Query 037092
Match_columns 76
No_of_seqs 168 out of 1086
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 08:35:11 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037092.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037092hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 99.9 4.4E-22 9.6E-27 134.3 6.7 61 1-62 60-120 (238)
2 PLN03212 Transcription repress 99.8 2.2E-21 4.7E-26 131.4 6.5 65 1-66 76-140 (249)
3 PLN03212 Transcription repress 99.8 1.7E-20 3.8E-25 127.0 5.8 75 1-76 23-99 (249)
4 KOG0048 Transcription factor, 99.8 2E-20 4.4E-25 126.2 5.1 73 3-76 9-83 (238)
5 PLN03091 hypothetical protein; 99.8 3.8E-20 8.1E-25 133.3 6.4 67 1-68 65-131 (459)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.8 4.2E-19 9.2E-24 97.0 3.9 58 6-64 1-58 (60)
7 PF00249 Myb_DNA-binding: Myb- 99.8 7.7E-19 1.7E-23 92.6 4.6 45 3-48 1-47 (48)
8 PLN03091 hypothetical protein; 99.8 9E-19 2E-23 126.2 5.2 75 1-76 12-88 (459)
9 smart00717 SANT SANT SWI3, AD 99.7 2.8E-16 6E-21 81.0 5.6 46 3-49 1-47 (49)
10 cd00167 SANT 'SWI3, ADA2, N-Co 99.6 5.7E-15 1.2E-19 75.0 5.4 42 5-47 1-43 (45)
11 KOG0049 Transcription factor, 99.4 2.5E-13 5.5E-18 102.1 6.8 73 1-74 358-431 (939)
12 COG5147 REB1 Myb superfamily p 98.9 5.8E-10 1.3E-14 82.4 2.6 74 1-75 18-92 (512)
13 KOG0051 RNA polymerase I termi 98.9 3E-09 6.6E-14 79.7 5.0 68 2-71 383-452 (607)
14 KOG0050 mRNA splicing protein 98.8 7.4E-09 1.6E-13 76.6 3.8 71 1-72 5-76 (617)
15 COG5147 REB1 Myb superfamily p 98.6 4.1E-08 9E-13 72.7 4.5 53 1-54 70-122 (512)
16 KOG0049 Transcription factor, 98.5 1.2E-07 2.5E-12 72.2 3.7 72 2-74 304-379 (939)
17 TIGR01557 myb_SHAQKYF myb-like 98.4 1.4E-06 3E-11 47.5 5.4 45 3-48 3-53 (57)
18 KOG0457 Histone acetyltransfer 98.4 1E-06 2.2E-11 64.1 6.2 47 3-49 72-119 (438)
19 TIGR02894 DNA_bind_RsfA transc 98.3 1.4E-06 3E-11 56.3 4.1 51 2-54 3-60 (161)
20 KOG0050 mRNA splicing protein 98.1 2.4E-06 5.1E-11 63.6 2.9 52 1-54 57-108 (617)
21 PF08914 Myb_DNA-bind_2: Rap1 98.0 1.2E-05 2.7E-10 44.9 4.1 49 3-52 2-60 (65)
22 PF13837 Myb_DNA-bind_4: Myb/S 97.9 1.1E-05 2.3E-10 46.4 2.9 52 3-56 1-70 (90)
23 KOG1279 Chromatin remodeling f 97.9 2.9E-05 6.3E-10 57.8 5.2 42 3-44 253-294 (506)
24 COG5259 RSC8 RSC chromatin rem 97.8 4.3E-05 9.4E-10 56.4 4.7 42 3-44 279-320 (531)
25 COG5114 Histone acetyltransfer 97.6 6.5E-05 1.4E-09 53.6 3.8 46 4-49 64-110 (432)
26 PRK13923 putative spore coat p 97.6 7.2E-05 1.6E-09 48.8 3.5 50 2-53 4-60 (170)
27 PF13873 Myb_DNA-bind_5: Myb/S 97.4 0.00058 1.2E-08 38.5 5.3 43 2-44 1-65 (78)
28 KOG0051 RNA polymerase I termi 96.7 0.0025 5.5E-08 48.5 4.3 58 1-59 434-518 (607)
29 PF12776 Myb_DNA-bind_3: Myb/S 96.5 0.011 2.3E-07 34.2 5.1 46 5-52 1-64 (96)
30 PF09111 SLIDE: SLIDE; InterP 96.5 0.0053 1.2E-07 37.9 3.9 47 3-50 49-111 (118)
31 KOG2656 DNA methyltransferase 96.2 0.0072 1.6E-07 44.2 3.9 56 2-58 129-190 (445)
32 COG5118 BDP1 Transcription ini 95.6 0.025 5.3E-07 41.5 4.5 41 4-44 366-406 (507)
33 KOG4282 Transcription factor G 95.5 0.068 1.5E-06 37.7 6.4 50 4-55 55-118 (345)
34 PF08281 Sigma70_r4_2: Sigma-7 95.2 0.058 1.3E-06 28.0 4.1 36 8-44 12-47 (54)
35 PF13325 MCRS_N: N-terminal re 94.4 0.12 2.6E-06 34.6 5.0 50 3-53 73-130 (199)
36 PF07750 GcrA: GcrA cell cycle 94.4 0.06 1.3E-06 34.8 3.4 39 5-44 2-40 (162)
37 KOG1194 Predicted DNA-binding 93.9 0.16 3.4E-06 38.1 5.0 41 4-44 188-228 (534)
38 PLN03142 Probable chromatin-re 93.2 0.19 4.1E-06 40.7 4.9 47 3-50 926-985 (1033)
39 PF11626 Rap1_C: TRF2-interact 90.9 0.27 5.8E-06 28.4 2.5 13 3-15 47-59 (87)
40 TIGR02985 Sig70_bacteroi1 RNA 90.6 0.86 1.9E-05 27.6 4.8 35 9-44 116-150 (161)
41 PF13325 MCRS_N: N-terminal re 90.0 0.88 1.9E-05 30.5 4.7 43 5-49 1-46 (199)
42 PF04545 Sigma70_r4: Sigma-70, 89.7 0.93 2E-05 23.0 3.8 35 9-44 7-41 (50)
43 KOG4167 Predicted DNA-binding 89.6 0.78 1.7E-05 36.4 4.7 41 4-44 620-660 (907)
44 PRK11179 DNA-binding transcrip 88.5 1.6 3.6E-05 27.3 5.0 36 8-44 8-44 (153)
45 KOG2009 Transcription initiati 88.5 0.56 1.2E-05 36.0 3.2 42 3-44 409-450 (584)
46 PF13936 HTH_38: Helix-turn-he 87.6 0.54 1.2E-05 23.8 1.9 37 4-42 3-39 (44)
47 cd08319 Death_RAIDD Death doma 85.2 1.8 3.9E-05 25.0 3.5 31 11-42 2-32 (83)
48 PRK11169 leucine-responsive tr 85.1 2.4 5.2E-05 26.9 4.4 36 8-44 13-49 (164)
49 KOG4468 Polycomb-group transcr 83.5 4.5 9.7E-05 31.7 5.8 58 3-62 88-155 (782)
50 cd08803 Death_ank3 Death domai 83.3 2.7 5.8E-05 24.3 3.7 31 11-42 4-34 (84)
51 PRK09643 RNA polymerase sigma 83.2 3.6 7.7E-05 26.4 4.7 36 8-44 136-171 (192)
52 smart00595 MADF subfamily of S 83.2 1.4 3.1E-05 24.8 2.5 19 25-44 30-48 (89)
53 PRK09641 RNA polymerase sigma 83.0 3.6 7.7E-05 25.8 4.5 35 9-44 139-173 (187)
54 COG5352 Uncharacterized protei 82.7 1.9 4E-05 27.8 3.1 37 5-42 2-38 (169)
55 PF13404 HTH_AsnC-type: AsnC-t 82.1 4.3 9.4E-05 20.3 3.8 35 9-44 3-38 (42)
56 TIGR02937 sigma70-ECF RNA poly 81.7 4.4 9.5E-05 23.7 4.4 34 10-44 114-147 (158)
57 PRK09652 RNA polymerase sigma 81.1 4.8 0.0001 24.8 4.6 34 10-44 132-165 (182)
58 PRK09645 RNA polymerase sigma 81.1 6.4 0.00014 24.4 5.2 35 9-44 121-155 (173)
59 PRK11924 RNA polymerase sigma 80.8 4.7 0.0001 24.8 4.4 34 10-44 129-162 (179)
60 TIGR02939 RpoE_Sigma70 RNA pol 80.7 3.4 7.4E-05 25.9 3.8 35 9-44 141-175 (190)
61 cd08317 Death_ank Death domain 80.3 2.7 5.8E-05 23.9 2.9 31 11-42 4-34 (84)
62 PRK12532 RNA polymerase sigma 80.2 6.3 0.00014 25.1 5.0 47 11-58 141-189 (195)
63 PF07638 Sigma70_ECF: ECF sigm 79.9 5.4 0.00012 25.6 4.6 36 8-44 137-172 (185)
64 PRK12530 RNA polymerase sigma 77.9 7.1 0.00015 24.9 4.7 34 10-44 138-171 (189)
65 TIGR02948 SigW_bacill RNA poly 77.6 6 0.00013 24.7 4.3 34 10-44 140-173 (187)
66 PF11035 SnAPC_2_like: Small n 77.2 9.1 0.0002 27.7 5.4 40 5-44 23-66 (344)
67 PRK09637 RNA polymerase sigma 77.0 7.5 0.00016 24.7 4.6 35 9-44 109-143 (181)
68 PRK11923 algU RNA polymerase s 77.0 6.7 0.00015 24.8 4.4 34 10-44 142-175 (193)
69 PRK09642 RNA polymerase sigma 76.9 8.7 0.00019 23.5 4.8 35 9-44 109-143 (160)
70 cd08804 Death_ank2 Death domai 76.6 4.9 0.00011 23.0 3.3 31 11-42 4-34 (84)
71 PRK12514 RNA polymerase sigma 76.5 8.1 0.00018 24.1 4.6 35 9-44 132-166 (179)
72 TIGR02943 Sig70_famx1 RNA poly 76.4 8.9 0.00019 24.5 4.9 33 11-44 136-168 (188)
73 PRK12515 RNA polymerase sigma 76.4 8.6 0.00019 24.3 4.8 35 9-44 134-168 (189)
74 TIGR02952 Sig70_famx2 RNA poly 76.2 8.2 0.00018 23.7 4.5 35 9-44 125-159 (170)
75 PRK09047 RNA polymerase factor 75.7 10 0.00022 23.0 4.9 34 10-44 110-143 (161)
76 PRK12529 RNA polymerase sigma 75.6 11 0.00024 23.7 5.1 41 9-51 130-170 (178)
77 TIGR02954 Sig70_famx3 RNA poly 75.5 8.6 0.00019 23.8 4.5 36 8-44 121-156 (169)
78 smart00344 HTH_ASNC helix_turn 75.3 13 0.00028 21.4 5.0 39 8-48 2-41 (108)
79 PRK12531 RNA polymerase sigma 75.1 9.7 0.00021 24.3 4.8 34 10-44 145-178 (194)
80 PF10545 MADF_DNA_bdg: Alcohol 74.9 3.3 7.2E-05 22.6 2.3 20 25-44 29-49 (85)
81 PF01388 ARID: ARID/BRIGHT DNA 74.5 10 0.00022 21.4 4.4 37 13-50 40-89 (92)
82 PRK08241 RNA polymerase factor 74.4 18 0.00039 25.1 6.3 41 12-55 159-199 (339)
83 PRK09636 RNA polymerase sigma 74.4 19 0.0004 24.7 6.3 43 10-55 119-161 (293)
84 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 74.2 8.7 0.00019 20.2 3.6 36 7-44 6-41 (50)
85 smart00005 DEATH DEATH domain, 73.3 6 0.00013 22.0 3.1 32 10-42 4-36 (88)
86 PRK09649 RNA polymerase sigma 72.9 10 0.00023 24.0 4.5 35 9-44 133-167 (185)
87 cd08318 Death_NMPP84 Death dom 72.4 7.5 0.00016 22.3 3.4 25 17-42 13-37 (86)
88 PRK04217 hypothetical protein; 71.7 14 0.00031 22.4 4.6 36 7-44 44-79 (110)
89 PRK12527 RNA polymerase sigma 71.6 15 0.00032 22.5 4.9 36 8-44 107-142 (159)
90 PRK06811 RNA polymerase factor 71.5 15 0.00033 23.3 5.0 46 8-56 133-178 (189)
91 cd08311 Death_p75NR Death doma 71.3 5.7 0.00012 22.5 2.7 34 8-43 2-35 (77)
92 smart00501 BRIGHT BRIGHT, ARID 71.2 12 0.00026 21.4 4.1 38 13-51 36-86 (93)
93 KOG4329 DNA-binding protein [G 71.0 12 0.00026 27.7 4.8 41 4-44 278-319 (445)
94 PRK12523 RNA polymerase sigma 70.7 19 0.00041 22.4 5.3 35 9-44 122-156 (172)
95 PRK09648 RNA polymerase sigma 70.5 14 0.00031 23.2 4.8 35 9-44 142-176 (189)
96 PRK12536 RNA polymerase sigma 70.5 14 0.00031 23.2 4.7 35 9-44 132-166 (181)
97 PRK12520 RNA polymerase sigma 70.3 15 0.00032 23.3 4.7 34 10-44 135-168 (191)
98 cd08777 Death_RIP1 Death Domai 70.2 7.4 0.00016 22.4 3.0 30 13-43 4-33 (86)
99 TIGR02983 SigE-fam_strep RNA p 70.1 14 0.0003 22.6 4.5 35 9-44 113-147 (162)
100 TIGR02957 SigX4 RNA polymerase 70.0 32 0.0007 23.5 6.9 42 11-55 113-154 (281)
101 PRK12545 RNA polymerase sigma 69.9 14 0.00031 23.8 4.7 33 11-44 144-176 (201)
102 TIGR02999 Sig-70_X6 RNA polyme 69.9 16 0.00034 22.8 4.8 36 8-44 136-171 (183)
103 TIGR02960 SigX5 RNA polymerase 69.5 12 0.00026 25.7 4.5 32 12-44 148-179 (324)
104 cd08805 Death_ank1 Death domai 68.8 8.8 0.00019 22.2 3.2 33 11-44 4-39 (84)
105 PRK12512 RNA polymerase sigma 68.6 20 0.00042 22.5 5.0 35 9-44 134-168 (184)
106 PRK12542 RNA polymerase sigma 68.1 17 0.00037 22.9 4.7 34 10-44 126-159 (185)
107 PRK06759 RNA polymerase factor 67.8 19 0.0004 21.7 4.7 34 10-44 110-143 (154)
108 PRK12524 RNA polymerase sigma 67.3 18 0.00038 23.1 4.7 35 9-44 139-173 (196)
109 TIGR02950 SigM_subfam RNA poly 66.7 4.5 9.7E-05 24.5 1.7 23 21-44 120-142 (154)
110 PF09420 Nop16: Ribosome bioge 66.7 21 0.00046 22.7 4.9 41 4-44 115-159 (164)
111 PRK12528 RNA polymerase sigma 66.5 18 0.00039 22.1 4.5 35 9-44 116-150 (161)
112 TIGR02984 Sig-70_plancto1 RNA 66.5 19 0.00041 22.4 4.6 34 10-44 144-177 (189)
113 PRK05602 RNA polymerase sigma 66.3 17 0.00037 22.8 4.4 35 9-44 131-165 (186)
114 PRK12516 RNA polymerase sigma 65.6 20 0.00043 22.9 4.7 48 8-56 118-167 (187)
115 COG2963 Transposase and inacti 65.6 25 0.00055 20.6 6.2 41 3-44 5-46 (116)
116 cd08779 Death_PIDD Death Domai 65.5 9 0.0002 22.0 2.7 32 12-44 3-37 (86)
117 PRK13919 putative RNA polymera 65.2 21 0.00045 22.4 4.6 35 9-44 138-172 (186)
118 PRK11922 RNA polymerase sigma 65.1 8.3 0.00018 25.5 2.9 34 10-44 153-186 (231)
119 PRK09647 RNA polymerase sigma 64.9 21 0.00046 23.2 4.8 34 10-44 142-175 (203)
120 cd08306 Death_FADD Fas-associa 63.9 15 0.00032 21.1 3.4 30 12-42 3-32 (86)
121 PRK12547 RNA polymerase sigma 63.8 25 0.00055 21.7 4.8 35 9-44 115-149 (164)
122 TIGR02989 Sig-70_gvs1 RNA poly 63.7 25 0.00053 21.3 4.7 35 9-44 114-148 (159)
123 PRK09639 RNA polymerase sigma 63.7 23 0.0005 21.6 4.6 34 9-44 115-148 (166)
124 cd06171 Sigma70_r4 Sigma70, re 63.6 15 0.00033 17.4 4.1 37 6-44 11-47 (55)
125 PF10440 WIYLD: Ubiquitin-bind 63.5 6.3 0.00014 21.9 1.7 19 12-30 30-48 (65)
126 PRK12537 RNA polymerase sigma 62.7 24 0.00052 22.2 4.6 34 10-44 137-170 (182)
127 PRK09651 RNA polymerase sigma 62.5 20 0.00043 22.4 4.2 35 9-44 122-156 (172)
128 PRK09646 RNA polymerase sigma 61.8 26 0.00056 22.3 4.7 35 9-44 145-179 (194)
129 KOG0384 Chromodomain-helicase 61.8 6 0.00013 33.3 2.0 26 4-29 1134-1160(1373)
130 PRK12546 RNA polymerase sigma 61.6 22 0.00049 22.7 4.4 35 9-44 116-150 (188)
131 PF04504 DUF573: Protein of un 61.3 31 0.00068 20.3 5.2 18 4-21 5-22 (98)
132 KOG1194 Predicted DNA-binding 59.7 6.5 0.00014 29.8 1.7 40 4-44 471-510 (534)
133 PF13384 HTH_23: Homeodomain-l 59.6 13 0.00029 18.4 2.5 34 8-43 4-37 (50)
134 PRK12543 RNA polymerase sigma 59.1 40 0.00087 21.0 5.2 35 9-44 120-154 (179)
135 PF09846 DUF2073: Uncharacteri 58.6 9.6 0.00021 23.1 2.1 17 4-20 27-43 (104)
136 PRK09415 RNA polymerase factor 58.3 28 0.0006 21.9 4.3 35 9-44 130-164 (179)
137 PRK12544 RNA polymerase sigma 58.3 34 0.00073 22.3 4.8 32 12-44 154-185 (206)
138 PRK12526 RNA polymerase sigma 57.6 34 0.00074 22.1 4.7 34 10-44 157-190 (206)
139 PRK12535 RNA polymerase sigma 57.3 32 0.00069 22.2 4.5 34 10-44 137-170 (196)
140 PRK12511 RNA polymerase sigma 57.0 35 0.00076 21.7 4.7 35 9-44 114-148 (182)
141 PRK09638 RNA polymerase sigma 56.9 11 0.00024 23.4 2.2 35 9-44 129-163 (176)
142 PRK00118 putative DNA-binding 55.9 43 0.00092 20.1 4.8 36 8-44 19-54 (104)
143 PRK12538 RNA polymerase sigma 55.7 27 0.00059 23.3 4.1 35 9-44 174-208 (233)
144 PRK12541 RNA polymerase sigma 55.2 35 0.00075 20.8 4.3 34 10-44 116-149 (161)
145 PRK08295 RNA polymerase factor 54.8 37 0.00081 21.5 4.5 30 13-44 162-191 (208)
146 PLN03142 Probable chromatin-re 54.6 31 0.00068 28.5 4.9 41 4-44 825-866 (1033)
147 TIGR02959 SigZ RNA polymerase 54.6 44 0.00096 20.8 4.8 35 9-44 103-137 (170)
148 PRK12522 RNA polymerase sigma 54.0 42 0.0009 20.8 4.6 32 12-44 125-156 (173)
149 PRK12519 RNA polymerase sigma 53.4 32 0.00068 21.7 4.0 35 9-44 144-178 (194)
150 PF09905 DUF2132: Uncharacteri 51.8 21 0.00045 19.8 2.5 31 11-43 12-45 (64)
151 PRK12518 RNA polymerase sigma 51.6 14 0.0003 22.9 2.1 25 19-44 133-157 (175)
152 PRK09644 RNA polymerase sigma 51.4 47 0.001 20.3 4.5 35 9-44 111-145 (165)
153 PRK12540 RNA polymerase sigma 51.4 48 0.001 21.0 4.6 47 9-56 114-162 (182)
154 cd01670 Death Death Domain: a 51.1 23 0.0005 19.1 2.8 27 15-42 3-29 (79)
155 cd00569 HTH_Hin_like Helix-tur 51.1 21 0.00045 15.0 4.7 37 4-42 4-40 (42)
156 PRK06704 RNA polymerase factor 51.0 74 0.0016 21.4 6.5 46 10-56 120-167 (228)
157 PF00531 Death: Death domain; 50.9 36 0.00078 18.3 3.5 24 18-42 8-31 (83)
158 TIGR03001 Sig-70_gmx1 RNA poly 50.6 47 0.001 22.4 4.7 34 10-44 165-198 (244)
159 PRK06930 positive control sigm 50.5 51 0.0011 21.2 4.6 33 11-44 119-151 (170)
160 PF01527 HTH_Tnp_1: Transposas 50.1 31 0.00067 18.4 3.1 40 3-44 4-43 (76)
161 PRK12534 RNA polymerase sigma 49.3 54 0.0012 20.5 4.6 34 10-44 141-174 (187)
162 PRK06986 fliA flagellar biosyn 48.5 42 0.00091 22.1 4.1 35 9-44 187-221 (236)
163 PRK12513 RNA polymerase sigma 46.9 20 0.00044 22.7 2.3 32 12-44 145-176 (194)
164 PF05263 DUF722: Protein of un 46.6 55 0.0012 20.5 4.2 36 6-43 82-119 (130)
165 PF09197 Rap1-DNA-bind: Rap1, 46.4 22 0.00047 21.6 2.2 44 5-49 1-75 (105)
166 TIGR02947 SigH_actino RNA poly 46.0 24 0.00051 22.4 2.6 30 14-44 139-168 (193)
167 PRK02866 cyanate hydratase; Va 45.8 51 0.0011 21.1 4.0 32 12-44 8-39 (147)
168 PRK07037 extracytoplasmic-func 45.5 53 0.0012 19.9 4.1 34 10-44 113-146 (163)
169 PRK12533 RNA polymerase sigma 45.4 56 0.0012 21.5 4.4 35 9-44 137-171 (216)
170 PRK09635 sigI RNA polymerase s 45.1 1E+02 0.0022 21.3 6.7 40 13-55 125-164 (290)
171 PRK08301 sporulation sigma fac 44.8 56 0.0012 21.4 4.3 23 21-44 197-219 (234)
172 PRK12525 RNA polymerase sigma 44.1 71 0.0015 19.7 4.5 34 10-44 122-155 (168)
173 PF08074 CHDCT2: CHDCT2 (NUC03 43.8 16 0.00036 24.0 1.5 40 5-44 5-58 (173)
174 KOG0431 Auxilin-like protein a 43.2 37 0.0008 25.4 3.5 61 12-73 376-441 (453)
175 PF10892 DUF2688: Protein of u 42.5 23 0.00051 19.2 1.8 16 3-18 42-57 (60)
176 PRK07670 RNA polymerase sigma 42.5 63 0.0014 21.6 4.3 35 9-44 204-238 (251)
177 COG1522 Lrp Transcriptional re 42.3 77 0.0017 19.1 5.0 36 8-44 7-43 (154)
178 PRK09413 IS2 repressor TnpA; R 42.2 34 0.00073 20.5 2.7 26 10-35 93-119 (121)
179 PF11198 DUF2857: Protein of u 41.6 69 0.0015 20.8 4.2 35 9-44 74-108 (180)
180 TIGR02980 SigBFG RNA polymeras 41.5 69 0.0015 20.8 4.3 33 11-44 183-215 (227)
181 PF00046 Homeobox: Homeobox do 40.2 52 0.0011 16.6 3.6 41 3-44 4-48 (57)
182 PF02954 HTH_8: Bacterial regu 39.6 49 0.0011 16.1 3.6 33 9-42 5-37 (42)
183 PRK10100 DNA-binding transcrip 39.5 87 0.0019 20.6 4.6 36 6-44 156-191 (216)
184 PRK12517 RNA polymerase sigma 39.5 99 0.0022 19.6 4.8 35 9-44 131-165 (188)
185 COG2197 CitB Response regulato 39.5 68 0.0015 21.0 4.0 43 5-51 148-190 (211)
186 TIGR02479 FliA_WhiG RNA polyme 38.5 86 0.0019 20.4 4.4 35 9-44 178-212 (224)
187 PRK15201 fimbriae regulatory p 38.4 1E+02 0.0022 20.8 4.6 37 5-44 133-169 (198)
188 PRK01905 DNA-binding protein F 38.3 72 0.0016 17.6 4.3 35 8-43 36-70 (77)
189 PRK09640 RNA polymerase sigma 37.1 28 0.0006 22.0 1.8 27 17-44 145-171 (188)
190 TIGR00673 cynS cyanate hydrata 37.0 84 0.0018 20.2 4.0 32 12-44 11-42 (150)
191 PF09633 DUF2023: Protein of u 37.0 21 0.00045 21.6 1.1 11 5-15 74-84 (101)
192 PRK09191 two-component respons 36.8 77 0.0017 20.5 4.0 35 9-44 91-125 (261)
193 PRK15411 rcsA colanic acid cap 36.5 86 0.0019 20.4 4.1 36 6-44 138-173 (207)
194 COG4628 Uncharacterized conser 36.0 40 0.00087 21.0 2.3 20 11-32 21-40 (136)
195 PRK06288 RNA polymerase sigma 35.5 1E+02 0.0022 20.8 4.5 34 10-44 216-249 (268)
196 PRK00430 fis global DNA-bindin 35.3 95 0.0021 18.1 4.1 33 9-42 55-87 (95)
197 PF04218 CENP-B_N: CENP-B N-te 34.4 60 0.0013 16.7 2.6 40 3-44 4-43 (53)
198 TIGR01636 phage_rinA phage tra 34.2 1.1E+02 0.0024 18.7 5.0 35 7-43 84-120 (134)
199 PRK07122 RNA polymerase sigma 33.8 89 0.0019 21.2 4.0 34 10-44 219-252 (264)
200 PRK12539 RNA polymerase sigma 33.6 1.2E+02 0.0027 18.9 4.5 35 9-44 134-168 (184)
201 PRK07408 RNA polymerase sigma 32.9 1.1E+02 0.0023 20.6 4.3 35 9-44 206-240 (256)
202 TIGR00696 wecB_tagA_cpsF bacte 32.4 64 0.0014 20.9 3.0 23 3-25 81-103 (177)
203 TIGR02859 spore_sigH RNA polym 31.9 1.2E+02 0.0027 18.8 4.3 22 22-44 165-186 (198)
204 COG3793 TerB Tellurite resista 31.9 60 0.0013 20.8 2.7 20 3-22 117-136 (144)
205 PRK05911 RNA polymerase sigma 31.8 1.2E+02 0.0026 20.5 4.3 35 9-44 208-242 (257)
206 PRK10360 DNA-binding transcrip 31.3 1.2E+02 0.0027 18.3 4.5 37 5-44 137-173 (196)
207 KOG3554 Histone deacetylase co 30.8 88 0.0019 24.2 3.8 41 5-45 287-328 (693)
208 COG2992 Bax Uncharacterized Fl 30.7 30 0.00066 24.0 1.3 25 3-27 95-119 (262)
209 PRK08583 RNA polymerase sigma 30.4 1.4E+02 0.0029 19.9 4.4 32 12-44 211-242 (257)
210 PF06461 DUF1086: Domain of Un 30.1 1.5E+02 0.0033 19.0 4.5 40 5-44 40-82 (145)
211 cd08780 Death_TRADD Death Doma 28.8 77 0.0017 18.7 2.6 26 16-42 7-37 (90)
212 cd08312 Death_MyD88 Death doma 28.3 59 0.0013 18.2 2.0 23 19-42 13-35 (79)
213 KOG3841 TEF-1 and related tran 28.0 1.9E+02 0.0041 21.7 5.0 42 3-44 76-138 (455)
214 COG4654 Cytochrome c551/c552 [ 28.0 36 0.00078 20.8 1.1 24 19-42 44-67 (110)
215 COG1595 RpoE DNA-directed RNA 26.6 1.2E+02 0.0027 18.9 3.5 35 9-44 130-164 (182)
216 PRK03692 putative UDP-N-acetyl 26.4 86 0.0019 21.4 2.9 22 3-24 138-159 (243)
217 PLN03162 golden-2 like transcr 26.0 2.3E+02 0.0049 21.4 5.1 42 3-44 237-283 (526)
218 KOG3200 Uncharacterized conser 25.9 71 0.0015 21.5 2.3 25 6-30 21-46 (224)
219 PF13934 ELYS: Nuclear pore co 25.4 59 0.0013 21.8 1.9 17 4-20 198-214 (226)
220 KOG0703 Predicted GTPase-activ 24.9 1.2E+02 0.0026 21.6 3.4 52 3-58 70-123 (287)
221 PF09862 DUF2089: Protein of u 24.8 1.7E+02 0.0038 17.8 6.2 41 8-50 35-75 (113)
222 PHA02291 hypothetical protein 23.9 30 0.00066 21.3 0.3 18 27-44 75-93 (132)
223 PF11084 DUF2621: Protein of u 23.5 74 0.0016 20.2 2.0 27 3-29 56-82 (141)
224 TIGR03209 P21_Cbot clostridium 23.4 1.3E+02 0.0027 17.9 3.0 9 14-22 101-109 (142)
225 PRK05572 sporulation sigma fac 23.4 2E+02 0.0043 19.2 4.2 34 10-44 206-239 (252)
226 PF03808 Glyco_tran_WecB: Glyc 23.3 1.1E+02 0.0024 19.4 2.8 29 3-31 82-110 (172)
227 smart00760 Bac_DnaA_C Bacteria 23.0 84 0.0018 16.4 1.9 19 18-36 41-59 (60)
228 PF08899 DUF1844: Domain of un 22.6 1.3E+02 0.0028 17.0 2.7 18 3-20 52-69 (74)
229 PRK03906 mannonate dehydratase 22.5 59 0.0013 23.8 1.6 27 4-30 38-64 (385)
230 TIGR03879 near_KaiC_dom probab 22.5 1.6E+02 0.0035 16.6 4.2 36 8-44 17-53 (73)
231 KOG0724 Zuotin and related mol 21.8 37 0.0008 23.8 0.4 40 5-44 33-82 (335)
232 PRK15328 invasion protein IagB 21.7 1.8E+02 0.0039 18.6 3.6 32 13-44 98-131 (160)
233 TIGR02835 spore_sigmaE RNA pol 21.5 2.5E+02 0.0054 18.4 4.5 22 22-44 198-219 (234)
234 PF03832 WSK: WSK motif; Inte 21.3 56 0.0012 15.5 0.9 14 22-35 4-17 (31)
235 TIGR01765 tspaseT_teng_N trans 20.8 1.1E+02 0.0023 16.7 2.2 35 5-41 7-44 (73)
236 cd06571 Bac_DnaA_C C-terminal 20.8 1.8E+02 0.0038 16.4 5.2 28 17-44 39-66 (90)
237 TIGR00695 uxuA mannonate dehyd 20.7 69 0.0015 23.7 1.6 27 4-30 38-64 (394)
238 cd09235 V_Alix Middle V-domain 20.7 65 0.0014 22.9 1.5 33 9-44 104-154 (339)
239 PF13725 tRNA_bind_2: Possible 20.6 60 0.0013 18.5 1.1 23 9-32 71-93 (101)
240 PF01466 Skp1: Skp1 family, di 20.6 77 0.0017 17.5 1.5 20 25-44 36-55 (78)
241 PF04219 DUF413: Protein of un 20.5 93 0.002 18.4 1.9 18 2-23 14-31 (93)
242 COG1168 MalY Bifunctional PLP- 20.3 98 0.0021 23.0 2.3 20 4-23 173-192 (388)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.86 E-value=4.4e-22 Score=134.27 Aligned_cols=61 Identities=48% Similarity=0.769 Sum_probs=56.8
Q ss_pred CCCCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHhhCCCCCCC
Q 037092 1 MKPWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEEGGLKVPM 62 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~~~~~~~ 62 (76)
|++|+||+|||.+|+++|..+|++|+.||++|||||||.|||+| ++.+++++......+..
T Consensus 60 ikrg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~W-nt~lkkkl~~~~~~~~~ 120 (238)
T KOG0048|consen 60 LKRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHW-NTHLKKKLLKMGIDPST 120 (238)
T ss_pred ccCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHH-HHHHHHHHHHcCCCCCc
Confidence 68999999999999999999999999999999999999999999 99999999987754443
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.85 E-value=2.2e-21 Score=131.42 Aligned_cols=65 Identities=43% Similarity=0.762 Sum_probs=60.7
Q ss_pred CCCCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHhhCCCCCCCchhH
Q 037092 1 MKPWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEEGGLKVPMKKNL 66 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~~~ 66 (76)
|++++||+|||++|+++|..||++|+.||++|||||+++||||| ++.+++++...+..|.+.+++
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRW-ns~LrK~l~r~~i~p~~~kp~ 140 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYW-NTHLRKKLLRQGIDPQTHKPL 140 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHH-HHHHhHHHHhcCCCCCCCCCC
Confidence 68999999999999999999999999999999999999999999 999999999888888776654
No 3
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.82 E-value=1.7e-20 Score=127.03 Aligned_cols=75 Identities=20% Similarity=0.299 Sum_probs=70.0
Q ss_pred CCCCCCChHHHHHHHHHHHHhC-CchhhhhhcC-CCCCHHHHHHHHhhchhhhHHhhCCCCCCCchhHHHHHHHhhcC
Q 037092 1 MKPWGFPDEEDRLICRLFAISG-SRWSVIGAHL-PGRTDNETNNYYRNTKLKRKHEEGGLKVPMKKNLERDLRIVKNH 76 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G-~~W~~Ia~~~-~gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~h 76 (76)
|++++||+|||++|+++|.+|| .+|+.||..+ +|||+.||+.|| ..+|.+.+.+++|+++++..+.+.+..++++
T Consensus 23 lKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW-~N~L~P~I~kgpWT~EED~lLlel~~~~GnK 99 (249)
T PLN03212 23 MKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRW-MNYLRPSVKRGGITSDEEDLILRLHRLLGNR 99 (249)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHH-HHhhchhcccCCCChHHHHHHHHHHHhcccc
Confidence 6899999999999999999999 6899999998 699999999999 9999999999999999999999888877753
No 4
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.81 E-value=2e-20 Score=126.21 Aligned_cols=73 Identities=12% Similarity=0.083 Sum_probs=70.1
Q ss_pred CCCCChHHHHHHHHHHHHhC-CchhhhhhcCC-CCCHHHHHHHHhhchhhhHHhhCCCCCCCchhHHHHHHHhhcC
Q 037092 3 PWGFPDEEDRLICRLFAISG-SRWSVIGAHLP-GRTDNETNNYYRNTKLKRKHEEGGLKVPMKKNLERDLRIVKNH 76 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G-~~W~~Ia~~~~-gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~h 76 (76)
+||||+|||++|+++|.+|| .+|..||+.++ ||++.+||-|| .+||++.++++.|+++++..+.++.++++|.
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW-~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRW-TNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHh-hcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 49999999999999999999 56999999999 99999999999 9999999999999999999999999999874
No 5
>PLN03091 hypothetical protein; Provisional
Probab=99.81 E-value=3.8e-20 Score=133.26 Aligned_cols=67 Identities=43% Similarity=0.701 Sum_probs=60.5
Q ss_pred CCCCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHhhCCCCCCCchhHHH
Q 037092 1 MKPWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEEGGLKVPMKKNLER 68 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~~~~~ 68 (76)
|++|+||+|||++|+++|..||++|+.||.+|||||+++||||| +..++++++..+..+.+..++.+
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRW-nslLKKklr~~~I~p~t~kpl~e 131 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLW-NSCLKKKLRQRGIDPNTHKPLSE 131 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHH-HHHHHHHHHHcCCCCCCCCCccc
Confidence 68999999999999999999999999999999999999999999 99999999887777666655443
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.77 E-value=4.2e-19 Score=97.05 Aligned_cols=58 Identities=28% Similarity=0.466 Sum_probs=49.7
Q ss_pred CChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHhhCCCCCCCch
Q 037092 6 FPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEEGGLKVPMKK 64 (76)
Q Consensus 6 wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~ 64 (76)
||+|||++|+.+|..||++|+.||..|+.||..+|++|| ...|.+.+...+|++.++.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~-~~~l~~~~~~~~wt~eEd~ 58 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRW-RNHLRPKISRGPWTKEEDQ 58 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHH-HHTTSTTSTSSSSSHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHH-HHHCcccccCCCcCHHHHh
Confidence 999999999999999999999999999669999999999 7778888888888776554
No 7
>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=99.76 E-value=7.7e-19 Score=92.64 Aligned_cols=45 Identities=24% Similarity=0.462 Sum_probs=40.7
Q ss_pred CCCCChHHHHHHHHHHHHhCCc-hhhhhhcCC-CCCHHHHHHHHhhch
Q 037092 3 PWGFPDEEDRLICRLFAISGSR-WSVIGAHLP-GRTDNETNNYYRNTK 48 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~-W~~Ia~~~~-gRt~~~~knrw~~~~ 48 (76)
|++||+|||++|++++.+||.. |..||..|| |||+.||++|| +.+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~-~~~ 47 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRY-QNL 47 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHH-HHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHH-Hhh
Confidence 6899999999999999999988 999999999 99999999999 654
No 8
>PLN03091 hypothetical protein; Provisional
Probab=99.75 E-value=9e-19 Score=126.19 Aligned_cols=75 Identities=15% Similarity=0.183 Sum_probs=70.0
Q ss_pred CCCCCCChHHHHHHHHHHHHhC-CchhhhhhcC-CCCCHHHHHHHHhhchhhhHHhhCCCCCCCchhHHHHHHHhhcC
Q 037092 1 MKPWGFPDEEDRLICRLFAISG-SRWSVIGAHL-PGRTDNETNNYYRNTKLKRKHEEGGLKVPMKKNLERDLRIVKNH 76 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G-~~W~~Ia~~~-~gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~h 76 (76)
|++++||+|||++|+++|.+|| .+|+.||+.+ +|||+.||+.|| ..+|.+.+.+++|+++++..+.+.++.++++
T Consensus 12 lrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW-~NyLdP~IkKgpWT~EED~lLLeL~k~~GnK 88 (459)
T PLN03091 12 LRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRW-INYLRPDLKRGTFSQQEENLIIELHAVLGNR 88 (459)
T ss_pred CcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHH-HhccCCcccCCCCCHHHHHHHHHHHHHhCcc
Confidence 5799999999999999999999 5799999988 499999999999 9999999999999999999999998887753
No 9
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.66 E-value=2.8e-16 Score=80.99 Aligned_cols=46 Identities=33% Similarity=0.588 Sum_probs=42.9
Q ss_pred CCCCChHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHHhhchh
Q 037092 3 PWGFPDEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYYRNTKL 49 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw~~~~l 49 (76)
+++||++||.+|+.++..|| ..|..||..||+||+.+|+++| +.++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~-~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERW-NNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHH-HHHc
Confidence 47999999999999999999 9999999999999999999999 6544
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=99.58 E-value=5.7e-15 Score=75.01 Aligned_cols=42 Identities=29% Similarity=0.582 Sum_probs=40.2
Q ss_pred CCChHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHHhhc
Q 037092 5 GFPDEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYYRNT 47 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw~~~ 47 (76)
+||+|||..|+.++..+| .+|..||..|++||+.+|+++| +.
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~-~~ 43 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERW-RN 43 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHH-HH
Confidence 699999999999999999 8999999999999999999999 54
No 11
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.44 E-value=2.5e-13 Score=102.13 Aligned_cols=73 Identities=19% Similarity=0.368 Sum_probs=68.5
Q ss_pred CCCCCCChHHHHHHHHHHHHhCCc-hhhhhhcCCCCCHHHHHHHHhhchhhhHHhhCCCCCCCchhHHHHHHHhh
Q 037092 1 MKPWGFPDEEDRLICRLFAISGSR-WSVIGAHLPGRTDNETNNYYRNTKLKRKHEEGGLKVPMKKNLERDLRIVK 74 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G~~-W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 74 (76)
|++|+||++||-+|+.+|.+||.+ |.+|-..||||++.||+.|| .+.|...++.+.|+..++..+...+...+
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY-~nvL~~s~K~~rW~l~edeqL~~~V~~YG 431 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERY-TNVLNRSAKVERWTLVEDEQLLYAVKVYG 431 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHH-HHHHHHhhccCceeecchHHHHHHHHHHc
Confidence 689999999999999999999955 99999999999999999999 99999999999999999999988887665
No 12
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.92 E-value=5.8e-10 Score=82.41 Aligned_cols=74 Identities=18% Similarity=0.203 Sum_probs=67.0
Q ss_pred CCCCCCChHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHHhhchhhhHHhhCCCCCCCchhHHHHHHHhhc
Q 037092 1 MKPWGFPDEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEEGGLKVPMKKNLERDLRIVKN 75 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ 75 (76)
++.|+|+..||+.+..++..|| ++|+.||..|.-+++++|++|| +.++.+.+....++..++..+...-..++.
T Consensus 18 ~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw-~~~lnp~lk~~~~~~eed~~li~l~~~~~~ 92 (512)
T COG5147 18 RKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRW-NNHLNPQLKKKNWSEEEDEQLIDLDKELGT 92 (512)
T ss_pred ecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchh-hhhhchhcccccccHHHHHHHHHHHHhcCc
Confidence 3679999999999999999999 6799999999999999999999 999999999999999888888777666554
No 13
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.87 E-value=3e-09 Score=79.69 Aligned_cols=68 Identities=21% Similarity=0.382 Sum_probs=58.4
Q ss_pred CCCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhH--HhhCCCCCCCchhHHHHHH
Q 037092 2 KPWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRK--HEEGGLKVPMKKNLERDLR 71 (76)
Q Consensus 2 ~~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~--~~~~~~~~~~~~~~~~~~~ 71 (76)
.+|.||+||++.|..+|.++|+.|..|+..| ||.+..|+.+| ..+.... ...+.|+-++...+...+.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~w-r~~~~~g~~~~r~~Ws~eEe~~Llk~V~ 452 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRW-RQYVKCGSKRNRGAWSIEEEEKLLKTVN 452 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHH-HHhhccccccccCcchHHHHHHHHHHHH
Confidence 5899999999999999999999999999998 99999999999 6555544 4777788877777776665
No 14
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.76 E-value=7.4e-09 Score=76.61 Aligned_cols=71 Identities=15% Similarity=0.199 Sum_probs=63.2
Q ss_pred CCCCCCChHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHHhhchhhhHHhhCCCCCCCchhHHHHHHH
Q 037092 1 MKPWGFPDEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEEGGLKVPMKKNLERDLRI 72 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~ 72 (76)
|+-|.|+.-||++|-..|.+|| +.|+.|++.++-.|..||++|| +.++.+.+++..|+..++..+......
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw-~e~ldp~i~~tews~eederlLhlakl 76 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARW-EEWLDPAIKKTEWSREEDERLLHLAKL 76 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHH-HHHhCHHHhhhhhhhhHHHHHHHHHHh
Confidence 4668999999999999999999 6799999999999999999999 899999999999988877766655443
No 15
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.63 E-value=4.1e-08 Score=72.73 Aligned_cols=53 Identities=25% Similarity=0.343 Sum_probs=47.9
Q ss_pred CCCCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHh
Q 037092 1 MKPWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHE 54 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~ 54 (76)
|+++.|+.|||..|+.+..++|++|+.||..+||||+.+|.++| ...+.....
T Consensus 70 lk~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery-~~~~~~~~s 122 (512)
T COG5147 70 LKKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERY-VNTLEDLSS 122 (512)
T ss_pred cccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHH-HHHhhhhhc
Confidence 57899999999999999999999999999999999999999999 766555444
No 16
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.49 E-value=1.2e-07 Score=72.20 Aligned_cols=72 Identities=19% Similarity=0.273 Sum_probs=65.0
Q ss_pred CCCCCChHHHHHHHHHHHHhC--C--chhhhhhcCCCCCHHHHHHHHhhchhhhHHhhCCCCCCCchhHHHHHHHhh
Q 037092 2 KPWGFPDEEDRLICRLFAISG--S--RWSVIGAHLPGRTDNETNNYYRNTKLKRKHEEGGLKVPMKKNLERDLRIVK 74 (76)
Q Consensus 2 ~~~~wT~eED~~L~~~~~~~G--~--~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ 74 (76)
+...||+|||.+|+.+|.... + .|.+|-.+||||+..++--|| ...|.+.++.+.|++.++..+..++...+
T Consensus 304 ~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~-~~~LdPsikhg~wt~~ED~~L~~AV~~Yg 379 (939)
T KOG0049|consen 304 SEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRF-SHTLDPSVKHGRWTDQEDVLLVCAVSRYG 379 (939)
T ss_pred HhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhh-eeccCccccCCCCCCHHHHHHHHHHHHhC
Confidence 346799999999999999976 2 399999999999999999999 89999999999999999999988887655
No 17
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.39 E-value=1.4e-06 Score=47.54 Aligned_cols=45 Identities=9% Similarity=0.098 Sum_probs=38.9
Q ss_pred CCCCChHHHHHHHHHHHHhCC-ch---hhhhhcCC-CC-CHHHHHHHHhhch
Q 037092 3 PWGFPDEEDRLICRLFAISGS-RW---SVIGAHLP-GR-TDNETNNYYRNTK 48 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~-~W---~~Ia~~~~-gR-t~~~~knrw~~~~ 48 (76)
+-.||+||....++++..+|. .| ..|+..|. .+ |..+|+.+. ..|
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~-QKy 53 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHL-QKY 53 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHH-HHH
Confidence 557999999999999999995 99 99999874 34 999999998 544
No 18
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.38 E-value=1e-06 Score=64.09 Aligned_cols=47 Identities=19% Similarity=0.337 Sum_probs=42.4
Q ss_pred CCCCChHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHHhhchh
Q 037092 3 PWGFPDEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYYRNTKL 49 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw~~~~l 49 (76)
.+.||.+|+-+|++++..|| ++|..||.++..+|...|+.+|++.++
T Consensus 72 ~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 72 DPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 46899999999999999999 899999999999999999999943333
No 19
>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=98.26 E-value=1.4e-06 Score=56.26 Aligned_cols=51 Identities=24% Similarity=0.365 Sum_probs=43.5
Q ss_pred CCCCCChHHHHHHHHHHHHh---CCc----hhhhhhcCCCCCHHHHHHHHhhchhhhHHh
Q 037092 2 KPWGFPDEEDRLICRLFAIS---GSR----WSVIGAHLPGRTDNETNNYYRNTKLKRKHE 54 (76)
Q Consensus 2 ~~~~wT~eED~~L~~~~~~~---G~~----W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~ 54 (76)
+...||.|||.+|-+.|-.| |+. ...++..+ +||+-+|.-|| |+++++...
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRW-Ns~VRkqY~ 60 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRW-NAYVRKQYE 60 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchH-HHHHHHHHH
Confidence 46789999999999988887 433 67788888 99999999999 999997664
No 20
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.09 E-value=2.4e-06 Score=63.63 Aligned_cols=52 Identities=25% Similarity=0.398 Sum_probs=46.3
Q ss_pred CCCCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHh
Q 037092 1 MKPWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHE 54 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~ 54 (76)
|++..||.|||+.|+.+...+...|..|+..| |||++||-.|| +..+--...
T Consensus 57 i~~tews~eederlLhlakl~p~qwrtIa~i~-gr~~~qc~eRy-~~ll~~~~s 108 (617)
T KOG0050|consen 57 IKKTEWSREEDERLLHLAKLEPTQWRTIADIM-GRTSQQCLERY-NNLLDVYVS 108 (617)
T ss_pred HhhhhhhhhHHHHHHHHHHhcCCccchHHHHh-hhhHHHHHHHH-HHHHHHHHh
Confidence 57788999999999999999999999999998 99999999999 766654444
No 21
>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=98.01 E-value=1.2e-05 Score=44.89 Aligned_cols=49 Identities=16% Similarity=0.303 Sum_probs=31.3
Q ss_pred CCCCChHHHHHHHHHHHHhC--------Cc-hhhhhhcCC-CCCHHHHHHHHhhchhhhH
Q 037092 3 PWGFPDEEDRLICRLFAISG--------SR-WSVIGAHLP-GRTDNETNNYYRNTKLKRK 52 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G--------~~-W~~Ia~~~~-gRt~~~~knrw~~~~l~~~ 52 (76)
+-+||.|||.+|++.+..+. ++ |..++..-| .+|-.+.++|| ...|..+
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry-~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRY-LKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHH-HHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHH-HHHHhcc
Confidence 46899999999999996542 22 999999887 99999999999 5545443
No 22
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.91 E-value=1.1e-05 Score=46.40 Aligned_cols=52 Identities=27% Similarity=0.424 Sum_probs=35.1
Q ss_pred CCCCChHHHHHHHHHHHH------hC--C------chhhhhhcC----CCCCHHHHHHHHhhchhhhHHhhC
Q 037092 3 PWGFPDEEDRLICRLFAI------SG--S------RWSVIGAHL----PGRTDNETNNYYRNTKLKRKHEEG 56 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~------~G--~------~W~~Ia~~~----~gRt~~~~knrw~~~~l~~~~~~~ 56 (76)
+..||++|...||+++.. ++ + -|..||..| ..||+.||+++| ++ |++.....
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw-~~-L~~~Yk~~ 70 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKW-KN-LKKKYKKI 70 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHH-HH-HHHHHHCS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHH-HH-HHHHHHHH
Confidence 458999999999999888 32 1 399999887 479999999999 54 55555443
No 23
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.87 E-value=2.9e-05 Score=57.80 Aligned_cols=42 Identities=12% Similarity=0.343 Sum_probs=40.7
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++.||.+|..+|++.+..||..|.+||.++.+||..+|--++
T Consensus 253 ~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kF 294 (506)
T KOG1279|consen 253 RPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKF 294 (506)
T ss_pred CCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHH
Confidence 578999999999999999999999999999999999999998
No 24
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.77 E-value=4.3e-05 Score=56.43 Aligned_cols=42 Identities=14% Similarity=0.277 Sum_probs=40.6
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..+||.+|-.+|++.+..||..|.+||.++..+|..||--+|
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~F 320 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHF 320 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHH
Confidence 458999999999999999999999999999999999999999
No 25
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.64 E-value=6.5e-05 Score=53.59 Aligned_cols=46 Identities=20% Similarity=0.333 Sum_probs=41.9
Q ss_pred CCCChHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHHhhchh
Q 037092 4 WGFPDEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYYRNTKL 49 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw~~~~l 49 (76)
..|+..|+.+|++....+| ++|..||.++..|+...||.+|++.|+
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 4799999999999999999 899999999999999999999944444
No 26
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=97.62 E-value=7.2e-05 Score=48.83 Aligned_cols=50 Identities=16% Similarity=0.274 Sum_probs=40.5
Q ss_pred CCCCCChHHHHHHHHHHHHhCCc-------hhhhhhcCCCCCHHHHHHHHhhchhhhHH
Q 037092 2 KPWGFPDEEDRLICRLFAISGSR-------WSVIGAHLPGRTDNETNNYYRNTKLKRKH 53 (76)
Q Consensus 2 ~~~~wT~eED~~L~~~~~~~G~~-------W~~Ia~~~~gRt~~~~knrw~~~~l~~~~ 53 (76)
+...||.|||.+|-+.|-.|+.. ...++..+ +||.-+|.-|| |+++++..
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRw-Ns~vrk~Y 60 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRW-NSVVRKQY 60 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHH-HHHHHHHH
Confidence 56789999999998888888732 34556666 89999999999 99988654
No 27
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=97.43 E-value=0.00058 Score=38.47 Aligned_cols=43 Identities=21% Similarity=0.389 Sum_probs=36.1
Q ss_pred CCCCCChHHHHHHHHHHHHh-----C--C----------chhhhhhcC-----CCCCHHHHHHHH
Q 037092 2 KPWGFPDEEDRLICRLFAIS-----G--S----------RWSVIGAHL-----PGRTDNETNNYY 44 (76)
Q Consensus 2 ~~~~wT~eED~~L~~~~~~~-----G--~----------~W~~Ia~~~-----~gRt~~~~knrw 44 (76)
++..||++|..+|++++.++ | . -|..|+..| +.||..+++..|
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW 65 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKW 65 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Confidence 35689999999999999987 3 1 199999876 369999999999
No 28
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=96.72 E-value=0.0025 Score=48.47 Aligned_cols=58 Identities=9% Similarity=0.122 Sum_probs=44.6
Q ss_pred CCCCCCChHHHHHHHHHHH-------Hh-------------------CCchhhhhhcCCCCCHHHHHHHHhhchhh-hHH
Q 037092 1 MKPWGFPDEEDRLICRLFA-------IS-------------------GSRWSVIGAHLPGRTDNETNNYYRNTKLK-RKH 53 (76)
Q Consensus 1 i~~~~wT~eED~~L~~~~~-------~~-------------------G~~W~~Ia~~~~gRt~~~~knrw~~~~l~-~~~ 53 (76)
+++|+||-||.+.|+++|. ++ +-.|+.|+..+..|+--||+-.| +..+. +..
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw-~kl~~~~s~ 512 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKW-YKLTTSPSF 512 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHH-HHHHhhHHh
Confidence 3689999999999999996 33 12499999999999999999999 55444 444
Q ss_pred hhCCCC
Q 037092 54 EEGGLK 59 (76)
Q Consensus 54 ~~~~~~ 59 (76)
....+.
T Consensus 513 n~~~~~ 518 (607)
T KOG0051|consen 513 NKRQES 518 (607)
T ss_pred hccccc
Confidence 444443
No 29
>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=96.50 E-value=0.011 Score=34.16 Aligned_cols=46 Identities=24% Similarity=0.490 Sum_probs=34.0
Q ss_pred CCChHHHHHHHHHHHHh---CCc----------hhhhhhcC---C--CCCHHHHHHHHhhchhhhH
Q 037092 5 GFPDEEDRLICRLFAIS---GSR----------WSVIGAHL---P--GRTDNETNNYYRNTKLKRK 52 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~---G~~----------W~~Ia~~~---~--gRt~~~~knrw~~~~l~~~ 52 (76)
.||++++..|++++.+. |+. |..|+..| + .-|..+|+||| ..|++.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~--~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKW--KTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHH--HHHHHH
Confidence 49999999999998664 211 88888877 2 34778999999 344443
No 30
>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=96.46 E-value=0.0053 Score=37.88 Aligned_cols=47 Identities=28% Similarity=0.419 Sum_probs=35.8
Q ss_pred CCCCChHHHHHHHHHHHHhCC----chhhhhhcC------------CCCCHHHHHHHHhhchhh
Q 037092 3 PWGFPDEEDRLICRLFAISGS----RWSVIGAHL------------PGRTDNETNNYYRNTKLK 50 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~----~W~~Ia~~~------------~gRt~~~~knrw~~~~l~ 50 (76)
+..||++||..|+-++.+||- .|..|...+ ..||+..+..|. ++.++
T Consensus 49 ~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~-~tLi~ 111 (118)
T PF09111_consen 49 KKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRC-NTLIK 111 (118)
T ss_dssp -SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHH-HHHHH
T ss_pred CCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHH-HHHHH
Confidence 568999999999999999996 687766533 579999999998 55443
No 31
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=96.20 E-value=0.0072 Score=44.16 Aligned_cols=56 Identities=16% Similarity=0.172 Sum_probs=46.6
Q ss_pred CCCCCChHHHHHHHHHHHHhCCchhhhhhc-----CCC-CCHHHHHHHHhhchhhhHHhhCCC
Q 037092 2 KPWGFPDEEDRLICRLFAISGSRWSVIGAH-----LPG-RTDNETNNYYRNTKLKRKHEEGGL 58 (76)
Q Consensus 2 ~~~~wT~eED~~L~~~~~~~G~~W~~Ia~~-----~~g-Rt~~~~knrw~~~~l~~~~~~~~~ 58 (76)
+...||.||-+-|.+|+..|--+|..|+.. ++. ||-..+|.|| +...++-++....
T Consensus 129 ~dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRy-Y~v~r~l~kAr~~ 190 (445)
T KOG2656|consen 129 NDNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERY-YSVCRKLLKARAP 190 (445)
T ss_pred ccccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHH-HHHHHHHHHccCC
Confidence 446799999999999999999999999987 665 9999999999 6666655554433
No 32
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.60 E-value=0.025 Score=41.51 Aligned_cols=41 Identities=17% Similarity=0.380 Sum_probs=39.7
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
-+||.+|-++...+...+|...+.||..||.|.-.||+..|
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKf 406 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKF 406 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHH
Confidence 47999999999999999999999999999999999999998
No 33
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=95.51 E-value=0.068 Score=37.72 Aligned_cols=50 Identities=16% Similarity=0.278 Sum_probs=38.2
Q ss_pred CCCChHHHHHHHHHHHHh----------CCchhhhhhcC----CCCCHHHHHHHHhhchhhhHHhh
Q 037092 4 WGFPDEEDRLICRLFAIS----------GSRWSVIGAHL----PGRTDNETNNYYRNTKLKRKHEE 55 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~----------G~~W~~Ia~~~----~gRt~~~~knrw~~~~l~~~~~~ 55 (76)
..|+.+|=..||++...+ +..|..||..+ .-||+.+|+++| .+ |.+++++
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~-~n-l~k~Yk~ 118 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKI-EN-LKKKYKK 118 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHH-HH-HHHHHHH
Confidence 579999999999988764 23499999855 359999999999 44 4444443
No 34
>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=95.21 E-value=0.058 Score=27.96 Aligned_cols=36 Identities=22% Similarity=0.279 Sum_probs=28.4
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++++..++.++...|-.+..||..+ |.|.+.|+.+.
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l 47 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRL 47 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHH
Confidence 5778888899999999999999999 89999999987
No 35
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=94.45 E-value=0.12 Score=34.61 Aligned_cols=50 Identities=16% Similarity=0.181 Sum_probs=35.5
Q ss_pred CCCCChHHHHHHHHHHHHhCCc---hhhhhh-----cCCCCCHHHHHHHHhhchhhhHH
Q 037092 3 PWGFPDEEDRLICRLFAISGSR---WSVIGA-----HLPGRTDNETNNYYRNTKLKRKH 53 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~---W~~Ia~-----~~~gRt~~~~knrw~~~~l~~~~ 53 (76)
+-+||.+|+++|........+. +..|=. +-++||+.++.++| ....+..+
T Consensus 73 kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW-~lmkqy~L 130 (199)
T PF13325_consen 73 KALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHW-RLMKQYHL 130 (199)
T ss_pred cCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHH-HHHHHhch
Confidence 5789999999999877666543 444322 33799999999999 54333333
No 36
>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=94.40 E-value=0.06 Score=34.80 Aligned_cols=39 Identities=26% Similarity=0.262 Sum_probs=35.4
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 5 GFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.||+|+.+.|-+|..+ |-.=++||..|.|.|-|+|--+-
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~ 40 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKA 40 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhh
Confidence 5999999999999977 99999999999889999988765
No 37
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=93.89 E-value=0.16 Score=38.07 Aligned_cols=41 Identities=24% Similarity=0.330 Sum_probs=39.1
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..||.||--++-.++..||....+|-+.||.|+-.++...|
T Consensus 188 d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyY 228 (534)
T KOG1194|consen 188 DEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYY 228 (534)
T ss_pred ccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHH
Confidence 57999999999999999999999999999999999999988
No 38
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=93.24 E-value=0.19 Score=40.73 Aligned_cols=47 Identities=21% Similarity=0.331 Sum_probs=38.5
Q ss_pred CCCCChHHHHHHHHHHHHhC-Cchhhhhhc------------CCCCCHHHHHHHHhhchhh
Q 037092 3 PWGFPDEEDRLICRLFAISG-SRWSVIGAH------------LPGRTDNETNNYYRNTKLK 50 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G-~~W~~Ia~~------------~~gRt~~~~knrw~~~~l~ 50 (76)
+..||.|||..|+-++.+|| .+|..|-.. |..||+..+..|. ++.++
T Consensus 926 ~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~-~~l~~ 985 (1033)
T PLN03142 926 GKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRC-DTLIR 985 (1033)
T ss_pred CCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHH-HHHHH
Confidence 44699999999999999999 779887332 2589999999999 65554
No 39
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=90.86 E-value=0.27 Score=28.44 Aligned_cols=13 Identities=23% Similarity=0.434 Sum_probs=8.4
Q ss_pred CCCCChHHHHHHH
Q 037092 3 PWGFPDEEDRLIC 15 (76)
Q Consensus 3 ~~~wT~eED~~L~ 15 (76)
.|-||+|+|..|.
T Consensus 47 ~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 47 PGIWTPEDDEMLR 59 (87)
T ss_dssp TT---HHHHHHHT
T ss_pred CCCcCHHHHHHHH
Confidence 4679999999994
No 40
>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=90.62 E-value=0.86 Score=27.59 Aligned_cols=35 Identities=23% Similarity=0.241 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++...|-.+..||..+ |.|...|+++.
T Consensus 116 ~~~r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~ 150 (161)
T TIGR02985 116 EQCRKIFILSRFEGKSYKEIAEEL-GISVKTVEYHI 150 (161)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 456666677666788999999998 89999999998
No 41
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=89.95 E-value=0.88 Score=30.52 Aligned_cols=43 Identities=14% Similarity=0.095 Sum_probs=33.7
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhhcC---CCCCHHHHHHHHhhchh
Q 037092 5 GFPDEEDRLICRLFAISGSRWSVIGAHL---PGRTDNETNNYYRNTKL 49 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~~W~~Ia~~~---~gRt~~~~knrw~~~~l 49 (76)
.|++++|-+|+..|.. |+.-..|+..+ -.-|-..|..|| +..|
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW-~~ll 46 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERW-YALL 46 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHH-HHHH
Confidence 4999999999999877 77777766644 356889999999 6544
No 42
>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=89.72 E-value=0.93 Score=23.05 Aligned_cols=35 Identities=20% Similarity=0.269 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++-..|-.+..||..+ |-|...|+.+-
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~ 41 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRIL 41 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHH
Confidence 445555556555577899999998 88999998877
No 43
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=89.63 E-value=0.78 Score=36.35 Aligned_cols=41 Identities=12% Similarity=0.193 Sum_probs=39.2
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..||+.|-.+.-+++..|-...-.|++.++|.|..+|-..|
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyY 660 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYY 660 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHH
Confidence 46999999999999999999999999999999999999988
No 44
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=88.48 E-value=1.6 Score=27.30 Aligned_cols=36 Identities=14% Similarity=0.194 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++-|..|+.+...-| ..|+.||..+ |-|...|.+|+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri 44 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRV 44 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHH
Confidence 457888888888878 5799999999 99999999999
No 45
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=88.46 E-value=0.56 Score=35.98 Aligned_cols=42 Identities=19% Similarity=0.320 Sum_probs=40.2
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+.||.+|=++.-.....+|.+-+.||..+|+|+..|||..+
T Consensus 409 ~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~ 450 (584)
T KOG2009|consen 409 TDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKF 450 (584)
T ss_pred cCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHH
Confidence 478999999999999999999999999999999999999988
No 46
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=87.57 E-value=0.54 Score=23.76 Aligned_cols=37 Identities=24% Similarity=0.299 Sum_probs=18.8
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
..+|++|-..|..++. -|-.=..||..| ||+..-|.+
T Consensus 3 ~~Lt~~eR~~I~~l~~-~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE-QGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp ---------HHHHHHC-S---HHHHHHHT-T--HHHHHH
T ss_pred cchhhhHHHHHHHHHH-cCCCHHHHHHHH-CcCcHHHHH
Confidence 4678899888888865 588888999999 899887765
No 47
>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=85.16 E-value=1.8 Score=25.02 Aligned_cols=31 Identities=23% Similarity=0.395 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
|+-|..+....|..|..+|.++ |=|..+|..
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 4567888999999999999998 666665443
No 48
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=85.10 E-value=2.4 Score=26.88 Aligned_cols=36 Identities=17% Similarity=0.113 Sum_probs=31.6
Q ss_pred hHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++-|..|+.+...-| -.|+.||..+ |=|...|.+|+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri 49 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERV 49 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHH
Confidence 456888888888877 5699999998 99999999999
No 49
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=83.49 E-value=4.5 Score=31.67 Aligned_cols=58 Identities=10% Similarity=0.205 Sum_probs=40.1
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhhcC----------CCCCHHHHHHHHhhchhhhHHhhCCCCCCC
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSVIGAHL----------PGRTDNETNNYYRNTKLKRKHEEGGLKVPM 62 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~----------~gRt~~~~knrw~~~~l~~~~~~~~~~~~~ 62 (76)
+..||-+|.+-...+..++|.....|-..+ .-.|-.|++.+| +..+.+..+-- |.+.-
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~y-Y~~~~~m~k~~-F~~~l 155 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYY-YRLVRRMNKLL-FGPDL 155 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHH-HHHHHHHHhhh-ccccc
Confidence 458999999999999999999998773222 234566888888 55444443333 54433
No 50
>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=83.33 E-value=2.7 Score=24.29 Aligned_cols=31 Identities=19% Similarity=0.284 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
|..|..+....|..|..+|..| |=+...|.+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 5677888899999999999998 666655444
No 51
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=83.25 E-value=3.6 Score=26.38 Aligned_cols=36 Identities=14% Similarity=0.112 Sum_probs=31.1
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
|+++..++.+....|-....||..+ |-|.+.|+++.
T Consensus 136 p~~~r~i~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl 171 (192)
T PRK09643 136 PVEQRAALVAVDMQGYSVADAARML-GVAEGTVKSRC 171 (192)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 3566777888888899999999999 89999999998
No 52
>smart00595 MADF subfamily of SANT domain.
Probab=83.21 E-value=1.4 Score=24.76 Aligned_cols=19 Identities=21% Similarity=0.424 Sum_probs=17.3
Q ss_pred hhhhhhcCCCCCHHHHHHHH
Q 037092 25 WSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 25 W~~Ia~~~~gRt~~~~knrw 44 (76)
|..||..|. -|...|+.+|
T Consensus 30 W~~Ia~~l~-~~~~~~~~kw 48 (89)
T smart00595 30 WEEIAEELG-LSVEECKKRW 48 (89)
T ss_pred HHHHHHHHC-cCHHHHHHHH
Confidence 999999994 4999999999
No 53
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=82.96 E-value=3.6 Score=25.78 Aligned_cols=35 Identities=17% Similarity=0.039 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.+....|.....||..+ |-|...|+++.
T Consensus 139 ~~~r~il~l~~~~~~s~~eIA~~l-gis~~~v~~~l 173 (187)
T PRK09641 139 EKYRTVIVLKYIEDLSLKEISEIL-DLPVGTVKTRI 173 (187)
T ss_pred HHHHHHhhhHHhhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 445566666666788899999998 89999999987
No 54
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.74 E-value=1.9 Score=27.82 Aligned_cols=37 Identities=27% Similarity=0.333 Sum_probs=32.5
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 5 GFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
.||+|--+.|-+|..+ |-.=|+||..+.|=|-|+|--
T Consensus 2 nWtdERve~LkKLWse-GLSASQIAaQLGGVsRnAVIG 38 (169)
T COG5352 2 NWTDERVETLKKLWSE-GLSASQIAAQLGGVSRNAVIG 38 (169)
T ss_pred CchHHHHHHHHHHHHc-ccCHHHHHHHhcCcchhhhhe
Confidence 6999999999999888 888899999999988887654
No 55
>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=82.12 E-value=4.3 Score=20.30 Aligned_cols=35 Identities=26% Similarity=0.416 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+=|..|+.+...-| -.+..||..+ |=|...|..|+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri 38 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRI 38 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHH
Confidence 55888898888888 4599999998 89999999998
No 56
>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=81.73 E-value=4.4 Score=23.72 Aligned_cols=34 Identities=18% Similarity=0.213 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.++...|-.+..||..+ |=|...|+++.
T Consensus 114 ~~~~ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~ 147 (158)
T TIGR02937 114 REREVLVLRYLEGLSYKEIAEIL-GISVGTVKRRL 147 (158)
T ss_pred HHHHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34444455555688999999998 67899999987
No 57
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=81.11 E-value=4.8 Score=24.81 Aligned_cols=34 Identities=21% Similarity=0.173 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.++...|-++..||..+ |-|...|+++.
T Consensus 132 ~~r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l 165 (182)
T PRK09652 132 ELRTAITLREIEGLSYEEIAEIM-GCPIGTVRSRI 165 (182)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34445556666788999999998 89999999987
No 58
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=81.09 E-value=6.4 Score=24.42 Aligned_cols=35 Identities=20% Similarity=0.156 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++...|-.-..||..+ |-+.+.|+.+.
T Consensus 121 ~~~r~vl~L~~~~g~s~~EIA~~l-gis~~tV~~~l 155 (173)
T PRK09645 121 PEHRAVLVRSYYRGWSTAQIAADL-GIPEGTVKSRL 155 (173)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 445556667666788889999998 89999999987
No 59
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=80.78 E-value=4.7 Score=24.76 Aligned_cols=34 Identities=18% Similarity=0.204 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.++...|-....||..| |-|...|+++.
T Consensus 129 ~~r~i~~l~~~~~~~~~eIA~~l-gis~~tv~~~~ 162 (179)
T PRK11924 129 KQREVFLLRYVEGLSYREIAEIL-GVPVGTVKSRL 162 (179)
T ss_pred HHHHHhhHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34455556666788899999998 89999999987
No 60
>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=80.74 E-value=3.4 Score=25.93 Aligned_cols=35 Identities=14% Similarity=0.114 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.+....|-....||..+ |=|.+.|+++.
T Consensus 141 ~~~r~v~~l~~~~~~s~~EIA~~l-gis~~tv~~~l 175 (190)
T TIGR02939 141 EDLRTAITLRELEGLSYEDIARIM-DCPVGTVRSRI 175 (190)
T ss_pred HHHhhhhhhhhhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 344445555555678889999998 88899999987
No 61
>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=80.27 E-value=2.7 Score=23.90 Aligned_cols=31 Identities=19% Similarity=0.461 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
|..|..+....|..|..+|..+ |=+...|..
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 4567778889999999999998 666655444
No 62
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=80.17 E-value=6.3 Score=25.10 Aligned_cols=47 Identities=13% Similarity=0.055 Sum_probs=31.3
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHh--hchhhhHHhhCCC
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYR--NTKLKRKHEEGGL 58 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~--~~~l~~~~~~~~~ 58 (76)
...++.++...|-+-..||..+ |-|.+.|+++.. ...|++.+....+
T Consensus 141 ~r~i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~~l~~~~~ 189 (195)
T PRK12532 141 TARVFTLKEILGFSSDEIQQMC-GISTSNYHTIMHRARESLRQCLQIKWF 189 (195)
T ss_pred HHHHhhhHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4445555566677789999998 899999999872 1344455444433
No 63
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=79.87 E-value=5.4 Score=25.59 Aligned_cols=36 Identities=19% Similarity=0.258 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++...++.+...-|-.+..||..+ |-|...|+.+|
T Consensus 137 ~~~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l 172 (185)
T PF07638_consen 137 DPRQRRVVELRFFEGLSVEEIAERL-GISERTVRRRL 172 (185)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHH
Confidence 4566777778777899999999999 99999999999
No 64
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=77.88 E-value=7.1 Score=24.91 Aligned_cols=34 Identities=3% Similarity=-0.106 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.++...|-+...||..| |-|.+.|+.+.
T Consensus 138 ~~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l 171 (189)
T PRK12530 138 QQARVFMMREYLELSSEQICQEC-DISTSNLHVLL 171 (189)
T ss_pred HHHHHHhHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 44555566666688899999998 99999999987
No 65
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=77.64 E-value=6 Score=24.72 Aligned_cols=34 Identities=12% Similarity=0.030 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.+....|-.-..||..+ |-|.+.|+++.
T Consensus 140 ~~r~v~~l~~~~g~s~~eIA~~l-gis~~~v~~~l 173 (187)
T TIGR02948 140 KYRMVIVLKYMEDLSLKEISEIL-DLPVGTVKTRI 173 (187)
T ss_pred HHhHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 33444455555577788999988 88999999987
No 66
>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=77.23 E-value=9.1 Score=27.67 Aligned_cols=40 Identities=25% Similarity=0.541 Sum_probs=32.8
Q ss_pred CCChHHHHHHHHHHHHh-CCc---hhhhhhcCCCCCHHHHHHHH
Q 037092 5 GFPDEEDRLICRLFAIS-GSR---WSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~-G~~---W~~Ia~~~~gRt~~~~knrw 44 (76)
.||.-|...|+++.... |.. -..|++.++||+..+|++.-
T Consensus 23 ~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl 66 (344)
T PF11035_consen 23 AWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFL 66 (344)
T ss_pred cCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHH
Confidence 69999999888887765 433 56899999999999999864
No 67
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=77.02 E-value=7.5 Score=24.72 Aligned_cols=35 Identities=20% Similarity=0.155 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.+....|-....||..| |-|.+.|+++.
T Consensus 109 ~~~r~i~~l~~~~g~~~~EIA~~l-gis~~tV~~~l 143 (181)
T PRK09637 109 EKYAEALRLTELEGLSQKEIAEKL-GLSLSGAKSRV 143 (181)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 456667777777899999999999 89999999987
No 68
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=77.02 E-value=6.7 Score=24.84 Aligned_cols=34 Identities=12% Similarity=0.071 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.+....|-....||..+ |-|.+.|+++.
T Consensus 142 ~~r~v~~l~~~~g~s~~eIA~~l-gis~~tv~~~l 175 (193)
T PRK11923 142 DLRTALTLREFDGLSYEDIASVM-QCPVGTVRSRI 175 (193)
T ss_pred HHhHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34555666556677889999988 88899999987
No 69
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=76.87 E-value=8.7 Score=23.50 Aligned_cols=35 Identities=9% Similarity=-0.028 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.++...|-+-..||..+ |-+.+.|+++-
T Consensus 109 ~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 143 (160)
T PRK09642 109 ENYRDVVLAHYLEEKSYQEIALQE-KIEVKTVEMKL 143 (160)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 344556666667788889999998 89999999986
No 70
>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=76.55 E-value=4.9 Score=23.04 Aligned_cols=31 Identities=13% Similarity=0.309 Sum_probs=25.3
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
|..|-.+....|..|..+|..| |=|+..|.+
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 4566777889999999999998 777777666
No 71
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=76.53 E-value=8.1 Score=24.14 Aligned_cols=35 Identities=9% Similarity=0.124 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.+....|-.-..||..| |.|...|+++.
T Consensus 132 ~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l 166 (179)
T PRK12514 132 KDRAAAVRRAYLEGLSYKELAERH-DVPLNTMRTWL 166 (179)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCChHHHHHHH
Confidence 344555556656688899999999 99999999987
No 72
>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=76.41 E-value=8.9 Score=24.48 Aligned_cols=33 Identities=9% Similarity=0.030 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+..++.++...|-+...||..| |-|.+.|+.|.
T Consensus 136 ~r~v~~l~~~~g~s~~EIA~~l-gis~~tvk~rl 168 (188)
T TIGR02943 136 TARVFMMREVLGFESDEICQEL-EISTSNCHVLL 168 (188)
T ss_pred HHHHHHHHHHhCCCHHHHHHHh-CCCHHHHHHHH
Confidence 4445666666678889999998 89999999987
No 73
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=76.38 E-value=8.6 Score=24.33 Aligned_cols=35 Identities=14% Similarity=0.160 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.+....|-....||..| |-|.+.|+++.
T Consensus 134 ~~~r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l 168 (189)
T PRK12515 134 PAHREIIDLVYYHEKSVEEVGEIV-GIPESTVKTRM 168 (189)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 445666667777788899999999 88999999997
No 74
>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=76.19 E-value=8.2 Score=23.66 Aligned_cols=35 Identities=11% Similarity=0.075 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++.-.|-+-..||..+ |-+.+.|+++-
T Consensus 125 ~~~r~vl~l~~~~g~s~~eIA~~l-~is~~tv~~~l 159 (170)
T TIGR02952 125 PKQQHVIALRFGQNLPIAEVARIL-GKTEGAVKILQ 159 (170)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345556666666688889999998 88899999886
No 75
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=75.67 E-value=10 Score=23.03 Aligned_cols=34 Identities=12% Similarity=0.037 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+...++.++...|-.-..||..+ |-|.+.|+++.
T Consensus 110 ~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 143 (161)
T PRK09047 110 RQREAFLLRYWEDMDVAETAAAM-GCSEGSVKTHC 143 (161)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHH-CCCHHHHHHHH
Confidence 44455666666788889999998 89999999987
No 76
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=75.63 E-value=11 Score=23.69 Aligned_cols=41 Identities=10% Similarity=0.079 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhh
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKR 51 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~ 51 (76)
++...++.|+...|-....||..+ |-+.+.|+.+. ..-+..
T Consensus 130 ~~~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l-~rAl~~ 170 (178)
T PRK12529 130 PRVKQAFLMATLDGMKQKDIAQAL-DIALPTVKKYI-HQAYVT 170 (178)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH-HHHHHH
Confidence 455666777777889999999998 89999999998 544443
No 77
>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=75.50 E-value=8.6 Score=23.79 Aligned_cols=36 Identities=8% Similarity=0.111 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++++..++.++...|-+...||..+ |-|.+.|+++.
T Consensus 121 ~~~~r~i~~l~~~~g~s~~eiA~~l-gis~~tv~~~l 156 (169)
T TIGR02954 121 NDKYQTAIILRYYHDLTIKEIAEVM-NKPEGTVKTYL 156 (169)
T ss_pred CHHHhHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 3455666667777788899999998 78999999988
No 78
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=75.30 E-value=13 Score=21.40 Aligned_cols=39 Identities=18% Similarity=0.191 Sum_probs=32.1
Q ss_pred hHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHHhhch
Q 037092 8 DEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYYRNTK 48 (76)
Q Consensus 8 ~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw~~~~ 48 (76)
++.|..|+.+....| -.++.||..+ |-+...|..+. +..
T Consensus 2 d~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l-~~L 41 (108)
T smart00344 2 DEIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRV-KRL 41 (108)
T ss_pred CHHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHH-HHH
Confidence 457888888888877 4699999998 89999999998 443
No 79
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=75.09 E-value=9.7 Score=24.29 Aligned_cols=34 Identities=3% Similarity=-0.029 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.++...|-....||..| |-|.+.|+.|.
T Consensus 145 ~~r~v~~l~~~eg~s~~EIA~~l-gis~~tVk~rl 178 (194)
T PRK12531 145 AQRDVLQAVYLEELPHQQVAEMF-DIPLGTVKSRL 178 (194)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHH
Confidence 44456666666688889999998 89999999987
No 80
>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=74.86 E-value=3.3 Score=22.56 Aligned_cols=20 Identities=15% Similarity=0.365 Sum_probs=17.1
Q ss_pred hhhhhhcCCC-CCHHHHHHHH
Q 037092 25 WSVIGAHLPG-RTDNETNNYY 44 (76)
Q Consensus 25 W~~Ia~~~~g-Rt~~~~knrw 44 (76)
|..||..+.+ -+...|+.+|
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w 49 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRW 49 (85)
T ss_pred HHHHHHHHccchhHHHHHHHH
Confidence 9999999953 5778899999
No 81
>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=74.50 E-value=10 Score=21.44 Aligned_cols=37 Identities=16% Similarity=0.286 Sum_probs=24.8
Q ss_pred HHHHHHHHhC--------CchhhhhhcCCC---CC--HHHHHHHHhhchhh
Q 037092 13 LICRLFAISG--------SRWSVIGAHLPG---RT--DNETNNYYRNTKLK 50 (76)
Q Consensus 13 ~L~~~~~~~G--------~~W~~Ia~~~~g---Rt--~~~~knrw~~~~l~ 50 (76)
.|-.+|...| ..|..||..|.- -+ +.+++..| ..+|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y-~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHY-EKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHH-HHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHH-HHHhH
Confidence 4556677776 349999998832 22 36788888 66654
No 82
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=74.44 E-value=18 Score=25.11 Aligned_cols=41 Identities=15% Similarity=0.122 Sum_probs=28.8
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHhh
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEE 55 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~ 55 (76)
..++.|+...|-+-..||..| |-|.+.|+++. ...++++++
T Consensus 159 R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l--~RAr~~Lr~ 199 (339)
T PRK08241 159 RAVLILRDVLGWSAAEVAELL-DTSVAAVNSAL--QRARATLAE 199 (339)
T ss_pred hhhhhhHHhhCCCHHHHHHHh-CCCHHHHHHHH--HHHHHHHhh
Confidence 334445555677778999998 89999999997 334455555
No 83
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=74.43 E-value=19 Score=24.68 Aligned_cols=43 Identities=16% Similarity=0.290 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHhh
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEE 55 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~ 55 (76)
++..++.|+..+|-+-..||..+ |.|...|+++. ...++++..
T Consensus 119 ~~R~v~~L~~~~g~s~~EIA~~l-g~s~~tVk~~l--~RAr~~Lr~ 161 (293)
T PRK09636 119 LERAAFLLHDVFGVPFDEIASTL-GRSPAACRQLA--SRARKHVRA 161 (293)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH--HHHHHHHHh
Confidence 34445556666788889999998 99999999997 334444444
No 84
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=74.23 E-value=8.7 Score=20.21 Aligned_cols=36 Identities=19% Similarity=0.291 Sum_probs=23.4
Q ss_pred ChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 7 PDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 7 T~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
|+.| +-.+.+..+.|-+=..||..+ ||+-+.|++.-
T Consensus 6 t~~E-qaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 6 TDAE-QAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp -HHH-HHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred CHHH-HHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 4444 455566677799999999998 89999888754
No 85
>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=73.29 E-value=6 Score=22.04 Aligned_cols=32 Identities=13% Similarity=0.356 Sum_probs=22.7
Q ss_pred HHHHHHHHHHH-hCCchhhhhhcCCCCCHHHHHH
Q 037092 10 EDRLICRLFAI-SGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 10 ED~~L~~~~~~-~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
-++.+..+... .|..|..+|..++ =++..|..
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~Lg-~~~~~i~~ 36 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKLG-LSEADIDQ 36 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHcC-CCHHHHHH
Confidence 35566677777 8999999999984 45555433
No 86
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=72.90 E-value=10 Score=24.05 Aligned_cols=35 Identities=14% Similarity=0.078 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.+....|-.-..||..+ |-|.+.|+++.
T Consensus 133 ~~~r~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l 167 (185)
T PRK09649 133 TDQREALLLTQLLGLSYADAAAVC-GCPVGTIRSRV 167 (185)
T ss_pred HHHhHHhhhHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 455666667777788889999998 89999999998
No 87
>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=72.42 E-value=7.5 Score=22.27 Aligned_cols=25 Identities=24% Similarity=0.477 Sum_probs=20.2
Q ss_pred HHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 17 LFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 17 ~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
+....|..|..+|..+ |=++..|..
T Consensus 13 ia~~iG~~Wk~Lar~L-Gls~~dI~~ 37 (86)
T cd08318 13 FANKLGEDWKTLAPHL-EMKDKEIRA 37 (86)
T ss_pred HHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 5688899999999998 777776644
No 88
>PRK04217 hypothetical protein; Provisional
Probab=71.74 E-value=14 Score=22.42 Aligned_cols=36 Identities=19% Similarity=0.127 Sum_probs=30.2
Q ss_pred ChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 7 PDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 7 T~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
|++| ..++.++..-|-+...||..+ |-|.+.|++++
T Consensus 44 t~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L 79 (110)
T PRK04217 44 TYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRAL 79 (110)
T ss_pred CHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 4444 677778877788999999998 99999999998
No 89
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=71.63 E-value=15 Score=22.48 Aligned_cols=36 Identities=19% Similarity=0.131 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++++..++.++...|-.-..||..| |-+.+.|+++.
T Consensus 107 ~~~~r~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l 142 (159)
T PRK12527 107 PPACRDSFLLRKLEGLSHQQIAEHL-GISRSLVEKHI 142 (159)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 3556677777777788889999998 89999999987
No 90
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=71.51 E-value=15 Score=23.27 Aligned_cols=46 Identities=22% Similarity=0.271 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHhhC
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEEG 56 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~ 56 (76)
++++..++.++..-|-.-..||..+ |-|.+.|+++- ...++++.+.
T Consensus 133 ~~~~r~i~~l~~~~g~s~~EIAe~l-gis~~~V~~~l--~Ra~~~Lr~~ 178 (189)
T PRK06811 133 EKLDREIFIRRYLLGEKIEEIAKKL-GLTRSAIDNRL--SRGRKKLQKN 178 (189)
T ss_pred CHHHHHHHHHHHHccCCHHHHHHHH-CCCHHHHHHHH--HHHHHHHHHc
Confidence 3456666767666688889999998 89999999986 3334445544
No 91
>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=71.34 E-value=5.7 Score=22.55 Aligned_cols=34 Identities=21% Similarity=0.456 Sum_probs=25.8
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNY 43 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knr 43 (76)
.||-++|+.. ...|..|...|..| |=++..|.+.
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHHH
Confidence 5788888732 24688999999999 7788777763
No 92
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=71.25 E-value=12 Score=21.43 Aligned_cols=38 Identities=21% Similarity=0.314 Sum_probs=25.7
Q ss_pred HHHHHHHHhCC--------chhhhhhcCCCC-----CHHHHHHHHhhchhhh
Q 037092 13 LICRLFAISGS--------RWSVIGAHLPGR-----TDNETNNYYRNTKLKR 51 (76)
Q Consensus 13 ~L~~~~~~~G~--------~W~~Ia~~~~gR-----t~~~~knrw~~~~l~~ 51 (76)
.|-.+|..+|+ .|..||..|.-. .+.+++..| ..+|.+
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y-~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHY-ERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHH-HHHhHH
Confidence 35566777763 599999988322 356788888 666654
No 93
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=70.97 E-value=12 Score=27.73 Aligned_cols=41 Identities=27% Similarity=0.410 Sum_probs=37.6
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhh-cCCCCCHHHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGA-HLPGRTDNETNNYY 44 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~-~~~gRt~~~~knrw 44 (76)
..||.+|=...-+....||.....|.. .++.|+...|-..|
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyY 319 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYY 319 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHH
Confidence 479999999999999999999999875 68999999999987
No 94
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=70.72 E-value=19 Score=22.36 Aligned_cols=35 Identities=17% Similarity=0.244 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++...|-+...||..+ |-+.+.|+.+-
T Consensus 122 ~~~r~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l 156 (172)
T PRK12523 122 SKARAAFLYNRLDGMGHAEIAERL-GVSVSRVRQYL 156 (172)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 456667777777788999999998 89999999987
No 95
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=70.52 E-value=14 Score=23.23 Aligned_cols=35 Identities=20% Similarity=0.130 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++...|-+...||..+ |-+.+.|+.+.
T Consensus 142 ~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 176 (189)
T PRK09648 142 EKQREILILRVVVGLSAEETAEAV-GSTPGAVRVAQ 176 (189)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345666677777788899999999 88999999987
No 96
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=70.46 E-value=14 Score=23.17 Aligned_cols=35 Identities=11% Similarity=0.084 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++...|-+...||..| |-+...|+++-
T Consensus 132 ~~~r~v~~l~~~~g~s~~EIA~~l-~is~~tV~~~l 166 (181)
T PRK12536 132 DRQRLPIVHVKLEGLSVAETAQLT-GLSESAVKVGI 166 (181)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345556677778899999999999 99999999987
No 97
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=70.28 E-value=15 Score=23.31 Aligned_cols=34 Identities=9% Similarity=-0.124 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.++...|-+-..||..| |-|.+.|+++.
T Consensus 135 ~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 168 (191)
T PRK12520 135 RTGRVFMMREWLELETEEICQEL-QITATNAWVLL 168 (191)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34445555555677788999998 89999999987
No 98
>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=70.19 E-value=7.4 Score=22.44 Aligned_cols=30 Identities=23% Similarity=0.336 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCchhhhhhcCCCCCHHHHHHH
Q 037092 13 LICRLFAISGSRWSVIGAHLPGRTDNETNNY 43 (76)
Q Consensus 13 ~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knr 43 (76)
-|-.+....|..|..+|..| |=|+..|.+-
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~i 33 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEEI 33 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHHH
Confidence 34455688899999999999 7888877763
No 99
>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=70.14 E-value=14 Score=22.57 Aligned_cols=35 Identities=11% Similarity=0.068 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.+....|-+-..||..| |-+...|+++.
T Consensus 113 ~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l 147 (162)
T TIGR02983 113 ARQRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRL 147 (162)
T ss_pred HHHHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHH
Confidence 456666777777788889999998 89999999987
No 100
>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=69.97 E-value=32 Score=23.47 Aligned_cols=42 Identities=12% Similarity=0.302 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHhh
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEE 55 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~ 55 (76)
+..++.|+..+|-.-..||..| |.|...|+.+. ...++++..
T Consensus 113 ~R~v~~L~~~~g~s~~EIA~~l-g~s~~tVr~~l--~RAr~~Lr~ 154 (281)
T TIGR02957 113 ERAVFVLREVFDYPYEEIASIV-GKSEANCRQLV--SRARRHLDA 154 (281)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH--HHHHHHHHh
Confidence 3344556667788889999999 89999999987 334444444
No 101
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=69.91 E-value=14 Score=23.77 Aligned_cols=33 Identities=12% Similarity=-0.059 Sum_probs=25.5
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
...++.++...|-+-..||..+ |-+.+.|+++.
T Consensus 144 ~r~v~~L~~~eg~s~~EIA~~l-gis~~tVk~~l 176 (201)
T PRK12545 144 IGRVFMMREFLDFEIDDICTEL-TLTANHCSVLL 176 (201)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 4445555555677789999998 89999999986
No 102
>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=69.90 E-value=16 Score=22.83 Aligned_cols=36 Identities=17% Similarity=0.175 Sum_probs=29.2
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
|+....++.++...|-+...||..+ |-+...|+++.
T Consensus 136 p~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tVk~~l 171 (183)
T TIGR02999 136 DPRQAEVVELRFFAGLTVEEIAELL-GVSVRTVERDW 171 (183)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 3455666777777788899999998 89999999987
No 103
>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=69.51 E-value=12 Score=25.68 Aligned_cols=32 Identities=22% Similarity=0.213 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..++.|+...|-+-..||..| |-|.+.|+++-
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 334455556677789999998 99999999987
No 104
>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=68.85 E-value=8.8 Score=22.17 Aligned_cols=33 Identities=12% Similarity=0.123 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCH---HHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTD---NETNNYY 44 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~---~~~knrw 44 (76)
|-.|..+....|..|..+|..| |=+. +.|+.-+
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~dI~~I~~e~ 39 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVEDINRIRVEN 39 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHHHHHHHHHhC
Confidence 4567778899999999999987 4444 3455544
No 105
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=68.64 E-value=20 Score=22.48 Aligned_cols=35 Identities=11% Similarity=0.187 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++...|-+...||..| |-|.+.|+.+.
T Consensus 134 ~~~r~v~~l~~~~g~s~~eIA~~l-~is~~tV~~~l 168 (184)
T PRK12512 134 PRQRDVVQSISVEGASIKETAAKL-SMSEGAVRVAL 168 (184)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 456666677766788899999999 89999999987
No 106
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=68.11 E-value=17 Score=22.89 Aligned_cols=34 Identities=12% Similarity=0.273 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.+....|-+-..||..| |-|...|+++.
T Consensus 126 ~~r~i~~l~~~~g~s~~EIA~~l-gis~~tVk~~l 159 (185)
T PRK12542 126 SNRQVFKYKVFYNLTYQEISSVM-GITEANVRKQF 159 (185)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 45555666667788889999998 89999999987
No 107
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=67.77 E-value=19 Score=21.74 Aligned_cols=34 Identities=15% Similarity=0.058 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.+....|-+...||..+ |-+.+.|+++-
T Consensus 110 ~~r~ii~l~~~~~~s~~EIA~~l-~is~~tV~~~~ 143 (154)
T PRK06759 110 KEKYIIFERFFVGKTMGEIALET-EMTYYQVRWIY 143 (154)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34455555556677788999988 89999999876
No 108
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=67.32 E-value=18 Score=23.10 Aligned_cols=35 Identities=17% Similarity=0.074 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.++...|-.+..||..+ |=+.+.|+++-
T Consensus 139 ~~~r~i~~L~~~~g~s~~eIA~~l-gis~~tV~~~l 173 (196)
T PRK12524 139 ERQRQAVVLRHIEGLSNPEIAEVM-EIGVEAVESLT 173 (196)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 445556667777788899999998 88889999986
No 109
>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=66.72 E-value=4.5 Score=24.49 Aligned_cols=23 Identities=9% Similarity=0.033 Sum_probs=19.2
Q ss_pred hCCchhhhhhcCCCCCHHHHHHHH
Q 037092 21 SGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 21 ~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
-|-++..||..| |=|...|+++.
T Consensus 120 ~g~s~~eIA~~l-gis~~tv~~~l 142 (154)
T TIGR02950 120 KEFSYKEIAELL-NLSLAKVKSNL 142 (154)
T ss_pred ccCcHHHHHHHH-CCCHHHHHHHH
Confidence 466788899988 88899999987
No 110
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=66.71 E-value=21 Score=22.73 Aligned_cols=41 Identities=12% Similarity=0.118 Sum_probs=33.3
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhhcC----CCCCHHHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGAHL----PGRTDNETNNYY 44 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~~~----~gRt~~~~knrw 44 (76)
-.-|+.|...|..|+.+||..+..++.=. -=-|..+|+.+.
T Consensus 115 ~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki 159 (164)
T PF09420_consen 115 RRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKI 159 (164)
T ss_pred CCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHH
Confidence 35688999999999999999999888632 146888888876
No 111
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=66.52 E-value=18 Score=22.13 Aligned_cols=35 Identities=17% Similarity=0.206 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++.-.|-+...||..+ |-+.+.|+++.
T Consensus 116 ~~~r~v~~L~~~~g~s~~EIA~~l-~is~~tV~~~l 150 (161)
T PRK12528 116 PLVKRAFLLAQVDGLGYGEIATEL-GISLATVKRYL 150 (161)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345566667777788899999998 89999999987
No 112
>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=66.51 E-value=19 Score=22.41 Aligned_cols=34 Identities=12% Similarity=0.305 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.++...|-.-..||..+ |-|.+.|+.+.
T Consensus 144 ~~r~vi~l~~~~g~s~~eIA~~l-gis~~~v~~~l 177 (189)
T TIGR02984 144 DYREVILLRHLEGLSFAEVAERM-DRSEGAVSMLW 177 (189)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 34445556556677888899988 88999999887
No 113
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=66.25 E-value=17 Score=22.82 Aligned_cols=35 Identities=14% Similarity=0.007 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.+....|-+...||..+ |-|.+.|+++.
T Consensus 131 ~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 165 (186)
T PRK05602 131 ERQREAIVLQYYQGLSNIEAAAVM-DISVDALESLL 165 (186)
T ss_pred HHHHHHhhHHHhcCCCHHHHHHHh-CcCHHHHHHHH
Confidence 345556666666688899999988 88999999986
No 114
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=65.62 E-value=20 Score=22.88 Aligned_cols=48 Identities=13% Similarity=0.105 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHh--hchhhhHHhhC
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYR--NTKLKRKHEEG 56 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~--~~~l~~~~~~~ 56 (76)
++++..++.|....|-....||..| |-|.+.|+++-. ...|++.+...
T Consensus 118 p~~~r~i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~Lr~~l~~~ 167 (187)
T PRK12516 118 PDDQREAIILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQRLQEILQIE 167 (187)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 3456677778777889999999998 899999999861 23344444443
No 115
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=65.59 E-value=25 Score=20.64 Aligned_cols=41 Identities=12% Similarity=0.140 Sum_probs=34.0
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhhcCCCC-CHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSVIGAHLPGR-TDNETNNYY 44 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gR-t~~~~knrw 44 (76)
+..||+|.-..+++++..-|..=+.||..+ |- +.+++...+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~ 46 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWR 46 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHH
Confidence 357999999999999999898889999998 65 666766544
No 116
>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=65.45 E-value=9 Score=21.98 Aligned_cols=32 Identities=25% Similarity=0.371 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHH---HHHHH
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNE---TNNYY 44 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~---~knrw 44 (76)
.-|..+....|..|..++..+ |=|+.. |+..|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~~Id~Ie~~~ 37 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYRELQRIKYNN 37 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHHHHHHHHHHC
Confidence 357788899999999999998 444443 45554
No 117
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=65.23 E-value=21 Score=22.37 Aligned_cols=35 Identities=14% Similarity=0.115 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.+....|-+-..||..+ |-|.+.|+++.
T Consensus 138 ~~~r~vl~l~~~~~~s~~eIA~~l-gis~~~V~~~l 172 (186)
T PRK13919 138 PEERRVIEVLYYQGYTHREAAQLL-GLPLGTLKTRA 172 (186)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 445555566666677889999998 89999999987
No 118
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=65.06 E-value=8.3 Score=25.47 Aligned_cols=34 Identities=12% Similarity=0.066 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.++...|-+...||..| |-|...|+++.
T Consensus 153 ~~r~i~~l~~~~g~s~~EIAe~l-gis~~tVk~~l 186 (231)
T PRK11922 153 AFRAVFVLRVVEELSVEETAQAL-GLPEETVKTRL 186 (231)
T ss_pred HHhhhheeehhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 34445555555577789999998 89999999987
No 119
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=64.93 E-value=21 Score=23.18 Aligned_cols=34 Identities=26% Similarity=0.236 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+...++.+....|-+-..||..| |-+.+.|+++.
T Consensus 142 ~~r~v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l 175 (203)
T PRK09647 142 EFRAAVVLCDIEGLSYEEIAATL-GVKLGTVRSRI 175 (203)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 44455556666778889999998 89999999987
No 120
>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=63.89 E-value=15 Score=21.05 Aligned_cols=30 Identities=13% Similarity=0.328 Sum_probs=22.2
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
..+--+....|..|..+|..+ |=|+++|..
T Consensus 3 ~~f~~i~~~lG~~Wk~laR~L-Glse~~Id~ 32 (86)
T cd08306 3 AAFDVICENVGRDWRKLARKL-GLSETKIES 32 (86)
T ss_pred HHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 344455677899999999998 677776554
No 121
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=63.78 E-value=25 Score=21.67 Aligned_cols=35 Identities=17% Similarity=0.117 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++...|-+-..||..+ |-+...|+++-
T Consensus 115 ~~~r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l 149 (164)
T PRK12547 115 ADQREAIILIGASGFSYEDAAAIC-GCAVGTIKSRV 149 (164)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 445556667666788889999998 88899999986
No 122
>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=63.72 E-value=25 Score=21.28 Aligned_cols=35 Identities=26% Similarity=0.314 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++...|-+-..||..+ |=|.+.|+.+.
T Consensus 114 ~~~r~v~~l~~~~g~~~~eIA~~l-~is~~tv~~~l 148 (159)
T TIGR02989 114 ERQRELLQLRYQRGVSLTALAEQL-GRTVNAVYKAL 148 (159)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 344455555555677778888887 77888888876
No 123
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=63.70 E-value=23 Score=21.62 Aligned_cols=34 Identities=26% Similarity=0.333 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.++. .|-.-..||..+ |-|.+.|+++.
T Consensus 115 ~~~r~il~l~~-~g~s~~eIA~~l-gis~~tV~~~i 148 (166)
T PRK09639 115 ERDRTVLLLRF-SGYSYKEIAEAL-GIKESSVGTTL 148 (166)
T ss_pred HHHHHHHHHHH-cCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34455566666 788889999998 89999999987
No 124
>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=63.56 E-value=15 Score=17.44 Aligned_cols=37 Identities=19% Similarity=0.269 Sum_probs=25.6
Q ss_pred CChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 6 FPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 6 wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+++ +..++.++...|-.+..||..+ |=+...|+.+.
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~ 47 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRL 47 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 4444 4555555556678899999988 67777777655
No 125
>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=63.48 E-value=6.3 Score=21.93 Aligned_cols=19 Identities=16% Similarity=0.490 Sum_probs=14.9
Q ss_pred HHHHHHHHHhCCchhhhhh
Q 037092 12 RLICRLFAISGSRWSVIGA 30 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~ 30 (76)
..|.+|...||++|..|-.
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3567788899988998864
No 126
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=62.70 E-value=24 Score=22.17 Aligned_cols=34 Identities=15% Similarity=0.142 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.+....|-.-..||..+ |-|.+.|+++.
T Consensus 137 ~~r~i~~l~~~~~~s~~eIA~~l-gis~~tV~~~l 170 (182)
T PRK12537 137 ARRNCILHAYVDGCSHAEIAQRL-GAPLGTVKAWI 170 (182)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCChhhHHHHH
Confidence 34445666666677788899988 88999999987
No 127
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=62.53 E-value=20 Score=22.36 Aligned_cols=35 Identities=23% Similarity=0.310 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++...|-+...||..+ |-+.+.|+++.
T Consensus 122 ~~~r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 156 (172)
T PRK09651 122 GKTREAFLLSQLDGLTYSEIAHKL-GVSVSSVKKYV 156 (172)
T ss_pred HHHhHHhhhhhccCCCHHHHHHHh-CCCHHHHHHHH
Confidence 345556667777788899999998 89999999987
No 128
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=61.84 E-value=26 Score=22.28 Aligned_cols=35 Identities=11% Similarity=0.110 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++...|-....||..+ |-+.+.|+++-
T Consensus 145 ~~~r~vl~l~~~~~~s~~EIA~~L-gis~~tVk~~l 179 (194)
T PRK09646 145 DTQRESVTLAYYGGLTYREVAERL-AVPLGTVKTRM 179 (194)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCChHhHHHHH
Confidence 455556667777788899999998 77999999976
No 129
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=61.78 E-value=6 Score=33.26 Aligned_cols=26 Identities=19% Similarity=0.391 Sum_probs=23.3
Q ss_pred CCCChHHHHHHHHHHHHhC-Cchhhhh
Q 037092 4 WGFPDEEDRLICRLFAISG-SRWSVIG 29 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G-~~W~~Ia 29 (76)
..|+.++|..|+-.+-+|| .+|..|-
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~Ir 1160 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAIR 1160 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHhc
Confidence 4699999999999999999 8898764
No 130
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=61.55 E-value=22 Score=22.74 Aligned_cols=35 Identities=17% Similarity=0.132 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.++...|-....||..+ |-|...|+++-
T Consensus 116 ~~~r~v~~L~~~~g~s~~EIA~~L-giS~~tVk~~l 150 (188)
T PRK12546 116 DEQREALILVGASGFSYEEAAEMC-GVAVGTVKSRA 150 (188)
T ss_pred HHHhHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 455666677777889999999998 89999999986
No 131
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=61.35 E-value=31 Score=20.27 Aligned_cols=18 Identities=11% Similarity=0.064 Sum_probs=15.8
Q ss_pred CCCChHHHHHHHHHHHHh
Q 037092 4 WGFPDEEDRLICRLFAIS 21 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~ 21 (76)
.-||+|++-.|++....|
T Consensus 5 R~WS~eDEi~iL~gl~~~ 22 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDF 22 (98)
T ss_pred CCCCchHHHHHHHHHHHH
Confidence 359999999999998887
No 132
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=59.71 E-value=6.5 Score=29.78 Aligned_cols=40 Identities=20% Similarity=0.469 Sum_probs=37.0
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
-.||++|-. +++...-||.+.-.||..+...|..|++.+|
T Consensus 471 ~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy 510 (534)
T KOG1194|consen 471 YGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFY 510 (534)
T ss_pred CCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHh
Confidence 479999988 8888999999999999999999999999999
No 133
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=59.65 E-value=13 Score=18.39 Aligned_cols=34 Identities=24% Similarity=0.315 Sum_probs=20.2
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNY 43 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knr 43 (76)
.++-..++.++.. |-....||..+ |-+.+.|.+.
T Consensus 4 ~~~R~~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~w 37 (50)
T PF13384_consen 4 EERRAQIIRLLRE-GWSIREIAKRL-GVSRSTVYRW 37 (50)
T ss_dssp ------HHHHHHH-T--HHHHHHHH-TS-HHHHHHH
T ss_pred hhHHHHHHHHHHC-CCCHHHHHHHH-CcCHHHHHHH
Confidence 3445567778887 99999999998 7777777663
No 134
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=59.15 E-value=40 Score=21.05 Aligned_cols=35 Identities=11% Similarity=-0.085 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.+....|-+-..||..+ |-|.+.|+++-
T Consensus 120 ~~~r~i~~l~~~e~~s~~EIA~~l-gis~~tV~~~l 154 (179)
T PRK12543 120 YKLRQVIILRYLHDYSQEEIAQLL-QIPIGTVKSRI 154 (179)
T ss_pred HHHHHHHHHHHHccCCHHHHHHHH-CCCHHHHHHHH
Confidence 445556667666788888999988 88889999886
No 135
>PF09846 DUF2073: Uncharacterized protein conserved in archaea (DUF2073); InterPro: IPR012017 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=58.60 E-value=9.6 Score=23.11 Aligned_cols=17 Identities=18% Similarity=0.251 Sum_probs=14.3
Q ss_pred CCCChHHHHHHHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAI 20 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~ 20 (76)
+.|||+|+..|++.-..
T Consensus 27 ~GLtPeEe~~LIE~TM~ 43 (104)
T PF09846_consen 27 EGLTPEEESKLIEMTMT 43 (104)
T ss_pred CCCChHHHHHHHHHHHH
Confidence 67999999999987644
No 136
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=58.33 E-value=28 Score=21.86 Aligned_cols=35 Identities=17% Similarity=0.113 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++.-.|-+-..||..| |-+.+.|+++.
T Consensus 130 ~~~r~v~~l~~~~g~s~~EIA~~l-~is~~tv~~~l 164 (179)
T PRK09415 130 IKYREVIYLFYYEELSIKEIAEVT-GVNENTVKTRL 164 (179)
T ss_pred HHHhhHhHhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 445556666666677888899988 77889999987
No 137
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=58.25 E-value=34 Score=22.30 Aligned_cols=32 Identities=6% Similarity=-0.097 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..++.+..-.|-.-..||..| |-|.+.|+++.
T Consensus 154 r~v~~L~~~~g~s~~EIAe~l-gis~~tV~~~l 185 (206)
T PRK12544 154 ARVFMMREFIELETNEICHAV-DLSVSNLNVLL 185 (206)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 334444455567778999998 89999999987
No 138
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=57.63 E-value=34 Score=22.07 Aligned_cols=34 Identities=3% Similarity=-0.022 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.++...|-+-..||..+ |-|.+.|+++.
T Consensus 157 ~~r~vl~l~~~~g~s~~EIA~~l-gis~~tV~~~l 190 (206)
T PRK12526 157 AQQTVVKGVYFQELSQEQLAQQL-NVPLGTVKSRL 190 (206)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34445555555577778899988 89999999987
No 139
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=57.27 E-value=32 Score=22.16 Aligned_cols=34 Identities=12% Similarity=-0.008 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.+....|-.-..||..| |-+.+.|+++.
T Consensus 137 ~~r~v~~l~~~~g~s~~EIAe~l-gis~~tV~~~l 170 (196)
T PRK12535 137 ERREALILTQVLGYTYEEAAKIA-DVRVGTIRSRV 170 (196)
T ss_pred HHHHHhhhHHHhCCCHHHHHHHh-CCCHHHHHHHH
Confidence 34455555666677788999998 89999999997
No 140
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=57.02 E-value=35 Score=21.69 Aligned_cols=35 Identities=29% Similarity=0.260 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+....++.+....|-.-..||..| |-+...|+++.
T Consensus 114 ~~~R~v~~L~~~eg~s~~EIA~~l-gis~~tV~~~l 148 (182)
T PRK12511 114 EEQRAALHLVAIEGLSYQEAAAVL-GIPIGTLMSRI 148 (182)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CcCHHHHHHHH
Confidence 344555666666788889999998 88999999987
No 141
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=56.92 E-value=11 Score=23.38 Aligned_cols=35 Identities=17% Similarity=0.078 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++..+|-+...||..| |-+...|+.+.
T Consensus 129 ~~~r~v~~l~~~~g~s~~eIA~~l-~is~~~V~~~l 163 (176)
T PRK09638 129 PEFRAPVILKHYYGYTYEEIAKML-NIPEGTVKSRV 163 (176)
T ss_pred HHHhheeeehhhcCCCHHHHHHHH-CCChhHHHHHH
Confidence 445555666666788899999998 77889898876
No 142
>PRK00118 putative DNA-binding protein; Validated
Probab=55.93 E-value=43 Score=20.11 Aligned_cols=36 Identities=11% Similarity=0.170 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++.+..++.++...|-+...||..+ |-|.+.|+++-
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L 54 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNI 54 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 5566777788888889999999998 89999988875
No 143
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=55.68 E-value=27 Score=23.28 Aligned_cols=35 Identities=14% Similarity=0.074 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.+....|-.-..||..| |-|.+.|+++-
T Consensus 174 ~~~R~v~~L~~~eg~s~~EIA~~L-gis~~tVk~~l 208 (233)
T PRK12538 174 EQQRIAVILSYHENMSNGEIAEVM-DTTVAAVESLL 208 (233)
T ss_pred HHHHHHhhhHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 344555666666788889999998 89999999986
No 144
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=55.16 E-value=35 Score=20.83 Aligned_cols=34 Identities=18% Similarity=0.083 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+...++.+....|-....||..| |=|...|+.+-
T Consensus 116 ~~r~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l 149 (161)
T PRK12541 116 ERRNVLLLRDYYGFSYKEIAEMT-GLSLAKVKIEL 149 (161)
T ss_pred HHHHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34455556566677778899888 78888888876
No 145
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=54.83 E-value=37 Score=21.53 Aligned_cols=30 Identities=20% Similarity=0.315 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 13 LICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 13 ~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.++.+ .-.|-+-..||..+ |-|.+.|+++-
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 33444 34577788899988 88899998876
No 146
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=54.60 E-value=31 Score=28.50 Aligned_cols=41 Identities=17% Similarity=0.280 Sum_probs=35.2
Q ss_pred CCCChHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.||.-+=...+.+..+|| ..-..||..|.|.|...|+.+.
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~ 866 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYA 866 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHH
Confidence 3588888888888999999 6688999999999999999764
No 147
>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=54.59 E-value=44 Score=20.76 Aligned_cols=35 Identities=23% Similarity=0.225 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.++...|-.=..||..| |-|...|+++.
T Consensus 103 ~~~r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l 137 (170)
T TIGR02959 103 DEYREAIRLTELEGLSQQEIAEKL-GLSLSGAKSRV 137 (170)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345566667777788889999998 88999999986
No 148
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=53.99 E-value=42 Score=20.77 Aligned_cols=32 Identities=6% Similarity=0.039 Sum_probs=22.3
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..++.+....|-+-..||..+ |-+...|+.+-
T Consensus 125 r~i~~l~~~~~~s~~EIA~~l-gis~~tV~~~l 156 (173)
T PRK12522 125 KTVLVLYYYEQYSYKEMSEIL-NIPIGTVKYRL 156 (173)
T ss_pred HHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 344445555566677888887 78888888875
No 149
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=53.42 E-value=32 Score=21.70 Aligned_cols=35 Identities=23% Similarity=0.159 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..++.+....|-+-..||..| |-|.+.|+++-
T Consensus 144 ~~~~~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 178 (194)
T PRK12519 144 ESQRQVLELAYYEGLSQSEIAKRL-GIPLGTVKARA 178 (194)
T ss_pred HHHhhhhhhhhhcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 344555556556677788899888 78888888876
No 150
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=51.76 E-value=21 Score=19.83 Aligned_cols=31 Identities=13% Similarity=0.388 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCC---CHHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGR---TDNETNNY 43 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gR---t~~~~knr 43 (76)
+.+|-+|+..|| |..++..++=| ++.+|+.-
T Consensus 12 e~il~~Lv~~yG--W~~L~~~i~i~CF~~~PsikSS 45 (64)
T PF09905_consen 12 ETILTELVEHYG--WEELGERININCFKNNPSIKSS 45 (64)
T ss_dssp HHHHHHHHHHT---HHHHHHHTTSSSTTSS--HHHH
T ss_pred HHHHHHHHHHhC--HHHHHhhcccccCCCCCchHHH
Confidence 578889999997 98888877533 34455553
No 151
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=51.61 E-value=14 Score=22.91 Aligned_cols=25 Identities=8% Similarity=-0.037 Sum_probs=19.5
Q ss_pred HHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 19 AISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 19 ~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.-.|-+-..||..| |-|.+.|+++.
T Consensus 133 ~~~g~s~~eIA~~l-g~s~~tv~~~l 157 (175)
T PRK12518 133 DLEDLPQKEIAEIL-NIPVGTVKSRL 157 (175)
T ss_pred HhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 33455668899988 88899999987
No 152
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=51.44 E-value=47 Score=20.34 Aligned_cols=35 Identities=9% Similarity=-0.045 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.++...|-.-..||..+ |-+.+.|+.+-
T Consensus 111 ~~~r~v~~l~~~~g~s~~eIA~~l-gis~~tv~~~l 145 (165)
T PRK09644 111 VIEAQAILLCDVHELTYEEAASVL-DLKLNTYKSHL 145 (165)
T ss_pred HHHHHHHHhHHHhcCCHHHHHHHH-CCCHHHHHHHH
Confidence 344555566666788888999998 78999998875
No 153
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=51.37 E-value=48 Score=21.02 Aligned_cols=47 Identities=17% Similarity=0.093 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHh--hchhhhHHhhC
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYR--NTKLKRKHEEG 56 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~--~~~l~~~~~~~ 56 (76)
+....++.+....|-+-..||..| |-|.+.|+.+-. ...|++.+...
T Consensus 114 ~~~R~v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l~RAr~~Lr~~l~~~ 162 (182)
T PRK12540 114 QDQREALILVGASGFSYEDAAAIC-GCAVGTIKSRVNRARSKLSALLYVD 162 (182)
T ss_pred HHHHHHhhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 445556666666788889999998 888999998851 23344444433
No 154
>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=51.10 E-value=23 Score=19.08 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=19.1
Q ss_pred HHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 15 CRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 15 ~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
..+....|+.|..+|..+ |=+...|..
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 456677899999999988 444544443
No 155
>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=51.08 E-value=21 Score=15.04 Aligned_cols=37 Identities=22% Similarity=0.196 Sum_probs=23.1
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
..+++++-..++.++. -|.....|+..+ |.+...+.+
T Consensus 4 ~~~~~~~~~~i~~~~~-~~~s~~~ia~~~-~is~~tv~~ 40 (42)
T cd00569 4 PKLTPEQIEEARRLLA-AGESVAEIARRL-GVSRSTLYR 40 (42)
T ss_pred CcCCHHHHHHHHHHHH-cCCCHHHHHHHH-CCCHHHHHH
Confidence 3466655555555543 466788888877 666665544
No 156
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=51.02 E-value=74 Score=21.40 Aligned_cols=46 Identities=17% Similarity=0.125 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHh--hchhhhHHhhC
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYR--NTKLKRKHEEG 56 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~--~~~l~~~~~~~ 56 (76)
++..++.+....|-+-..||..+ |-+.+.|+++-. ...|+..+...
T Consensus 120 ~~R~v~lL~~~eg~S~~EIAe~L-giS~~tVksrL~Rark~Lr~~l~~~ 167 (228)
T PRK06704 120 QQSAILLLKDVFQYSIADIAKVC-SVSEGAVKASLFRSRNRLKTVSEEG 167 (228)
T ss_pred HHhhHhhhHHhhCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 34555556666677889999998 789999999851 23445554443
No 157
>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=50.89 E-value=36 Score=18.34 Aligned_cols=24 Identities=29% Similarity=0.516 Sum_probs=17.3
Q ss_pred HHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 18 FAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 18 ~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
....|+.|..+|..+ |=+...+.+
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 455689999999998 776666554
No 158
>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=50.55 E-value=47 Score=22.39 Aligned_cols=34 Identities=21% Similarity=0.315 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.++...|-....||..+ |=+.+.|+.+-
T Consensus 165 ~~R~v~~L~~~eg~S~~EIA~~L-gis~~TVk~rl 198 (244)
T TIGR03001 165 RERHLLRLHFVDGLSMDRIGAMY-QVHRSTVSRWV 198 (244)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 44555666666678899999998 89999999986
No 159
>PRK06930 positive control sigma-like factor; Validated
Probab=50.52 E-value=51 Score=21.19 Aligned_cols=33 Identities=12% Similarity=0.138 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+..++.++...|-.-..||..| |-|.+.|+.+.
T Consensus 119 er~V~~L~~~eg~s~~EIA~~l-giS~~tVk~~l 151 (170)
T PRK06930 119 EKEVYLMHRGYGLSYSEIADYL-NIKKSTVQSMI 151 (170)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 3444556566788899999998 88999999886
No 160
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=50.08 E-value=31 Score=18.42 Aligned_cols=40 Identities=18% Similarity=0.176 Sum_probs=29.0
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+..||+|+-..++..+..-|..-..+|..+ |=+...+.+ |
T Consensus 4 r~~ys~e~K~~~v~~~~~~g~sv~~va~~~-gi~~~~l~~-W 43 (76)
T PF01527_consen 4 RRRYSPEFKLQAVREYLESGESVSEVAREY-GISPSTLYN-W 43 (76)
T ss_dssp S----HHHHHHHHHHHHHHHCHHHHHHHHH-TS-HHHHHH-H
T ss_pred CCCCCHHHHHHHHHHHHHCCCceEeeeccc-ccccccccH-H
Confidence 468999999999999988889999999887 446666665 6
No 161
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=49.30 E-value=54 Score=20.49 Aligned_cols=34 Identities=9% Similarity=0.115 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.++...|-+...||..| |=|.+.|+++-
T Consensus 141 ~~r~i~~l~~~~g~s~~eIA~~l-gis~~~v~~~l 174 (187)
T PRK12534 141 PRSELIRTAFFEGITYEELAART-DTPIGTVKSWI 174 (187)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHh-CCChhHHHHHH
Confidence 34444556656678888999988 77888888875
No 162
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=48.45 E-value=42 Score=22.12 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++...|-+...||..+ |-|...|+.+-
T Consensus 187 ~~~r~vl~l~~~~g~s~~EIA~~l-gis~~tV~~~~ 221 (236)
T PRK06986 187 EREQLVLSLYYQEELNLKEIGAVL-GVSESRVSQIH 221 (236)
T ss_pred HHHHHHHHhHhccCCCHHHHHHHH-CCCHHHHHHHH
Confidence 445556666666677889999998 89999999886
No 163
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=46.94 E-value=20 Score=22.67 Aligned_cols=32 Identities=13% Similarity=0.069 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..++.++...|-....||..+ |-+...|+++.
T Consensus 145 r~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 176 (194)
T PRK12513 145 REVFLLREHGDLELEEIAELT-GVPEETVKSRL 176 (194)
T ss_pred hhheeeehccCCCHHHHHHHH-CCCHHHHHHHH
Confidence 334444445567788899988 78999999876
No 164
>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=46.64 E-value=55 Score=20.47 Aligned_cols=36 Identities=19% Similarity=0.328 Sum_probs=21.3
Q ss_pred CChHHHHHHHHHHHHhC--CchhhhhhcCCCCCHHHHHHH
Q 037092 6 FPDEEDRLICRLFAISG--SRWSVIGAHLPGRTDNETNNY 43 (76)
Q Consensus 6 wT~eED~~L~~~~~~~G--~~W~~Ia~~~~gRt~~~~knr 43 (76)
++++ +..++.+.-.-+ ..|..||..+ +=+..+|+..
T Consensus 82 l~de-~k~Ii~lry~~r~~~TW~~IA~~l-~i~erta~r~ 119 (130)
T PF05263_consen 82 LIDE-EKRIIKLRYDRRSRRTWYQIAQKL-HISERTARRW 119 (130)
T ss_pred hCHH-HHHHHHHHHcccccchHHHHHHHh-CccHHHHHHH
Confidence 3444 555555554433 6799999987 3455555543
No 165
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=46.40 E-value=22 Score=21.58 Aligned_cols=44 Identities=20% Similarity=0.420 Sum_probs=28.5
Q ss_pred CCChHHHHHHHHHHHHh------------CC-c------------------hhhhhhcCCCCCHHHHHHHHhhchh
Q 037092 5 GFPDEEDRLICRLFAIS------------GS-R------------------WSVIGAHLPGRTDNETNNYYRNTKL 49 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~------------G~-~------------------W~~Ia~~~~gRt~~~~knrw~~~~l 49 (76)
.||.+||..|...+.++ |. . ....+...|.-|.++=+.|| ...+
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~-RKfv 75 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRY-RKFV 75 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHH-HHTH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHH-HHHH
Confidence 38999999999988664 11 1 23456677889999999998 4433
No 166
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 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 (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=46.02 E-value=24 Score=22.36 Aligned_cols=30 Identities=13% Similarity=0.142 Sum_probs=21.6
Q ss_pred HHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 14 ICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 14 L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++.+....|-+-..||..+ |-|...|+++-
T Consensus 139 i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l 168 (193)
T TIGR02947 139 AVYLADVEGFAYKEIAEIM-GTPIGTVMSRL 168 (193)
T ss_pred heeehhhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 3334444456678899888 89999999986
No 167
>PRK02866 cyanate hydratase; Validated
Probab=45.81 E-value=51 Score=21.10 Aligned_cols=32 Identities=16% Similarity=0.169 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.|+.+-.+-|-.|..||..+ |++..-+..-.
T Consensus 8 e~Ll~AK~~kGLTw~~IA~~i-G~S~v~vaaa~ 39 (147)
T PRK02866 8 EKILAAKKEKGLTWADIAEAI-GLSEVWVTAAL 39 (147)
T ss_pred HHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 567888888899999999998 89988777765
No 168
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=45.53 E-value=53 Score=19.92 Aligned_cols=34 Identities=18% Similarity=0.258 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..++.+....|-+-..||..+ |-|.+.|+.+-
T Consensus 113 ~~r~v~~l~~~~~~s~~EIA~~l-gis~~tV~~~l 146 (163)
T PRK07037 113 RTRYAFEMYRLHGETQKDIAREL-GVSPTLVNFMI 146 (163)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34445555555566777888877 77777777764
No 169
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=45.44 E-value=56 Score=21.54 Aligned_cols=35 Identities=14% Similarity=0.009 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++...|-.-..||..| |=|.+.|+.+-
T Consensus 137 ~~~R~v~~L~y~eg~s~~EIAe~L-giS~~tVk~~L 171 (216)
T PRK12533 137 VEYREVLVLRELEDMSYREIAAIA-DVPVGTVMSRL 171 (216)
T ss_pred HHHHhHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 345566666666777788999998 89999999986
No 170
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=45.06 E-value=1e+02 Score=21.32 Aligned_cols=40 Identities=20% Similarity=0.339 Sum_probs=29.9
Q ss_pred HHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhhHHhh
Q 037092 13 LICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKRKHEE 55 (76)
Q Consensus 13 ~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~~~~~ 55 (76)
.++.|+..+|-.-..||..+ |.|.+.|+.+. ...++++..
T Consensus 125 ~vf~L~~~~g~s~~EIA~~L-gis~~tVr~~l--~RAr~~Lr~ 164 (290)
T PRK09635 125 VVFVLHEIFGLPYQQIATTI-GSQASTCRQLA--HRARRKINE 164 (290)
T ss_pred HHhhHHHHhCCCHHHHHHHH-CcCHHHHHHHH--HHHHHHHHh
Confidence 34456677788889999998 99999999987 334455544
No 171
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=44.77 E-value=56 Score=21.40 Aligned_cols=23 Identities=9% Similarity=0.053 Sum_probs=19.1
Q ss_pred hCCchhhhhhcCCCCCHHHHHHHH
Q 037092 21 SGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 21 ~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.|-+...||..+ |-|.+.|+++-
T Consensus 197 eg~s~~EIA~~l-gis~~tVk~~~ 219 (234)
T PRK08301 197 EEKTQKEVADML-GISQSYISRLE 219 (234)
T ss_pred CCCCHHHHHHHH-CCCHHHHHHHH
Confidence 467788999988 88999998875
No 172
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=44.09 E-value=71 Score=19.67 Aligned_cols=34 Identities=21% Similarity=0.358 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.++.--|-+...||..+ |-+.+.|+++-
T Consensus 122 ~~r~v~~L~~~eg~s~~EIA~~l-~is~~tV~~~l 155 (168)
T PRK12525 122 KARAAFLMSQLEGLTYVEIGERL-GVSLSRIHQYM 155 (168)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34455566666677889999988 78888888876
No 173
>PF08074 CHDCT2: CHDCT2 (NUC038) domain; InterPro: IPR012957 The CHDCT2 C-terminal domain is found in PHD/RING fingers and chromo domain-associated CHD-like helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=43.77 E-value=16 Score=23.97 Aligned_cols=40 Identities=23% Similarity=0.351 Sum_probs=30.1
Q ss_pred CCChHHHHHHHHHHHHhC-Cchhhhhhc--C-----CCCCH------HHHHHHH
Q 037092 5 GFPDEEDRLICRLFAISG-SRWSVIGAH--L-----PGRTD------NETNNYY 44 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G-~~W~~Ia~~--~-----~gRt~------~~~knrw 44 (76)
-|-..-|-.|+..+..+| .+|..|..- | |=++. ..+||+|
T Consensus 5 iw~r~hdywll~gi~~hgy~rwqdi~nd~~f~IiNEPFk~e~~kgnfle~KNkF 58 (173)
T PF08074_consen 5 IWHRRHDYWLLAGIVKHGYGRWQDIQNDPRFAIINEPFKTESQKGNFLEMKNKF 58 (173)
T ss_pred hhhhhhhHHHHhHHhhccchhHHHHhcCCceeeecccccccccccchHHHHHHH
Confidence 477788999999999999 899988752 1 22332 3789988
No 174
>KOG0431 consensus Auxilin-like protein and related proteins containing DnaJ domain [General function prediction only]
Probab=43.18 E-value=37 Score=25.41 Aligned_cols=61 Identities=20% Similarity=0.230 Sum_probs=39.6
Q ss_pred HHHHHHHHHhC--CchhhhhhcCCCCCHHHHHHHHhhchhh---hHHhhCCCCCCCchhHHHHHHHh
Q 037092 12 RLICRLFAISG--SRWSVIGAHLPGRTDNETNNYYRNTKLK---RKHEEGGLKVPMKKNLERDLRIV 73 (76)
Q Consensus 12 ~~L~~~~~~~G--~~W~~Ia~~~~gRt~~~~knrw~~~~l~---~~~~~~~~~~~~~~~~~~~~~~~ 73 (76)
.+|-.|+..++ ++|..|+-. .=.|+.+||-.|++..|. .++.+.+.....+...++...++
T Consensus 376 ALLSTLh~VLW~es~WqpVslt-DLVtp~~VKKaYrKA~L~VHPDKlqq~gas~~qK~Iaekvfd~l 441 (453)
T KOG0431|consen 376 ALLSTLHYVLWPESGWQPVSLT-DLVTPAQVKKAYRKAVLCVHPDKLQQKGASLEQKYIAEKVFDAL 441 (453)
T ss_pred HHHHHHhHhhcCccCcccCchh-hccCHHHHHHHHHhhhheeCcccccCCcccHHHHHHHHHHHHHH
Confidence 46777888887 689887642 237899999999544432 35556666655555555555544
No 175
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=42.47 E-value=23 Score=19.25 Aligned_cols=16 Identities=31% Similarity=0.104 Sum_probs=12.7
Q ss_pred CCCCChHHHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLF 18 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~ 18 (76)
.+.-|||||..|.+..
T Consensus 42 ~~CitpEE~~~I~e~~ 57 (60)
T PF10892_consen 42 GDCITPEEDREILEAT 57 (60)
T ss_pred hccCCHHHHHHHHHHH
Confidence 4567999999998754
No 176
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=42.45 E-value=63 Score=21.55 Aligned_cols=35 Identities=20% Similarity=0.278 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.+...-|-.-..||..+ |-|...|+++-
T Consensus 204 ~~~r~vl~l~~~~~~s~~EIA~~l-gis~~tV~~~~ 238 (251)
T PRK07670 204 EKEQLVISLFYKEELTLTEIGQVL-NLSTSRISQIH 238 (251)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 455666666666677889999988 89999998886
No 177
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=42.27 E-value=77 Score=19.12 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHHhC-CchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFAISG-SRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~~~G-~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++-|..|+++...-| -.++.||..+ |-|...|.+|=
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri 43 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRI 43 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHH
Confidence 466888888888877 4599999998 89999999997
No 178
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=42.17 E-value=34 Score=20.53 Aligned_cols=26 Identities=23% Similarity=0.489 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHhC-CchhhhhhcCCCC
Q 037092 10 EDRLICRLFAISG-SRWSVIGAHLPGR 35 (76)
Q Consensus 10 ED~~L~~~~~~~G-~~W~~Ia~~~~gR 35 (76)
|-++|-.+...|+ .+|...+.++||-
T Consensus 93 E~diLKKa~~~~~~~~~~~~~~~~~~~ 119 (121)
T PRK09413 93 ENELLKEAVEYGRAKKWIAHAPLLPGD 119 (121)
T ss_pred HHHHHHHHHHHhchhhhhhcCCCCCCC
Confidence 3344555555566 5699999998874
No 179
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=41.56 E-value=69 Score=20.81 Aligned_cols=35 Identities=9% Similarity=0.109 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+++..+++-.-.+|.....+..+| |-|...|..|=
T Consensus 74 ~~~~~~idr~L~lGAS~~mm~~~F-Gls~~ev~~rR 108 (180)
T PF11198_consen 74 QQEQQLIDRALRLGASIEMMQRLF-GLSSAEVAARR 108 (180)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 455666777778899999999998 88988888764
No 180
>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=41.49 E-value=69 Score=20.82 Aligned_cols=33 Identities=21% Similarity=0.183 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 11 DRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+..++.++...|-.-..||..+ |-|.+.|+.+-
T Consensus 183 ~r~vl~l~y~~~~s~~eIA~~l-gis~~~v~~~~ 215 (227)
T TIGR02980 183 ERRILLLRFFEDKTQSEIAERL-GISQMHVSRLL 215 (227)
T ss_pred HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 3444555555577788899988 78888888876
No 181
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=40.23 E-value=52 Score=16.56 Aligned_cols=41 Identities=17% Similarity=0.336 Sum_probs=32.2
Q ss_pred CCCCChHHHHHHHHHHHHhC-Cc---hhhhhhcCCCCCHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAISG-SR---WSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G-~~---W~~Ia~~~~gRt~~~~knrw 44 (76)
+..||++.-..|...+.... +. -..||..+ |=+..+|.+.|
T Consensus 4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF 48 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWF 48 (57)
T ss_dssp SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCH
Confidence 56799999999998888833 11 45688777 89999999977
No 182
>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=39.59 E-value=49 Score=16.07 Aligned_cols=33 Identities=21% Similarity=0.175 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
=|.+.|.+....+|++-+..|..+ |=+...+..
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~ 37 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHH
Confidence 377889999999999999999887 555444443
No 183
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=39.50 E-value=87 Score=20.65 Aligned_cols=36 Identities=17% Similarity=0.248 Sum_probs=28.2
Q ss_pred CChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 6 FPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 6 wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.|+-|-+.| .++.. |-.-..||..+ +-+...|+++-
T Consensus 156 Lt~rE~~Vl-~l~~~-G~s~~eIA~~L-~iS~~TVk~~~ 191 (216)
T PRK10100 156 LTHREKEIL-NKLRI-GASNNEIARSL-FISENTVKTHL 191 (216)
T ss_pred CCHHHHHHH-HHHHc-CCCHHHHHHHh-CCCHHHHHHHH
Confidence 677665555 45555 98899999998 79999999987
No 184
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=39.50 E-value=99 Score=19.59 Aligned_cols=35 Identities=23% Similarity=0.051 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++...|-.-..||..+ |-|.+.|+.+-
T Consensus 131 ~~~r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l 165 (188)
T PRK12517 131 PEYREPLLLQVIGGFSGEEIAEIL-DLNKNTVMTRL 165 (188)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 344555556666677788899988 88889998875
No 185
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=39.46 E-value=68 Score=21.03 Aligned_cols=43 Identities=16% Similarity=0.181 Sum_probs=31.9
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhhh
Q 037092 5 GFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLKR 51 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~~ 51 (76)
..|+.|-+.|. +..+ |-.=..||..+ +.|..-||++. .+.+++
T Consensus 148 ~LT~RE~eVL~-lla~-G~snkeIA~~L-~iS~~TVk~h~-~~i~~K 190 (211)
T COG2197 148 LLTPRELEVLR-LLAE-GLSNKEIAEEL-NLSEKTVKTHV-SNILRK 190 (211)
T ss_pred CCCHHHHHHHH-HHHC-CCCHHHHHHHH-CCCHhHHHHHH-HHHHHH
Confidence 47777776654 4444 77788999999 89999999998 544433
No 186
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=38.48 E-value=86 Score=20.41 Aligned_cols=35 Identities=23% Similarity=0.355 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++...|-.-..||..+ |-+...|+.+.
T Consensus 178 ~~~r~il~l~y~~~~s~~eIA~~l-gis~~tV~~~~ 212 (224)
T TIGR02479 178 EREQLVLSLYYYEELNLKEIGEVL-GLTESRVSQIH 212 (224)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHh-CCCHHHHHHHH
Confidence 344445555555566778888887 78888888876
No 187
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=38.43 E-value=1e+02 Score=20.77 Aligned_cols=37 Identities=27% Similarity=0.301 Sum_probs=29.1
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 5 GFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..|+-|-+.|. ++.+ |-....||..| +-|...|+++-
T Consensus 133 ~LSpRErEVLr-LLAq-GkTnKEIAe~L-~IS~rTVkth~ 169 (198)
T PRK15201 133 HFSVTERHLLK-LIAS-GYHLSETAALL-SLSEEQTKSLR 169 (198)
T ss_pred CCCHHHHHHHH-HHHC-CCCHHHHHHHh-CCCHHHHHHHH
Confidence 46777766654 5555 88999999998 88899998876
No 188
>PRK01905 DNA-binding protein Fis; Provisional
Probab=38.28 E-value=72 Score=17.65 Aligned_cols=35 Identities=20% Similarity=0.177 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHH
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNY 43 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knr 43 (76)
.-|...+.+++..+|.+.+..|..+ |=+...+..+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 3477788999999999999999887 5555554443
No 189
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=37.15 E-value=28 Score=21.99 Aligned_cols=27 Identities=15% Similarity=0.085 Sum_probs=20.0
Q ss_pred HHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 17 LFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 17 ~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...|-....||..| |-|...|+++-
T Consensus 145 l~~~~g~s~~EIA~~l-gis~~tV~~~l 171 (188)
T PRK09640 145 LRFVAELEFQEIADIM-HMGLSATKMRY 171 (188)
T ss_pred eHHhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 3333456678899988 88888998886
No 190
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=37.03 E-value=84 Score=20.21 Aligned_cols=32 Identities=13% Similarity=0.045 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.|+.+-..-|-.|..||..+ |++..-+-.-.
T Consensus 11 ~~Ll~AK~~KGLTwe~IAe~i-G~sevwvaaa~ 42 (150)
T TIGR00673 11 DALLESKKKKGLTFADIADGL-GLAEVFVAAAL 42 (150)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 467777788899999999998 78887665544
No 191
>PF09633 DUF2023: Protein of unknown function (DUF2023); InterPro: IPR018594 This protein of approx.120 residues consists of three beta strands and five alpha helices, thought to fold into a homo-dimer. ; PDB: 2GUK_B.
Probab=37.02 E-value=21 Score=21.56 Aligned_cols=11 Identities=27% Similarity=0.392 Sum_probs=7.3
Q ss_pred CCChHHHHHHH
Q 037092 5 GFPDEEDRLIC 15 (76)
Q Consensus 5 ~wT~eED~~L~ 15 (76)
.+|||||-+|=
T Consensus 74 ~lTpEEDFiLG 84 (101)
T PF09633_consen 74 ELTPEEDFILG 84 (101)
T ss_dssp G--HHHHHHHH
T ss_pred hCCcHHHHHHH
Confidence 58999998873
No 192
>PRK09191 two-component response regulator; Provisional
Probab=36.80 E-value=77 Score=20.50 Aligned_cols=35 Identities=20% Similarity=0.114 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.+...-|-+...||..+ |.+.+.|+.+-
T Consensus 91 ~~~r~v~~l~~~~~~s~~eIA~~l-~~s~~tV~~~l 125 (261)
T PRK09191 91 PLPRQAFLLTALEGFSVEEAAEIL-GVDPAEAEALL 125 (261)
T ss_pred HHHhHHHHHHHHhcCCHHHHHHHH-CCCHHHHHHHH
Confidence 456777778888888999999988 88888888876
No 193
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=36.49 E-value=86 Score=20.37 Aligned_cols=36 Identities=11% Similarity=0.226 Sum_probs=28.2
Q ss_pred CChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 6 FPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 6 wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.|+-|-+.| .++.+ |.....||..+ |-|.+-|+++-
T Consensus 138 LT~RE~eVL-~lla~-G~snkeIA~~L-~iS~~TVk~h~ 173 (207)
T PRK15411 138 LSRTESSML-RMWMA-GQGTIQISDQM-NIKAKTVSSHK 173 (207)
T ss_pred CCHHHHHHH-HHHHc-CCCHHHHHHHc-CCCHHHHHHHH
Confidence 677777665 45554 88889999999 78999999876
No 194
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=35.97 E-value=40 Score=21.02 Aligned_cols=20 Identities=20% Similarity=0.624 Sum_probs=15.8
Q ss_pred HHHHHHHHHHhCCchhhhhhcC
Q 037092 11 DRLICRLFAISGSRWSVIGAHL 32 (76)
Q Consensus 11 D~~L~~~~~~~G~~W~~Ia~~~ 32 (76)
+.+|-++|..|| |...+..+
T Consensus 21 E~llt~Lvd~YG--Wd~L~~ri 40 (136)
T COG4628 21 ETLLTELVDFYG--WDGLATRI 40 (136)
T ss_pred HHHHHHHHHHhC--hHHHHhhc
Confidence 578889999998 77766655
No 195
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=35.52 E-value=1e+02 Score=20.84 Aligned_cols=34 Identities=18% Similarity=0.263 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.++...|-.-..||..+ |-|.+.|+.+.
T Consensus 216 ~~r~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~~ 249 (268)
T PRK06288 216 REKKVLILYYYEDLTLKEIGKVL-GVTESRISQLH 249 (268)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 34445555555567788888888 88888888765
No 196
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=35.26 E-value=95 Score=18.11 Aligned_cols=33 Identities=12% Similarity=0.089 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
-|...|..+...+|.+.+..|..+ |=+.+.++.
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~r 87 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRK 87 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHH
Confidence 467788899999999999999887 555555444
No 197
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=34.43 E-value=60 Score=16.74 Aligned_cols=40 Identities=15% Similarity=0.111 Sum_probs=25.8
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+-..|.+|--.+++.+.. |..=..||..| |=+..+|.+-+
T Consensus 4 R~~LTl~eK~~iI~~~e~-g~s~~~ia~~f-gv~~sTv~~I~ 43 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEE-GESKRDIAREF-GVSRSTVSTIL 43 (53)
T ss_dssp SSS--HHHHHHHHHHHHC-TT-HHHHHHHH-T--CCHHHHHH
T ss_pred CccCCHHHHHHHHHHHHc-CCCHHHHHHHh-CCCHHHHHHHH
Confidence 557889999999999877 66788899887 44444454444
No 198
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=34.18 E-value=1.1e+02 Score=18.65 Aligned_cols=35 Identities=6% Similarity=0.056 Sum_probs=21.7
Q ss_pred ChHHHHHHHHHHHHhCC--chhhhhhcCCCCCHHHHHHH
Q 037092 7 PDEEDRLICRLFAISGS--RWSVIGAHLPGRTDNETNNY 43 (76)
Q Consensus 7 T~eED~~L~~~~~~~G~--~W~~Ia~~~~gRt~~~~knr 43 (76)
+++|- .|+.+.---+. .|..||..+ |=|...|..+
T Consensus 84 d~~er-~II~~rY~~~~~~t~~~Ia~~l-~iS~~t~~r~ 120 (134)
T TIGR01636 84 DEQTR-VIIQELYMKKRPLTLVGLAQQL-FISKSTAYRL 120 (134)
T ss_pred CHHHH-HHHHHHHccCCCCCHHHHHHHh-CCCHHHHHHH
Confidence 44444 44444333344 799999998 7777777643
No 199
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=33.81 E-value=89 Score=21.25 Aligned_cols=34 Identities=12% Similarity=0.147 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.++..-|-.-..||..+ |-|...|+.+.
T Consensus 219 rer~vl~l~y~~~~t~~EIA~~l-gis~~~V~~~~ 252 (264)
T PRK07122 219 RERTVLVLRFFESMTQTQIAERV-GISQMHVSRLL 252 (264)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHH-CcCHHHHHHHH
Confidence 34445555555577788999988 88888888876
No 200
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=33.59 E-value=1.2e+02 Score=18.90 Aligned_cols=35 Identities=14% Similarity=0.163 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++.+....|-.-..||..+ |-+.+.|+++-
T Consensus 134 ~~~r~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l 168 (184)
T PRK12539 134 EKMRLAIQAVKLEGLSVAEAATRS-GMSESAVKVSV 168 (184)
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHH-CcCHHHHHHHH
Confidence 344445555555577778888888 66888888875
No 201
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=32.92 E-value=1.1e+02 Score=20.63 Aligned_cols=35 Identities=11% Similarity=0.087 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++..-|-.-..||..+ |-|...|+.+.
T Consensus 206 ~~~r~vl~l~y~~~~s~~eIA~~l-gvs~~~V~~~~ 240 (256)
T PRK07408 206 ERTREVLEFVFLHDLTQKEAAERL-GISPVTVSRRV 240 (256)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHH
Confidence 344455555555567788899988 88888888876
No 202
>TIGR00696 wecB_tagA_cpsF bacterial polymer biosynthesis proteins, WecB/TagA/CpsF family. The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.
Probab=32.40 E-value=64 Score=20.89 Aligned_cols=23 Identities=22% Similarity=0.044 Sum_probs=19.7
Q ss_pred CCCCChHHHHHHHHHHHHhCCch
Q 037092 3 PWGFPDEEDRLICRLFAISGSRW 25 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W 25 (76)
.|+|+++|++.+++.+...|..=
T Consensus 81 ~g~f~~~~~~~i~~~I~~s~~di 103 (177)
T TIGR00696 81 FGPLEPEERKAALAKIARSGAGI 103 (177)
T ss_pred CCCCChHHHHHHHHHHHHcCCCE
Confidence 48899999999999999988763
No 203
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=31.87 E-value=1.2e+02 Score=18.85 Aligned_cols=22 Identities=23% Similarity=0.371 Sum_probs=15.8
Q ss_pred CCchhhhhhcCCCCCHHHHHHHH
Q 037092 22 GSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 22 G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
|-+-..||..+ |-+...|+++.
T Consensus 165 ~~s~~eIA~~l-~~s~~tV~~~l 186 (198)
T TIGR02859 165 GKSYQEIACDL-NRHVKSIDNAL 186 (198)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHH
Confidence 45567788777 67777787776
No 204
>COG3793 TerB Tellurite resistance protein [Inorganic ion transport and metabolism]
Probab=31.85 E-value=60 Score=20.80 Aligned_cols=20 Identities=20% Similarity=0.243 Sum_probs=18.2
Q ss_pred CCCCChHHHHHHHHHHHHhC
Q 037092 3 PWGFPDEEDRLICRLFAISG 22 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G 22 (76)
-|.+.++|+..|.+...-+|
T Consensus 117 DG~~d~~E~avl~eI~~aLG 136 (144)
T COG3793 117 DGEFEAEERAVLREIAGALG 136 (144)
T ss_pred CCCCCHHHHHHHHHHHHHhC
Confidence 47899999999999999888
No 205
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=31.81 E-value=1.2e+02 Score=20.48 Aligned_cols=35 Identities=20% Similarity=0.302 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
+.+..++.++..-|-.-..||..| |-|...|+.+.
T Consensus 208 ~~er~vi~l~y~e~~t~~EIA~~l-gis~~~V~~~~ 242 (257)
T PRK05911 208 EKERKVMALYYYEELVLKEIGKIL-GVSESRVSQIH 242 (257)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 344455555555567788899988 78888888876
No 206
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=31.28 E-value=1.2e+02 Score=18.26 Aligned_cols=37 Identities=19% Similarity=0.189 Sum_probs=28.0
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 5 GFPDEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..|+.|-++|.-+.. |-.-..||..+ +-+.+.|+++-
T Consensus 137 ~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~ 173 (196)
T PRK10360 137 PLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHR 173 (196)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHH
Confidence 577777766654443 66788999998 67889998887
No 207
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=30.76 E-value=88 Score=24.21 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=36.1
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhh-cCCCCCHHHHHHHHh
Q 037092 5 GFPDEEDRLICRLFAISGSRWSVIGA-HLPGRTDNETNNYYR 45 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~~W~~Ia~-~~~gRt~~~~knrw~ 45 (76)
.||..|-.+.-++.++||.....|.. ++|=.+-.+|-..||
T Consensus 287 EWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 287 EWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 59999999999999999999998875 678888888888773
No 208
>COG2992 Bax Uncharacterized FlgJ-related protein [General function prediction only]
Probab=30.72 E-value=30 Score=24.01 Aligned_cols=25 Identities=16% Similarity=0.126 Sum_probs=20.5
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhh
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSV 27 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~ 27 (76)
++.||++|-..|-++...|.-.|+.
T Consensus 95 k~~~s~~e~a~l~~lat~ykv~~~e 119 (262)
T COG2992 95 KEQLSPSERARLKDLATRYKVKWSE 119 (262)
T ss_pred hccCCHHHHHHHHHHHHHHHhhhcc
Confidence 5789999999999998888766654
No 209
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=30.38 E-value=1.4e+02 Score=19.94 Aligned_cols=32 Identities=16% Similarity=0.124 Sum_probs=23.6
Q ss_pred HHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 12 RLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 12 ~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
..++.++...|-+...||..+ |=+...|+.+.
T Consensus 211 r~vl~l~~~~g~s~~eIA~~l-~is~~tV~~~~ 242 (257)
T PRK08583 211 KSIIQCTFIENLSQKETGERL-GISQMHVSRLQ 242 (257)
T ss_pred HHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHH
Confidence 344555555677788999988 78888888876
No 210
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=30.09 E-value=1.5e+02 Score=18.97 Aligned_cols=40 Identities=20% Similarity=0.405 Sum_probs=34.9
Q ss_pred CCChHHHHHHHHHHHHhCC---chhhhhhcCCCCCHHHHHHHH
Q 037092 5 GFPDEEDRLICRLFAISGS---RWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~---~W~~Ia~~~~gRt~~~~knrw 44 (76)
.|++-.-...+..+..||- .|+-+...|.+.|...++.+=
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~aY~ 82 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIRAYG 82 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHHHHH
Confidence 5788889999999999993 699899999999999998853
No 211
>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=28.79 E-value=77 Score=18.73 Aligned_cols=26 Identities=23% Similarity=0.484 Sum_probs=18.7
Q ss_pred HHHHHhCCchhhhhhcCCC-----CCHHHHHH
Q 037092 16 RLFAISGSRWSVIGAHLPG-----RTDNETNN 42 (76)
Q Consensus 16 ~~~~~~G~~W~~Ia~~~~g-----Rt~~~~kn 42 (76)
......|.+|..++..+ | =|+.+|-+
T Consensus 7 ~~~~nvGr~WK~laR~L-g~~cral~d~~ID~ 37 (90)
T cd08780 7 HFAKSVGKKWKPVGRSL-QKNCRALRDPAIDN 37 (90)
T ss_pred HHHHHHhHHHHHHHHHH-cccccccchhHHHH
Confidence 44577899999999998 4 35555544
No 212
>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=28.30 E-value=59 Score=18.21 Aligned_cols=23 Identities=17% Similarity=0.432 Sum_probs=16.4
Q ss_pred HHhCCchhhhhhcCCCCCHHHHHH
Q 037092 19 AISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 19 ~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
...|+.|..+|..+ |-+...|++
T Consensus 13 ~~~g~DWr~LA~~L-g~~~~~I~~ 35 (79)
T cd08312 13 RVVAADWTALAEEM-GFEYLEIRN 35 (79)
T ss_pred CCcccCHHHHHHHc-CCCHHHHHH
Confidence 34688999999999 555545543
No 213
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=28.02 E-value=1.9e+02 Score=21.74 Aligned_cols=42 Identities=14% Similarity=0.120 Sum_probs=30.5
Q ss_pred CCCCChHHHHHHHHHHHHhCC---c-------------hhhhhhcC-----CCCCHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAISGS---R-------------WSVIGAHL-----PGRTDNETNNYY 44 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~---~-------------W~~Ia~~~-----~gRt~~~~knrw 44 (76)
-|.||++=|+...++...|.+ + =..||.++ ..||-.||..+=
T Consensus 76 egvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHI 138 (455)
T KOG3841|consen 76 EGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHI 138 (455)
T ss_pred ccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHH
Confidence 378999999999988887642 1 24577665 346777888875
No 214
>COG4654 Cytochrome c551/c552 [Energy production and conversion]
Probab=27.97 E-value=36 Score=20.76 Aligned_cols=24 Identities=17% Similarity=0.268 Sum_probs=19.5
Q ss_pred HHhCCchhhhhhcCCCCCHHHHHH
Q 037092 19 AISGSRWSVIGAHLPGRTDNETNN 42 (76)
Q Consensus 19 ~~~G~~W~~Ia~~~~gRt~~~~kn 42 (76)
...|+.|+.||..+.|..+..++-
T Consensus 44 ktVGPS~kdIAakYag~~~~~~kl 67 (110)
T COG4654 44 KTVGPSYKDIAAKYAGKAGALAKL 67 (110)
T ss_pred cccCccHHHHHHHHccchhHHHHH
Confidence 456888999999999988877654
No 215
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=26.61 E-value=1.2e+02 Score=18.90 Aligned_cols=35 Identities=17% Similarity=0.159 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++...++-++...|-+-..||..+ |-+...|+.+-
T Consensus 130 ~~~R~~~~l~~~~gls~~EIA~~l-~i~~~tVks~l 164 (182)
T COG1595 130 PRQREAFLLRYLEGLSYEEIAEIL-GISVGTVKSRL 164 (182)
T ss_pred HHHhHHhhhHhhcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 344556667777788899999998 88999999986
No 216
>PRK03692 putative UDP-N-acetyl-D-mannosaminuronic acid transferase; Provisional
Probab=26.35 E-value=86 Score=21.39 Aligned_cols=22 Identities=18% Similarity=0.232 Sum_probs=19.3
Q ss_pred CCCCChHHHHHHHHHHHHhCCc
Q 037092 3 PWGFPDEEDRLICRLFAISGSR 24 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~ 24 (76)
.|.|+++|++.+++.+...|..
T Consensus 138 ~Gyf~~~e~~~i~~~I~~s~~d 159 (243)
T PRK03692 138 DGYFTPEQRQALFERIHASGAK 159 (243)
T ss_pred CCCCCHHHHHHHHHHHHhcCCC
Confidence 6899999999999999998876
No 217
>PLN03162 golden-2 like transcription factor; Provisional
Probab=25.99 E-value=2.3e+02 Score=21.40 Aligned_cols=42 Identities=14% Similarity=-0.001 Sum_probs=33.7
Q ss_pred CCCCChHHHHHHHHHHHHhCCc---hhhhhhcC--CCCCHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAISGSR---WSVIGAHL--PGRTDNETNNYY 44 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~---W~~Ia~~~--~gRt~~~~knrw 44 (76)
|=.||+|=-+..+++|.++|.. =+.|=..| +|=|-..|+.+.
T Consensus 237 RLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHL 283 (526)
T PLN03162 237 KVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHL 283 (526)
T ss_pred cccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHH
Confidence 3469999999999999999932 45566655 788999999886
No 218
>KOG3200 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.89 E-value=71 Score=21.53 Aligned_cols=25 Identities=20% Similarity=0.492 Sum_probs=15.4
Q ss_pred CChHHHHHHHHHHH-HhCCchhhhhh
Q 037092 6 FPDEEDRLICRLFA-ISGSRWSVIGA 30 (76)
Q Consensus 6 wT~eED~~L~~~~~-~~G~~W~~Ia~ 30 (76)
-|+||+.+++.-+. .-|++|...+.
T Consensus 21 It~EEe~~~lshIe~ap~pkW~~L~N 46 (224)
T KOG3200|consen 21 ITEEEENLYLSHIENAPQPKWRVLAN 46 (224)
T ss_pred cChHHHHHHHHHHhcCCCchhHHHHh
Confidence 36666666655443 34588988764
No 219
>PF13934 ELYS: Nuclear pore complex assembly
Probab=25.43 E-value=59 Score=21.78 Aligned_cols=17 Identities=12% Similarity=0.268 Sum_probs=13.8
Q ss_pred CCCChHHHHHHHHHHHH
Q 037092 4 WGFPDEEDRLICRLFAI 20 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~ 20 (76)
=||+++|++.|.++...
T Consensus 198 LPl~~~EE~~l~~~L~~ 214 (226)
T PF13934_consen 198 LPLDEEEEQWLEKYLRE 214 (226)
T ss_pred CCCChHHHHHHHHHHcc
Confidence 38999999999986553
No 220
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=24.89 E-value=1.2e+02 Score=21.58 Aligned_cols=52 Identities=8% Similarity=0.112 Sum_probs=32.2
Q ss_pred CCCCChHHHHHHHHHHHHhCC-chh-hhhhcCCCCCHHHHHHHHhhchhhhHHhhCCC
Q 037092 3 PWGFPDEEDRLICRLFAISGS-RWS-VIGAHLPGRTDNETNNYYRNTKLKRKHEEGGL 58 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~-~W~-~Ia~~~~gRt~~~~knrw~~~~l~~~~~~~~~ 58 (76)
-..||+|+-+.++.+=..-.+ -|. .+...+...++.++++.| ++.+.....|
T Consensus 70 LD~W~~eqv~~m~~~GN~~an~~~ea~~p~~~~~p~~d~~~e~F----IR~KYE~kkf 123 (287)
T KOG0703|consen 70 LDEWTDEQVDFMISMGNAKANSYYEAKLPDPFRRPGPDDLVEQF----IRDKYERKKF 123 (287)
T ss_pred ccccCHHHHHHHHHHcchhhhhhccccCCccccCCChHHHHHHH----HHHHHhhhhh
Confidence 357999998887654322112 164 457777778888877777 4445444433
No 221
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=24.80 E-value=1.7e+02 Score=17.84 Aligned_cols=41 Identities=15% Similarity=0.184 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHHhhchhh
Q 037092 8 DEEDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYYRNTKLK 50 (76)
Q Consensus 8 ~eED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw~~~~l~ 50 (76)
.+||...+..+-...++=+.+++.+ |=|-.-+|+|- ...+.
T Consensus 35 ~~E~~~Fi~~Fi~~rGnlKe~e~~l-giSYPTvR~rL-d~ii~ 75 (113)
T PF09862_consen 35 SPEQLEFIKLFIKNRGNLKEMEKEL-GISYPTVRNRL-DKIIE 75 (113)
T ss_pred CHHHHHHHHHHHHhcCCHHHHHHHH-CCCcHHHHHHH-HHHHH
Confidence 4677777777777788899999988 78888899998 54443
No 222
>PHA02291 hypothetical protein
Probab=23.85 E-value=30 Score=21.34 Aligned_cols=18 Identities=33% Similarity=0.610 Sum_probs=12.7
Q ss_pred hhhhcCCCCCHH-HHHHHH
Q 037092 27 VIGAHLPGRTDN-ETNNYY 44 (76)
Q Consensus 27 ~Ia~~~~gRt~~-~~knrw 44 (76)
.+..++||||+. .|--+|
T Consensus 75 ~LP~~LPGRT~~~sID~~~ 93 (132)
T PHA02291 75 TLPTYLPGRTGDNSIDMRY 93 (132)
T ss_pred hccccCCCCCCCcccceee
Confidence 467789999975 355555
No 223
>PF11084 DUF2621: Protein of unknown function (DUF2621); InterPro: IPR020203 This entry represents a group of uncharacterised proteins.
Probab=23.50 E-value=74 Score=20.21 Aligned_cols=27 Identities=15% Similarity=0.172 Sum_probs=20.3
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhh
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSVIG 29 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~Ia 29 (76)
+.-||+|+-++|-+||+-...-...||
T Consensus 56 rhlW~de~K~lL~eLV~PVPelFRdvA 82 (141)
T PF11084_consen 56 RHLWTDEQKALLEELVSPVPELFRDVA 82 (141)
T ss_pred HhhcCHHHHHHHHHHhhcCcHHHHHHH
Confidence 346999999999999988765444433
No 224
>TIGR03209 P21_Cbot clostridium toxin-associated regulator BotR. Similarly, tetanus toxin production of Clostridium tetani is regulated by TetR which is a very close relative of BotR. Both BotR and TetR are members of the TIGR02937 subfamily of sigma-70 RNA polymerase sigma factors. Functional complementation experiments have been done for botR and tetR in highly transformable strain of Clostridium perfringens host cells to assess functional interchangeability of sigma factors and it has been confirmed that they are interchangeable in vivo.
Probab=23.44 E-value=1.3e+02 Score=17.88 Aligned_cols=9 Identities=22% Similarity=0.198 Sum_probs=3.5
Q ss_pred HHHHHHHhC
Q 037092 14 ICRLFAISG 22 (76)
Q Consensus 14 L~~~~~~~G 22 (76)
|.+++..+.
T Consensus 101 l~~~l~~Lp 109 (142)
T TIGR03209 101 FNDLISILP 109 (142)
T ss_pred HHHHHHhCC
Confidence 333344433
No 225
>PRK05572 sporulation sigma factor SigF; Validated
Probab=23.42 E-value=2e+02 Score=19.16 Aligned_cols=34 Identities=21% Similarity=0.234 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 10 EDRLICRLFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 10 ED~~L~~~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
.+..++.++..-|-.=..||..+ |-|.+.|+.+-
T Consensus 206 ~~~~v~~l~~~~~~s~~eIA~~l-gis~~~V~~~~ 239 (252)
T PRK05572 206 RERLIVYLRYFKDKTQSEVAKRL-GISQVQVSRLE 239 (252)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHH
Confidence 33444444444455667788877 77777777655
No 226
>PF03808 Glyco_tran_WecB: Glycosyl transferase WecB/TagA/CpsF family; InterPro: IPR004629 The WecG member of this superfamily, believed to be UDP-N-acetyl-D-mannosaminuronic acid transferase, plays a role in Enterobacterial common antigen (eca) synthesis in Escherichia coli. Another family member, the Bacillus subtilis TagA protein, is involved in the biosynthesis of the cell wall polymer poly(glycerol phosphate). The third family member, CpsF, CMP-N-acetylneuraminic acid synthetase has a role in the capsular polysaccharide biosynthesis pathway.; GO: 0009058 biosynthetic process
Probab=23.27 E-value=1.1e+02 Score=19.39 Aligned_cols=29 Identities=24% Similarity=0.268 Sum_probs=22.9
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhhc
Q 037092 3 PWGFPDEEDRLICRLFAISGSRWSVIGAH 31 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~~G~~W~~Ia~~ 31 (76)
.|+|+++|++.+++.+...|..---++--
T Consensus 82 ~g~f~~~~~~~i~~~I~~~~pdiv~vglG 110 (172)
T PF03808_consen 82 HGYFDEEEEEAIINRINASGPDIVFVGLG 110 (172)
T ss_pred CCCCChhhHHHHHHHHHHcCCCEEEEECC
Confidence 57899999999999999988875444433
No 227
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=23.02 E-value=84 Score=16.36 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=12.3
Q ss_pred HHHhCCchhhhhhcCCCCC
Q 037092 18 FAISGSRWSVIGAHLPGRT 36 (76)
Q Consensus 18 ~~~~G~~W~~Ia~~~~gRt 36 (76)
...+|-.-+.|+..|.||+
T Consensus 41 ~~~~~~sl~~Ig~~fg~rd 59 (60)
T smart00760 41 RELTDLSLPEIGKIFGGRD 59 (60)
T ss_pred HHHHCCCHHHHHHHhCCCC
Confidence 3445666777777776664
No 228
>PF08899 DUF1844: Domain of unknown function (DUF1844); InterPro: IPR014995 This group of proteins are functionally uncharacterised.
Probab=22.60 E-value=1.3e+02 Score=17.03 Aligned_cols=18 Identities=22% Similarity=0.259 Sum_probs=14.7
Q ss_pred CCCCChHHHHHHHHHHHH
Q 037092 3 PWGFPDEEDRLICRLFAI 20 (76)
Q Consensus 3 ~~~wT~eED~~L~~~~~~ 20 (76)
+|.-|++|..+|-.+...
T Consensus 52 kGNL~~~E~~lL~~~L~e 69 (74)
T PF08899_consen 52 KGNLDEEEERLLESALYE 69 (74)
T ss_pred ccCCCHHHHHHHHHHHHH
Confidence 788999999998877654
No 229
>PRK03906 mannonate dehydratase; Provisional
Probab=22.50 E-value=59 Score=23.82 Aligned_cols=27 Identities=26% Similarity=0.267 Sum_probs=24.0
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhh
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGA 30 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~ 30 (76)
..||.||=..+.+.+..+|-.|+.|.+
T Consensus 38 ~~W~~~~i~~~~~~ie~~Gl~~~vvEs 64 (385)
T PRK03906 38 EVWPVEEILARKAEIEAAGLEWSVVES 64 (385)
T ss_pred CCCCHHHHHHHHHHHHHcCCeEEEEeC
Confidence 479999999999999999999987643
No 230
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=22.48 E-value=1.6e+02 Score=16.56 Aligned_cols=36 Identities=28% Similarity=0.286 Sum_probs=27.3
Q ss_pred hHHHHHHHHHHH-HhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 8 DEEDRLICRLFA-ISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 8 ~eED~~L~~~~~-~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
|+--+....+.. ..|-+...||..+ |-|.+.|+++.
T Consensus 17 ~~~~r~af~L~R~~eGlS~kEIAe~L-GIS~~TVk~~l 53 (73)
T TIGR03879 17 DSLAEAAAALAREEAGKTASEIAEEL-GRTEQTVRNHL 53 (73)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHH
Confidence 444455555554 3678899999999 89999999987
No 231
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=21.83 E-value=37 Score=23.76 Aligned_cols=40 Identities=25% Similarity=0.444 Sum_probs=24.8
Q ss_pred CCChHHHHHHHHHHHHhCCc--------hhhhhhcCCC--CCHHHHHHHH
Q 037092 5 GFPDEEDRLICRLFAISGSR--------WSVIGAHLPG--RTDNETNNYY 44 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~~--------W~~Ia~~~~g--Rt~~~~knrw 44 (76)
-|+.++...+.+++..++.. |..++..+|+ |..+.+...+
T Consensus 33 ~~~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~ 82 (335)
T KOG0724|consen 33 LWTEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALPLEKRLEDKIEEYI 82 (335)
T ss_pred hhHHHHHHHHHHHHHHHhccccccchhhhhHHHhcCccccccchhHHhhh
Confidence 37777777777777777721 5566666764 4444444443
No 232
>PRK15328 invasion protein IagB; Provisional
Probab=21.74 E-value=1.8e+02 Score=18.63 Aligned_cols=32 Identities=22% Similarity=0.556 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCchhhhhhcCCC--CCHHHHHHHH
Q 037092 13 LICRLFAISGSRWSVIGAHLPG--RTDNETNNYY 44 (76)
Q Consensus 13 ~L~~~~~~~G~~W~~Ia~~~~g--Rt~~~~knrw 44 (76)
.|..+...||..|..|+.+=.| +.....+.+|
T Consensus 98 ~L~~~~~~~g~~~~alaaYNaG~~~~~~~~~~~Y 131 (160)
T PRK15328 98 ILSDMMKIYGYSWEAVGAYNAGTSPKRSDIRKRY 131 (160)
T ss_pred HHHHHHHHcCChHHhhhhccCCCCCCCCHHHHHH
Confidence 5678889999999999886544 3333445555
No 233
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=21.55 E-value=2.5e+02 Score=18.44 Aligned_cols=22 Identities=9% Similarity=0.052 Sum_probs=17.0
Q ss_pred CCchhhhhhcCCCCCHHHHHHHH
Q 037092 22 GSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 22 G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
|-+-..||..+ |-|.+.|+++-
T Consensus 198 g~s~~EIA~~L-gis~~tV~~~l 219 (234)
T TIGR02835 198 EKTQKEVADML-GISQSYISRLE 219 (234)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHH
Confidence 45677888887 78888888875
No 234
>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=21.27 E-value=56 Score=15.50 Aligned_cols=14 Identities=29% Similarity=0.603 Sum_probs=10.9
Q ss_pred CCchhhhhhcCCCC
Q 037092 22 GSRWSVIGAHLPGR 35 (76)
Q Consensus 22 G~~W~~Ia~~~~gR 35 (76)
+..|..|-..+++|
T Consensus 4 ~~~W~S~KrlVt~r 17 (31)
T PF03832_consen 4 GSTWASFKRLVTPR 17 (31)
T ss_pred cchhHHHHhhcCcc
Confidence 35699999888766
No 235
>TIGR01765 tspaseT_teng_N transposase, putative, N-terminal domain. This model represents the N-terminal region of a family of putative transposases found in the largest copy number in Thermoanaerobacter tengcongensis. The three homologs in Bacillus anthracis are each split into two ORFs and This model represents the upstream ORF.
Probab=20.83 E-value=1.1e+02 Score=16.67 Aligned_cols=35 Identities=23% Similarity=0.333 Sum_probs=24.1
Q ss_pred CCChHHHHHHHHHHHHhCC--chh-hhhhcCCCCCHHHHH
Q 037092 5 GFPDEEDRLICRLFAISGS--RWS-VIGAHLPGRTDNETN 41 (76)
Q Consensus 5 ~wT~eED~~L~~~~~~~G~--~W~-~Ia~~~~gRt~~~~k 41 (76)
.+++|+++.|.+....|.. +|. ..+ +.|.+-+.++
T Consensus 7 ~~~~e~~~~L~~tm~~f~~A~n~~~~~~--~e~~~~~~~k 44 (73)
T TIGR01765 7 NFEDKEKEYLLDLIRAFSSAVNFVIKRL--LEGKSHSELK 44 (73)
T ss_pred ecChhhHHHHHHHHHHHHHHHHHHHHHH--HCCCChhHHH
Confidence 3688999999999999873 333 333 5677776433
No 236
>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=20.81 E-value=1.8e+02 Score=16.40 Aligned_cols=28 Identities=18% Similarity=0.228 Sum_probs=22.1
Q ss_pred HHHHhCCchhhhhhcCCCCCHHHHHHHH
Q 037092 17 LFAISGSRWSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 17 ~~~~~G~~W~~Ia~~~~gRt~~~~knrw 44 (76)
++..+|-.-+.|+..|.||+-..|..-.
T Consensus 39 ~~~~~~~s~~~Ig~~fg~r~hStV~~a~ 66 (90)
T cd06571 39 ARELTGLSLPEIGRAFGGRDHSTVLHAV 66 (90)
T ss_pred HHHHhCCCHHHHHHHhCCCCHhHHHHHH
Confidence 3444578889999999889998887765
No 237
>TIGR00695 uxuA mannonate dehydratase. This Fe2+-requiring enzyme plays a role in D-glucuronate catabolism in Escherichia coli. Mannonate dehydratase converts D-mannonate to 2-dehydro-3-deoxy-D-gluconate. An apparent equivalog is found in a glucuronate utilization operon in Bacillus stearothermophilus T-6.
Probab=20.72 E-value=69 Score=23.72 Aligned_cols=27 Identities=26% Similarity=0.320 Sum_probs=23.9
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhh
Q 037092 4 WGFPDEEDRLICRLFAISGSRWSVIGA 30 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~~W~~Ia~ 30 (76)
..||.+|=..+.+.+..+|-+|+.|-+
T Consensus 38 evW~~~~i~~~k~~ie~~GL~~~vvEs 64 (394)
T TIGR00695 38 EVWEKEEIRKRKEYIESAGLHWSVVES 64 (394)
T ss_pred CCCCHHHHHHHHHHHHHcCCeEEEEeC
Confidence 479999999999999999999987643
No 238
>cd09235 V_Alix Middle V-domain of mammalian Alix and related domains are dimerization and protein interaction modules. This family contains the middle V-shaped (V) domain of mammalian Alix (apoptosis-linked gene-2 interacting protein X) and related domains. It belongs to the V_Alix_like superfamily which includes the V-domains of Bro1 and Rim20 (also known as PalA) from Saccharomyces cerevisiae, mammalian His-Domain type N23 protein tyrosine phosphatase (HD-PTP, also known as PTPN23), and related domains. Alix, also known as apoptosis-linked gene-2 interacting protein 1 (AIP1), is part of the ESCRT (Endosomal Sorting Complexes Required for Transport) system, and participates in membrane remodeling processes, including the budding of enveloped viruses, vesicle budding inside late endosomal multivesicular bodies (MVBs), the abscission reactions of mammalian cell division, and in apoptosis. The Alix V-domain is a dimerization domain, and contains a binding site, partially conserved in the
Probab=20.70 E-value=65 Score=22.86 Aligned_cols=33 Identities=21% Similarity=0.294 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHhCCchhhhhh----------------cC--CCCCHHHHHHHH
Q 037092 9 EEDRLICRLFAISGSRWSVIGA----------------HL--PGRTDNETNNYY 44 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~----------------~~--~gRt~~~~knrw 44 (76)
.||+.+. .+||.+|+.-++ .+ .+.++..|+..|
T Consensus 104 ~ed~~~R---~k~g~~Wtr~pS~~~~~~l~~~~~kyr~~L~~A~~sD~~v~~k~ 154 (339)
T cd09235 104 ASDNQLR---AQFKERWTRTPSNKLTKPLRAEGSKYRTILDNAVQADKIVREKY 154 (339)
T ss_pred hHHHHHH---HHhCCcCCCCChHHHhHHHHHHHHHHHHHHHHHHhhHHHHHHHH
Confidence 4555544 778988843221 11 356888888888
No 239
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=20.62 E-value=60 Score=18.53 Aligned_cols=23 Identities=17% Similarity=0.299 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHhCCchhhhhhcC
Q 037092 9 EEDRLICRLFAISGSRWSVIGAHL 32 (76)
Q Consensus 9 eED~~L~~~~~~~G~~W~~Ia~~~ 32 (76)
.+..+|+..+-+ +..|..||+.+
T Consensus 71 ~q~~lLi~k~LQ-~ksw~~~a~~l 93 (101)
T PF13725_consen 71 LQQALLIAKGLQ-GKSWEEVAKEL 93 (101)
T ss_dssp S--HHHHHHHCS----HHHHHHHC
T ss_pred HHHHHHHHHHHC-CCCHHHHHHHc
Confidence 344444444333 56788888766
No 240
>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=20.59 E-value=77 Score=17.52 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=16.5
Q ss_pred hhhhhhcCCCCCHHHHHHHH
Q 037092 25 WSVIGAHLPGRTDNETNNYY 44 (76)
Q Consensus 25 W~~Ia~~~~gRt~~~~knrw 44 (76)
-..||..+.|+|..+++..+
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 35688899999999999988
No 241
>PF04219 DUF413: Protein of unknown function, DUF; InterPro: IPR007335 This is a family of uncharacterised proteins.
Probab=20.52 E-value=93 Score=18.39 Aligned_cols=18 Identities=22% Similarity=0.333 Sum_probs=12.9
Q ss_pred CCCCCChHHHHHHHHHHHHhCC
Q 037092 2 KPWGFPDEEDRLICRLFAISGS 23 (76)
Q Consensus 2 ~~~~wT~eED~~L~~~~~~~G~ 23 (76)
+.|.||-.|-++| ..||.
T Consensus 14 RsGdFTi~Ea~lL----e~~G~ 31 (93)
T PF04219_consen 14 RSGDFTIKEAQLL----EQYGH 31 (93)
T ss_pred cCCcccHHHHHHH----HHHHH
Confidence 4577999888887 45554
No 242
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=20.34 E-value=98 Score=22.96 Aligned_cols=20 Identities=30% Similarity=0.252 Sum_probs=17.8
Q ss_pred CCCChHHHHHHHHHHHHhCC
Q 037092 4 WGFPDEEDRLICRLFAISGS 23 (76)
Q Consensus 4 ~~wT~eED~~L~~~~~~~G~ 23 (76)
..||.||=..|.+++.+||-
T Consensus 173 rvwt~eeL~~i~elc~kh~v 192 (388)
T COG1168 173 RVWTKEELRKIAELCLRHGV 192 (388)
T ss_pred ccccHHHHHHHHHHHHHcCC
Confidence 36999999999999999983
Done!