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
...|-....||..| |-|...|+++-....+
T Consensus 126 ~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~ 155 (188)
T PRK12546 126 GASGFSYEEAAEMC-GVAVGTVKSRANRARA 155 (188)
T ss_pred HhcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 34567899999999 8899999988765543
No 171
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=22.78 E-value=1.6e+02 Score=23.80 Aligned_cols=43 Identities=12% Similarity=0.112 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 70 NISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
..|+-|-+.|..+. -|..-.+||..| +-+...|++|-.+++++
T Consensus 137 ~LT~RE~eVL~lla--~G~snkeIA~~L-~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 137 SLSRTESSMLRMWM--AGQGTIQISDQM-NIKAKTVSSHKGNIKRK 179 (207)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHc-CCCHHHHHHHHHHHHHH
Confidence 48888887654333 377789999999 89999999988776655
No 172
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=22.70 E-value=1.7e+02 Score=23.38 Aligned_cols=26 Identities=19% Similarity=0.012 Sum_probs=21.0
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSH 112 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~ 112 (202)
.|..-..||..| |.+...|+.|....
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RA 179 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRA 179 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 356789999999 99999999876543
No 173
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=22.67 E-value=2.2e+02 Score=23.53 Aligned_cols=43 Identities=26% Similarity=0.246 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 70 NISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
..|+-|-+.|. ++.+ |.....||..| +-+...|+++-..++++
T Consensus 133 ~LSpRErEVLr-LLAq-GkTnKEIAe~L-~IS~rTVkth~srImkK 175 (198)
T PRK15201 133 HFSVTERHLLK-LIAS-GYHLSETAALL-SLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCHHHHHHHH-HHHC-CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 57888877654 4433 88899999999 99999999888777655
No 174
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=22.08 E-value=2.2e+02 Score=20.44 Aligned_cols=34 Identities=15% Similarity=0.080 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHH
Q 028922 74 QEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNY 108 (202)
Q Consensus 74 eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~r 108 (202)
-|...|..++..+|++....|+.+ |=+...++.+
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rK 88 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKK 88 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHH
Confidence 467788899999999999999998 5555555443
No 175
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=22.00 E-value=62 Score=30.48 Aligned_cols=39 Identities=21% Similarity=0.250 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhHHhhhhccCcCccccch
Q 028922 17 AWTAEEDQKLAQAIEVHGPKKWKSVAAKAGLNRCGKSCRL 56 (202)
Q Consensus 17 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~Rt~~qcr~ 56 (202)
.|+..|-.++.+++++|| ++++.|...+-+=++-.++.+
T Consensus 287 EWSasEanLFEeALeKyG-KDFndIrqdfLPWKSl~sIve 325 (693)
T KOG3554|consen 287 EWSASEANLFEEALEKYG-KDFNDIRQDFLPWKSLTSIVE 325 (693)
T ss_pred hccchhhHHHHHHHHHhc-ccHHHHHHhhcchHHHHHHHH
Confidence 699999999999999999 777777665433455544444
No 176
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.95 E-value=2.2e+02 Score=22.30 Aligned_cols=28 Identities=32% Similarity=0.376 Sum_probs=22.2
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 87 GNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 87 G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
|-.=..||..| |-|...|+++-....++
T Consensus 147 g~s~~EIAe~l-gis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 147 GEKIEEIAKKL-GLTRSAIDNRLSRGRKK 174 (189)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55678999999 99999999887665443
No 177
>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=21.78 E-value=1.9e+02 Score=22.35 Aligned_cols=29 Identities=24% Similarity=0.514 Sum_probs=22.4
Q ss_pred HhCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 85 LLGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 85 ~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
..|-.-..||..+ |-|...|+.+....+.
T Consensus 154 ~~g~s~~eIA~~l-gis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 154 LEGLSFAEVAERM-DRSEGAVSMLWVRGLA 182 (189)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3466789999998 8899999888765543
No 178
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.41 E-value=2.8e+02 Score=20.03 Aligned_cols=44 Identities=20% Similarity=0.209 Sum_probs=35.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhccCCCC-CHHHHHHHHHHhh
Q 028922 68 RGNISDQEEDLILRLHKLLGNRWSLIAGRLPGR-TDNEIKNYWNSHL 113 (202)
Q Consensus 68 k~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gR-T~~q~k~rw~~~l 113 (202)
+..||.|.-..+++++..-|..=+.||+.+ |- .+++++ +|...+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~-~W~~~~ 49 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLY-KWRIQL 49 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHH-HHHHHH
Confidence 568999999999999999888889999999 75 666665 454433
No 179
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=21.29 E-value=93 Score=25.57 Aligned_cols=26 Identities=15% Similarity=0.070 Sum_probs=21.4
Q ss_pred CCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 87 GNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 87 G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
|-.-..||..| |-|..+|+++.....
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar 190 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRAR 190 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 45689999999 899999998877544
No 180
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=21.19 E-value=83 Score=21.00 Aligned_cols=23 Identities=35% Similarity=0.492 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCCChhHHhhhhcc
Q 028922 25 KLAQAIEVHGPKKWKSVAAKAGL 47 (202)
Q Consensus 25 ~L~~~v~~~g~~~W~~Ia~~l~~ 47 (202)
.|..++......+|..+|..++.
T Consensus 2 ~l~~~l~~~~~~~Wk~La~~Lg~ 24 (83)
T PF00531_consen 2 KLFDLLAEDLGSDWKRLARKLGL 24 (83)
T ss_dssp HHHHHHHHSHSTCHHHHHHHTTS
T ss_pred hHHHHHhhcchhhHHHHHHHhCc
Confidence 46666666655899999999973
No 181
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=20.74 E-value=2e+02 Score=22.49 Aligned_cols=27 Identities=15% Similarity=-0.111 Sum_probs=21.7
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHL 113 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l 113 (202)
.|..-..||..| |-|...|++|.....
T Consensus 146 ~g~s~~EIA~~l-gis~~tV~~~l~Rar 172 (191)
T PRK12520 146 LELETEEICQEL-QITATNAWVLLYRAR 172 (191)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 356789999999 999999998876543
No 182
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=20.35 E-value=1.7e+02 Score=25.12 Aligned_cols=28 Identities=21% Similarity=0.210 Sum_probs=22.7
Q ss_pred hCCChHHHhccCCCCCHHHHHHHHHHhhh
Q 028922 86 LGNRWSLIAGRLPGRTDNEIKNYWNSHLS 114 (202)
Q Consensus 86 ~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~ 114 (202)
.|-.-..||..| |.+...|+.|.....+
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 184 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARA 184 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466789999999 9999999988765443
No 183
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=20.13 E-value=2.1e+02 Score=23.41 Aligned_cols=43 Identities=19% Similarity=0.273 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhccCCCCCHHHHHHHHHHhhhH
Q 028922 70 NISDQEEDLILRLHKLLGNRWSLIAGRLPGRTDNEIKNYWNSHLSK 115 (202)
Q Consensus 70 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~gRT~~q~k~rw~~~l~~ 115 (202)
..|+-|-+.| .++.. |..-..||..| +-+...|+.+-..++++
T Consensus 155 ~Lt~rE~~Vl-~l~~~-G~s~~eIA~~L-~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 155 LLTHREKEIL-NKLRI-GASNNEIARSL-FISENTVKTHLYNLFKK 197 (216)
T ss_pred CCCHHHHHHH-HHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 4777666554 45545 98899999999 89999999988877655
Done!