Query 039547
Match_columns 67
No_of_seqs 113 out of 1068
Neff 7.1
Searched_HMMs 46136
Date Fri Mar 29 10:47:16 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039547.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039547hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 99.8 4.1E-19 8.9E-24 117.3 5.3 52 1-54 69-120 (238)
2 PLN03212 Transcription repress 99.7 6.3E-17 1.4E-21 107.9 5.3 54 1-56 85-138 (249)
3 PLN03091 hypothetical protein; 99.6 1E-15 2.2E-20 108.6 5.4 52 1-54 74-125 (459)
4 PF13921 Myb_DNA-bind_6: Myb-l 99.5 2.8E-14 6.1E-19 76.3 5.1 56 1-63 5-60 (60)
5 PF00249 Myb_DNA-binding: Myb- 99.4 6.2E-13 1.3E-17 68.7 3.6 38 1-39 8-47 (48)
6 PLN03212 Transcription repress 99.3 1.3E-12 2.8E-17 87.3 4.8 59 1-66 32-92 (249)
7 KOG0048 Transcription factor, 99.3 2.5E-12 5.3E-17 85.1 3.4 60 1-67 16-77 (238)
8 smart00717 SANT SANT SWI3, AD 99.3 8.3E-12 1.8E-16 62.7 3.9 39 1-40 8-47 (49)
9 PLN03091 hypothetical protein; 99.2 1.8E-11 3.9E-16 87.1 4.3 60 1-67 21-82 (459)
10 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 4E-11 8.6E-16 59.4 4.0 37 1-38 6-43 (45)
11 KOG0049 Transcription factor, 98.3 1.1E-06 2.4E-11 65.9 4.7 58 1-65 367-425 (939)
12 KOG0050 mRNA splicing protein 98.2 1.5E-06 3.3E-11 63.5 4.3 58 1-65 14-72 (617)
13 COG5147 REB1 Myb superfamily p 98.2 1.7E-06 3.7E-11 63.0 3.7 58 1-65 27-85 (512)
14 COG5147 REB1 Myb superfamily p 97.8 1.9E-05 4.1E-10 57.7 3.2 44 1-45 79-122 (512)
15 KOG0051 RNA polymerase I termi 97.4 0.00036 7.8E-09 51.9 5.1 59 1-65 391-449 (607)
16 KOG0050 mRNA splicing protein 96.5 0.0027 5.8E-08 47.0 2.9 41 1-43 66-106 (617)
17 KOG0457 Histone acetyltransfer 96.3 0.0065 1.4E-07 43.9 3.9 35 1-35 79-114 (438)
18 KOG0049 Transcription factor, 96.2 0.0054 1.2E-07 46.7 3.4 59 1-66 312-374 (939)
19 PF13837 Myb_DNA-bind_4: Myb/S 95.4 0.012 2.6E-07 32.8 1.8 31 15-47 36-70 (90)
20 COG5114 Histone acetyltransfer 95.0 0.066 1.4E-06 38.0 5.0 40 1-40 70-110 (432)
21 TIGR01557 myb_SHAQKYF myb-like 94.3 0.11 2.4E-06 27.7 3.7 35 1-35 10-50 (57)
22 PF08914 Myb_DNA-bind_2: Rap1 94.2 0.09 1.9E-06 28.7 3.3 41 1-42 9-59 (65)
23 TIGR02894 DNA_bind_RsfA transc 93.3 0.13 2.8E-06 32.9 3.3 29 16-46 33-61 (161)
24 PF08281 Sigma70_r4_2: Sigma-7 92.8 0.3 6.6E-06 24.7 3.8 33 2-35 15-47 (54)
25 KOG1279 Chromatin remodeling f 92.4 0.2 4.2E-06 37.1 3.7 35 1-35 260-294 (506)
26 COG5259 RSC8 RSC chromatin rem 92.2 0.18 3.9E-06 37.2 3.2 35 1-35 286-320 (531)
27 PF13873 Myb_DNA-bind_5: Myb/S 89.2 0.69 1.5E-05 25.2 3.2 20 16-35 41-65 (78)
28 PRK13923 putative spore coat p 89.1 0.6 1.3E-05 30.1 3.2 36 6-43 21-59 (170)
29 cd08319 Death_RAIDD Death doma 84.8 1.9 4.1E-05 24.5 3.4 31 2-33 2-32 (83)
30 TIGR02985 Sig70_bacteroi1 RNA 83.9 3.2 7E-05 24.4 4.4 33 2-35 118-150 (161)
31 smart00595 MADF subfamily of S 81.3 2.3 5.1E-05 23.4 2.9 21 16-38 30-50 (89)
32 PF04545 Sigma70_r4: Sigma-70, 79.7 4.9 0.00011 19.9 3.6 37 2-40 9-45 (50)
33 cd08317 Death_ank Death domain 79.7 3.1 6.8E-05 23.2 3.1 31 2-33 4-34 (84)
34 PRK11179 DNA-binding transcrip 79.4 6.2 0.00013 24.1 4.6 33 2-35 11-44 (153)
35 PF10545 MADF_DNA_bdg: Alcohol 79.3 2.7 6E-05 22.4 2.7 22 16-38 29-51 (85)
36 cd08803 Death_ank3 Death domai 79.1 4.9 0.00011 22.8 3.7 32 2-34 4-35 (84)
37 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 78.0 3.3 7.1E-05 21.5 2.6 33 2-35 9-41 (50)
38 PF13404 HTH_AsnC-type: AsnC-t 76.5 7.1 0.00015 19.2 3.5 33 2-35 5-38 (42)
39 PF09111 SLIDE: SLIDE; InterP 75.5 3.5 7.6E-05 24.9 2.6 40 1-41 56-111 (118)
40 PRK11169 leucine-responsive tr 75.3 6.8 0.00015 24.3 4.0 33 2-35 16-49 (164)
41 cd08804 Death_ank2 Death domai 73.1 6.3 0.00014 22.2 3.1 30 3-33 5-34 (84)
42 PF13936 HTH_38: Helix-turn-he 72.8 6.3 0.00014 19.4 2.8 32 2-34 9-40 (44)
43 smart00005 DEATH DEATH domain, 72.3 5.8 0.00013 21.7 2.8 29 4-33 7-36 (88)
44 cd08318 Death_NMPP84 Death dom 70.6 8.7 0.00019 21.6 3.3 28 5-33 10-37 (86)
45 TIGR02937 sigma70-ECF RNA poly 70.0 12 0.00027 21.2 4.0 32 3-35 116-147 (158)
46 KOG4282 Transcription factor G 69.3 8.7 0.00019 26.5 3.7 26 14-40 84-113 (345)
47 PF12776 Myb_DNA-bind_3: Myb/S 69.0 6.8 0.00015 21.7 2.7 20 16-35 34-58 (96)
48 PRK09652 RNA polymerase sigma 68.9 12 0.00026 22.4 4.0 32 3-35 134-165 (182)
49 COG5118 BDP1 Transcription ini 68.7 6.9 0.00015 28.6 3.2 31 5-35 376-406 (507)
50 cd08306 Death_FADD Fas-associa 68.6 9.6 0.00021 21.4 3.2 30 4-34 4-33 (86)
51 cd08777 Death_RIP1 Death Domai 68.4 8.7 0.00019 21.7 3.0 29 5-34 5-33 (86)
52 PRK09636 RNA polymerase sigma 68.0 28 0.0006 23.3 5.9 41 3-46 121-161 (293)
53 PRK09641 RNA polymerase sigma 68.0 15 0.00032 22.4 4.3 33 2-35 141-173 (187)
54 PRK11924 RNA polymerase sigma 66.8 15 0.00033 21.9 4.1 32 3-35 131-162 (179)
55 PF01388 ARID: ARID/BRIGHT DNA 66.4 20 0.00044 19.8 4.4 36 5-41 41-89 (92)
56 PF07638 Sigma70_ECF: ECF sigm 64.8 21 0.00045 22.4 4.6 32 3-35 141-172 (185)
57 PF10440 WIYLD: Ubiquitin-bind 64.4 6.4 0.00014 21.6 1.9 18 4-21 31-48 (65)
58 cd08779 Death_PIDD Death Domai 64.2 9.9 0.00022 21.4 2.7 27 3-30 3-29 (86)
59 TIGR02939 RpoE_Sigma70 RNA pol 63.9 15 0.00033 22.4 3.7 32 3-35 144-175 (190)
60 PRK09643 RNA polymerase sigma 63.7 20 0.00043 22.4 4.3 33 2-35 139-171 (192)
61 smart00501 BRIGHT BRIGHT, ARID 63.0 25 0.00054 19.7 4.5 28 14-42 54-86 (93)
62 TIGR02960 SigX5 RNA polymerase 62.5 34 0.00073 22.9 5.5 32 3-35 148-179 (324)
63 TIGR02948 SigW_bacill RNA poly 60.5 24 0.00052 21.4 4.2 32 3-35 142-173 (187)
64 cd08805 Death_ank1 Death domai 59.2 17 0.00037 20.6 3.1 32 3-35 5-39 (84)
65 PRK09637 RNA polymerase sigma 58.7 27 0.00059 21.6 4.2 33 2-35 111-143 (181)
66 PRK04217 hypothetical protein; 58.6 27 0.00059 20.8 4.0 33 2-35 47-79 (110)
67 PF00531 Death: Death domain; 58.5 26 0.00055 18.6 3.7 24 9-33 8-31 (83)
68 PF13384 HTH_23: Homeodomain-l 57.7 19 0.0004 17.5 2.8 30 4-35 9-38 (50)
69 PRK12532 RNA polymerase sigma 56.2 42 0.00092 20.7 4.8 44 3-48 142-188 (195)
70 PF13325 MCRS_N: N-terminal re 55.9 34 0.00073 22.6 4.4 26 22-48 109-134 (199)
71 TIGR02952 Sig70_famx2 RNA poly 55.9 34 0.00075 20.3 4.3 33 2-35 127-159 (170)
72 PRK12536 RNA polymerase sigma 55.7 37 0.00081 20.8 4.5 32 3-35 135-166 (181)
73 PRK12515 RNA polymerase sigma 55.0 36 0.00079 20.9 4.4 32 3-35 137-168 (189)
74 cd01670 Death Death Domain: a 54.2 19 0.0004 19.1 2.6 27 6-33 3-29 (79)
75 TIGR02943 Sig70_famx1 RNA poly 54.1 38 0.00082 21.1 4.4 32 3-35 137-168 (188)
76 PRK12523 RNA polymerase sigma 54.1 35 0.00076 20.7 4.2 33 2-35 124-156 (172)
77 PRK08241 RNA polymerase factor 54.0 48 0.001 22.5 5.2 41 3-46 159-199 (339)
78 PRK09645 RNA polymerase sigma 53.3 48 0.001 19.9 4.9 32 3-35 124-155 (173)
79 KOG1194 Predicted DNA-binding 53.0 34 0.00073 25.7 4.4 36 2-38 194-230 (534)
80 PRK12514 RNA polymerase sigma 52.7 38 0.00081 20.6 4.1 31 4-35 136-166 (179)
81 PRK11923 algU RNA polymerase s 52.7 38 0.00083 20.8 4.2 32 3-35 144-175 (193)
82 TIGR02957 SigX4 RNA polymerase 52.0 69 0.0015 21.4 6.7 41 3-46 114-154 (281)
83 PRK12530 RNA polymerase sigma 51.9 42 0.0009 20.8 4.3 32 3-35 140-171 (189)
84 cd08311 Death_p75NR Death doma 51.6 19 0.00042 20.0 2.5 23 11-34 13-35 (77)
85 PRK09642 RNA polymerase sigma 51.4 50 0.0011 19.6 4.5 32 3-35 112-143 (160)
86 PF09905 DUF2132: Uncharacteri 51.3 25 0.00055 19.2 2.8 30 2-33 12-44 (64)
87 PRK09047 RNA polymerase factor 47.9 50 0.0011 19.4 4.1 32 3-35 112-143 (161)
88 PLN03142 Probable chromatin-re 47.9 30 0.00066 28.0 3.8 40 1-41 933-985 (1033)
89 PRK12512 RNA polymerase sigma 47.0 52 0.0011 20.1 4.1 33 2-35 136-168 (184)
90 PRK13919 putative RNA polymera 46.8 64 0.0014 19.6 4.5 32 3-35 141-172 (186)
91 PRK12531 RNA polymerase sigma 46.4 54 0.0012 20.3 4.2 32 3-35 147-178 (194)
92 PRK12529 RNA polymerase sigma 45.8 56 0.0012 20.0 4.2 37 3-41 133-169 (178)
93 TIGR02954 Sig70_famx3 RNA poly 44.9 60 0.0013 19.5 4.1 32 3-35 125-156 (169)
94 PF11035 SnAPC_2_like: Small n 44.5 56 0.0012 23.4 4.3 32 4-35 32-66 (344)
95 PRK05602 RNA polymerase sigma 44.4 73 0.0016 19.5 5.1 45 3-48 134-180 (186)
96 PRK06811 RNA polymerase factor 44.4 68 0.0015 19.8 4.4 33 2-35 136-168 (189)
97 PRK12527 RNA polymerase sigma 43.4 68 0.0015 19.0 4.2 33 2-35 110-142 (159)
98 smart00344 HTH_ASNC helix_turn 43.1 60 0.0013 18.1 4.1 38 2-41 5-43 (108)
99 PRK09651 RNA polymerase sigma 43.0 54 0.0012 19.9 3.8 32 3-35 125-156 (172)
100 cd08312 Death_MyD88 Death doma 42.9 29 0.00063 19.1 2.3 23 10-33 13-35 (79)
101 cd06171 Sigma70_r4 Sigma70, re 42.4 38 0.00082 15.6 3.8 32 3-35 16-47 (55)
102 PRK12520 RNA polymerase sigma 42.4 73 0.0016 19.6 4.3 32 3-35 137-168 (191)
103 PRK12528 RNA polymerase sigma 42.0 72 0.0016 18.9 4.2 32 3-35 119-150 (161)
104 PRK09648 RNA polymerase sigma 41.6 77 0.0017 19.4 4.3 32 3-35 145-176 (189)
105 KOG2656 DNA methyltransferase 41.0 18 0.0004 26.4 1.5 45 3-48 139-189 (445)
106 PRK09649 RNA polymerase sigma 40.8 74 0.0016 19.6 4.2 32 3-35 136-167 (185)
107 COG4654 Cytochrome c551/c552 [ 40.0 21 0.00045 21.5 1.5 24 10-33 44-67 (110)
108 PRK06759 RNA polymerase factor 39.9 78 0.0017 18.5 4.5 32 3-35 112-143 (154)
109 PRK12545 RNA polymerase sigma 39.8 82 0.0018 19.7 4.3 45 3-48 145-191 (201)
110 PRK09647 RNA polymerase sigma 39.8 84 0.0018 19.9 4.4 31 4-35 145-175 (203)
111 PRK10100 DNA-binding transcrip 39.6 85 0.0018 20.3 4.4 31 3-35 161-191 (216)
112 TIGR02950 SigM_subfam RNA poly 39.4 27 0.00059 20.5 1.9 27 8-35 116-142 (154)
113 PF03832 WSK: WSK motif; Inte 38.9 22 0.00048 16.7 1.2 14 13-26 4-17 (31)
114 PRK12524 RNA polymerase sigma 38.4 90 0.0019 19.3 4.3 32 3-35 142-173 (196)
115 PRK01905 DNA-binding protein F 38.3 69 0.0015 17.4 3.4 33 1-34 38-70 (77)
116 TIGR02983 SigE-fam_strep RNA p 38.1 85 0.0018 18.6 4.0 32 3-35 116-147 (162)
117 TIGR02999 Sig-70_X6 RNA polyme 36.1 1E+02 0.0022 18.6 4.4 32 3-35 140-171 (183)
118 PRK12537 RNA polymerase sigma 35.5 99 0.0021 18.9 4.1 31 4-35 140-170 (182)
119 PF02954 HTH_8: Bacterial regu 35.4 57 0.0012 15.6 2.8 32 1-33 6-37 (42)
120 PRK09646 RNA polymerase sigma 35.4 1E+02 0.0022 19.1 4.2 33 2-35 147-179 (194)
121 PRK12516 RNA polymerase sigma 35.2 98 0.0021 19.2 4.1 32 3-35 122-153 (187)
122 PHA02291 hypothetical protein 34.9 14 0.00031 22.5 0.2 18 18-35 75-93 (132)
123 COG4628 Uncharacterized conser 34.8 46 0.001 20.5 2.4 21 2-24 21-41 (136)
124 PRK00118 putative DNA-binding 34.5 1E+02 0.0022 18.2 4.4 32 3-35 23-54 (104)
125 PRK09639 RNA polymerase sigma 33.8 1E+02 0.0023 18.2 4.0 31 3-35 118-148 (166)
126 PRK00430 fis global DNA-bindin 33.7 92 0.002 17.8 3.5 32 1-33 56-87 (95)
127 PRK12547 RNA polymerase sigma 33.3 1.1E+02 0.0024 18.3 4.2 32 3-35 118-149 (164)
128 PRK09415 RNA polymerase factor 33.1 1E+02 0.0022 18.8 3.9 32 3-35 133-164 (179)
129 PRK12546 RNA polymerase sigma 32.7 1.1E+02 0.0024 19.1 4.1 32 3-35 119-150 (188)
130 TIGR02984 Sig-70_plancto1 RNA 32.7 1.1E+02 0.0025 18.3 4.1 31 4-35 147-177 (189)
131 cd06571 Bac_DnaA_C C-terminal 32.4 61 0.0013 18.0 2.6 28 8-35 39-66 (90)
132 PRK09635 sigI RNA polymerase s 31.8 1.7E+02 0.0036 19.9 6.1 41 3-46 124-164 (290)
133 PRK12526 RNA polymerase sigma 31.2 1.3E+02 0.0027 19.0 4.1 32 3-35 159-190 (206)
134 PRK09638 RNA polymerase sigma 31.2 45 0.00097 20.1 2.0 31 4-35 133-163 (176)
135 TIGR02989 Sig-70_gvs1 RNA poly 31.2 1.1E+02 0.0025 17.8 4.5 32 3-35 117-148 (159)
136 KOG2009 Transcription initiati 30.8 37 0.0008 25.9 1.8 29 7-35 422-450 (584)
137 PRK11922 RNA polymerase sigma 30.6 60 0.0013 20.9 2.6 41 4-45 156-198 (231)
138 KOG0051 RNA polymerase I termi 30.4 68 0.0015 24.7 3.1 28 15-44 542-570 (607)
139 PRK12513 RNA polymerase sigma 29.8 53 0.0011 20.2 2.2 31 4-35 146-176 (194)
140 PRK12519 RNA polymerase sigma 29.6 1.1E+02 0.0024 18.7 3.7 32 3-35 147-178 (194)
141 PRK12518 RNA polymerase sigma 29.3 58 0.0013 19.6 2.3 29 6-35 129-157 (175)
142 PRK12538 RNA polymerase sigma 29.2 1.1E+02 0.0024 19.9 3.7 32 3-35 177-208 (233)
143 PRK12542 RNA polymerase sigma 28.0 1.5E+02 0.0032 18.1 4.2 32 3-35 128-159 (185)
144 smart00760 Bac_DnaA_C Bacteria 27.7 69 0.0015 16.4 2.1 19 9-27 41-59 (60)
145 TIGR02959 SigZ RNA polymerase 27.6 1.5E+02 0.0032 17.9 4.2 32 3-35 106-137 (170)
146 COG1522 Lrp Transcriptional re 27.5 1.4E+02 0.003 17.6 4.6 33 2-35 10-43 (154)
147 cd08778 Death_TNFRSF21 Death d 27.0 63 0.0014 18.2 1.9 27 8-34 9-35 (84)
148 PRK06986 fliA flagellar biosyn 26.9 1.7E+02 0.0038 18.7 4.3 32 3-35 190-221 (236)
149 cd00569 HTH_Hin_like Helix-tur 26.8 59 0.0013 13.1 3.3 21 12-33 20-40 (42)
150 PRK12535 RNA polymerase sigma 26.4 1.7E+02 0.0037 18.3 4.3 31 4-35 140-170 (196)
151 PRK08295 RNA polymerase factor 26.1 1.7E+02 0.0036 18.1 4.4 30 4-35 162-191 (208)
152 PRK12544 RNA polymerase sigma 25.1 1.9E+02 0.004 18.4 4.1 31 4-35 155-185 (206)
153 TIGR03001 Sig-70_gmx1 RNA poly 24.9 2.1E+02 0.0046 18.8 5.4 60 3-64 167-231 (244)
154 cd08781 Death_UNC5-like Death 24.9 52 0.0011 18.3 1.4 14 11-24 18-31 (83)
155 PF01466 Skp1: Skp1 family, di 24.5 62 0.0013 17.6 1.6 20 16-35 36-55 (78)
156 PRK12541 RNA polymerase sigma 24.3 1.6E+02 0.0036 17.3 4.1 32 3-35 118-149 (161)
157 cd08780 Death_TRADD Death Doma 23.9 84 0.0018 18.3 2.1 26 8-34 8-38 (90)
158 PRK15201 fimbriae regulatory p 23.7 2.3E+02 0.005 18.8 4.4 30 4-35 140-169 (198)
159 TIGR02980 SigBFG RNA polymeras 23.2 2.1E+02 0.0045 18.1 4.4 32 3-35 184-215 (227)
160 PRK06930 positive control sigm 22.6 2.1E+02 0.0045 18.0 4.4 32 3-35 120-151 (170)
161 PRK12511 RNA polymerase sigma 22.0 2.1E+02 0.0045 17.7 4.5 31 4-35 118-148 (182)
162 PRK12522 RNA polymerase sigma 22.0 1.9E+02 0.0042 17.3 4.2 31 4-35 126-156 (173)
163 PRK09644 RNA polymerase sigma 21.9 1.9E+02 0.0041 17.2 4.3 32 3-35 114-145 (165)
164 PF03444 HrcA_DNA-bdg: Winged 21.8 1.7E+02 0.0036 16.5 3.4 31 4-35 12-44 (78)
165 PF13725 tRNA_bind_2: Possible 21.8 77 0.0017 17.7 1.7 10 14-23 84-93 (101)
166 PRK13719 conjugal transfer tra 21.4 2.6E+02 0.0057 18.7 4.4 30 4-35 150-179 (217)
167 PRK12533 RNA polymerase sigma 21.2 2.4E+02 0.0052 18.1 4.2 32 3-35 140-171 (216)
168 PF05263 DUF722: Protein of un 20.9 88 0.0019 19.2 1.9 22 2-23 86-109 (130)
169 PF07750 GcrA: GcrA cell cycle 20.4 1.4E+02 0.003 18.8 2.8 31 4-35 10-40 (162)
170 PRK15328 invasion protein IagB 20.2 2.4E+02 0.0052 17.7 4.4 32 4-35 98-131 (160)
171 PRK09413 IS2 repressor TnpA; R 20.2 73 0.0016 18.7 1.4 23 4-26 96-119 (121)
172 COG4707 Uncharacterized protei 20.1 16 0.00034 21.8 -1.5 12 12-23 78-89 (107)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.77 E-value=4.1e-19 Score=117.29 Aligned_cols=52 Identities=50% Similarity=0.786 Sum_probs=47.8
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhhCCCCCCCC
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEEGGLMVPMK 54 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~~~~~~~~~ 54 (67)
||++|+++|..+||+|+.||++|||||||+|||+| ++.+++++.... ..+..
T Consensus 69 Ee~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~W-nt~lkkkl~~~~-~~~~~ 120 (238)
T KOG0048|consen 69 EEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHW-NTHLKKKLLKMG-IDPST 120 (238)
T ss_pred HHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHH-HHHHHHHHHHcC-CCCCc
Confidence 79999999999999999999999999999999999 999999998876 44443
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.68 E-value=6.3e-17 Score=107.87 Aligned_cols=54 Identities=46% Similarity=0.817 Sum_probs=48.9
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhhCCCCCCCCCC
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEEGGLMVPMKKN 56 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~ 56 (67)
||++|+++|.++|++|+.||++|||||+++||||| ++.+++++...+ ++|.+..
T Consensus 85 ED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRW-ns~LrK~l~r~~-i~p~~~k 138 (249)
T PLN03212 85 EEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYW-NTHLRKKLLRQG-IDPQTHK 138 (249)
T ss_pred HHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHH-HHHHhHHHHhcC-CCCCCCC
Confidence 79999999999999999999999999999999999 999999988877 6655433
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.61 E-value=1e-15 Score=108.57 Aligned_cols=52 Identities=50% Similarity=0.788 Sum_probs=47.3
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhhCCCCCCCC
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEEGGLMVPMK 54 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~~~~~~~~~ 54 (67)
||++|+++|.++|++|+.||++|||||+++||||| +..++++++..+ +++..
T Consensus 74 ED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRW-nslLKKklr~~~-I~p~t 125 (459)
T PLN03091 74 EENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLW-NSCLKKKLRQRG-IDPNT 125 (459)
T ss_pred HHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHH-HHHHHHHHHHcC-CCCCC
Confidence 79999999999999999999999999999999999 999999988776 55443
No 4
>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=99.52 E-value=2.8e-14 Score=76.35 Aligned_cols=56 Identities=30% Similarity=0.436 Sum_probs=44.3
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhhCCCCCCCCCCHHHHHHH
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEEGGLMVPMKKNLERDLRI 63 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 63 (67)
||++|+++|..+|+.|..||..|+.||+.+|++|| ...+++. ....+++.++|..|
T Consensus 5 Ed~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~-~~~l~~~------~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 5 EDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRW-RNHLRPK------ISRGPWTKEEDQRL 60 (60)
T ss_dssp HHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHH-HHTTSTT------STSSSSSHHHHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHH-HHHCccc------ccCCCcCHHHHhcC
Confidence 79999999999999999999999669999999999 7767655 33444777776543
No 5
>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=99.37 E-value=6.2e-13 Score=68.71 Aligned_cols=38 Identities=26% Similarity=0.468 Sum_probs=35.8
Q ss_pred ChHHHHHHHHhcCCc-HHHHHhhCC-CCChhhHHHHHHHhh
Q 039547 1 EDRLICRLFAISESR-WSVIAAHLP-GRTDNETNNYYKNTK 39 (67)
Q Consensus 1 Ed~ll~~~~~~~G~k-W~~Ia~~lp-gRt~~~vknrw~~~~ 39 (67)
||++|++++.++|.. |..||..|| |||+.+|++|| +.+
T Consensus 8 E~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~-~~~ 47 (48)
T PF00249_consen 8 EDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRY-QNL 47 (48)
T ss_dssp HHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHH-HHH
T ss_pred HHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHH-Hhh
Confidence 789999999999988 999999999 99999999999 654
No 6
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.34 E-value=1.3e-12 Score=87.31 Aligned_cols=59 Identities=15% Similarity=0.274 Sum_probs=51.2
Q ss_pred ChHHHHHHHHhcC-CcHHHHHhhC-CCCChhhHHHHHHHhhhhhhhhhCCCCCCCCCCHHHHHHHHhc
Q 039547 1 EDRLICRLFAISE-SRWSVIAAHL-PGRTDNETNNYYKNTKLKRKHEEGGLMVPMKKNLERDLRIVKN 66 (67)
Q Consensus 1 Ed~ll~~~~~~~G-~kW~~Ia~~l-pgRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 (67)
||++|+++++++| ++|..||+.+ +|||++||+.|| ..+|++.+.+.. ++.++|..++..
T Consensus 32 EDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW-~N~L~P~I~kgp------WT~EED~lLlel 92 (249)
T PLN03212 32 EDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRW-MNYLRPSVKRGG------ITSDEEDLILRL 92 (249)
T ss_pred HHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHH-HHhhchhcccCC------CChHHHHHHHHH
Confidence 8999999999999 5899999998 699999999999 999999977766 667777666554
No 7
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.28 E-value=2.5e-12 Score=85.07 Aligned_cols=60 Identities=17% Similarity=0.104 Sum_probs=54.2
Q ss_pred ChHHHHHHHHhcCC-cHHHHHhhCC-CCChhhHHHHHHHhhhhhhhhhCCCCCCCCCCHHHHHHHHhcC
Q 039547 1 EDRLICRLFAISES-RWSVIAAHLP-GRTDNETNNYYKNTKLKRKHEEGGLMVPMKKNLERDLRIVKNH 67 (67)
Q Consensus 1 Ed~ll~~~~~~~G~-kW~~Ia~~lp-gRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 (67)
||++|++++..+|. .|..||+.++ ||++.+|+-|| .+||++.+++.. .+.+++..++.+|
T Consensus 16 ED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW-~NyLrP~ikrg~------fT~eEe~~Ii~lH 77 (238)
T KOG0048|consen 16 EDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRW-TNYLRPDLKRGN------FSDEEEDLIIKLH 77 (238)
T ss_pred HHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHh-hcccCCCccCCC------CCHHHHHHHHHHH
Confidence 89999999999996 5999999999 99999999999 999999988888 6777777777665
No 8
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.26 E-value=8.3e-12 Score=62.69 Aligned_cols=39 Identities=36% Similarity=0.606 Sum_probs=36.3
Q ss_pred ChHHHHHHHHhcC-CcHHHHHhhCCCCChhhHHHHHHHhhh
Q 039547 1 EDRLICRLFAISE-SRWSVIAAHLPGRTDNETNNYYKNTKL 40 (67)
Q Consensus 1 Ed~ll~~~~~~~G-~kW~~Ia~~lpgRt~~~vknrw~~~~l 40 (67)
||.+|+.++..+| ..|..||..||+||+.+|+++| +..+
T Consensus 8 E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~-~~~~ 47 (49)
T smart00717 8 EDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERW-NNLL 47 (49)
T ss_pred HHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHH-HHHc
Confidence 7899999999999 9999999999999999999999 6544
No 9
>PLN03091 hypothetical protein; Provisional
Probab=99.20 E-value=1.8e-11 Score=87.15 Aligned_cols=60 Identities=17% Similarity=0.216 Sum_probs=52.3
Q ss_pred ChHHHHHHHHhcCC-cHHHHHhhC-CCCChhhHHHHHHHhhhhhhhhhCCCCCCCCCCHHHHHHHHhcC
Q 039547 1 EDRLICRLFAISES-RWSVIAAHL-PGRTDNETNNYYKNTKLKRKHEEGGLMVPMKKNLERDLRIVKNH 67 (67)
Q Consensus 1 Ed~ll~~~~~~~G~-kW~~Ia~~l-pgRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~ 67 (67)
||++|++++.+||. .|..||+.+ +|||+++|+.|| ..+|.+.+.+.. ++.++|..++..|
T Consensus 21 EDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW-~NyLdP~IkKgp------WT~EED~lLLeL~ 82 (459)
T PLN03091 21 EDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRW-INYLRPDLKRGT------FSQQEENLIIELH 82 (459)
T ss_pred HHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHH-HhccCCcccCCC------CCHHHHHHHHHHH
Confidence 89999999999995 799999988 599999999999 999999876665 8888887777643
No 10
>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=99.18 E-value=4e-11 Score=59.39 Aligned_cols=37 Identities=30% Similarity=0.536 Sum_probs=35.0
Q ss_pred ChHHHHHHHHhcC-CcHHHHHhhCCCCChhhHHHHHHHh
Q 039547 1 EDRLICRLFAISE-SRWSVIAAHLPGRTDNETNNYYKNT 38 (67)
Q Consensus 1 Ed~ll~~~~~~~G-~kW~~Ia~~lpgRt~~~vknrw~~~ 38 (67)
||.+|+.++..+| ..|..||..||+||+.+|+++| +.
T Consensus 6 E~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~-~~ 43 (45)
T cd00167 6 EDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERW-RN 43 (45)
T ss_pred HHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHH-HH
Confidence 7899999999999 8999999999999999999999 54
No 11
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.29 E-value=1.1e-06 Score=65.89 Aligned_cols=58 Identities=21% Similarity=0.379 Sum_probs=48.0
Q ss_pred ChHHHHHHHHhcCCc-HHHHHhhCCCCChhhHHHHHHHhhhhhhhhhCCCCCCCCCCHHHHHHHHh
Q 039547 1 EDRLICRLFAISESR-WSVIAAHLPGRTDNETNNYYKNTKLKRKHEEGGLMVPMKKNLERDLRIVK 65 (67)
Q Consensus 1 Ed~ll~~~~~~~G~k-W~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (67)
||.+|+..+.+||.+ |..|-..+|||++.||+.|| ...|....+... |+..+|-+++.
T Consensus 367 ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY-~nvL~~s~K~~r------W~l~edeqL~~ 425 (939)
T KOG0049|consen 367 EDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERY-TNVLNRSAKVER------WTLVEDEQLLY 425 (939)
T ss_pred HHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHH-HHHHHHhhccCc------eeecchHHHHH
Confidence 799999999999975 99999999999999999999 777777766655 66665555543
No 12
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.24 E-value=1.5e-06 Score=63.50 Aligned_cols=58 Identities=21% Similarity=0.271 Sum_probs=50.7
Q ss_pred ChHHHHHHHHhcC-CcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhhCCCCCCCCCCHHHHHHHHh
Q 039547 1 EDRLICRLFAISE-SRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEEGGLMVPMKKNLERDLRIVK 65 (67)
Q Consensus 1 Ed~ll~~~~~~~G-~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (67)
||++|-..+..|| |+|+.|++.++-.|..+|++|| +.++.+.+.... ++-+.|.+++.
T Consensus 14 Edeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw-~e~ldp~i~~te------ws~eederlLh 72 (617)
T KOG0050|consen 14 EDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARW-EEWLDPAIKKTE------WSREEDERLLH 72 (617)
T ss_pred HHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHH-HHHhCHHHhhhh------hhhhHHHHHHH
Confidence 7899999999999 6899999999999999999999 999999988777 66666666654
No 13
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.19 E-value=1.7e-06 Score=63.01 Aligned_cols=58 Identities=22% Similarity=0.330 Sum_probs=49.7
Q ss_pred ChHHHHHHHHhcC-CcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhhCCCCCCCCCCHHHHHHHHh
Q 039547 1 EDRLICRLFAISE-SRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEEGGLMVPMKKNLERDLRIVK 65 (67)
Q Consensus 1 Ed~ll~~~~~~~G-~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (67)
||..+..++..+| +.|+.||..|.-+++++|++|| +.++.+.+.... ++.++|-.++.
T Consensus 27 EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw-~~~lnp~lk~~~------~~~eed~~li~ 85 (512)
T COG5147 27 EDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRW-NNHLNPQLKKKN------WSEEEDEQLID 85 (512)
T ss_pred chhHHHHHHhhcccccHHHHHHHhcccccccccchh-hhhhchhccccc------ccHHHHHHHHH
Confidence 8999999999999 5799999999889999999999 999999977766 56666555543
No 14
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=97.80 E-value=1.9e-05 Score=57.68 Aligned_cols=44 Identities=25% Similarity=0.276 Sum_probs=39.3
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhh
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHE 45 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~ 45 (67)
||..|+.++.++|++|+.||..+||||+.+|.++| ...+.....
T Consensus 79 ed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery-~~~~~~~~s 122 (512)
T COG5147 79 EDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERY-VNTLEDLSS 122 (512)
T ss_pred HHHHHHHHHHhcCchhhhhccccCccchHHHHHHH-HHHhhhhhc
Confidence 68999999999999999999999999999999999 866655433
No 15
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=97.40 E-value=0.00036 Score=51.94 Aligned_cols=59 Identities=17% Similarity=0.260 Sum_probs=43.5
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhhCCCCCCCCCCHHHHHHHHh
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEEGGLMVPMKKNLERDLRIVK 65 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 65 (67)
|++.|..++.++|+.|..|++.| ||.+.+|+.+| ..+.+..- ..+...|+.++.-.++.
T Consensus 391 e~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~w-r~~~~~g~----~~~r~~Ws~eEe~~Llk 449 (607)
T KOG0051|consen 391 EEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRW-RQYVKCGS----KRNRGAWSIEEEEKLLK 449 (607)
T ss_pred hHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHH-HHhhcccc----ccccCcchHHHHHHHHH
Confidence 57889999999999999999999 99999999999 43332221 02445566666555543
No 16
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=96.46 E-value=0.0027 Score=46.98 Aligned_cols=41 Identities=29% Similarity=0.477 Sum_probs=36.7
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhh
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRK 43 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~ 43 (67)
||..|+.+...+.+.|..||..| |||+++|-.|| +..+--.
T Consensus 66 ederlLhlakl~p~qwrtIa~i~-gr~~~qc~eRy-~~ll~~~ 106 (617)
T KOG0050|consen 66 EDERLLHLAKLEPTQWRTIADIM-GRTSQQCLERY-NNLLDVY 106 (617)
T ss_pred HHHHHHHHHHhcCCccchHHHHh-hhhHHHHHHHH-HHHHHHH
Confidence 78999999999999999999998 99999999999 7665443
No 17
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.27 E-value=0.0065 Score=43.86 Aligned_cols=35 Identities=26% Similarity=0.422 Sum_probs=32.7
Q ss_pred ChHHHHHHHHhcC-CcHHHHHhhCCCCChhhHHHHH
Q 039547 1 EDRLICRLFAISE-SRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 1 Ed~ll~~~~~~~G-~kW~~Ia~~lpgRt~~~vknrw 35 (67)
|+-+|++....|| .+|..||.++..+|.-.|+.+|
T Consensus 79 EEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy 114 (438)
T KOG0457|consen 79 EEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHY 114 (438)
T ss_pred HHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHH
Confidence 5678999999999 7999999999999999999999
No 18
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.23 E-value=0.0054 Score=46.72 Aligned_cols=59 Identities=22% Similarity=0.386 Sum_probs=50.4
Q ss_pred ChHHHHHHHHhcCC----cHHHHHhhCCCCChhhHHHHHHHhhhhhhhhhCCCCCCCCCCHHHHHHHHhc
Q 039547 1 EDRLICRLFAISES----RWSVIAAHLPGRTDNETNNYYKNTKLKRKHEEGGLMVPMKKNLERDLRIVKN 66 (67)
Q Consensus 1 Ed~ll~~~~~~~G~----kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 66 (67)
||..|+.++....- .|..|-.+||||+..++=-|| ...|-+.++... +.+++|+.++.|
T Consensus 312 ed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~-~~~LdPsikhg~------wt~~ED~~L~~A 374 (939)
T KOG0049|consen 312 EDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRF-SHTLDPSVKHGR------WTDQEDVLLVCA 374 (939)
T ss_pred hhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhh-eeccCccccCCC------CCCHHHHHHHHH
Confidence 68899999988762 599999999999999999999 877888766666 788888888765
No 19
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.36 E-value=0.012 Score=32.76 Aligned_cols=31 Identities=32% Similarity=0.467 Sum_probs=20.9
Q ss_pred cHHHHHhhC----CCCChhhHHHHHHHhhhhhhhhhC
Q 039547 15 RWSVIAAHL----PGRTDNETNNYYKNTKLKRKHEEG 47 (67)
Q Consensus 15 kW~~Ia~~l----pgRt~~~vknrw~~~~l~~~~~~~ 47 (67)
-|..||..| ..||+.+|+++| ++ |++.....
T Consensus 36 ~w~~Ia~~l~~~G~~rt~~qc~~Kw-~~-L~~~Yk~~ 70 (90)
T PF13837_consen 36 VWKEIAEELAEHGYNRTPEQCRNKW-KN-LKKKYKKI 70 (90)
T ss_dssp HHHHHHHHHHHHC----HHHHHHHH-HH-HHHHHHCS
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHH-HH-HHHHHHHH
Confidence 399999988 479999999999 55 55555443
No 20
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.03 E-value=0.066 Score=37.99 Aligned_cols=40 Identities=20% Similarity=0.282 Sum_probs=34.8
Q ss_pred ChHHHHHHHHhcC-CcHHHHHhhCCCCChhhHHHHHHHhhh
Q 039547 1 EDRLICRLFAISE-SRWSVIAAHLPGRTDNETNNYYKNTKL 40 (67)
Q Consensus 1 Ed~ll~~~~~~~G-~kW~~Ia~~lpgRt~~~vknrw~~~~l 40 (67)
|+-+|++.-..+| ..|..||.++..|+...||.+|...++
T Consensus 70 EEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 70 EELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred HHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 6778899999999 799999999999999999999944444
No 21
>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=94.25 E-value=0.11 Score=27.66 Aligned_cols=35 Identities=9% Similarity=0.076 Sum_probs=29.1
Q ss_pred ChHHHHHHHHhcCC-cH---HHHHhhCC-CC-ChhhHHHHH
Q 039547 1 EDRLICRLFAISES-RW---SVIAAHLP-GR-TDNETNNYY 35 (67)
Q Consensus 1 Ed~ll~~~~~~~G~-kW---~~Ia~~lp-gR-t~~~vknrw 35 (67)
|....++.+..+|. .| ..|+..|. .+ |..+|+.+.
T Consensus 10 eh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~ 50 (57)
T TIGR01557 10 LHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHL 50 (57)
T ss_pred HHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHH
Confidence 34677889999996 99 99999884 34 999999988
No 22
>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=94.20 E-value=0.09 Score=28.74 Aligned_cols=41 Identities=15% Similarity=0.286 Sum_probs=28.2
Q ss_pred ChHHHHHHHHhc--------CCc-HHHHHhhCC-CCChhhHHHHHHHhhhhh
Q 039547 1 EDRLICRLFAIS--------ESR-WSVIAAHLP-GRTDNETNNYYKNTKLKR 42 (67)
Q Consensus 1 Ed~ll~~~~~~~--------G~k-W~~Ia~~lp-gRt~~~vknrw~~~~l~~ 42 (67)
||.+|+..+.++ ||+ |..++..-| .+|-.+.++|| .-.++.
T Consensus 9 dD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry-~K~L~~ 59 (65)
T PF08914_consen 9 DDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRY-LKHLRG 59 (65)
T ss_dssp HHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHH-HHHT--
T ss_pred HHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHH-HHHHhc
Confidence 688899888543 333 999999888 99999999999 544443
No 23
>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=93.29 E-value=0.13 Score=32.89 Aligned_cols=29 Identities=21% Similarity=0.349 Sum_probs=24.0
Q ss_pred HHHHHhhCCCCChhhHHHHHHHhhhhhhhhh
Q 039547 16 WSVIAAHLPGRTDNETNNYYKNTKLKRKHEE 46 (67)
Q Consensus 16 W~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~ 46 (67)
...++..| +||+-+|.=|| |+++++++..
T Consensus 33 FeEvg~~L-~RTsAACGFRW-Ns~VRkqY~~ 61 (161)
T TIGR02894 33 FEEVGRAL-NRTAAACGFRW-NAYVRKQYEE 61 (161)
T ss_pred HHHHHHHH-cccHHHhcchH-HHHHHHHHHH
Confidence 45677887 99999999999 9999976543
No 24
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=92.81 E-value=0.3 Score=24.68 Aligned_cols=33 Identities=21% Similarity=0.216 Sum_probs=25.5
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.++-..|-.|..||..+ |.|.+.|+++.
T Consensus 15 ~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l 47 (54)
T PF08281_consen 15 QREIFLLRYFQGMSYAEIAEIL-GISESTVKRRL 47 (54)
T ss_dssp HHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHH
Confidence 4567888888999999999999 89999999987
No 25
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=92.42 E-value=0.2 Score=37.08 Aligned_cols=35 Identities=14% Similarity=0.335 Sum_probs=33.0
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
|..+|++.+..||-.|..||.+...||-.+|=-+|
T Consensus 260 E~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kF 294 (506)
T KOG1279|consen 260 ETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKF 294 (506)
T ss_pred HHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHH
Confidence 56789999999999999999999999999999988
No 26
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=92.19 E-value=0.18 Score=37.20 Aligned_cols=35 Identities=17% Similarity=0.264 Sum_probs=32.6
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
|..+|++.+.+||-.|..||+++..+|.-+|=-+|
T Consensus 286 E~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~F 320 (531)
T COG5259 286 ELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHF 320 (531)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHH
Confidence 45689999999999999999999999999999998
No 27
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=89.23 E-value=0.69 Score=25.15 Aligned_cols=20 Identities=25% Similarity=0.441 Sum_probs=17.9
Q ss_pred HHHHHhhC-----CCCChhhHHHHH
Q 039547 16 WSVIAAHL-----PGRTDNETNNYY 35 (67)
Q Consensus 16 W~~Ia~~l-----pgRt~~~vknrw 35 (67)
|..|+..| +.||..+++..|
T Consensus 41 W~~I~~~lN~~~~~~Rs~~~lkkkW 65 (78)
T PF13873_consen 41 WEEIAEELNALGPGKRSWKQLKKKW 65 (78)
T ss_pred HHHHHHHHHhcCCCCCCHHHHHHHH
Confidence 99999877 369999999999
No 28
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=89.05 E-value=0.6 Score=30.10 Aligned_cols=36 Identities=14% Similarity=0.211 Sum_probs=24.6
Q ss_pred HHHHHhcCCcH---HHHHhhCCCCChhhHHHHHHHhhhhhh
Q 039547 6 CRLFAISESRW---SVIAAHLPGRTDNETNNYYKNTKLKRK 43 (67)
Q Consensus 6 ~~~~~~~G~kW---~~Ia~~lpgRt~~~vknrw~~~~l~~~ 43 (67)
++...+-|.+- ...+..| +||.-+|.-|| |+.++++
T Consensus 21 l~~i~eg~tql~afe~~g~~L-~rt~aac~fRw-Ns~vrk~ 59 (170)
T PRK13923 21 LRHIREGGTQLKAFEEVGDAL-KRTAAACGFRW-NSVVRKQ 59 (170)
T ss_pred HHHHhccchHHHHHHHHHHHH-hhhHHHHHhHH-HHHHHHH
Confidence 34444444443 3455666 89999999999 9988864
No 29
>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=84.79 E-value=1.9 Score=24.50 Aligned_cols=31 Identities=19% Similarity=0.350 Sum_probs=25.4
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
|+-|..+...+|..|..+|.+| |=|...|..
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~~ 32 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIYR 32 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 4567788999999999999999 777776654
No 30
>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=83.90 E-value=3.2 Score=24.41 Aligned_cols=33 Identities=21% Similarity=0.146 Sum_probs=27.2
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.++-..|-.+..||..+ |.|...|+++.
T Consensus 118 ~r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~ 150 (161)
T TIGR02985 118 CRKIFILSRFEGKSYKEIAEEL-GISVKTVEYHI 150 (161)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 3456667556788999999998 89999999998
No 31
>smart00595 MADF subfamily of SANT domain.
Probab=81.34 E-value=2.3 Score=23.38 Aligned_cols=21 Identities=24% Similarity=0.400 Sum_probs=18.4
Q ss_pred HHHHHhhCCCCChhhHHHHHHHh
Q 039547 16 WSVIAAHLPGRTDNETNNYYKNT 38 (67)
Q Consensus 16 W~~Ia~~lpgRt~~~vknrw~~~ 38 (67)
|..||..|.. |...|+.+| ++
T Consensus 30 W~~Ia~~l~~-~~~~~~~kw-~~ 50 (89)
T smart00595 30 WEEIAEELGL-SVEECKKRW-KN 50 (89)
T ss_pred HHHHHHHHCc-CHHHHHHHH-HH
Confidence 9999999954 999999999 54
No 32
>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=79.74 E-value=4.9 Score=19.87 Aligned_cols=37 Identities=22% Similarity=0.244 Sum_probs=26.9
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhh
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKL 40 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l 40 (67)
+..|+.++-.-|-.+..||..| |-|...|+.+. ...+
T Consensus 9 er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~-~~al 45 (50)
T PF04545_consen 9 EREVIRLRYFEGLTLEEIAERL-GISRSTVRRIL-KRAL 45 (50)
T ss_dssp HHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHH-HHHH
T ss_pred HHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHH-HHHH
Confidence 4456666666667899999999 88999999887 4433
No 33
>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=79.72 E-value=3.1 Score=23.15 Aligned_cols=31 Identities=19% Similarity=0.402 Sum_probs=23.7
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
|..|..+...+|..|..+|..| |=+...|..
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~~ 34 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDIDL 34 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHHH
Confidence 3456667788999999999999 677666554
No 34
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=79.38 E-value=6.2 Score=24.14 Aligned_cols=33 Identities=15% Similarity=0.197 Sum_probs=28.3
Q ss_pred hHHHHHHHHhcC-CcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISE-SRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G-~kW~~Ia~~lpgRt~~~vknrw 35 (67)
|..|+.+-..-| ..|+.||+.+ |-|...|.+|+
T Consensus 11 D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri 44 (153)
T PRK11179 11 DRGILEALMENARTPYAELAKQF-GVSPGTIHVRV 44 (153)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHH
Confidence 566777777777 4799999999 99999999999
No 35
>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=79.32 E-value=2.7 Score=22.42 Aligned_cols=22 Identities=18% Similarity=0.380 Sum_probs=18.4
Q ss_pred HHHHHhhCCC-CChhhHHHHHHHh
Q 039547 16 WSVIAAHLPG-RTDNETNNYYKNT 38 (67)
Q Consensus 16 W~~Ia~~lpg-Rt~~~vknrw~~~ 38 (67)
|..||..|.+ -+.+.|+.+| ++
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w-~~ 51 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRW-KN 51 (85)
T ss_pred HHHHHHHHccchhHHHHHHHH-HH
Confidence 9999999953 5788899999 54
No 36
>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=79.08 E-value=4.9 Score=22.77 Aligned_cols=32 Identities=19% Similarity=0.211 Sum_probs=24.5
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNY 34 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknr 34 (67)
|..|..+-..+|..|..+|..| |=+...|.+.
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~i 35 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQI 35 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHHH
Confidence 4456677788999999999999 6776665553
No 37
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=78.01 E-value=3.3 Score=21.52 Aligned_cols=33 Identities=12% Similarity=0.192 Sum_probs=23.6
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
|+--+....++|-+-..||+.+ ||+-+.|++.-
T Consensus 9 Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 9 EQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 4455667788999999999999 99999998865
No 38
>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=76.49 E-value=7.1 Score=19.18 Aligned_cols=33 Identities=24% Similarity=0.378 Sum_probs=25.2
Q ss_pred hHHHHHHHHhcCC-cHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISES-RWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~-kW~~Ia~~lpgRt~~~vknrw 35 (67)
|..|+.....-|. .|..||..+ |=|...|.+|+
T Consensus 5 D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri 38 (42)
T PF13404_consen 5 DRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRI 38 (42)
T ss_dssp HHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHH
Confidence 5667777777774 699999998 89999999998
No 39
>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=75.46 E-value=3.5 Score=24.90 Aligned_cols=40 Identities=28% Similarity=0.393 Sum_probs=31.1
Q ss_pred ChHHHHHHHHhcCC----cHHHHHhh------------CCCCChhhHHHHHHHhhhh
Q 039547 1 EDRLICRLFAISES----RWSVIAAH------------LPGRTDNETNNYYKNTKLK 41 (67)
Q Consensus 1 Ed~ll~~~~~~~G~----kW~~Ia~~------------lpgRt~~~vknrw~~~~l~ 41 (67)
||..|+-....+|- .|..|... |..||+..+..|. ++.++
T Consensus 56 EDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~-~tLi~ 111 (118)
T PF09111_consen 56 EDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRC-NTLIK 111 (118)
T ss_dssp HHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHH-HHHHH
T ss_pred HHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHH-HHHHH
Confidence 68888889999996 78777653 3689999999999 77654
No 40
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=75.35 E-value=6.8 Score=24.29 Aligned_cols=33 Identities=12% Similarity=0.048 Sum_probs=27.9
Q ss_pred hHHHHHHHHhcCC-cHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISES-RWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~-kW~~Ia~~lpgRt~~~vknrw 35 (67)
|..|+.+-..-|. .|+.||+.+ |=|...|.+|+
T Consensus 16 D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri 49 (164)
T PRK11169 16 DRNILNELQKDGRISNVELSKRV-GLSPTPCLERV 49 (164)
T ss_pred HHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHH
Confidence 5667777666664 799999999 99999999999
No 41
>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=73.10 E-value=6.3 Score=22.17 Aligned_cols=30 Identities=13% Similarity=0.228 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
..|-.+-..+|..|..+|..| |=|+..|.+
T Consensus 5 ~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 5 ERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 345566688999999999999 788888777
No 42
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=72.80 E-value=6.3 Score=19.39 Aligned_cols=32 Identities=19% Similarity=0.158 Sum_probs=17.9
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNY 34 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknr 34 (67)
|...|...-.-|-.=..||+.| ||+...|.+.
T Consensus 9 eR~~I~~l~~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 9 ERNQIEALLEQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp ---HHHHHHCS---HHHHHHHT-T--HHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CcCcHHHHHH
Confidence 3344555556777778899999 8998888764
No 43
>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=72.34 E-value=5.8 Score=21.66 Aligned_cols=29 Identities=14% Similarity=0.329 Sum_probs=20.1
Q ss_pred HHHHHHHh-cCCcHHHHHhhCCCCChhhHHH
Q 039547 4 LICRLFAI-SESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 4 ll~~~~~~-~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
.+..+... .|+.|..+|..|+ -+++.|..
T Consensus 7 ~~~~l~~~~~g~~W~~la~~Lg-~~~~~i~~ 36 (88)
T smart00005 7 KLAKLLDHPLGLDWRELARKLG-LSEADIDQ 36 (88)
T ss_pred HHHHHHcCccchHHHHHHHHcC-CCHHHHHH
Confidence 34455556 8999999999994 45555443
No 44
>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=70.64 E-value=8.7 Score=21.60 Aligned_cols=28 Identities=25% Similarity=0.379 Sum_probs=21.9
Q ss_pred HHHHHHhcCCcHHHHHhhCCCCChhhHHH
Q 039547 5 ICRLFAISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 5 l~~~~~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
|-.+-..+|..|..+|..| |-++..|..
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI~~ 37 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEIRA 37 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 3346678899999999999 777777654
No 45
>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=70.05 E-value=12 Score=21.20 Aligned_cols=32 Identities=19% Similarity=0.136 Sum_probs=25.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.+..||..+ |=|...|+++.
T Consensus 116 ~~ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~ 147 (158)
T TIGR02937 116 REVLVLRYLEGLSYKEIAEIL-GISVGTVKRRL 147 (158)
T ss_pred HHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345555555788999999998 77999999987
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=69.30 E-value=8.7 Score=26.49 Aligned_cols=26 Identities=12% Similarity=0.216 Sum_probs=20.2
Q ss_pred CcHHHHHhhC----CCCChhhHHHHHHHhhh
Q 039547 14 SRWSVIAAHL----PGRTDNETNNYYKNTKL 40 (67)
Q Consensus 14 ~kW~~Ia~~l----pgRt~~~vknrw~~~~l 40 (67)
.-|..||+.+ .-||+.+|+++| .+..
T Consensus 84 ~~We~va~k~~~~g~~rs~~qck~K~-~nl~ 113 (345)
T KOG4282|consen 84 PLWEEVARKMAELGYPRSPKQCKAKI-ENLK 113 (345)
T ss_pred cHHHHHHHHHHHhCCCCCHHHHHHHH-HHHH
Confidence 3499999866 359999999999 5433
No 47
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=68.96 E-value=6.8 Score=21.66 Aligned_cols=20 Identities=30% Similarity=0.624 Sum_probs=16.3
Q ss_pred HHHHHhhC---CC--CChhhHHHHH
Q 039547 16 WSVIAAHL---PG--RTDNETNNYY 35 (67)
Q Consensus 16 W~~Ia~~l---pg--Rt~~~vknrw 35 (67)
|..|+..| +| -|..+|+|+|
T Consensus 34 w~~i~~~~~~~~~~~~t~~qlknk~ 58 (96)
T PF12776_consen 34 WNNIAEEFNEKTGLNYTKKQLKNKW 58 (96)
T ss_pred HHHHHHHHHHHhCCcccHHHHHHHH
Confidence 99999887 33 4778999999
No 48
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=68.90 E-value=12 Score=22.42 Aligned_cols=32 Identities=19% Similarity=0.130 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.+..||..| |.|...|+++.
T Consensus 134 r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l 165 (182)
T PRK09652 134 RTAITLREIEGLSYEEIAEIM-GCPIGTVRSRI 165 (182)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 445666666788999999999 89999999987
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=68.69 E-value=6.9 Score=28.63 Aligned_cols=31 Identities=16% Similarity=0.408 Sum_probs=27.1
Q ss_pred HHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 5 ICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 5 l~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.......+|.-.+.|+..||.|.-.+||-.|
T Consensus 376 FYKALs~wGtdF~LIs~lfP~R~RkqIKaKf 406 (507)
T COG5118 376 FYKALSIWGTDFSLISSLFPNRERKQIKAKF 406 (507)
T ss_pred HHHHHHHhcchHHHHHHhcCchhHHHHHHHH
Confidence 3455567888999999999999999999999
No 50
>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=68.62 E-value=9.6 Score=21.43 Aligned_cols=30 Identities=13% Similarity=0.266 Sum_probs=22.6
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNY 34 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknr 34 (67)
.+--+...+|..|..+|+.| |=|+++|...
T Consensus 4 ~f~~i~~~lG~~Wk~laR~L-Glse~~Id~i 33 (86)
T cd08306 4 AFDVICENVGRDWRKLARKL-GLSETKIESI 33 (86)
T ss_pred HHHHHHHHHhhhHHHHHHHc-CCCHHHHHHH
Confidence 34445577899999999999 7777776653
No 51
>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=68.36 E-value=8.7 Score=21.74 Aligned_cols=29 Identities=24% Similarity=0.306 Sum_probs=23.5
Q ss_pred HHHHHHhcCCcHHHHHhhCCCCChhhHHHH
Q 039547 5 ICRLFAISESRWSVIAAHLPGRTDNETNNY 34 (67)
Q Consensus 5 l~~~~~~~G~kW~~Ia~~lpgRt~~~vknr 34 (67)
|-.+-..+|..|..+|..| |=|++.|.+.
T Consensus 5 l~~l~~~lG~~Wk~lar~L-G~s~~eI~~i 33 (86)
T cd08777 5 LDLLRENLGKKWKRCARKL-GFTESEIEEI 33 (86)
T ss_pred HHHHHHHHHHHHHHHHHHc-CCCHHHHHHH
Confidence 3445578899999999999 8888888774
No 52
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=67.99 E-value=28 Score=23.28 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhh
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEE 46 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~ 46 (67)
..++.++...|-.-..||..| |.|...|+++. . .-++++.+
T Consensus 121 R~v~~L~~~~g~s~~EIA~~l-g~s~~tVk~~l-~-RAr~~Lr~ 161 (293)
T PRK09636 121 RAAFLLHDVFGVPFDEIASTL-GRSPAACRQLA-S-RARKHVRA 161 (293)
T ss_pred HHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH-H-HHHHHHHh
Confidence 445667777888899999999 99999999987 3 34444444
No 53
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=67.97 E-value=15 Score=22.40 Aligned_cols=33 Identities=15% Similarity=0.026 Sum_probs=26.9
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.+.-..|-.+..||..| |-|...|+++.
T Consensus 141 ~r~il~l~~~~~~s~~eIA~~l-gis~~~v~~~l 173 (187)
T PRK09641 141 YRTVIVLKYIEDLSLKEISEIL-DLPVGTVKTRI 173 (187)
T ss_pred HHHHhhhHHhhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 3455666666788999999999 99999999987
No 54
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=66.83 E-value=15 Score=21.93 Aligned_cols=32 Identities=19% Similarity=0.137 Sum_probs=26.5
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.+..||..| |-|.+.|+++.
T Consensus 131 r~i~~l~~~~~~~~~eIA~~l-gis~~tv~~~~ 162 (179)
T PRK11924 131 REVFLLRYVEGLSYREIAEIL-GVPVGTVKSRL 162 (179)
T ss_pred HHHhhHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345666666788999999999 89999999987
No 55
>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=66.36 E-value=20 Score=19.79 Aligned_cols=36 Identities=17% Similarity=0.256 Sum_probs=22.9
Q ss_pred HHHHHHhcC--------CcHHHHHhhCCCC---C--hhhHHHHHHHhhhh
Q 039547 5 ICRLFAISE--------SRWSVIAAHLPGR---T--DNETNNYYKNTKLK 41 (67)
Q Consensus 5 l~~~~~~~G--------~kW~~Ia~~lpgR---t--~~~vknrw~~~~l~ 41 (67)
|...+...| .+|..||..|.-- + +.++++.| ..+|.
T Consensus 41 Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y-~~~L~ 89 (92)
T PF01388_consen 41 LYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHY-EKYLL 89 (92)
T ss_dssp HHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHH-HHHTH
T ss_pred HHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHH-HHHhH
Confidence 444555555 3599999998321 1 35688888 66553
No 56
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=64.81 E-value=21 Score=22.35 Aligned_cols=32 Identities=19% Similarity=0.176 Sum_probs=27.7
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.+..--|=.+..||..+ |-|...|+++|
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l 172 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRL 172 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHH
Confidence 456667767788999999999 99999999999
No 57
>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=64.45 E-value=6.4 Score=21.58 Aligned_cols=18 Identities=17% Similarity=0.597 Sum_probs=14.4
Q ss_pred HHHHHHHhcCCcHHHHHh
Q 039547 4 LICRLFAISESRWSVIAA 21 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~ 21 (67)
.|.+|.+.||+.|..|..
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 467788889988999873
No 58
>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=64.19 E-value=9.9 Score=21.41 Aligned_cols=27 Identities=22% Similarity=0.322 Sum_probs=20.7
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhh
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNE 30 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~ 30 (67)
.-|..+-..+|..|..+|..| |=|+..
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~~ 29 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYRE 29 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHHH
Confidence 346678899999999999998 444444
No 59
>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=63.92 E-value=15 Score=22.42 Aligned_cols=32 Identities=13% Similarity=0.043 Sum_probs=25.6
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-|.+.|+++.
T Consensus 144 r~v~~l~~~~~~s~~EIA~~l-gis~~tv~~~l 175 (190)
T TIGR02939 144 RTAITLRELEGLSYEDIARIM-DCPVGTVRSRI 175 (190)
T ss_pred hhhhhhhhhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 345556556777899999999 88999999987
No 60
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=63.66 E-value=20 Score=22.37 Aligned_cols=33 Identities=12% Similarity=0.057 Sum_probs=28.1
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.++-..|-....||..| |-|.+.|+++.
T Consensus 139 ~r~i~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl 171 (192)
T PRK09643 139 QRAALVAVDMQGYSVADAARML-GVAEGTVKSRC 171 (192)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 3456777777888999999999 89999999998
No 61
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=62.99 E-value=25 Score=19.66 Aligned_cols=28 Identities=21% Similarity=0.297 Sum_probs=19.4
Q ss_pred CcHHHHHhhCCCC-----ChhhHHHHHHHhhhhh
Q 039547 14 SRWSVIAAHLPGR-----TDNETNNYYKNTKLKR 42 (67)
Q Consensus 14 ~kW~~Ia~~lpgR-----t~~~vknrw~~~~l~~ 42 (67)
++|..||..|.-. .+..++..| ..+|.+
T Consensus 54 ~~W~~Va~~lg~~~~~~~~~~~lk~~Y-~k~L~~ 86 (93)
T smart00501 54 KKWKEIARELGIPDTSTSAASSLRKHY-ERYLLP 86 (93)
T ss_pred CCHHHHHHHhCCCcccchHHHHHHHHH-HHHhHH
Confidence 3699999988332 356788888 665543
No 62
>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=62.48 E-value=34 Score=22.92 Aligned_cols=32 Identities=22% Similarity=0.156 Sum_probs=26.9
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++...|-....||..| |-|.+.|+++.
T Consensus 148 R~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l 179 (324)
T TIGR02960 148 RAVLLLRDVLGWRAAETAELL-GTSTASVNSAL 179 (324)
T ss_pred hhHhhhHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 446667777788899999999 99999999987
No 63
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=60.47 E-value=24 Score=21.44 Aligned_cols=32 Identities=13% Similarity=0.082 Sum_probs=25.7
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.+.-..|-....||..| |-|.+.|+++.
T Consensus 142 r~v~~l~~~~g~s~~eIA~~l-gis~~~v~~~l 173 (187)
T TIGR02948 142 RMVIVLKYMEDLSLKEISEIL-DLPVGTVKTRI 173 (187)
T ss_pred hHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 445566556678899999998 88999999987
No 64
>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=59.18 E-value=17 Score=20.58 Aligned_cols=32 Identities=13% Similarity=0.042 Sum_probs=21.7
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCCh---hhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTD---NETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~---~~vknrw 35 (67)
-.|-.+-..+|..|..+|..| |=++ +.|+.-+
T Consensus 5 ~~l~~Ia~~LG~dW~~Lar~L-~vs~~dI~~I~~e~ 39 (84)
T cd08805 5 MKMAVIREHLGLSWAELAREL-QFSVEDINRIRVEN 39 (84)
T ss_pred hHHHHHHHHhcchHHHHHHHc-CCCHHHHHHHHHhC
Confidence 345566788999999999988 4443 3444444
No 65
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=58.69 E-value=27 Score=21.63 Aligned_cols=33 Identities=18% Similarity=0.061 Sum_probs=27.5
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.+.-..|-....||..| |-|.+.|+++.
T Consensus 111 ~r~i~~l~~~~g~~~~EIA~~l-gis~~tV~~~l 143 (181)
T PRK09637 111 YAEALRLTELEGLSQKEIAEKL-GLSLSGAKSRV 143 (181)
T ss_pred HHHHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 3456667777888999999999 89999999987
No 66
>PRK04217 hypothetical protein; Provisional
Probab=58.62 E-value=27 Score=20.80 Aligned_cols=33 Identities=9% Similarity=-0.016 Sum_probs=27.4
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.++..-|-....||+.+ |-|.+.|++++
T Consensus 47 ereai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L 79 (110)
T PRK04217 47 EFEALRLVDYEGLTQEEAGKRM-GVSRGTVWRAL 79 (110)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 3456666766777899999999 99999999998
No 67
>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=58.51 E-value=26 Score=18.57 Aligned_cols=24 Identities=29% Similarity=0.440 Sum_probs=18.3
Q ss_pred HHhcCCcHHHHHhhCCCCChhhHHH
Q 039547 9 FAISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 9 ~~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
-...|+.|..+|..| |=+...|.+
T Consensus 8 ~~~~~~~Wk~La~~L-g~~~~~i~~ 31 (83)
T PF00531_consen 8 AEDLGSDWKRLARKL-GLSESEIEN 31 (83)
T ss_dssp HHSHSTCHHHHHHHT-TS-HHHHHH
T ss_pred hhcchhhHHHHHHHh-CcCHHHHHH
Confidence 456788999999999 777777665
No 68
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=57.67 E-value=19 Score=17.51 Aligned_cols=30 Identities=23% Similarity=0.224 Sum_probs=20.3
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.++.+ |-....||+.+ |-+.+.|.+.-
T Consensus 9 ~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~w~ 38 (50)
T PF13384_consen 9 QIIRLLRE-GWSIREIAKRL-GVSRSTVYRWI 38 (50)
T ss_dssp -HHHHHHH-T--HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHC-CCCHHHHHHHH-CcCHHHHHHHH
Confidence 45667777 88899999999 77777777643
No 69
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=56.23 E-value=42 Score=20.75 Aligned_cols=44 Identities=11% Similarity=-0.004 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHH---hhhhhhhhhCC
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYYKN---TKLKRKHEEGG 48 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~---~~l~~~~~~~~ 48 (67)
..++.++...|-.-..||..| |-|.+.|+++. . ..|++.+....
T Consensus 142 r~i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l-~Rar~~Lr~~l~~~~ 188 (195)
T PRK12532 142 ARVFTLKEILGFSSDEIQQMC-GISTSNYHTIM-HRARESLRQCLQIKW 188 (195)
T ss_pred HHHhhhHHHhCCCHHHHHHHH-CCCHHHHHHHH-HHHHHHHHHHHHHhh
Confidence 345556666788889999999 99999999987 4 24444444333
No 70
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=55.91 E-value=34 Score=22.60 Aligned_cols=26 Identities=12% Similarity=0.093 Sum_probs=17.6
Q ss_pred hCCCCChhhHHHHHHHhhhhhhhhhCC
Q 039547 22 HLPGRTDNETNNYYKNTKLKRKHEEGG 48 (67)
Q Consensus 22 ~lpgRt~~~vknrw~~~~l~~~~~~~~ 48 (67)
+-++||+..+.++| ....+-.+....
T Consensus 109 Fh~sRTak~L~~HW-~lmkqy~LL~DQ 134 (199)
T PF13325_consen 109 FHPSRTAKSLQDHW-RLMKQYHLLPDQ 134 (199)
T ss_pred hccccCHHHHHHHH-HHHHHhchhhcc
Confidence 34899999999999 643333444433
No 71
>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=55.87 E-value=34 Score=20.34 Aligned_cols=33 Identities=15% Similarity=0.096 Sum_probs=26.7
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.++--.|-....||..| |-+.+.|+++-
T Consensus 127 ~r~vl~l~~~~g~s~~eIA~~l-~is~~tv~~~l 159 (170)
T TIGR02952 127 QQHVIALRFGQNLPIAEVARIL-GKTEGAVKILQ 159 (170)
T ss_pred HHHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 3456667666788899999998 89999999986
No 72
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=55.75 E-value=37 Score=20.77 Aligned_cols=32 Identities=13% Similarity=-0.007 Sum_probs=27.6
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-+...|+++-
T Consensus 135 r~v~~l~~~~g~s~~EIA~~l-~is~~tV~~~l 166 (181)
T PRK12536 135 RLPIVHVKLEGLSVAETAQLT-GLSESAVKVGI 166 (181)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 446677778888999999999 99999999987
No 73
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=54.97 E-value=36 Score=20.93 Aligned_cols=32 Identities=16% Similarity=0.158 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-|.++|+++.
T Consensus 137 r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l 168 (189)
T PRK12515 137 REIIDLVYYHEKSVEEVGEIV-GIPESTVKTRM 168 (189)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 456667777888899999999 88999999998
No 74
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=54.17 E-value=19 Score=19.08 Aligned_cols=27 Identities=26% Similarity=0.425 Sum_probs=19.5
Q ss_pred HHHHHhcCCcHHHHHhhCCCCChhhHHH
Q 039547 6 CRLFAISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 6 ~~~~~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
..+-..+|+.|..+|..+ |=+...|..
T Consensus 3 ~~ia~~lg~~W~~la~~L-gl~~~~I~~ 29 (79)
T cd01670 3 DKLAKKLGKDWKKLARKL-GLSDGEIDQ 29 (79)
T ss_pred HHHHHHHhhHHHHHHHHh-CCCHHHHHH
Confidence 345678899999999999 455555544
No 75
>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=54.12 E-value=38 Score=21.06 Aligned_cols=32 Identities=6% Similarity=-0.020 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-.-|-....||..| |-|.+.|+.+.
T Consensus 137 r~v~~l~~~~g~s~~EIA~~l-gis~~tvk~rl 168 (188)
T TIGR02943 137 ARVFMMREVLGFESDEICQEL-EISTSNCHVLL 168 (188)
T ss_pred HHHHHHHHHhCCCHHHHHHHh-CCCHHHHHHHH
Confidence 345666666788899999999 99999999987
No 76
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=54.10 E-value=35 Score=20.67 Aligned_cols=33 Identities=18% Similarity=0.189 Sum_probs=27.7
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.++-..|-....||..| |-+.+.|+++-
T Consensus 124 ~r~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l 156 (172)
T PRK12523 124 ARAAFLYNRLDGMGHAEIAERL-GVSVSRVRQYL 156 (172)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 3456677777788999999999 99999999987
No 77
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=54.02 E-value=48 Score=22.46 Aligned_cols=41 Identities=15% Similarity=0.083 Sum_probs=29.8
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhh
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEE 46 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~ 46 (67)
..++.++...|-.-..||..| |-|.+.|+++. . ..++++++
T Consensus 159 R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l-~-RAr~~Lr~ 199 (339)
T PRK08241 159 RAVLILRDVLGWSAAEVAELL-DTSVAAVNSAL-Q-RARATLAE 199 (339)
T ss_pred hhhhhhHHhhCCCHHHHHHHh-CCCHHHHHHHH-H-HHHHHHhh
Confidence 345556666777889999999 99999999987 3 33444444
No 78
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=53.33 E-value=48 Score=19.94 Aligned_cols=32 Identities=19% Similarity=0.077 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |.+.+.|+.+.
T Consensus 124 r~vl~L~~~~g~s~~EIA~~l-gis~~tV~~~l 155 (173)
T PRK09645 124 RAVLVRSYYRGWSTAQIAADL-GIPEGTVKSRL 155 (173)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 345566666677889999999 89999999987
No 79
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=52.98 E-value=34 Score=25.66 Aligned_cols=36 Identities=22% Similarity=0.349 Sum_probs=30.2
Q ss_pred hHHH-HHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHh
Q 039547 2 DRLI-CRLFAISESRWSVIAAHLPGRTDNETNNYYKNT 38 (67)
Q Consensus 2 d~ll-~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~ 38 (67)
|..| -+.|..||.....|-+.||.|+-.++..+| ++
T Consensus 194 d~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyY-y~ 230 (534)
T KOG1194|consen 194 DIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYY-YS 230 (534)
T ss_pred HHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHH-HH
Confidence 4433 467899999999999999999999999887 54
No 80
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=52.73 E-value=38 Score=20.59 Aligned_cols=31 Identities=10% Similarity=0.049 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.+.-..|-.-..||..| |.|...|+++.
T Consensus 136 ~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l 166 (179)
T PRK12514 136 AAVRRAYLEGLSYKELAERH-DVPLNTMRTWL 166 (179)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCChHHHHHHH
Confidence 34555556677899999999 99999999987
No 81
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=52.68 E-value=38 Score=20.81 Aligned_cols=32 Identities=13% Similarity=0.032 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.+.-..|-....||..| |-|.+.|+++.
T Consensus 144 r~v~~l~~~~g~s~~eIA~~l-gis~~tv~~~l 175 (193)
T PRK11923 144 RTALTLREFDGLSYEDIASVM-QCPVGTVRSRI 175 (193)
T ss_pred hHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345566556777889999998 88999999987
No 82
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=52.00 E-value=69 Score=21.35 Aligned_cols=41 Identities=15% Similarity=0.319 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhh
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEE 46 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~ 46 (67)
..++.++..+|-.-..||..| |.|...|+.+. . ..++++..
T Consensus 114 R~v~~L~~~~g~s~~EIA~~l-g~s~~tVr~~l-~-RAr~~Lr~ 154 (281)
T TIGR02957 114 RAVFVLREVFDYPYEEIASIV-GKSEANCRQLV-S-RARRHLDA 154 (281)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH-H-HHHHHHHh
Confidence 345667777888899999999 89999999987 3 34444444
No 83
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=51.86 E-value=42 Score=20.85 Aligned_cols=32 Identities=6% Similarity=-0.068 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-|.+.|+.+.
T Consensus 140 R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l 171 (189)
T PRK12530 140 ARVFMMREYLELSSEQICQEC-DISTSNLHVLL 171 (189)
T ss_pred HHHHhHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345556656677899999999 99999999987
No 84
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=51.62 E-value=19 Score=19.99 Aligned_cols=23 Identities=22% Similarity=0.541 Sum_probs=19.5
Q ss_pred hcCCcHHHHHhhCCCCChhhHHHH
Q 039547 11 ISESRWSVIAAHLPGRTDNETNNY 34 (67)
Q Consensus 11 ~~G~kW~~Ia~~lpgRt~~~vknr 34 (67)
..|..|...|..| |=++..|.+.
T Consensus 13 nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 13 RPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred CCccCHHHHHHHc-CCCHHHHHHH
Confidence 4678999999999 8888888774
No 85
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=51.45 E-value=50 Score=19.59 Aligned_cols=32 Identities=13% Similarity=0.017 Sum_probs=26.3
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |-+.+.|+++.
T Consensus 112 r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 143 (160)
T PRK09642 112 RDVVLAHYLEEKSYQEIALQE-KIEVKTVEMKL 143 (160)
T ss_pred HHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345666667778889999999 99999999987
No 86
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=51.28 E-value=25 Score=19.22 Aligned_cols=30 Identities=7% Similarity=0.273 Sum_probs=19.9
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCC---ChhhHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGR---TDNETNN 33 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgR---t~~~vkn 33 (67)
+.+|-+|+..|| |..++..++=| ++.+||.
T Consensus 12 e~il~~Lv~~yG--W~~L~~~i~i~CF~~~PsikS 44 (64)
T PF09905_consen 12 ETILTELVEHYG--WEELGERININCFKNNPSIKS 44 (64)
T ss_dssp HHHHHHHHHHT---HHHHHHHTTSSSTTSS--HHH
T ss_pred HHHHHHHHHHhC--HHHHHhhcccccCCCCCchHH
Confidence 567888999997 99999887543 3444554
No 87
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=47.90 E-value=50 Score=19.45 Aligned_cols=32 Identities=16% Similarity=0.072 Sum_probs=26.3
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-.-|-....||..| |-|.+.|+++.
T Consensus 112 r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 143 (161)
T PRK09047 112 REAFLLRYWEDMDVAETAAAM-GCSEGSVKTHC 143 (161)
T ss_pred HHHHHHHHHhcCCHHHHHHHH-CCCHHHHHHHH
Confidence 345666666777889999999 89999999987
No 88
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=47.86 E-value=30 Score=27.99 Aligned_cols=40 Identities=20% Similarity=0.330 Sum_probs=32.0
Q ss_pred ChHHHHHHHHhcC-CcHHHHHh------------hCCCCChhhHHHHHHHhhhh
Q 039547 1 EDRLICRLFAISE-SRWSVIAA------------HLPGRTDNETNNYYKNTKLK 41 (67)
Q Consensus 1 Ed~ll~~~~~~~G-~kW~~Ia~------------~lpgRt~~~vknrw~~~~l~ 41 (67)
||..|+-....+| ..|..|-. +|..||+..+..|. ++.++
T Consensus 933 ~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~-~~l~~ 985 (1033)
T PLN03142 933 CDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRC-DTLIR 985 (1033)
T ss_pred HHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHH-HHHHH
Confidence 6888888888999 57988743 23689999999999 77654
No 89
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=46.97 E-value=52 Score=20.05 Aligned_cols=33 Identities=12% Similarity=0.144 Sum_probs=27.3
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.++-.-|-....||..| |-|.+.|+++.
T Consensus 136 ~r~v~~l~~~~g~s~~eIA~~l-~is~~tV~~~l 168 (184)
T PRK12512 136 QRDVVQSISVEGASIKETAAKL-SMSEGAVRVAL 168 (184)
T ss_pred HHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 3456667666788899999999 99999999998
No 90
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=46.81 E-value=64 Score=19.62 Aligned_cols=32 Identities=13% Similarity=0.008 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |-|.+.|+++.
T Consensus 141 r~vl~l~~~~~~s~~eIA~~l-gis~~~V~~~l 172 (186)
T PRK13919 141 RRVIEVLYYQGYTHREAAQLL-GLPLGTLKTRA 172 (186)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 445666667777889999998 89999999987
No 91
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=46.38 E-value=54 Score=20.34 Aligned_cols=32 Identities=9% Similarity=0.025 Sum_probs=26.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-.-|-....||..| |-|.+.|+++.
T Consensus 147 r~v~~l~~~eg~s~~EIA~~l-gis~~tVk~rl 178 (194)
T PRK12531 147 RDVLQAVYLEELPHQQVAEMF-DIPLGTVKSRL 178 (194)
T ss_pred HHHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHH
Confidence 346666666777889999999 99999999987
No 92
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=45.79 E-value=56 Score=19.99 Aligned_cols=37 Identities=11% Similarity=0.067 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhh
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLK 41 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~ 41 (67)
..++.+...-|-....||..| |-+.+.|+.+. ...+.
T Consensus 133 R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l-~rAl~ 169 (178)
T PRK12529 133 KQAFLMATLDGMKQKDIAQAL-DIALPTVKKYI-HQAYV 169 (178)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH-HHHHH
Confidence 456777777888999999999 99999999998 54333
No 93
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=44.87 E-value=60 Score=19.48 Aligned_cols=32 Identities=13% Similarity=0.136 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-|.+.|+++.
T Consensus 125 r~i~~l~~~~g~s~~eiA~~l-gis~~tv~~~l 156 (169)
T TIGR02954 125 QTAIILRYYHDLTIKEIAEVM-NKPEGTVKTYL 156 (169)
T ss_pred hHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345556666678899999998 78999999988
No 94
>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=44.53 E-value=56 Score=23.36 Aligned_cols=32 Identities=28% Similarity=0.421 Sum_probs=23.5
Q ss_pred HHHHHHHhcCCc---HHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESR---WSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~k---W~~Ia~~lpgRt~~~vknrw 35 (67)
+|--|...-|.. -..|++.++||+...|++.-
T Consensus 32 Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl 66 (344)
T PF11035_consen 32 LLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFL 66 (344)
T ss_pred HHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHH
Confidence 344444555654 56899999999999999965
No 95
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=44.44 E-value=73 Score=19.46 Aligned_cols=45 Identities=11% Similarity=-0.058 Sum_probs=30.5
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHH--HhhhhhhhhhCC
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYYK--NTKLKRKHEEGG 48 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~--~~~l~~~~~~~~ 48 (67)
..++.+.-..|-....||..| |-|.+.|+++.. ...|++.+...+
T Consensus 134 r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~~l~~~~ 180 (186)
T PRK05602 134 REAIVLQYYQGLSNIEAAAVM-DISVDALESLLARGRRALRAQLADLP 180 (186)
T ss_pred HHHhhHHHhcCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 445556556678899999998 899999999872 233444444433
No 96
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=44.38 E-value=68 Score=19.79 Aligned_cols=33 Identities=27% Similarity=0.212 Sum_probs=26.2
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.++-.-|-.-..||..| |-|.+.|+++-
T Consensus 136 ~r~i~~l~~~~g~s~~EIAe~l-gis~~~V~~~l 168 (189)
T PRK06811 136 DREIFIRRYLLGEKIEEIAKKL-GLTRSAIDNRL 168 (189)
T ss_pred HHHHHHHHHHccCCHHHHHHHH-CCCHHHHHHHH
Confidence 3456666556677888999999 99999999986
No 97
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=43.42 E-value=68 Score=19.01 Aligned_cols=33 Identities=21% Similarity=0.099 Sum_probs=26.9
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.+....|-.-..||..| |-+.+.|+++.
T Consensus 110 ~r~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l 142 (159)
T PRK12527 110 CRDSFLLRKLEGLSHQQIAEHL-GISRSLVEKHI 142 (159)
T ss_pred HHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 3456667666777889999999 99999999987
No 98
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=43.11 E-value=60 Score=18.12 Aligned_cols=38 Identities=16% Similarity=0.159 Sum_probs=29.5
Q ss_pred hHHHHHHHHhcCC-cHHHHHhhCCCCChhhHHHHHHHhhhh
Q 039547 2 DRLICRLFAISES-RWSVIAAHLPGRTDNETNNYYKNTKLK 41 (67)
Q Consensus 2 d~ll~~~~~~~G~-kW~~Ia~~lpgRt~~~vknrw~~~~l~ 41 (67)
|..|+.....-|. .++.||+.+ |-+...|..+. +....
T Consensus 5 D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l-~~L~~ 43 (108)
T smart00344 5 DRKILEELQKDARISLAELAKKV-GLSPSTVHNRV-KRLEE 43 (108)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHH-HHHHH
Confidence 5667777777664 799999998 99999999998 54333
No 99
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=43.02 E-value=54 Score=19.91 Aligned_cols=32 Identities=25% Similarity=0.278 Sum_probs=26.5
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-+.+.|+++.
T Consensus 125 r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 156 (172)
T PRK09651 125 REAFLLSQLDGLTYSEIAHKL-GVSVSSVKKYV 156 (172)
T ss_pred hHHhhhhhccCCCHHHHHHHh-CCCHHHHHHHH
Confidence 445666667777899999999 99999999987
No 100
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and
Probab=42.88 E-value=29 Score=19.15 Aligned_cols=23 Identities=22% Similarity=0.452 Sum_probs=17.0
Q ss_pred HhcCCcHHHHHhhCCCCChhhHHH
Q 039547 10 AISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 10 ~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
...|+.|..+|..| |-+...|++
T Consensus 13 ~~~g~DWr~LA~~L-g~~~~~I~~ 35 (79)
T cd08312 13 RVVAADWTALAEEM-GFEYLEIRN 35 (79)
T ss_pred CCcccCHHHHHHHc-CCCHHHHHH
Confidence 35789999999999 555555554
No 101
>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=42.43 E-value=38 Score=15.60 Aligned_cols=32 Identities=19% Similarity=0.094 Sum_probs=20.9
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-.-|-.+..||..+ |-+...|+.+.
T Consensus 16 ~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~ 47 (55)
T cd06171 16 REVILLRFGEGLSYEEIAEIL-GISRSTVRQRL 47 (55)
T ss_pred HHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 344455545667788888887 66666776654
No 102
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=42.42 E-value=73 Score=19.59 Aligned_cols=32 Identities=13% Similarity=-0.065 Sum_probs=26.0
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |-|.+.|+++.
T Consensus 137 r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 168 (191)
T PRK12520 137 GRVFMMREWLELETEEICQEL-QITATNAWVLL 168 (191)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345566666777889999999 99999999997
No 103
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=42.05 E-value=72 Score=18.93 Aligned_cols=32 Identities=19% Similarity=0.232 Sum_probs=26.5
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++--.|-....||..+ |-+.+.|+++.
T Consensus 119 r~v~~L~~~~g~s~~EIA~~l-~is~~tV~~~l 150 (161)
T PRK12528 119 KRAFLLAQVDGLGYGEIATEL-GISLATVKRYL 150 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 456667777788899999998 89999999987
No 104
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=41.56 E-value=77 Score=19.41 Aligned_cols=32 Identities=19% Similarity=0.025 Sum_probs=26.6
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-+.+.|+.+.
T Consensus 145 r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 176 (189)
T PRK09648 145 REILILRVVVGLSAEETAEAV-GSTPGAVRVAQ 176 (189)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 456666666788899999999 89999999987
No 105
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=40.98 E-value=18 Score=26.45 Aligned_cols=45 Identities=18% Similarity=0.200 Sum_probs=35.8
Q ss_pred HHHHHHHHhcCCcHHHHHhh-----CCC-CChhhHHHHHHHhhhhhhhhhCC
Q 039547 3 RLICRLFAISESRWSVIAAH-----LPG-RTDNETNNYYKNTKLKRKHEEGG 48 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~-----lpg-Rt~~~vknrw~~~~l~~~~~~~~ 48 (67)
+-|++|-+.|-=+|..||.. ++. ||--.+|.|| ++..+.-++...
T Consensus 139 D~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRy-Y~v~r~l~kAr~ 189 (445)
T KOG2656|consen 139 DYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERY-YSVCRKLLKARA 189 (445)
T ss_pred HHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHH-HHHHHHHHHccC
Confidence 45777778888899999987 676 9999999999 887776655544
No 106
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=40.79 E-value=74 Score=19.61 Aligned_cols=32 Identities=16% Similarity=-0.008 Sum_probs=26.6
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.+.-..|-....||..| |-|.+.|+++.
T Consensus 136 r~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l 167 (185)
T PRK09649 136 REALLLTQLLGLSYADAAAVC-GCPVGTIRSRV 167 (185)
T ss_pred hHHhhhHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 445666667777889999999 89999999998
No 107
>COG4654 Cytochrome c551/c552 [Energy production and conversion]
Probab=40.04 E-value=21 Score=21.46 Aligned_cols=24 Identities=17% Similarity=0.192 Sum_probs=20.6
Q ss_pred HhcCCcHHHHHhhCCCCChhhHHH
Q 039547 10 AISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 10 ~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
+..|+.|..||..+.|..+..++-
T Consensus 44 ktVGPS~kdIAakYag~~~~~~kl 67 (110)
T COG4654 44 KTVGPSYKDIAAKYAGKAGALAKL 67 (110)
T ss_pred cccCccHHHHHHHHccchhHHHHH
Confidence 567899999999999999888764
No 108
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=39.92 E-value=78 Score=18.50 Aligned_cols=32 Identities=16% Similarity=-0.036 Sum_probs=24.8
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.+.-.-|-....||..+ |-+.+.|+++-
T Consensus 112 r~ii~l~~~~~~s~~EIA~~l-~is~~tV~~~~ 143 (154)
T PRK06759 112 KYIIFERFFVGKTMGEIALET-EMTYYQVRWIY 143 (154)
T ss_pred HHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345555556677788999998 89999999986
No 109
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=39.79 E-value=82 Score=19.74 Aligned_cols=45 Identities=18% Similarity=0.130 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHH--HhhhhhhhhhCC
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYYK--NTKLKRKHEEGG 48 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~--~~~l~~~~~~~~ 48 (67)
..++.++-..|-.-..||..| |-+.+.|+++.. ...|+..+...+
T Consensus 145 r~v~~L~~~eg~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~~l~~~~ 191 (201)
T PRK12545 145 GRVFMMREFLDFEIDDICTEL-TLTANHCSVLLYRARTRLRTCLSEKG 191 (201)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 446666667777889999999 999999999872 134444444433
No 110
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=39.78 E-value=84 Score=19.91 Aligned_cols=31 Identities=23% Similarity=0.159 Sum_probs=25.7
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.+....|-.-..||..| |-+.+.|+++.
T Consensus 145 ~v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l 175 (203)
T PRK09647 145 AAVVLCDIEGLSYEEIAATL-GVKLGTVRSRI 175 (203)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 45556667778889999999 99999999987
No 111
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=39.60 E-value=85 Score=20.29 Aligned_cols=31 Identities=19% Similarity=0.115 Sum_probs=24.8
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.-++.+... |-....||..| +-+.+.|+++-
T Consensus 161 ~~Vl~l~~~-G~s~~eIA~~L-~iS~~TVk~~~ 191 (216)
T PRK10100 161 KEILNKLRI-GASNNEIARSL-FISENTVKTHL 191 (216)
T ss_pred HHHHHHHHc-CCCHHHHHHHh-CCCHHHHHHHH
Confidence 345666666 88889999998 78999999987
No 112
>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=39.40 E-value=27 Score=20.48 Aligned_cols=27 Identities=19% Similarity=0.128 Sum_probs=21.7
Q ss_pred HHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 8 LFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 8 ~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+.-.-|-.+..||..| |=|...|+++.
T Consensus 116 l~~~~g~s~~eIA~~l-gis~~tv~~~l 142 (154)
T TIGR02950 116 LREFKEFSYKEIAELL-NLSLAKVKSNL 142 (154)
T ss_pred ehhhccCcHHHHHHHH-CCCHHHHHHHH
Confidence 3334567789999998 88999999987
No 113
>PF03832 WSK: WSK motif; InterPro: IPR001573 Cell signalling mediated via GPCRs (G-protein-coupled receptors) involves the assembly of receptors, G-proteins, effectors and downstream elements into complexes that approach in design 'solid-state' signalling devices. Scaffold molecules, such as the AKAPs (A-kinase anchoring proteins), were discovered more than a decade ago and represent dynamic platforms, enabling multivalent signalling []. This family of functionally related proteins is classified on the basis of their ability to associate with the PKA holoenzyme inside cells. A shared property of most, if not all, AKAPs is the ability to form multivalent signal transduction complexes. Each anchoring protein contains at least two functional motifs []. The conserved PKA binding motif forms an amphipathic helix of 14-18 residues that interacts with hydrophobic determinants located in the extreme N terminus of the regulatory subunit dimmer. The subcellular address of each AKAP is encoded by a unique targeting motif. Gravin, an autoantigen recognised by serum from myasthenia gravis patients contains 3 repeats of this domain []. The WSK motif is short motif, named after three conserved residues found in the WXSXK motif, found in protein kinase A anchoring proteins. ; GO: 0006605 protein targeting, 0007165 signal transduction
Probab=38.86 E-value=22 Score=16.72 Aligned_cols=14 Identities=21% Similarity=0.444 Sum_probs=11.4
Q ss_pred CCcHHHHHhhCCCC
Q 039547 13 ESRWSVIAAHLPGR 26 (67)
Q Consensus 13 G~kW~~Ia~~lpgR 26 (67)
+..|+.|-+++++|
T Consensus 4 ~~~W~S~KrlVt~r 17 (31)
T PF03832_consen 4 GSTWASFKRLVTPR 17 (31)
T ss_pred cchhHHHHhhcCcc
Confidence 45799999999876
No 114
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=38.43 E-value=90 Score=19.34 Aligned_cols=32 Identities=16% Similarity=-0.028 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.+..||..| |=+.+.|+++.
T Consensus 142 r~i~~L~~~~g~s~~eIA~~l-gis~~tV~~~l 173 (196)
T PRK12524 142 RQAVVLRHIEGLSNPEIAEVM-EIGVEAVESLT 173 (196)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 346667667788899999998 88999999987
No 115
>PRK01905 DNA-binding protein Fis; Provisional
Probab=38.32 E-value=69 Score=17.42 Aligned_cols=33 Identities=21% Similarity=0.184 Sum_probs=23.0
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHH
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNNY 34 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknr 34 (67)
|...|.+....+|..++..|+.+ |=+.+.+..+
T Consensus 38 E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 38 EKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 34567888888998888888877 4454444443
No 116
>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=38.08 E-value=85 Score=18.55 Aligned_cols=32 Identities=16% Similarity=0.107 Sum_probs=25.1
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |-+...|+++.
T Consensus 116 r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l 147 (162)
T TIGR02983 116 RAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRL 147 (162)
T ss_pred HHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHH
Confidence 345555556677788999998 89999999987
No 117
>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=36.06 E-value=1e+02 Score=18.64 Aligned_cols=32 Identities=16% Similarity=0.082 Sum_probs=26.7
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-.-|-....||..| |-+...|+++.
T Consensus 140 r~v~~l~~~~g~s~~EIA~~l-gis~~tVk~~l 171 (183)
T TIGR02999 140 AEVVELRFFAGLTVEEIAELL-GVSVRTVERDW 171 (183)
T ss_pred HHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 456667777788899999999 89999999987
No 118
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=35.45 E-value=99 Score=18.86 Aligned_cols=31 Identities=13% Similarity=0.050 Sum_probs=24.8
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.+.-..|-.-..||..| |-|.+.|+++.
T Consensus 140 ~i~~l~~~~~~s~~eIA~~l-gis~~tV~~~l 170 (182)
T PRK12537 140 NCILHAYVDGCSHAEIAQRL-GAPLGTVKAWI 170 (182)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCChhhHHHHH
Confidence 45556656677788999998 89999999988
No 119
>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=35.37 E-value=57 Score=15.57 Aligned_cols=32 Identities=22% Similarity=0.163 Sum_probs=22.0
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHH
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
|.++|.+....+|.+-+..|+.| |=+...+..
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~ 37 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHH
Confidence 45788888899998888888887 444444433
No 120
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=35.37 E-value=1e+02 Score=19.09 Aligned_cols=33 Identities=12% Similarity=0.035 Sum_probs=26.6
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+..++.++-..|-....||..| |-+.+.|+++-
T Consensus 147 ~r~vl~l~~~~~~s~~EIA~~L-gis~~tVk~~l 179 (194)
T PRK09646 147 QRESVTLAYYGGLTYREVAERL-AVPLGTVKTRM 179 (194)
T ss_pred HHHHHHHHHHcCCCHHHHHHHh-CCChHhHHHHH
Confidence 3456667667778899999999 78999999986
No 121
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=35.16 E-value=98 Score=19.22 Aligned_cols=32 Identities=16% Similarity=0.006 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.|....|-....||..| |-|.+.|+++-
T Consensus 122 r~i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l 153 (187)
T PRK12516 122 REAIILVGASGFAYEEAAEIC-GCAVGTIKSRV 153 (187)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 456667777788999999999 89999999986
No 122
>PHA02291 hypothetical protein
Probab=34.90 E-value=14 Score=22.47 Aligned_cols=18 Identities=33% Similarity=0.658 Sum_probs=12.4
Q ss_pred HHHhhCCCCChhh-HHHHH
Q 039547 18 VIAAHLPGRTDNE-TNNYY 35 (67)
Q Consensus 18 ~Ia~~lpgRt~~~-vknrw 35 (67)
.+..+|||||+.. |--+|
T Consensus 75 ~LP~~LPGRT~~~sID~~~ 93 (132)
T PHA02291 75 TLPTYLPGRTGDNSIDMRY 93 (132)
T ss_pred hccccCCCCCCCcccceee
Confidence 3567899999754 55554
No 123
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=34.77 E-value=46 Score=20.46 Aligned_cols=21 Identities=19% Similarity=0.493 Sum_probs=16.5
Q ss_pred hHHHHHHHHhcCCcHHHHHhhCC
Q 039547 2 DRLICRLFAISESRWSVIAAHLP 24 (67)
Q Consensus 2 d~ll~~~~~~~G~kW~~Ia~~lp 24 (67)
+.++-+++..|| |...+..++
T Consensus 21 E~llt~Lvd~YG--Wd~L~~ri~ 41 (136)
T COG4628 21 ETLLTELVDFYG--WDGLATRIR 41 (136)
T ss_pred HHHHHHHHHHhC--hHHHHhhce
Confidence 567888999998 887777663
No 124
>PRK00118 putative DNA-binding protein; Validated
Probab=34.45 E-value=1e+02 Score=18.16 Aligned_cols=32 Identities=13% Similarity=0.178 Sum_probs=25.6
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..+ |-|.+.|+++-
T Consensus 23 Revl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L 54 (104)
T PRK00118 23 RNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNI 54 (104)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 445666667778889999998 89999998876
No 125
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=33.81 E-value=1e+02 Score=18.18 Aligned_cols=31 Identities=23% Similarity=0.213 Sum_probs=25.1
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++- .|-.-..||..| |-|.+.|+++.
T Consensus 118 r~il~l~~-~g~s~~eIA~~l-gis~~tV~~~i 148 (166)
T PRK09639 118 RTVLLLRF-SGYSYKEIAEAL-GIKESSVGTTL 148 (166)
T ss_pred HHHHHHHH-cCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34555666 788889999998 89999999987
No 126
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=33.68 E-value=92 Score=17.84 Aligned_cols=32 Identities=16% Similarity=0.146 Sum_probs=23.0
Q ss_pred ChHHHHHHHHhcCCcHHHHHhhCCCCChhhHHH
Q 039547 1 EDRLICRLFAISESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 1 Ed~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
|..+|......+|...+..|+.+ |=+.+.+..
T Consensus 56 Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~r 87 (95)
T PRK00430 56 EAPLLDMVMQYTRGNQTRAALML-GINRGTLRK 87 (95)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHH
Confidence 45677888888998899998887 545444443
No 127
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=33.33 E-value=1.1e+02 Score=18.30 Aligned_cols=32 Identities=19% Similarity=0.034 Sum_probs=26.3
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++..-|-....||..| |-+...|+++-
T Consensus 118 r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l 149 (164)
T PRK12547 118 REAIILIGASGFSYEDAAAIC-GCAVGTIKSRV 149 (164)
T ss_pred HHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 345667667788899999999 89999999987
No 128
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=33.13 E-value=1e+02 Score=18.77 Aligned_cols=32 Identities=25% Similarity=0.233 Sum_probs=25.5
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |-+.+.|+++.
T Consensus 133 r~v~~l~~~~g~s~~EIA~~l-~is~~tv~~~l 164 (179)
T PRK09415 133 REVIYLFYYEELSIKEIAEVT-GVNENTVKTRL 164 (179)
T ss_pred hhHhHhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345566666788889999998 77999999987
No 129
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=32.73 E-value=1.1e+02 Score=19.06 Aligned_cols=32 Identities=16% Similarity=0.012 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++...|-....||..| |-|...|+++.
T Consensus 119 r~v~~L~~~~g~s~~EIA~~L-giS~~tVk~~l 150 (188)
T PRK12546 119 REALILVGASGFSYEEAAEMC-GVAVGTVKSRA 150 (188)
T ss_pred hHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 456667777888999999999 89999999987
No 130
>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=32.69 E-value=1.1e+02 Score=18.34 Aligned_cols=31 Identities=10% Similarity=0.225 Sum_probs=24.5
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.++--.|-....||..| |-|.+.|+++.
T Consensus 147 ~vi~l~~~~g~s~~eIA~~l-gis~~~v~~~l 177 (189)
T TIGR02984 147 EVILLRHLEGLSFAEVAERM-DRSEGAVSMLW 177 (189)
T ss_pred HHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 45555556777888999988 89999999987
No 131
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=32.38 E-value=61 Score=18.00 Aligned_cols=28 Identities=11% Similarity=0.068 Sum_probs=22.7
Q ss_pred HHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 8 LFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 8 ~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
++..+|-.-+.|++.|.||+...|..-.
T Consensus 39 ~~~~~~~s~~~Ig~~fg~r~hStV~~a~ 66 (90)
T cd06571 39 ARELTGLSLPEIGRAFGGRDHSTVLHAV 66 (90)
T ss_pred HHHHhCCCHHHHHHHhCCCCHhHHHHHH
Confidence 4455677889999999889999887765
No 132
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=31.77 E-value=1.7e+02 Score=19.86 Aligned_cols=41 Identities=22% Similarity=0.324 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHHhhhhhhhhh
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYYKNTKLKRKHEE 46 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~~~l~~~~~~ 46 (67)
..++.++..+|-.-..||..| |.|.+.|+.+. ...++++..
T Consensus 124 R~vf~L~~~~g~s~~EIA~~L-gis~~tVr~~l--~RAr~~Lr~ 164 (290)
T PRK09635 124 RVVFVLHEIFGLPYQQIATTI-GSQASTCRQLA--HRARRKINE 164 (290)
T ss_pred HHHhhHHHHhCCCHHHHHHHH-CcCHHHHHHHH--HHHHHHHHh
Confidence 345667778888899999999 99999999987 334444444
No 133
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=31.23 E-value=1.3e+02 Score=18.97 Aligned_cols=32 Identities=9% Similarity=0.033 Sum_probs=24.9
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |-|.+.|+++.
T Consensus 159 r~vl~l~~~~g~s~~EIA~~l-gis~~tV~~~l 190 (206)
T PRK12526 159 QTVVKGVYFQELSQEQLAQQL-NVPLGTVKSRL 190 (206)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345555555667788899998 89999999987
No 134
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=31.17 E-value=45 Score=20.08 Aligned_cols=31 Identities=13% Similarity=-0.006 Sum_probs=24.6
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.++-..|-....||..| |-+.+.|+++.
T Consensus 133 ~v~~l~~~~g~s~~eIA~~l-~is~~~V~~~l 163 (176)
T PRK09638 133 APVILKHYYGYTYEEIAKML-NIPEGTVKSRV 163 (176)
T ss_pred heeeehhhcCCCHHHHHHHH-CCChhHHHHHH
Confidence 34555556788899999999 78999999887
No 135
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=31.16 E-value=1.1e+02 Score=17.82 Aligned_cols=32 Identities=25% Similarity=0.235 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |=|.+.|+++.
T Consensus 117 r~v~~l~~~~g~~~~eIA~~l-~is~~tv~~~l 148 (159)
T TIGR02989 117 RELLQLRYQRGVSLTALAEQL-GRTVNAVYKAL 148 (159)
T ss_pred HHHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 445566556677788888888 88888888876
No 136
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=30.82 E-value=37 Score=25.93 Aligned_cols=29 Identities=17% Similarity=0.327 Sum_probs=25.7
Q ss_pred HHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 7 RLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 7 ~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..-.++|..-+.|+..+|+|+..+||--|
T Consensus 422 ka~~~~gs~~slis~l~p~R~rk~iK~K~ 450 (584)
T KOG2009|consen 422 KALSERGSDFSLISNLFPLRDRKQIKAKF 450 (584)
T ss_pred hHHhhhcccccccccccccccHHHHHHHH
Confidence 34567888899999999999999999988
No 137
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=30.56 E-value=60 Score=20.86 Aligned_cols=41 Identities=15% Similarity=0.136 Sum_probs=28.6
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHH--Hhhhhhhhh
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYYK--NTKLKRKHE 45 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~--~~~l~~~~~ 45 (67)
.++.++-..|-....||..| |-|...|+++.. ...|++.+.
T Consensus 156 ~i~~l~~~~g~s~~EIAe~l-gis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 156 AVFVLRVVEELSVEETAQAL-GLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hhheeehhcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHHH
Confidence 34555555677889999999 899999999872 234444443
No 138
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=30.44 E-value=68 Score=24.68 Aligned_cols=28 Identities=29% Similarity=0.589 Sum_probs=23.0
Q ss_pred cHHHHHhhCCCCC-hhhHHHHHHHhhhhhhh
Q 039547 15 RWSVIAAHLPGRT-DNETNNYYKNTKLKRKH 44 (67)
Q Consensus 15 kW~~Ia~~lpgRt-~~~vknrw~~~~l~~~~ 44 (67)
-|..|+...||.+ +-+|+-+| . .|+..+
T Consensus 542 DW~~l~~~~~g~~~~~e~r~q~-~-~lk~~I 570 (607)
T KOG0051|consen 542 DWKSLAEYAPGESTGEELRLQF-E-RLKKKI 570 (607)
T ss_pred CHHHHHHhCCCCCcHHHHHHHH-H-hHhhcc
Confidence 5999999999998 99999999 3 344443
No 139
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=29.83 E-value=53 Score=20.24 Aligned_cols=31 Identities=13% Similarity=0.069 Sum_probs=24.5
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.++-..|-....||..| |-+...|+++.
T Consensus 146 ~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 176 (194)
T PRK12513 146 EVFLLREHGDLELEEIAELT-GVPEETVKSRL 176 (194)
T ss_pred hheeeehccCCCHHHHHHHH-CCCHHHHHHHH
Confidence 44555556677889999999 79999999886
No 140
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=29.63 E-value=1.1e+02 Score=18.70 Aligned_cols=32 Identities=22% Similarity=0.068 Sum_probs=24.2
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.+.-..|-.-..||..| |-|.+.|+++.
T Consensus 147 ~~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 178 (194)
T PRK12519 147 RQVLELAYYEGLSQSEIAKRL-GIPLGTVKARA 178 (194)
T ss_pred hhhhhhhhhcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 345555555677788899988 88999999876
No 141
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=29.27 E-value=58 Score=19.56 Aligned_cols=29 Identities=14% Similarity=0.024 Sum_probs=22.3
Q ss_pred HHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 6 CRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 6 ~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
+.++--.|-.-..||..| |-|.+.|+++.
T Consensus 129 l~l~~~~g~s~~eIA~~l-g~s~~tv~~~l 157 (175)
T PRK12518 129 LVLHDLEDLPQKEIAEIL-NIPVGTVKSRL 157 (175)
T ss_pred eeehHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 334444566678899998 89999999987
No 142
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=29.17 E-value=1.1e+02 Score=19.90 Aligned_cols=32 Identities=16% Similarity=0.041 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-|.+.|+++.
T Consensus 177 R~v~~L~~~eg~s~~EIA~~L-gis~~tVk~~l 208 (233)
T PRK12538 177 RIAVILSYHENMSNGEIAEVM-DTTVAAVESLL 208 (233)
T ss_pred HHHhhhHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 345666667778889999999 99999999987
No 143
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=27.98 E-value=1.5e+02 Score=18.08 Aligned_cols=32 Identities=13% Similarity=0.278 Sum_probs=25.8
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.+.-..|-....||..| |-|...|+++.
T Consensus 128 r~i~~l~~~~g~s~~EIA~~l-gis~~tVk~~l 159 (185)
T PRK12542 128 RQVFKYKVFYNLTYQEISSVM-GITEANVRKQF 159 (185)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345556666777889999999 89999999987
No 144
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=27.67 E-value=69 Score=16.40 Aligned_cols=19 Identities=16% Similarity=0.228 Sum_probs=13.4
Q ss_pred HHhcCCcHHHHHhhCCCCC
Q 039547 9 FAISESRWSVIAAHLPGRT 27 (67)
Q Consensus 9 ~~~~G~kW~~Ia~~lpgRt 27 (67)
...+|-.-..|++.|.||+
T Consensus 41 ~~~~~~sl~~Ig~~fg~rd 59 (60)
T smart00760 41 RELTDLSLPEIGKIFGGRD 59 (60)
T ss_pred HHHHCCCHHHHHHHhCCCC
Confidence 4456667788888887674
No 145
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=27.56 E-value=1.5e+02 Score=17.94 Aligned_cols=32 Identities=22% Similarity=0.152 Sum_probs=26.3
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |-|...|+++.
T Consensus 106 r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l 137 (170)
T TIGR02959 106 REAIRLTELEGLSQQEIAEKL-GLSLSGAKSRV 137 (170)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 456667777777889999999 89999999986
No 146
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=27.46 E-value=1.4e+02 Score=17.58 Aligned_cols=33 Identities=21% Similarity=0.220 Sum_probs=26.9
Q ss_pred hHHHHHHHHhcCC-cHHHHHhhCCCCChhhHHHHH
Q 039547 2 DRLICRLFAISES-RWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 2 d~ll~~~~~~~G~-kW~~Ia~~lpgRt~~~vknrw 35 (67)
|..|+.....-|. .++.||+.+ |-|...|.+|-
T Consensus 10 D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri 43 (154)
T COG1522 10 DRRILRLLQEDARISNAELAERV-GLSPSTVLRRI 43 (154)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHH
Confidence 5567777766664 699999998 89999999998
No 147
>cd08778 Death_TNFRSF21 Death domain of tumor necrosis factor receptor superfamily member 21. Death domain (DD) found in tumor necrosis factor receptor superfamily member 21 (TNFRSF21), also called death receptor-6, DR6. DR6 is an orphan receptor that is expressed ubiquitously, but shows high expression in lymphoid organs, heart, brain and pancreas. Results from DR6(-/-) mice indicate that DR6 plays an important regulatory role for the generation of adaptive immunity. It may also be involved in tumor cell survival and immune evasion. In neuronal cells, it binds beta-amyloid precursor protein (APP) and activates caspase-dependent cell death. It may contribute to the pathogenesis of Alzheimer's disease. 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 recruitme
Probab=27.05 E-value=63 Score=18.16 Aligned_cols=27 Identities=22% Similarity=0.348 Sum_probs=20.4
Q ss_pred HHHhcCCcHHHHHhhCCCCChhhHHHH
Q 039547 8 LFAISESRWSVIAAHLPGRTDNETNNY 34 (67)
Q Consensus 8 ~~~~~G~kW~~Ia~~lpgRt~~~vknr 34 (67)
.-.+.|++|..+-+.+..-|+..|-..
T Consensus 9 vaaqvgsqwid~y~sla~aterevaaf 35 (84)
T cd08778 9 VAAQVGSQWKDIYQFLCNASEREVAAF 35 (84)
T ss_pred HHHHHhhHHHHHHHHHhhhhHHHHHHH
Confidence 346889999999888877777666544
No 148
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=26.91 E-value=1.7e+02 Score=18.73 Aligned_cols=32 Identities=22% Similarity=0.305 Sum_probs=25.4
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-|...|+++.
T Consensus 190 r~vl~l~~~~g~s~~EIA~~l-gis~~tV~~~~ 221 (236)
T PRK06986 190 QLVLSLYYQEELNLKEIGAVL-GVSESRVSQIH 221 (236)
T ss_pred HHHHHhHhccCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345556656677889999998 89999999987
No 149
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=26.85 E-value=59 Score=13.10 Aligned_cols=21 Identities=19% Similarity=0.185 Sum_probs=13.1
Q ss_pred cCCcHHHHHhhCCCCChhhHHH
Q 039547 12 SESRWSVIAAHLPGRTDNETNN 33 (67)
Q Consensus 12 ~G~kW~~Ia~~lpgRt~~~vkn 33 (67)
-|..+..||..+ |.+...+.+
T Consensus 20 ~~~s~~~ia~~~-~is~~tv~~ 40 (42)
T cd00569 20 AGESVAEIARRL-GVSRSTLYR 40 (42)
T ss_pred cCCCHHHHHHHH-CCCHHHHHH
Confidence 455677788776 566555544
No 150
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=26.42 E-value=1.7e+02 Score=18.29 Aligned_cols=31 Identities=6% Similarity=-0.154 Sum_probs=25.0
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.+.--.|-.-..||..| |-+.+.|+++.
T Consensus 140 ~v~~l~~~~g~s~~EIAe~l-gis~~tV~~~l 170 (196)
T PRK12535 140 EALILTQVLGYTYEEAAKIA-DVRVGTIRSRV 170 (196)
T ss_pred HHhhhHHHhCCCHHHHHHHh-CCCHHHHHHHH
Confidence 45555656677788999999 99999999997
No 151
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=26.11 E-value=1.7e+02 Score=18.05 Aligned_cols=30 Identities=20% Similarity=0.254 Sum_probs=23.2
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.+ --.|-....||..| |-|.+.|+++-
T Consensus 162 ~vl~l-~~e~~s~~EIA~~l-gis~~tV~~~l 191 (208)
T PRK08295 162 EVLEL-YLDGKSYQEIAEEL-NRHVKSIDNAL 191 (208)
T ss_pred HHHHH-HHccCCHHHHHHHH-CCCHHHHHHHH
Confidence 34445 34577888999998 89999999987
No 152
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=25.08 E-value=1.9e+02 Score=18.36 Aligned_cols=31 Identities=10% Similarity=-0.020 Sum_probs=24.1
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.+.--.|-.-..||..| |-|.+.|+++.
T Consensus 155 ~v~~L~~~~g~s~~EIAe~l-gis~~tV~~~l 185 (206)
T PRK12544 155 RVFMMREFIELETNEICHAV-DLSVSNLNVLL 185 (206)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 34445555566778999999 99999999987
No 153
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=24.94 E-value=2.1e+02 Score=18.83 Aligned_cols=60 Identities=17% Similarity=0.146 Sum_probs=38.7
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHHHH---hhhhhhhhhCC--CCCCCCCCHHHHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYYKN---TKLKRKHEEGG--LMVPMKKNLERDLRIV 64 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw~~---~~l~~~~~~~~--~~~~~~~~~~~~~~~~ 64 (67)
..++.++-.-|-....||..| |-+.+.|+++. . ..|+..+.+.- ...+.+...++-+.++
T Consensus 167 R~v~~L~~~eg~S~~EIA~~L-gis~~TVk~rl-~RAr~~Lr~~l~~~~~~~~~~~~~~~~~~~~~~ 231 (244)
T TIGR03001 167 RHLLRLHFVDGLSMDRIGAMY-QVHRSTVSRWV-AQARERLLERTRRRLAERLKLSSPELESLLGLV 231 (244)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH-HHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Confidence 345666666777899999998 89999999987 3 22233222211 1456666666666554
No 154
>cd08781 Death_UNC5-like Death domain found in Uncoordinated-5 homolog family. Death Domain (DD) found in Uncoordinated-5 (UNC-5) homolog family, which includes Unc5A, B, C and D in vertebrates. UNC5 proteins are receptors for secreted netrins (netrin-1, -3 and -4) that are involved in diverse processes like axonal guidance, neuronal migration, blood vessel patterning, and apoptosis. They are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. 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
Probab=24.93 E-value=52 Score=18.33 Aligned_cols=14 Identities=21% Similarity=0.539 Sum_probs=11.9
Q ss_pred hcCCcHHHHHhhCC
Q 039547 11 ISESRWSVIAAHLP 24 (67)
Q Consensus 11 ~~G~kW~~Ia~~lp 24 (67)
..|+.|..+|..|.
T Consensus 18 ~~g~dWr~LA~~Lg 31 (83)
T cd08781 18 PRGNDWRLLAKKLS 31 (83)
T ss_pred CCCCCHHHHHHHhC
Confidence 46889999999995
No 155
>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=24.53 E-value=62 Score=17.59 Aligned_cols=20 Identities=25% Similarity=0.551 Sum_probs=16.7
Q ss_pred HHHHHhhCCCCChhhHHHHH
Q 039547 16 WSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 16 W~~Ia~~lpgRt~~~vknrw 35 (67)
-..||..+.|+|..+++..+
T Consensus 36 ~~~iA~~i~gks~eeir~~f 55 (78)
T PF01466_consen 36 CKYIANMIKGKSPEEIRKYF 55 (78)
T ss_dssp HHHHHHHHTTS-HHHHHHHH
T ss_pred HHHHHHHhcCCCHHHHHHHc
Confidence 35688999999999999998
No 156
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=24.27 E-value=1.6e+02 Score=17.35 Aligned_cols=32 Identities=16% Similarity=-0.004 Sum_probs=24.7
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.+.-..|-....||..| |=|...|+.+-
T Consensus 118 r~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l 149 (161)
T PRK12541 118 RNVLLLRDYYGFSYKEIAEMT-GLSLAKVKIEL 149 (161)
T ss_pred HHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345566666777788999998 88888899886
No 157
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. 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 s
Probab=23.94 E-value=84 Score=18.29 Aligned_cols=26 Identities=15% Similarity=0.304 Sum_probs=19.3
Q ss_pred HHHhcCCcHHHHHhhCCC-----CChhhHHHH
Q 039547 8 LFAISESRWSVIAAHLPG-----RTDNETNNY 34 (67)
Q Consensus 8 ~~~~~G~kW~~Ia~~lpg-----Rt~~~vknr 34 (67)
.-..+|.+|..+|+.| | =|+.+|-+.
T Consensus 8 ~~~nvGr~WK~laR~L-g~~cral~d~~ID~I 38 (90)
T cd08780 8 FAKSVGKKWKPVGRSL-QKNCRALRDPAIDNL 38 (90)
T ss_pred HHHHHhHHHHHHHHHH-cccccccchhHHHHH
Confidence 4467899999999999 4 456666553
No 158
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=23.69 E-value=2.3e+02 Score=18.80 Aligned_cols=30 Identities=27% Similarity=0.256 Sum_probs=23.2
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
-++.+.. -|-....||..| |-|...|+++-
T Consensus 140 EVLrLLA-qGkTnKEIAe~L-~IS~rTVkth~ 169 (198)
T PRK15201 140 HLLKLIA-SGYHLSETAALL-SLSEEQTKSLR 169 (198)
T ss_pred HHHHHHH-CCCCHHHHHHHh-CCCHHHHHHHH
Confidence 3455554 377899999999 88999999876
No 159
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=23.18 E-value=2.1e+02 Score=18.13 Aligned_cols=32 Identities=25% Similarity=0.207 Sum_probs=24.4
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..+ |-|.+.|+.+.
T Consensus 184 r~vl~l~y~~~~s~~eIA~~l-gis~~~v~~~~ 215 (227)
T TIGR02980 184 RRILLLRFFEDKTQSEIAERL-GISQMHVSRLL 215 (227)
T ss_pred HHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 345555555677888999998 88999998876
No 160
>PRK06930 positive control sigma-like factor; Validated
Probab=22.63 E-value=2.1e+02 Score=17.96 Aligned_cols=32 Identities=13% Similarity=0.057 Sum_probs=25.8
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-....||..| |-|.+.|+.+.
T Consensus 120 r~V~~L~~~eg~s~~EIA~~l-giS~~tVk~~l 151 (170)
T PRK06930 120 KEVYLMHRGYGLSYSEIADYL-NIKKSTVQSMI 151 (170)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 345566667788899999998 89999999987
No 161
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=22.04 E-value=2.1e+02 Score=17.69 Aligned_cols=31 Identities=23% Similarity=0.097 Sum_probs=25.6
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.++-..|-....||..| |-+...|+++.
T Consensus 118 ~v~~L~~~eg~s~~EIA~~l-gis~~tV~~~l 148 (182)
T PRK12511 118 AALHLVAIEGLSYQEAAAVL-GIPIGTLMSRI 148 (182)
T ss_pred HHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHH
Confidence 45666666788899999999 89999999987
No 162
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.03 E-value=1.9e+02 Score=17.31 Aligned_cols=31 Identities=6% Similarity=0.047 Sum_probs=23.9
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.++.++-.-|-.-..||..| |-+.+.|+.+-
T Consensus 126 ~i~~l~~~~~~s~~EIA~~l-gis~~tV~~~l 156 (173)
T PRK12522 126 TVLVLYYYEQYSYKEMSEIL-NIPIGTVKYRL 156 (173)
T ss_pred HHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 34555556677788899888 88899999886
No 163
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=21.89 E-value=1.9e+02 Score=17.19 Aligned_cols=32 Identities=16% Similarity=0.036 Sum_probs=25.0
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++.-.|-.-..||..| |-+.+.|+++-
T Consensus 114 r~v~~l~~~~g~s~~eIA~~l-gis~~tv~~~l 145 (165)
T PRK09644 114 AQAILLCDVHELTYEEAASVL-DLKLNTYKSHL 145 (165)
T ss_pred HHHHHhHHHhcCCHHHHHHHH-CCCHHHHHHHH
Confidence 345556666777888999998 88999999975
No 164
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=21.80 E-value=1.7e+02 Score=16.52 Aligned_cols=31 Identities=23% Similarity=0.296 Sum_probs=24.9
Q ss_pred HHHHHHHhcCC--cHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISES--RWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~--kW~~Ia~~lpgRt~~~vknrw 35 (67)
.|+++|.+-|. .-..||..+ |+++--|+|--
T Consensus 12 alV~~Y~~~~~PVgSk~ia~~l-~~s~aTIRN~M 44 (78)
T PF03444_consen 12 ALVELYIETGEPVGSKTIAEEL-GRSPATIRNEM 44 (78)
T ss_pred HHHHHHHhcCCCcCHHHHHHHH-CCChHHHHHHH
Confidence 46778888774 577899987 89999999976
No 165
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=21.77 E-value=77 Score=17.69 Aligned_cols=10 Identities=30% Similarity=0.730 Sum_probs=4.3
Q ss_pred CcHHHHHhhC
Q 039547 14 SRWSVIAAHL 23 (67)
Q Consensus 14 ~kW~~Ia~~l 23 (67)
..|..||+.+
T Consensus 84 ksw~~~a~~l 93 (101)
T PF13725_consen 84 KSWEEVAKEL 93 (101)
T ss_dssp --HHHHHHHC
T ss_pred CCHHHHHHHc
Confidence 3455555544
No 166
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=21.38 E-value=2.6e+02 Score=18.67 Aligned_cols=30 Identities=20% Similarity=0.087 Sum_probs=23.6
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
-+++++. -|-....||..| +-|...|+++=
T Consensus 150 eVL~Lia-~G~SnkEIA~~L-~IS~~TVk~hv 179 (217)
T PRK13719 150 DVFILYS-FGFSHEYIAQLL-NITVGSSKNKI 179 (217)
T ss_pred HHHHHHH-CCCCHHHHHHHh-CCCHHHHHHHH
Confidence 4555654 488899999999 88999999875
No 167
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.20 E-value=2.4e+02 Score=18.12 Aligned_cols=32 Identities=16% Similarity=0.068 Sum_probs=26.1
Q ss_pred HHHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 3 RLICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 3 ~ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
..++.++-..|-.-..||..| |=|.+.|+++-
T Consensus 140 R~v~~L~y~eg~s~~EIAe~L-giS~~tVk~~L 171 (216)
T PRK12533 140 REVLVLRELEDMSYREIAAIA-DVPVGTVMSRL 171 (216)
T ss_pred HhHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 456666666777889999999 89999999987
No 168
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.86 E-value=88 Score=19.20 Aligned_cols=22 Identities=27% Similarity=0.380 Sum_probs=13.5
Q ss_pred hHHHHHHHHh-c-CCcHHHHHhhC
Q 039547 2 DRLICRLFAI-S-ESRWSVIAAHL 23 (67)
Q Consensus 2 d~ll~~~~~~-~-G~kW~~Ia~~l 23 (67)
+..|+.++=. . |..|..||..|
T Consensus 86 ~k~Ii~lry~~r~~~TW~~IA~~l 109 (130)
T PF05263_consen 86 EKRIIKLRYDRRSRRTWYQIAQKL 109 (130)
T ss_pred HHHHHHHHHcccccchHHHHHHHh
Confidence 3444444333 3 36799999877
No 169
>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=20.36 E-value=1.4e+02 Score=18.81 Aligned_cols=31 Identities=23% Similarity=0.157 Sum_probs=23.1
Q ss_pred HHHHHHHhcCCcHHHHHhhCCCCChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPGRTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpgRt~~~vknrw 35 (67)
.|-+|+ .-|-.-+.||..|.|.|-|+|--.-
T Consensus 10 ~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~ 40 (162)
T PF07750_consen 10 RLRKLW-AEGLSASQIARQLGGVSRNAVIGKA 40 (162)
T ss_pred HHHHHH-HcCCCHHHHHHHhCCcchhhhhhhh
Confidence 334444 4466778999999889999988765
No 170
>PRK15328 invasion protein IagB; Provisional
Probab=20.24 E-value=2.4e+02 Score=17.73 Aligned_cols=32 Identities=16% Similarity=0.416 Sum_probs=22.4
Q ss_pred HHHHHHHhcCCcHHHHHhhCCC--CChhhHHHHH
Q 039547 4 LICRLFAISESRWSVIAAHLPG--RTDNETNNYY 35 (67)
Q Consensus 4 ll~~~~~~~G~kW~~Ia~~lpg--Rt~~~vknrw 35 (67)
.|..++..+|+.|..++..=.| +.....+.+|
T Consensus 98 ~L~~~~~~~g~~~~alaaYNaG~~~~~~~~~~~Y 131 (160)
T PRK15328 98 ILSDMMKIYGYSWEAVGAYNAGTSPKRSDIRKRY 131 (160)
T ss_pred HHHHHHHHcCChHHhhhhccCCCCCCCCHHHHHH
Confidence 4667889999999988877654 3333445556
No 171
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=20.20 E-value=73 Score=18.68 Aligned_cols=23 Identities=26% Similarity=0.511 Sum_probs=14.4
Q ss_pred HHHHHHHhcC-CcHHHHHhhCCCC
Q 039547 4 LICRLFAISE-SRWSVIAAHLPGR 26 (67)
Q Consensus 4 ll~~~~~~~G-~kW~~Ia~~lpgR 26 (67)
+|-....-++ .+|...+.++||-
T Consensus 96 iLKKa~~~~~~~~~~~~~~~~~~~ 119 (121)
T PRK09413 96 LLKEAVEYGRAKKWIAHAPLLPGD 119 (121)
T ss_pred HHHHHHHHhchhhhhhcCCCCCCC
Confidence 3333333444 3699999999874
No 172
>COG4707 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.05 E-value=16 Score=21.80 Aligned_cols=12 Identities=42% Similarity=0.830 Sum_probs=9.8
Q ss_pred cCCcHHHHHhhC
Q 039547 12 SESRWSVIAAHL 23 (67)
Q Consensus 12 ~G~kW~~Ia~~l 23 (67)
-|++|+.+|+.|
T Consensus 78 kg~rW~F~ak~M 89 (107)
T COG4707 78 KGERWSFIAKEM 89 (107)
T ss_pred CCceeeEeHHHH
Confidence 467899999877
Done!