Query 041165
Match_columns 85
No_of_seqs 136 out of 1079
Neff 7.6
Searched_HMMs 46136
Date Fri Mar 29 04:23:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041165.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041165hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03091 hypothetical protein; 100.0 1.5E-32 3.3E-37 199.0 9.4 85 1-85 1-85 (459)
2 PLN03212 Transcription repress 100.0 4.5E-32 9.7E-37 185.2 8.7 83 3-85 14-96 (249)
3 KOG0048 Transcription factor, 99.9 1.1E-27 2.3E-32 164.0 8.1 77 9-85 4-80 (238)
4 PF13921 Myb_DNA-bind_6: Myb-l 99.9 2.7E-23 5.8E-28 115.2 7.0 60 17-78 1-60 (60)
5 KOG0049 Transcription factor, 99.8 3E-20 6.5E-25 140.2 5.7 84 1-85 347-430 (939)
6 PF00249 Myb_DNA-binding: Myb- 99.8 1.8E-19 3.9E-24 96.1 5.1 48 14-61 1-48 (48)
7 KOG0049 Transcription factor, 99.7 1.4E-16 3.1E-21 120.6 5.8 54 5-58 244-297 (939)
8 PLN03212 Transcription repress 99.6 9.8E-17 2.1E-21 110.0 1.4 60 5-66 69-128 (249)
9 smart00717 SANT SANT SWI3, AD 99.6 3.9E-15 8.4E-20 77.7 5.5 48 14-62 1-48 (49)
10 KOG0051 RNA polymerase I termi 99.6 2.6E-15 5.7E-20 113.0 6.3 69 13-84 383-453 (607)
11 PLN03091 hypothetical protein; 99.6 5.2E-16 1.1E-20 113.3 2.5 57 5-63 58-114 (459)
12 cd00167 SANT 'SWI3, ADA2, N-Co 99.5 5.2E-14 1.1E-18 72.4 5.1 45 16-61 1-45 (45)
13 KOG0048 Transcription factor, 99.5 8.1E-14 1.8E-18 95.5 5.2 59 4-64 52-110 (238)
14 COG5147 REB1 Myb superfamily p 99.4 8E-14 1.7E-18 103.9 4.8 76 9-85 15-90 (512)
15 KOG0050 mRNA splicing protein 99.4 6.8E-14 1.5E-18 103.8 3.9 73 11-84 4-76 (617)
16 TIGR01557 myb_SHAQKYF myb-like 98.9 3.6E-09 7.8E-14 58.3 5.7 49 13-61 2-54 (57)
17 COG5147 REB1 Myb superfamily p 98.9 5E-10 1.1E-14 83.8 2.1 73 9-84 286-360 (512)
18 KOG0457 Histone acetyltransfer 98.8 8E-09 1.7E-13 75.7 6.3 51 10-61 68-118 (438)
19 KOG0050 mRNA splicing protein 98.6 2.8E-08 6.1E-13 74.4 2.6 52 8-62 53-104 (617)
20 KOG0051 RNA polymerase I termi 98.3 1.3E-06 2.8E-11 66.7 5.4 60 12-72 434-519 (607)
21 PF13837 Myb_DNA-bind_4: Myb/S 98.2 1.9E-06 4.1E-11 50.3 4.1 48 14-61 1-64 (90)
22 COG5259 RSC8 RSC chromatin rem 98.2 1.6E-06 3.4E-11 64.5 4.2 46 13-60 278-323 (531)
23 KOG1279 Chromatin remodeling f 98.1 3E-06 6.4E-11 63.8 4.4 47 12-60 251-297 (506)
24 PF08914 Myb_DNA-bind_2: Rap1 98.1 5.1E-06 1.1E-10 46.9 4.3 52 14-65 2-61 (65)
25 TIGR02894 DNA_bind_RsfA transc 97.9 1.3E-05 2.8E-10 52.4 3.6 48 13-62 3-56 (161)
26 COG5114 Histone acetyltransfer 97.9 1.7E-05 3.6E-10 57.1 3.7 51 11-62 60-110 (432)
27 PRK13923 putative spore coat p 97.6 6.3E-05 1.4E-09 49.6 3.1 49 12-62 3-57 (170)
28 PF13873 Myb_DNA-bind_5: Myb/S 97.6 0.00034 7.4E-09 39.9 5.5 48 14-61 2-69 (78)
29 PF00249 Myb_DNA-binding: Myb- 97.4 0.00016 3.5E-09 37.9 2.4 19 67-85 1-19 (48)
30 PF13325 MCRS_N: N-terminal re 97.0 0.0034 7.3E-08 42.5 6.3 65 16-82 1-88 (199)
31 smart00717 SANT SANT SWI3, AD 96.6 0.0022 4.8E-08 32.4 2.4 19 67-85 1-19 (49)
32 PF09111 SLIDE: SLIDE; InterP 96.4 0.014 2.9E-07 36.5 5.5 53 9-61 44-110 (118)
33 PF13921 Myb_DNA-bind_6: Myb-l 96.2 0.0053 1.1E-07 33.2 2.7 18 8-25 43-60 (60)
34 KOG4282 Transcription factor G 96.1 0.014 2.9E-07 41.9 4.9 47 15-61 55-113 (345)
35 PF12776 Myb_DNA-bind_3: Myb/S 96.0 0.03 6.4E-07 32.7 5.2 45 16-60 1-61 (96)
36 cd00167 SANT 'SWI3, ADA2, N-Co 95.7 0.01 2.3E-07 29.3 2.2 17 69-85 1-17 (45)
37 COG5118 BDP1 Transcription ini 95.7 0.019 4E-07 42.6 4.2 63 15-79 366-436 (507)
38 PF13404 HTH_AsnC-type: AsnC-t 95.6 0.039 8.5E-07 28.2 4.2 38 20-59 3-40 (42)
39 PRK11179 DNA-binding transcrip 94.4 0.11 2.3E-06 33.2 4.6 45 19-65 8-52 (153)
40 KOG2656 DNA methyltransferase 93.8 0.081 1.8E-06 39.3 3.5 50 11-61 127-181 (445)
41 PRK11169 leucine-responsive tr 93.7 0.14 3.1E-06 33.0 4.1 46 19-66 13-58 (164)
42 PF08281 Sigma70_r4_2: Sigma-7 92.0 0.37 8.1E-06 25.1 3.6 39 19-60 12-50 (54)
43 PF11626 Rap1_C: TRF2-interact 91.1 0.27 5.9E-06 28.8 2.7 17 10-26 43-59 (87)
44 KOG4167 Predicted DNA-binding 90.0 0.55 1.2E-05 37.6 4.2 44 14-59 619-662 (907)
45 PLN03142 Probable chromatin-re 90.0 1.5 3.1E-05 36.4 6.7 38 16-54 826-863 (1033)
46 PF01388 ARID: ARID/BRIGHT DNA 89.0 0.93 2E-05 26.3 3.8 40 23-62 39-89 (92)
47 smart00344 HTH_ASNC helix_turn 88.7 1.5 3.2E-05 25.9 4.6 44 20-65 3-46 (108)
48 smart00595 MADF subfamily of S 88.6 0.41 8.9E-06 27.5 2.1 23 36-60 29-51 (89)
49 smart00501 BRIGHT BRIGHT, ARID 87.7 0.92 2E-05 26.5 3.3 41 23-63 35-86 (93)
50 PLN03142 Probable chromatin-re 87.5 1.5 3.3E-05 36.3 5.4 52 11-62 923-985 (1033)
51 TIGR01557 myb_SHAQKYF myb-like 87.1 0.87 1.9E-05 24.8 2.7 19 67-85 3-21 (57)
52 COG1522 Lrp Transcriptional re 86.9 1.5 3.2E-05 27.4 4.1 44 20-65 8-51 (154)
53 PF10545 MADF_DNA_bdg: Alcohol 86.8 0.57 1.2E-05 26.1 2.0 26 36-61 28-53 (85)
54 KOG1194 Predicted DNA-binding 86.8 1.4 2.9E-05 33.6 4.3 44 14-59 187-230 (534)
55 PF13325 MCRS_N: N-terminal re 84.8 2 4.3E-05 29.2 4.0 49 12-60 71-125 (199)
56 PF04545 Sigma70_r4: Sigma-70, 84.6 3.4 7.3E-05 21.1 4.1 39 20-61 7-45 (50)
57 KOG0384 Chromodomain-helicase 82.6 0.78 1.7E-05 38.6 1.6 28 14-41 1133-1160(1373)
58 KOG4468 Polycomb-group transcr 81.8 2.3 5E-05 33.6 3.8 48 14-62 88-144 (782)
59 cd08319 Death_RAIDD Death doma 81.6 2.2 4.7E-05 24.9 2.9 23 22-45 2-24 (83)
60 KOG2009 Transcription initiati 81.0 2.5 5.4E-05 33.0 3.8 51 8-60 403-453 (584)
61 PF07750 GcrA: GcrA cell cycle 80.6 2.6 5.6E-05 27.5 3.3 37 16-54 2-39 (162)
62 cd08803 Death_ank3 Death domai 80.3 2.8 6E-05 24.5 3.0 23 22-45 4-26 (84)
63 PF09111 SLIDE: SLIDE; InterP 79.4 1.9 4.1E-05 26.9 2.2 22 64-85 46-67 (118)
64 PF09197 Rap1-DNA-bind: Rap1, 77.3 8.2 0.00018 23.6 4.6 46 16-62 1-76 (105)
65 PF09420 Nop16: Ribosome bioge 75.7 7.4 0.00016 25.2 4.4 48 12-60 112-162 (164)
66 KOG1194 Predicted DNA-binding 75.4 1.3 2.7E-05 33.8 0.8 42 15-59 471-512 (534)
67 TIGR02985 Sig70_bacteroi1 RNA 75.3 7.6 0.00017 23.7 4.2 25 35-61 130-154 (161)
68 PF02954 HTH_8: Bacterial regu 74.3 9.1 0.0002 19.0 4.0 30 20-50 5-34 (42)
69 cd08317 Death_ank Death domain 73.5 3.7 8.1E-05 23.6 2.3 23 22-45 4-26 (84)
70 cd08804 Death_ank2 Death domai 69.6 6.2 0.00013 22.9 2.7 29 22-53 4-32 (84)
71 cd08777 Death_RIP1 Death Domai 66.4 7.2 0.00016 22.8 2.5 28 23-53 3-30 (86)
72 cd08318 Death_NMPP84 Death dom 66.1 8.6 0.00019 22.3 2.8 27 24-53 9-35 (86)
73 PF00531 Death: Death domain; 65.3 8.3 0.00018 21.3 2.6 23 24-46 2-24 (83)
74 PF01466 Skp1: Skp1 family, di 64.6 19 0.0004 20.3 4.0 36 37-80 36-71 (78)
75 TIGR02937 sigma70-ECF RNA poly 61.4 19 0.00041 21.3 3.8 28 31-61 124-151 (158)
76 cd08805 Death_ank1 Death domai 61.0 11 0.00023 22.0 2.5 23 22-45 4-26 (84)
77 cd08311 Death_p75NR Death doma 60.5 8.9 0.00019 22.0 2.1 26 19-46 2-27 (77)
78 COG5201 SKP1 SCF ubiquitin lig 60.4 13 0.00028 24.0 3.0 36 37-80 115-150 (158)
79 PF07638 Sigma70_ECF: ECF sigm 59.7 22 0.00047 23.1 4.1 35 23-60 141-175 (185)
80 cd08779 Death_PIDD Death Domai 59.4 11 0.00024 21.9 2.4 23 23-46 3-25 (86)
81 TIGR02957 SigX4 RNA polymerase 57.6 61 0.0013 22.4 6.4 46 35-82 125-173 (281)
82 KOG1279 Chromatin remodeling f 57.4 9.5 0.0002 29.4 2.3 19 67-85 253-271 (506)
83 PF09356 Phage_BR0599: Phage c 57.3 6 0.00013 22.8 1.0 19 44-62 51-69 (80)
84 PF01527 HTH_Tnp_1: Transposas 57.0 19 0.00041 19.5 3.1 45 13-61 3-47 (76)
85 PF04435 SPK: Domain of unknow 56.8 12 0.00027 22.0 2.4 43 37-79 25-68 (109)
86 smart00005 DEATH DEATH domain, 56.5 14 0.0003 20.8 2.5 24 22-46 5-29 (88)
87 PRK11924 RNA polymerase sigma 55.5 27 0.00058 21.7 3.9 25 35-61 142-166 (179)
88 PF13936 HTH_38: Helix-turn-he 55.0 10 0.00023 19.1 1.6 36 15-54 3-38 (44)
89 cd06171 Sigma70_r4 Sigma70, re 54.8 24 0.00052 16.9 3.9 39 17-59 11-49 (55)
90 PRK09641 RNA polymerase sigma 54.8 27 0.00059 22.0 3.9 25 35-61 153-177 (187)
91 smart00351 PAX Paired Box doma 53.6 50 0.0011 20.3 7.4 70 13-84 14-90 (125)
92 PRK09652 RNA polymerase sigma 53.5 32 0.00069 21.4 4.0 24 35-60 145-168 (182)
93 PRK09643 RNA polymerase sigma 53.3 32 0.00069 22.3 4.1 24 35-60 151-174 (192)
94 PF10440 WIYLD: Ubiquitin-bind 53.1 12 0.00026 21.0 1.7 19 23-42 30-48 (65)
95 COG2963 Transposase and inacti 53.0 47 0.001 19.7 4.7 42 14-59 5-47 (116)
96 PF09846 DUF2073: Uncharacteri 52.1 14 0.0003 22.6 2.0 18 14-31 26-43 (104)
97 PRK02866 cyanate hydratase; Va 51.4 65 0.0014 20.9 5.5 50 23-82 8-57 (147)
98 PRK11923 algU RNA polymerase s 50.2 35 0.00075 21.9 3.9 25 35-61 155-179 (193)
99 PRK01905 DNA-binding protein F 49.8 46 0.001 18.7 4.2 32 18-50 35-66 (77)
100 cd08306 Death_FADD Fas-associa 48.9 25 0.00055 20.3 2.8 20 25-45 5-24 (86)
101 TIGR02939 RpoE_Sigma70 RNA pol 48.8 29 0.00064 22.0 3.3 25 35-61 155-179 (190)
102 PF03444 HrcA_DNA-bdg: Winged 48.7 53 0.0011 19.0 4.1 40 18-59 3-46 (78)
103 PRK09648 RNA polymerase sigma 48.6 44 0.00094 21.4 4.2 25 35-61 156-180 (189)
104 PRK04217 hypothetical protein; 48.3 50 0.0011 20.2 4.1 43 14-60 40-82 (110)
105 PRK09637 RNA polymerase sigma 47.8 42 0.00091 21.5 4.0 24 35-60 123-146 (181)
106 PRK12531 RNA polymerase sigma 47.5 46 0.001 21.5 4.2 25 35-61 158-182 (194)
107 PF11035 SnAPC_2_like: Small n 47.1 41 0.00089 24.7 4.1 43 14-57 21-66 (344)
108 TIGR02954 Sig70_famx3 RNA poly 47.1 45 0.00098 20.8 4.0 25 35-61 136-160 (169)
109 PF00674 DUP: DUP family; Int 46.9 62 0.0013 19.3 4.4 42 23-64 44-102 (108)
110 PRK12512 RNA polymerase sigma 46.9 48 0.001 21.0 4.1 25 35-61 148-172 (184)
111 TIGR02948 SigW_bacill RNA poly 46.9 39 0.00085 21.3 3.7 25 35-61 153-177 (187)
112 PF13412 HTH_24: Winged helix- 46.9 38 0.00081 16.8 3.9 39 21-61 4-42 (48)
113 KOG4329 DNA-binding protein [G 46.8 41 0.00088 25.3 4.1 43 15-59 278-321 (445)
114 COG1460 Uncharacterized protei 46.7 56 0.0012 20.3 4.2 63 15-85 46-111 (114)
115 PF05263 DUF722: Protein of un 46.7 43 0.00093 21.2 3.7 23 35-59 100-122 (130)
116 PRK09047 RNA polymerase factor 46.3 55 0.0012 20.1 4.2 25 35-61 123-147 (161)
117 PRK12523 RNA polymerase sigma 45.7 54 0.0012 20.6 4.2 25 35-61 136-160 (172)
118 PRK12524 RNA polymerase sigma 45.5 50 0.0011 21.3 4.1 24 35-60 153-176 (196)
119 PRK09642 RNA polymerase sigma 45.3 56 0.0012 20.1 4.2 25 35-61 123-147 (160)
120 PRK00430 fis global DNA-bindin 45.2 64 0.0014 19.1 4.2 30 20-50 55-84 (95)
121 PRK12529 RNA polymerase sigma 45.2 55 0.0012 20.8 4.2 25 35-61 144-168 (178)
122 KOG0457 Histone acetyltransfer 44.8 27 0.0006 26.5 3.0 21 65-85 70-90 (438)
123 PRK09645 RNA polymerase sigma 44.2 58 0.0012 20.4 4.2 25 35-61 135-159 (173)
124 PRK12515 RNA polymerase sigma 43.9 58 0.0013 20.8 4.2 25 35-61 148-172 (189)
125 PF06163 DUF977: Bacterial pro 43.7 84 0.0018 19.9 6.9 61 16-78 4-73 (127)
126 PF10668 Phage_terminase: Phag 43.7 56 0.0012 17.9 3.7 43 19-63 7-54 (60)
127 TIGR02943 Sig70_famx1 RNA poly 43.1 60 0.0013 20.9 4.2 25 35-61 148-172 (188)
128 PRK09636 RNA polymerase sigma 43.1 1.1E+02 0.0024 21.2 6.2 44 35-80 132-178 (293)
129 COG1168 MalY Bifunctional PLP- 41.5 39 0.00084 25.3 3.3 21 14-34 172-192 (388)
130 cd01670 Death Death Domain: a 41.4 30 0.00064 18.9 2.2 19 26-45 3-21 (79)
131 cd08313 Death_TNFR1 Death doma 41.2 19 0.00041 20.8 1.4 28 25-54 2-29 (80)
132 PLN03079 Uncharacterized prote 41.2 40 0.00086 20.2 2.8 27 51-80 26-52 (91)
133 PRK12530 RNA polymerase sigma 40.6 67 0.0014 20.7 4.1 25 35-61 151-175 (189)
134 PRK12527 RNA polymerase sigma 40.5 75 0.0016 19.6 4.2 25 35-61 122-146 (159)
135 PRK09635 sigI RNA polymerase s 40.3 82 0.0018 22.1 4.8 45 35-81 135-182 (290)
136 PF09905 DUF2132: Uncharacteri 40.2 34 0.00073 19.1 2.2 49 22-78 12-62 (64)
137 PRK09651 RNA polymerase sigma 39.6 51 0.0011 20.8 3.4 25 35-61 136-160 (172)
138 PF11198 DUF2857: Protein of u 38.9 1.1E+02 0.0025 20.1 7.6 57 22-82 76-135 (180)
139 TIGR00673 cynS cyanate hydrata 38.9 1.1E+02 0.0024 19.9 5.6 50 23-82 11-60 (150)
140 PRK12528 RNA polymerase sigma 38.6 82 0.0018 19.4 4.2 24 35-60 130-153 (161)
141 PF10892 DUF2688: Protein of u 37.6 30 0.00065 19.0 1.7 16 14-29 42-57 (60)
142 TIGR02999 Sig-70_X6 RNA polyme 37.6 82 0.0018 19.8 4.1 25 35-61 151-175 (183)
143 COG4628 Uncharacterized conser 37.5 97 0.0021 19.5 4.2 50 22-79 21-72 (136)
144 cd00086 homeodomain Homeodomai 37.3 59 0.0013 16.4 5.1 45 13-59 3-50 (59)
145 PF04504 DUF573: Protein of un 37.2 91 0.002 18.5 6.9 69 15-84 5-94 (98)
146 PRK06759 RNA polymerase factor 37.0 88 0.0019 19.0 4.1 25 35-61 123-147 (154)
147 PRK12536 RNA polymerase sigma 36.9 85 0.0018 19.9 4.1 24 35-60 146-169 (181)
148 TIGR02952 Sig70_famx2 RNA poly 36.9 87 0.0019 19.3 4.1 25 35-61 139-163 (170)
149 TIGR02984 Sig-70_plancto1 RNA 36.8 86 0.0019 19.7 4.1 25 35-61 157-181 (189)
150 TIGR02950 SigM_subfam RNA poly 36.5 21 0.00045 21.9 1.1 25 35-61 122-146 (154)
151 PRK12514 RNA polymerase sigma 36.5 88 0.0019 19.7 4.1 25 35-61 146-170 (179)
152 PRK12547 RNA polymerase sigma 36.4 89 0.0019 19.5 4.1 24 35-60 129-152 (164)
153 PRK12546 RNA polymerase sigma 36.2 74 0.0016 20.6 3.8 24 35-60 130-153 (188)
154 PRK11922 RNA polymerase sigma 35.9 36 0.00078 22.8 2.3 24 35-60 166-189 (231)
155 PRK09649 RNA polymerase sigma 35.7 81 0.0018 20.2 3.9 25 35-61 147-171 (185)
156 PRK12532 RNA polymerase sigma 34.9 86 0.0019 20.1 4.0 24 35-60 153-176 (195)
157 PRK12516 RNA polymerase sigma 34.6 95 0.0021 20.0 4.1 23 35-59 133-155 (187)
158 PRK05602 RNA polymerase sigma 34.5 84 0.0018 19.9 3.8 24 35-60 145-168 (186)
159 PRK12545 RNA polymerase sigma 34.4 94 0.002 20.2 4.1 24 35-60 156-179 (201)
160 TIGR02983 SigE-fam_strep RNA p 34.4 91 0.002 19.2 3.9 25 35-61 127-151 (162)
161 KOG2656 DNA methyltransferase 34.2 55 0.0012 24.8 3.1 27 55-85 122-148 (445)
162 smart00583 SPK domain in SET a 34.2 69 0.0015 19.6 3.2 34 46-79 37-71 (114)
163 cd08312 Death_MyD88 Death doma 34.1 12 0.00027 21.3 -0.1 15 31-46 14-28 (79)
164 PRK12542 RNA polymerase sigma 34.0 97 0.0021 19.7 4.1 25 35-61 139-163 (185)
165 PRK00118 putative DNA-binding 33.9 1.1E+02 0.0024 18.5 4.1 38 19-59 19-56 (104)
166 PF15603 Imm45: Immunity prote 33.6 58 0.0013 19.0 2.6 24 61-84 47-70 (82)
167 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 33.3 80 0.0017 16.6 3.6 35 19-57 6-40 (50)
168 PRK13919 putative RNA polymera 33.2 1.1E+02 0.0023 19.4 4.1 25 35-61 152-176 (186)
169 PF11216 DUF3012: Protein of u 33.2 24 0.00053 17.0 0.8 14 11-24 12-25 (32)
170 COG2901 Fis Factor for inversi 32.5 56 0.0012 19.6 2.4 31 20-50 57-87 (98)
171 PF06892 Phage_CP76: Phage reg 32.0 1.5E+02 0.0032 19.3 5.8 50 23-82 12-61 (162)
172 KOG3493 Ubiquitin-like protein 31.4 52 0.0011 18.6 2.1 28 38-66 29-56 (73)
173 PF11084 DUF2621: Protein of u 30.7 44 0.00096 21.4 1.9 27 14-41 56-82 (141)
174 PRK12519 RNA polymerase sigma 30.0 89 0.0019 19.9 3.4 25 35-61 158-182 (194)
175 PRK09415 RNA polymerase factor 29.9 1.1E+02 0.0023 19.4 3.7 25 35-61 144-168 (179)
176 PF07325 Curto_V2: Curtovirus 29.7 84 0.0018 19.5 3.0 35 50-84 20-56 (126)
177 PRK06811 RNA polymerase factor 29.5 1.3E+02 0.0029 19.2 4.2 24 35-60 148-171 (189)
178 COG5259 RSC8 RSC chromatin rem 29.3 50 0.0011 25.6 2.3 19 67-85 279-297 (531)
179 KOG1724 SCF ubiquitin ligase, 29.0 83 0.0018 20.6 3.1 33 38-78 121-153 (162)
180 PF13384 HTH_23: Homeodomain-l 28.8 84 0.0018 15.5 2.7 26 24-53 9-34 (50)
181 TIGR02960 SigX5 RNA polymerase 28.7 1.1E+02 0.0024 21.2 3.9 24 35-60 159-182 (324)
182 PF11784 DUF3320: Protein of u 28.7 77 0.0017 16.5 2.4 32 25-56 17-52 (52)
183 PRK09646 RNA polymerase sigma 28.5 1.4E+02 0.003 19.2 4.1 24 35-60 159-182 (194)
184 cd08780 Death_TRADD Death Doma 28.4 1.2E+02 0.0026 18.1 3.4 18 27-45 7-24 (90)
185 PHA00442 host recBCD nuclease 28.2 49 0.0011 18.0 1.6 37 8-44 6-50 (59)
186 PRK10365 transcriptional regul 28.2 58 0.0012 23.6 2.5 30 20-50 405-434 (441)
187 PRK12537 RNA polymerase sigma 28.1 1.5E+02 0.0032 18.8 4.1 25 35-61 150-174 (182)
188 PRK09638 RNA polymerase sigma 28.0 49 0.0011 20.7 1.8 24 35-60 143-166 (176)
189 PF15586 Imm47: Immunity prote 28.0 52 0.0011 20.3 1.9 22 24-45 84-105 (116)
190 PRK09647 RNA polymerase sigma 28.0 1.5E+02 0.0032 19.5 4.2 25 35-61 155-179 (203)
191 PF08074 CHDCT2: CHDCT2 (NUC03 27.9 37 0.00079 22.6 1.2 28 16-43 5-32 (173)
192 TIGR02980 SigBFG RNA polymeras 27.8 1.4E+02 0.003 19.7 4.1 25 35-61 195-219 (227)
193 PRK08241 RNA polymerase factor 27.7 1.9E+02 0.004 20.4 4.9 25 35-61 170-194 (339)
194 cd08310 Death_NFkB-like Death 27.6 43 0.00093 18.8 1.4 13 33-46 12-24 (72)
195 PF09019 EcoRII-C: EcoRII C te 27.6 9.4 0.0002 25.2 -1.5 12 51-62 96-107 (164)
196 PRK12534 RNA polymerase sigma 27.1 1.5E+02 0.0033 18.7 4.1 24 35-60 154-177 (187)
197 PF05546 She9_MDM33: She9 / Md 27.1 68 0.0015 22.0 2.5 20 13-32 82-101 (207)
198 PF00196 GerE: Bacterial regul 26.9 1E+02 0.0022 15.9 2.9 41 16-61 3-43 (58)
199 PRK09413 IS2 repressor TnpA; R 26.8 1.5E+02 0.0033 17.9 4.2 46 12-61 8-53 (121)
200 PRK07670 RNA polymerase sigma 26.8 1.4E+02 0.003 20.2 4.0 25 35-61 218-242 (251)
201 PF05373 Pro_3_hydrox_C: L-pro 26.7 27 0.00058 21.3 0.4 35 11-45 19-53 (101)
202 PRK12541 RNA polymerase sigma 26.6 1.4E+02 0.0031 18.3 3.8 25 35-61 129-153 (161)
203 PF14237 DUF4339: Domain of un 26.6 62 0.0013 16.1 1.8 18 63-80 7-24 (45)
204 PRK11388 DNA-binding transcrip 26.3 1E+02 0.0022 24.0 3.6 34 17-51 588-621 (638)
205 KOG3200 Uncharacterized conser 26.2 64 0.0014 21.9 2.2 27 17-43 21-47 (224)
206 PF01285 TEA: TEA/ATTS domain 26.2 1.3E+02 0.0029 22.7 4.1 49 12-60 47-112 (431)
207 PRK12520 RNA polymerase sigma 26.1 1.7E+02 0.0036 18.7 4.1 24 35-60 148-171 (191)
208 PRK09639 RNA polymerase sigma 26.0 1.6E+02 0.0035 18.1 4.0 25 35-61 128-152 (166)
209 cd08784 Death_DRs Death Domain 25.6 52 0.0011 18.6 1.5 20 26-45 3-22 (79)
210 PF12244 DUF3606: Protein of u 25.5 95 0.0021 16.6 2.4 22 23-45 35-56 (57)
211 cd08799 Death_UNC5C Death doma 25.2 35 0.00077 20.0 0.7 12 35-46 21-32 (84)
212 cd08801 Death_UNC5D Death doma 25.1 31 0.00068 20.8 0.5 22 32-62 19-40 (98)
213 PRK06986 fliA flagellar biosyn 24.9 1.5E+02 0.0032 19.8 3.8 25 35-61 201-225 (236)
214 PF09862 DUF2089: Protein of u 24.8 1.8E+02 0.0039 18.0 5.4 42 19-63 35-76 (113)
215 COG3795 Uncharacterized protei 24.7 40 0.00086 21.3 0.9 59 15-77 15-78 (123)
216 PF00046 Homeobox: Homeobox do 24.6 1.1E+02 0.0024 15.5 5.0 45 13-59 3-50 (57)
217 cd08802 Death_UNC5B Death doma 24.6 36 0.00079 19.9 0.7 12 35-46 21-32 (84)
218 PF08667 BetR: BetR domain; I 24.4 2.1E+02 0.0045 18.5 5.1 52 23-83 8-62 (147)
219 TIGR02915 PEP_resp_reg putativ 24.4 75 0.0016 23.2 2.5 29 21-50 406-434 (445)
220 TIGR01636 phage_rinA phage tra 24.3 1.8E+02 0.004 17.9 4.2 19 36-56 102-120 (134)
221 KOG1079 Transcriptional repres 24.2 1.1E+02 0.0024 24.8 3.4 45 10-59 402-449 (739)
222 PRK12511 RNA polymerase sigma 24.1 1.8E+02 0.0039 18.6 4.0 24 35-60 128-151 (182)
223 cd08781 Death_UNC5-like Death 24.0 40 0.00086 19.4 0.8 12 35-46 21-32 (83)
224 PRK12522 RNA polymerase sigma 23.9 1.8E+02 0.0039 18.1 4.0 24 35-60 136-159 (173)
225 PRK12526 RNA polymerase sigma 23.6 2E+02 0.0042 18.8 4.2 24 35-60 170-193 (206)
226 TIGR02989 Sig-70_gvs1 RNA poly 23.6 1.8E+02 0.0039 17.6 4.1 24 35-60 128-151 (159)
227 TIGR03001 Sig-70_gmx1 RNA poly 23.5 1.9E+02 0.004 19.8 4.2 24 35-60 178-201 (244)
228 KOG0724 Zuotin and related mol 23.4 29 0.00063 24.7 0.2 43 17-61 56-98 (335)
229 PRK12525 RNA polymerase sigma 23.3 2E+02 0.0043 17.9 4.2 25 35-61 135-159 (168)
230 cd00131 PAX Paired Box domain 23.2 1.9E+02 0.0042 17.8 7.4 68 14-83 15-89 (128)
231 PF09633 DUF2023: Protein of u 23.2 98 0.0021 18.9 2.4 27 52-80 59-85 (101)
232 PRK15328 invasion protein IagB 22.4 1.3E+02 0.0028 19.5 3.1 34 24-58 98-132 (160)
233 PRK09458 pspB phage shock prot 22.4 1.7E+02 0.0037 16.8 3.4 18 66-83 32-49 (75)
234 PRK11608 pspF phage shock prot 21.4 96 0.0021 22.1 2.5 29 21-50 287-315 (326)
235 smart00389 HOX Homeodomain. DN 21.0 1.3E+02 0.0028 15.0 5.0 45 13-59 3-50 (56)
236 cd08782 Death_DAPK1 Death doma 20.5 29 0.00062 20.1 -0.3 14 31-45 15-28 (82)
237 PF01498 HTH_Tnp_Tc3_2: Transp 20.5 1E+02 0.0022 16.5 2.0 37 22-58 1-40 (72)
238 PRK12538 RNA polymerase sigma 20.4 1.8E+02 0.004 19.6 3.6 25 35-61 188-212 (233)
239 PF05176 ATP-synt_10: ATP10 pr 20.4 47 0.001 23.2 0.7 20 66-85 233-252 (252)
240 PRK07408 RNA polymerase sigma 20.2 2.3E+02 0.0049 19.3 4.1 25 35-61 220-244 (256)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=99.98 E-value=1.5e-32 Score=199.05 Aligned_cols=85 Identities=62% Similarity=1.208 Sum_probs=82.1
Q ss_pred CCCCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHH
Q 041165 1 MGRQPCCDKVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQ 80 (85)
Q Consensus 1 m~r~~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~ 80 (85)
|||++||+|..++||+||+|||++|+++|.+||..+|..||+.++.+|+++|||+||.++|+|.+++++||+|||.+|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998756999999999999999999999999999999999
Q ss_pred HHHhC
Q 041165 81 LHSLL 85 (85)
Q Consensus 81 ~v~~~ 85 (85)
+|++|
T Consensus 81 L~k~~ 85 (459)
T PLN03091 81 LHAVL 85 (459)
T ss_pred HHHHh
Confidence 99875
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.97 E-value=4.5e-32 Score=185.18 Aligned_cols=83 Identities=66% Similarity=1.284 Sum_probs=79.1
Q ss_pred CCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHHHH
Q 041165 3 RQPCCDKVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQLH 82 (85)
Q Consensus 3 r~~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~~v 82 (85)
++|||+|+++++++||+|||++|+++|++||..+|..||+.++.+||++|||+||.++|+|.+++++||.|||++|+++|
T Consensus 14 ~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~ 93 (249)
T PLN03212 14 TTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLH 93 (249)
T ss_pred CCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHH
Confidence 57999999999999999999999999999998899999999864599999999999999999999999999999999999
Q ss_pred HhC
Q 041165 83 SLL 85 (85)
Q Consensus 83 ~~~ 85 (85)
..|
T Consensus 94 ~~~ 96 (249)
T PLN03212 94 RLL 96 (249)
T ss_pred Hhc
Confidence 865
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.95 E-value=1.1e-27 Score=163.98 Aligned_cols=77 Identities=61% Similarity=1.044 Sum_probs=72.2
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHhC
Q 041165 9 KVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 9 k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~~v~~~ 85 (85)
++.+.||+||+|||++|+++|.+||.++|..||+.+|..|++++||.||.|||+|++++++||+|||.+|++++..|
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~ 80 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALL 80 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHH
Confidence 45566899999999999999999999999999999995599999999999999999999999999999999999864
No 4
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.89 E-value=2.7e-23 Score=115.23 Aligned_cols=60 Identities=38% Similarity=0.830 Sum_probs=55.1
Q ss_pred CCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHH
Q 041165 17 WTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQI 78 (85)
Q Consensus 17 WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L 78 (85)
||+|||++|+.+|..|| .+|..||..|| +||+.||++||.++|+|.+++++||++||..|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 79999999998 69999999999999999999999999999987
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.81 E-value=3e-20 Score=140.24 Aligned_cols=84 Identities=25% Similarity=0.362 Sum_probs=80.3
Q ss_pred CCCCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHH
Q 041165 1 MGRQPCCDKVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQ 80 (85)
Q Consensus 1 m~r~~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~ 80 (85)
++|+.+...|++++|+||++||.+|+.+|.+||.++|-+|-..++ +|+..|||+||.|+|+...+.+.||-.||..|+.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 467788899999999999999999999999999999999999999 5999999999999999999999999999999999
Q ss_pred HHHhC
Q 041165 81 LHSLL 85 (85)
Q Consensus 81 ~v~~~ 85 (85)
+|.+|
T Consensus 426 ~V~~Y 430 (939)
T KOG0049|consen 426 AVKVY 430 (939)
T ss_pred HHHHH
Confidence 99887
No 6
>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=99.79 E-value=1.8e-19 Score=96.12 Aligned_cols=48 Identities=42% Similarity=0.711 Sum_probs=42.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
|++||+|||++|+++|.+||.++|..||..||++||+.||++||+++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 689999999999999999997669999999995599999999999875
No 7
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.66 E-value=1.4e-16 Score=120.63 Aligned_cols=54 Identities=19% Similarity=0.237 Sum_probs=48.2
Q ss_pred CCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHH
Q 041165 5 PCCDKVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWI 58 (85)
Q Consensus 5 ~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~ 58 (85)
+....|+++|..||+|||++|..+...++..+|..||..+|.+|++.||..+|+
T Consensus 244 ~n~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~ 297 (939)
T KOG0049|consen 244 YNELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFK 297 (939)
T ss_pred hhhcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHH
Confidence 346789999999999999999999999999999999999998899999987333
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.62 E-value=9.8e-17 Score=110.02 Aligned_cols=60 Identities=20% Similarity=0.271 Sum_probs=53.8
Q ss_pred CCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCC
Q 041165 5 PCCDKVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLK 66 (85)
Q Consensus 5 ~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~ 66 (85)
....+|.+++++||+|||++|++++..+| +.|..||..|++ ||+.||++||+.+|...+.
T Consensus 69 ~N~L~P~I~kgpWT~EED~lLlel~~~~G-nKWs~IAk~LpG-RTDnqIKNRWns~LrK~l~ 128 (249)
T PLN03212 69 MNYLRPSVKRGGITSDEEDLILRLHRLLG-NRWSLIAGRIPG-RTDNEIKNYWNTHLRKKLL 128 (249)
T ss_pred HHhhchhcccCCCChHHHHHHHHHHHhcc-ccHHHHHhhcCC-CCHHHHHHHHHHHHhHHHH
Confidence 34577999999999999999999999999 799999999995 9999999999998866433
No 9
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.59 E-value=3.9e-15 Score=77.72 Aligned_cols=48 Identities=35% Similarity=0.708 Sum_probs=44.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhC
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLR 62 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 62 (85)
+++||++||..|+.++..+|..+|..||..++ +||+.+|++||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 47899999999999999999779999999999 5999999999998764
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.59 E-value=2.6e-15 Score=113.03 Aligned_cols=69 Identities=33% Similarity=0.726 Sum_probs=66.1
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCC--CCCCCCCHHHHHHHHHHHHh
Q 041165 13 KRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPD--LKRGAFTEDEEDQIIQLHSL 84 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~--~~~~~wt~eEd~~L~~~v~~ 84 (85)
++|.||+||++.|..+|.++| +.|..|+..|| |.+..|++||+++..+. .++++||.||++.|+++|++
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~ 453 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNE 453 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHH
Confidence 899999999999999999999 89999999999 99999999999999887 48999999999999999974
No 11
>PLN03091 hypothetical protein; Provisional
Probab=99.59 E-value=5.2e-16 Score=113.31 Aligned_cols=57 Identities=18% Similarity=0.307 Sum_probs=51.9
Q ss_pred CCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCC
Q 041165 5 PCCDKVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRP 63 (85)
Q Consensus 5 ~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~ 63 (85)
.....|.+++|+||+|||++|++++..+| .+|..||..|+| ||+.||++||+.+|..
T Consensus 58 ~NyLdP~IkKgpWT~EED~lLLeL~k~~G-nKWskIAk~LPG-RTDnqIKNRWnslLKK 114 (459)
T PLN03091 58 INYLRPDLKRGTFSQQEENLIIELHAVLG-NRWSQIAAQLPG-RTDNEIKNLWNSCLKK 114 (459)
T ss_pred HhccCCcccCCCCCHHHHHHHHHHHHHhC-cchHHHHHhcCC-CCHHHHHHHHHHHHHH
Confidence 34578999999999999999999999999 799999999995 9999999999987643
No 12
>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=99.50 E-value=5.2e-14 Score=72.39 Aligned_cols=45 Identities=40% Similarity=0.699 Sum_probs=42.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 16 PWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
+||++||..|+.++..+|..+|..||..+++ ||+.||+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~-rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPG-RTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCC-CCHHHHHHHHHHhC
Confidence 6999999999999999997799999999994 99999999998763
No 13
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.46 E-value=8.1e-14 Score=95.51 Aligned_cols=59 Identities=19% Similarity=0.309 Sum_probs=53.6
Q ss_pred CCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCC
Q 041165 4 QPCCDKVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPD 64 (85)
Q Consensus 4 ~~~~~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~ 64 (85)
+--+.+|.|++|.||+|||..|++++..+| +.|..||.+|+| ||+..+++.|+..|...
T Consensus 52 W~NyLrP~ikrg~fT~eEe~~Ii~lH~~~G-NrWs~IA~~LPG-RTDNeIKN~Wnt~lkkk 110 (238)
T KOG0048|consen 52 WTNYLRPDLKRGNFSDEEEDLIIKLHALLG-NRWSLIAGRLPG-RTDNEVKNHWNTHLKKK 110 (238)
T ss_pred hhcccCCCccCCCCCHHHHHHHHHHHHHHC-cHHHHHHhhCCC-cCHHHHHHHHHHHHHHH
Confidence 345688999999999999999999999999 789999999996 99999999999887543
No 14
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.45 E-value=8e-14 Score=103.89 Aligned_cols=76 Identities=33% Similarity=0.573 Sum_probs=71.2
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHhC
Q 041165 9 KVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 9 k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~~v~~~ 85 (85)
...++.|.|+..||+.|..+|+.+|+++|..||..++. +++.||+.||+++++|.+++.+|+.+||..|+.+..++
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~-~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~ 90 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLIS-STGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKEL 90 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcc-cccccccchhhhhhchhcccccccHHHHHHHHHHHHhc
Confidence 44678899999999999999999999999999999994 99999999999999999999999999999999998753
No 15
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.44 E-value=6.8e-14 Score=103.85 Aligned_cols=73 Identities=25% Similarity=0.663 Sum_probs=68.9
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHh
Q 041165 11 GLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQLHSL 84 (85)
Q Consensus 11 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~~v~~ 84 (85)
-++-|.|+.-||+.|-.+|.+||.+.|+.|+..+. ..++.||+.||..+|||.|++..|+.+||..|+.++..
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl 76 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKL 76 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHh
Confidence 36788999999999999999999999999999999 59999999999999999999999999999999998764
No 16
>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=98.94 E-value=3.6e-09 Score=58.34 Aligned_cols=49 Identities=14% Similarity=0.213 Sum_probs=44.1
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCc---hhhhhhhCCCC-chhhHHHHHHhhh
Q 041165 13 KRGPWTIEEDHKLMSFILNNGIHCW---RMVPKLAGLLR-CGKSCRLRWINYL 61 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~g~~~W---~~Ia~~~~~~R-t~~qcr~Rw~~~l 61 (85)
++-.||+||...++.++..+|.++| +.|++.|+.++ |..||+.+.+.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3567999999999999999997799 99999988667 9999999998875
No 17
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.91 E-value=5e-10 Score=83.81 Aligned_cols=73 Identities=32% Similarity=0.666 Sum_probs=66.4
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCC--CCCCCCCCHHHHHHHHHHHHh
Q 041165 9 KVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRP--DLKRGAFTEDEEDQIIQLHSL 84 (85)
Q Consensus 9 k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~--~~~~~~wt~eEd~~L~~~v~~ 84 (85)
.+--.+|.||++|+..|..++..+| ..|..|+..++ |-+..|++||+++..+ .+++++|+.||+.+|...|++
T Consensus 286 ~~f~~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e 360 (512)
T COG5147 286 NIFEQRGKWTKEEEQELAKLVVEHG-GSWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNE 360 (512)
T ss_pred hHHhhhccCcccccccccccccccc-chhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHH
Confidence 3445689999999999999999999 79999999999 9999999999999988 677889999999999998874
No 18
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.85 E-value=8e-09 Score=75.71 Aligned_cols=51 Identities=16% Similarity=0.420 Sum_probs=47.1
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 10 VGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 10 ~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
..+-.+.||.+|+-.|++++..||.+||..||.++| +|+..+|+++|.+++
T Consensus 68 ~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 68 FPILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 356678899999999999999999999999999999 699999999999965
No 19
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.59 E-value=2.8e-08 Score=74.42 Aligned_cols=52 Identities=27% Similarity=0.559 Sum_probs=48.8
Q ss_pred CCCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhC
Q 041165 8 DKVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLR 62 (85)
Q Consensus 8 ~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 62 (85)
..|+|++.-|+.|||++|+.+..... ..|..||..|| |++.||.+||.+.|+
T Consensus 53 ldp~i~~tews~eederlLhlakl~p-~qwrtIa~i~g--r~~~qc~eRy~~ll~ 104 (617)
T KOG0050|consen 53 LDPAIKKTEWSREEDERLLHLAKLEP-TQWRTIADIMG--RTSQQCLERYNNLLD 104 (617)
T ss_pred hCHHHhhhhhhhhHHHHHHHHHHhcC-CccchHHHHhh--hhHHHHHHHHHHHHH
Confidence 46899999999999999999999999 79999999999 999999999999874
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.30 E-value=1.3e-06 Score=66.68 Aligned_cols=60 Identities=27% Similarity=0.633 Sum_probs=48.6
Q ss_pred CCcCCCCHHHHHHHHHHHH-------Hh------------------CCCCchhhhhhhCCCCchhhHHHHHHhhh-CCCC
Q 041165 12 LKRGPWTIEEDHKLMSFIL-------NN------------------GIHCWRMVPKLAGLLRCGKSCRLRWINYL-RPDL 65 (85)
Q Consensus 12 ~~kg~WT~eED~~L~~~v~-------~~------------------g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l-~~~~ 65 (85)
.++|+||.||.+.|+++|+ ++ ...+|..|++.+| +|+..|||..|...+ .|..
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 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLG-TRSRIQCRYKWYKLTTSPSF 512 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhc-CCCcchHHHHHHHHHhhHHh
Confidence 6899999999999999995 22 2247999999888 699999999999976 4455
Q ss_pred CCCCCCH
Q 041165 66 KRGAFTE 72 (85)
Q Consensus 66 ~~~~wt~ 72 (85)
+...|..
T Consensus 513 n~~~~~~ 519 (607)
T KOG0051|consen 513 NKRQESK 519 (607)
T ss_pred hcccccc
Confidence 5666654
No 21
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=98.24 E-value=1.9e-06 Score=50.31 Aligned_cols=48 Identities=27% Similarity=0.514 Sum_probs=33.5
Q ss_pred cCCCCHHHHHHHHHHHHH--h----C--C-----CCchhhhhhh---CCCCchhhHHHHHHhhh
Q 041165 14 RGPWTIEEDHKLMSFILN--N----G--I-----HCWRMVPKLA---GLLRCGKSCRLRWINYL 61 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~--~----g--~-----~~W~~Ia~~~---~~~Rt~~qcr~Rw~~~l 61 (85)
+..||.+|...|+.++.. + + . .-|..||..| |.+||+.||+++|.++.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 458999999999999877 1 1 1 1399999885 66799999999999865
No 22
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.22 E-value=1.6e-06 Score=64.51 Aligned_cols=46 Identities=22% Similarity=0.435 Sum_probs=42.6
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 13 KRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
...+||.+|-.+|++.|+.|| .+|.+||.++| ++|..||-.+|.++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 456999999999999999999 79999999999 69999999999874
No 23
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.15 E-value=3e-06 Score=63.83 Aligned_cols=47 Identities=26% Similarity=0.480 Sum_probs=43.3
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 12 LKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 12 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-.++.||.+|+-+|+++|..|| .+|.+||.++| +||..||-.+|.+.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYG-DDWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccC-CCCHHHHHHHHHhc
Confidence 4477899999999999999999 79999999999 59999999999864
No 24
>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=98.14 E-value=5.1e-06 Score=46.87 Aligned_cols=52 Identities=25% Similarity=0.401 Sum_probs=32.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCC--------CCchhhhhhhCCCCchhhHHHHHHhhhCCCC
Q 041165 14 RGPWTIEEDHKLMSFILNNGI--------HCWRMVPKLAGLLRCGKSCRLRWINYLRPDL 65 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~--------~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~ 65 (85)
+.+||.+||+.|+..|..+.. .=|+.+++.-..++|..+-|+||.+.|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 568999999999999976531 1299999886645999999999999987643
No 25
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.92 E-value=1.3e-05 Score=52.35 Aligned_cols=48 Identities=29% Similarity=0.576 Sum_probs=41.2
Q ss_pred CcCCCCHHHHHHHHHHHHHhCC------CCchhhhhhhCCCCchhhHHHHHHhhhC
Q 041165 13 KRGPWTIEEDHKLMSFILNNGI------HCWRMVPKLAGLLRCGKSCRLRWINYLR 62 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~g~------~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 62 (85)
+.-.||.|||..|.+.|-.|-. .....++..++ ||+..|.-||+.++.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VR 56 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVR 56 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHH
Confidence 4568999999999999998832 23788888898 999999999999986
No 26
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.86 E-value=1.7e-05 Score=57.10 Aligned_cols=51 Identities=14% Similarity=0.366 Sum_probs=46.5
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhC
Q 041165 11 GLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLR 62 (85)
Q Consensus 11 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 62 (85)
.|---.|+..|+-.|++.+.-.|.+||..||.++| .|+...|+++|...+.
T Consensus 60 pI~~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 60 PIGEEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred cccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 44556799999999999999999999999999999 6999999999999765
No 27
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=97.60 E-value=6.3e-05 Score=49.62 Aligned_cols=49 Identities=24% Similarity=0.464 Sum_probs=39.7
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCC------chhhhhhhCCCCchhhHHHHHHhhhC
Q 041165 12 LKRGPWTIEEDHKLMSFILNNGIHC------WRMVPKLAGLLRCGKSCRLRWINYLR 62 (85)
Q Consensus 12 ~~kg~WT~eED~~L~~~v~~~g~~~------W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 62 (85)
.+...||.|+|..|.+.|-.|+... ...++..++ ||+.+|..||+.++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 4567899999999999999886533 455556677 999999999977765
No 28
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=97.56 E-value=0.00034 Score=39.93 Aligned_cols=48 Identities=17% Similarity=0.278 Sum_probs=39.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCC----------------CCchhhhhhh----CCCCchhhHHHHHHhhh
Q 041165 14 RGPWTIEEDHKLMSFILNNGI----------------HCWRMVPKLA----GLLRCGKSCRLRWINYL 61 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~----------------~~W~~Ia~~~----~~~Rt~~qcr~Rw~~~l 61 (85)
+..||++|...|++++.+|.. .-|..|+..+ |+.||..|++..|.+..
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 568999999999999988721 1399999885 23599999999999875
No 29
>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=97.39 E-value=0.00016 Score=37.87 Aligned_cols=19 Identities=26% Similarity=0.643 Sum_probs=15.6
Q ss_pred CCCCCHHHHHHHHHHHHhC
Q 041165 67 RGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 67 ~~~wt~eEd~~L~~~v~~~ 85 (85)
+++||++||.+|+++|.+|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~ 19 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKY 19 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHS
T ss_pred CCCCCHHHHHHHHHHHHHh
Confidence 5789999999999999876
No 30
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.01 E-value=0.0034 Score=42.47 Aligned_cols=65 Identities=18% Similarity=0.257 Sum_probs=49.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhh--hCCCCchhhHHHHHHhhh-CCCC--------------------CCCCCCH
Q 041165 16 PWTIEEDHKLMSFILNNGIHCWRMVPKL--AGLLRCGKSCRLRWINYL-RPDL--------------------KRGAFTE 72 (85)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~--~~~~Rt~~qcr~Rw~~~l-~~~~--------------------~~~~wt~ 72 (85)
.|+++.|-.|+.+|..-. +-..|+.- |...-|-..+.+||+..| +|.+ .+.+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 599999999999997743 55555543 454578889999999876 3332 3458999
Q ss_pred HHHHHHHHHH
Q 041165 73 DEEDQIIQLH 82 (85)
Q Consensus 73 eEd~~L~~~v 82 (85)
+|+++|....
T Consensus 79 ~EE~lL~~v~ 88 (199)
T PF13325_consen 79 EEEQLLGTVA 88 (199)
T ss_pred HHHHHHHhhh
Confidence 9999998764
No 31
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=96.60 E-value=0.0022 Score=32.36 Aligned_cols=19 Identities=32% Similarity=0.660 Sum_probs=16.7
Q ss_pred CCCCCHHHHHHHHHHHHhC
Q 041165 67 RGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 67 ~~~wt~eEd~~L~~~v~~~ 85 (85)
+++||++||.+|+.++.+|
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~ 19 (49)
T smart00717 1 KGEWTEEEDELLIELVKKY 19 (49)
T ss_pred CCCCCHHHHHHHHHHHHHH
Confidence 3689999999999999865
No 32
>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=96.41 E-value=0.014 Score=36.49 Aligned_cols=53 Identities=17% Similarity=0.242 Sum_probs=38.8
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCC---CCchhhhhhhC-----------CCCchhhHHHHHHhhh
Q 041165 9 KVGLKRGPWTIEEDHKLMSFILNNGI---HCWRMVPKLAG-----------LLRCGKSCRLRWINYL 61 (85)
Q Consensus 9 k~~~~kg~WT~eED~~L~~~v~~~g~---~~W~~Ia~~~~-----------~~Rt~~qcr~Rw~~~l 61 (85)
.|.-++..||.+||..|+-.+.+||. +.|..|-..+- -+||+..+..|=..++
T Consensus 44 ~~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi 110 (118)
T PF09111_consen 44 PPNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLI 110 (118)
T ss_dssp TSTSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHH
Confidence 34677889999999999999999998 88988876631 0388888877755443
No 33
>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=96.23 E-value=0.0053 Score=33.19 Aligned_cols=18 Identities=50% Similarity=0.962 Sum_probs=16.3
Q ss_pred CCCCCCcCCCCHHHHHHH
Q 041165 8 DKVGLKRGPWTIEEDHKL 25 (85)
Q Consensus 8 ~k~~~~kg~WT~eED~~L 25 (85)
.+|.+++++||++||++|
T Consensus 43 l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 43 LRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp TSTTSTSSSSSHHHHHHH
T ss_pred CcccccCCCcCHHHHhcC
Confidence 568899999999999987
No 34
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=96.09 E-value=0.014 Score=41.93 Aligned_cols=47 Identities=23% Similarity=0.334 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHHHHh----C-----CCCchhhhhh---hCCCCchhhHHHHHHhhh
Q 041165 15 GPWTIEEDHKLMSFILNN----G-----IHCWRMVPKL---AGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 15 g~WT~eED~~L~~~v~~~----g-----~~~W~~Ia~~---~~~~Rt~~qcr~Rw~~~l 61 (85)
..|+.+|-..|+.+.... . ..-|..||.. .|..||+.||+.+|.++.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 679999999999988543 1 1459999985 466699999999999875
No 35
>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=95.96 E-value=0.03 Score=32.71 Aligned_cols=45 Identities=22% Similarity=0.484 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------Cchhhhhhh----CCCCchhhHHHHHHhh
Q 041165 16 PWTIEEDHKLMSFILNN---GIH---------CWRMVPKLA----GLLRCGKSCRLRWINY 60 (85)
Q Consensus 16 ~WT~eED~~L~~~v~~~---g~~---------~W~~Ia~~~----~~~Rt~~qcr~Rw~~~ 60 (85)
.||+++++.|++++... |.. .|..|+..| |...+..||++||...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999988554 211 388888774 4457889999998765
No 36
>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=95.71 E-value=0.01 Score=29.34 Aligned_cols=17 Identities=18% Similarity=0.436 Sum_probs=15.2
Q ss_pred CCCHHHHHHHHHHHHhC
Q 041165 69 AFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 69 ~wt~eEd~~L~~~v~~~ 85 (85)
+||++|+..|+.++.+|
T Consensus 1 ~Wt~eE~~~l~~~~~~~ 17 (45)
T cd00167 1 PWTEEEDELLLEAVKKY 17 (45)
T ss_pred CCCHHHHHHHHHHHHHH
Confidence 69999999999998764
No 37
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.69 E-value=0.019 Score=42.56 Aligned_cols=63 Identities=19% Similarity=0.319 Sum_probs=49.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhh--hCCC-----C-CCCCCCHHHHHHHH
Q 041165 15 GPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINY--LRPD-----L-KRGAFTEDEEDQII 79 (85)
Q Consensus 15 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~--l~~~-----~-~~~~wt~eEd~~L~ 79 (85)
-+||.+|-+++..+....| .++..||.+++ +|+.+|++-.|.+- .+|. + .+.|+..+|-..+.
T Consensus 366 ~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP-~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~ 436 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWG-TDFSLISSLFP-NRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLR 436 (507)
T ss_pred CcccHHHHHHHHHHHHHhc-chHHHHHHhcC-chhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHH
Confidence 3699999999999999999 69999999999 69999999998763 2331 1 24577777655443
No 38
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=95.63 E-value=0.039 Score=28.24 Aligned_cols=38 Identities=18% Similarity=0.311 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHh
Q 041165 20 EEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
+=|.+|+.+.+..|...+..||+.+| =|...|..|...
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 34889999999999999999999999 899999999865
No 39
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=94.42 E-value=0.11 Score=33.23 Aligned_cols=45 Identities=11% Similarity=0.130 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCC
Q 041165 19 IEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDL 65 (85)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~ 65 (85)
.+-|.+|+.+.+..|...|..||+.+| -|...|+.|+.+..+..+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 467999999999999999999999999 899999999999876654
No 40
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=93.84 E-value=0.081 Score=39.26 Aligned_cols=50 Identities=14% Similarity=0.167 Sum_probs=42.9
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhh-----hCCCCchhhHHHHHHhhh
Q 041165 11 GLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKL-----AGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 11 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~-----~~~~Rt~~qcr~Rw~~~l 61 (85)
.+.-..||++|...|.++++.|. -.|-.||.. ++..||-...++||+.+.
T Consensus 127 ~l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 34557899999999999999999 689999977 664599999999998764
No 41
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=93.65 E-value=0.14 Score=33.05 Aligned_cols=46 Identities=15% Similarity=0.120 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCC
Q 041165 19 IEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLK 66 (85)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~ 66 (85)
.+-|.+|+.+.+..|.-.|..||+.+| -|...|+.|+.+..+..+-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 567999999999999999999999999 8999999999998776543
No 42
>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=91.96 E-value=0.37 Score=25.12 Aligned_cols=39 Identities=10% Similarity=0.190 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 19 IEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
++++..++.++...| -++..||..+| .|...++.+....
T Consensus 12 ~~~~r~i~~l~~~~g-~s~~eIa~~l~--~s~~~v~~~l~ra 50 (54)
T PF08281_consen 12 PERQREIFLLRYFQG-MSYAEIAEILG--ISESTVKRRLRRA 50 (54)
T ss_dssp -HHHHHHHHHHHTS----HHHHHHHCT--S-HHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHC-cCHHHHHHHHC--cCHHHHHHHHHHH
Confidence 566777888888888 69999999999 9999999887764
No 43
>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=91.10 E-value=0.27 Score=28.76 Aligned_cols=17 Identities=35% Similarity=0.460 Sum_probs=9.9
Q ss_pred CCCCcCCCCHHHHHHHH
Q 041165 10 VGLKRGPWTIEEDHKLM 26 (85)
Q Consensus 10 ~~~~kg~WT~eED~~L~ 26 (85)
|.-..|-||+++|+.|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 44568899999999994
No 44
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=90.03 E-value=0.55 Score=37.59 Aligned_cols=44 Identities=14% Similarity=0.200 Sum_probs=39.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHh
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
.-.||+.|-..+.+++..|. +++-.|++++.+ +|-.||-+-|+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~-KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVKS-KTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhcc-ccHHHHHHHHHH
Confidence 34699999999999999999 899999999995 999999887765
No 45
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=89.99 E-value=1.5 Score=36.40 Aligned_cols=38 Identities=5% Similarity=0.090 Sum_probs=32.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHH
Q 041165 16 PWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCR 54 (85)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr 54 (85)
.||.-+=..++.++.+||..+-..||..|++ +|...++
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~-k~~~ev~ 863 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEG-KTEEEVE 863 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcC-CCHHHHH
Confidence 5888888888889999999899999999974 8887776
No 46
>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=88.96 E-value=0.93 Score=26.27 Aligned_cols=40 Identities=25% Similarity=0.428 Sum_probs=28.4
Q ss_pred HHHHHHHHHhCC-------CCchhhhhhhCCCCc----hhhHHHHHHhhhC
Q 041165 23 HKLMSFILNNGI-------HCWRMVPKLAGLLRC----GKSCRLRWINYLR 62 (85)
Q Consensus 23 ~~L~~~v~~~g~-------~~W~~Ia~~~~~~Rt----~~qcr~Rw~~~l~ 62 (85)
-.|..+|...|. +.|..||..+|...+ +.+++..|.++|.
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 356777777763 469999999875332 3678888888874
No 47
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=88.67 E-value=1.5 Score=25.91 Aligned_cols=44 Identities=14% Similarity=0.100 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCC
Q 041165 20 EEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDL 65 (85)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~ 65 (85)
+.|.+++.+....+.-.+..||+.+| -+...|+.|.....+..+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 56889999999998889999999999 899999999888766543
No 48
>smart00595 MADF subfamily of SANT domain.
Probab=88.55 E-value=0.41 Score=27.45 Aligned_cols=23 Identities=26% Similarity=0.710 Sum_probs=20.1
Q ss_pred CchhhhhhhCCCCchhhHHHHHHhh
Q 041165 36 CWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 36 ~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.|..||..|| -+..+|+.+|.+.
T Consensus 29 aW~~Ia~~l~--~~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELG--LSVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHC--cCHHHHHHHHHHH
Confidence 4999999999 5999999888876
No 49
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=87.67 E-value=0.92 Score=26.53 Aligned_cols=41 Identities=22% Similarity=0.459 Sum_probs=29.4
Q ss_pred HHHHHHHHHhCC-------CCchhhhhhhCCCC----chhhHHHHHHhhhCC
Q 041165 23 HKLMSFILNNGI-------HCWRMVPKLAGLLR----CGKSCRLRWINYLRP 63 (85)
Q Consensus 23 ~~L~~~v~~~g~-------~~W~~Ia~~~~~~R----t~~qcr~Rw~~~l~~ 63 (85)
-.|..+|...|. +.|..||..+|..- ...+.+..|.++|.|
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 457777877653 46999999998532 356778888888754
No 50
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=87.53 E-value=1.5 Score=36.26 Aligned_cols=52 Identities=15% Similarity=0.132 Sum_probs=40.8
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhC-----------CCCchhhHHHHHHhhhC
Q 041165 11 GLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAG-----------LLRCGKSCRLRWINYLR 62 (85)
Q Consensus 11 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~-----------~~Rt~~qcr~Rw~~~l~ 62 (85)
.-++..+|.|||..|+-.+.+||..+|..|-..+- -.||+..+..|=..+|.
T Consensus 923 ~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~ 985 (1033)
T PLN03142 923 QNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIR 985 (1033)
T ss_pred CCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHH
Confidence 34455699999999999999999999999855431 14999999888766553
No 51
>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=87.14 E-value=0.87 Score=24.78 Aligned_cols=19 Identities=37% Similarity=0.441 Sum_probs=16.3
Q ss_pred CCCCCHHHHHHHHHHHHhC
Q 041165 67 RGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 67 ~~~wt~eEd~~L~~~v~~~ 85 (85)
+-.||+||...++++++.|
T Consensus 3 r~~WT~eeh~~Fl~ai~~~ 21 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKL 21 (57)
T ss_pred CCCCCHHHHHHHHHHHHHh
Confidence 4579999999999998764
No 52
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=86.86 E-value=1.5 Score=27.41 Aligned_cols=44 Identities=7% Similarity=0.085 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCC
Q 041165 20 EEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDL 65 (85)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~ 65 (85)
+=|.+++.+.+..+...+..||+.+| -|...|+.|=.+..+..+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCc
Confidence 56889999999999999999999999 899999999888776554
No 53
>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=86.84 E-value=0.57 Score=26.14 Aligned_cols=26 Identities=23% Similarity=0.553 Sum_probs=21.4
Q ss_pred CchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 36 CWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 36 ~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-|..||..+|..-+..+|+.||.+..
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr 53 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLR 53 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHH
Confidence 49999999986567888999988764
No 54
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=86.78 E-value=1.4 Score=33.63 Aligned_cols=44 Identities=14% Similarity=0.065 Sum_probs=38.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHh
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
...||.||--++-++...|| .+..+|-+.|+. |+-..+..-|..
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP~-rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFG-KDFHKIRQALPH-RSLASLVQYYYS 230 (534)
T ss_pred cccchHHHHHHHHHHHHHhc-ccHHHHHHHccC-ccHHHHHHHHHH
Confidence 44699999999999999999 899999999994 999988877764
No 55
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=84.76 E-value=2 Score=29.21 Aligned_cols=49 Identities=14% Similarity=0.117 Sum_probs=34.7
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCC--CCchhhhhh----hCCCCchhhHHHHHHhh
Q 041165 12 LKRGPWTIEEDHKLMSFILNNGI--HCWRMVPKL----AGLLRCGKSCRLRWINY 60 (85)
Q Consensus 12 ~~kg~WT~eED~~L~~~v~~~g~--~~W~~Ia~~----~~~~Rt~~qcr~Rw~~~ 60 (85)
-.+-+||.+|++.|..+.....+ ..+..|-.. |-..||+.+..++|...
T Consensus 71 q~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lm 125 (199)
T PF13325_consen 71 QSKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLM 125 (199)
T ss_pred cccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHH
Confidence 35789999999999997765532 235444432 22249999999999974
No 56
>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=84.56 E-value=3.4 Score=21.12 Aligned_cols=39 Identities=10% Similarity=0.116 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 20 EEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
+++..++.+.-..+ ..+..||..+| -|...++.+....+
T Consensus 7 ~~er~vi~~~y~~~-~t~~eIa~~lg--~s~~~V~~~~~~al 45 (50)
T PF04545_consen 7 PREREVIRLRYFEG-LTLEEIAERLG--ISRSTVRRILKRAL 45 (50)
T ss_dssp HHHHHHHHHHHTST--SHHHHHHHHT--SCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCC-CCHHHHHHHHC--CcHHHHHHHHHHHH
Confidence 44555666655445 68999999999 78888887766554
No 57
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=82.56 E-value=0.78 Score=38.59 Aligned_cols=28 Identities=25% Similarity=0.551 Sum_probs=25.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhh
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVP 41 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia 41 (85)
---|..++|..|+-.|-+||.++|..|-
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGygswe~Ir 1160 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYGSWEAIR 1160 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccccHHHhc
Confidence 4469999999999999999999998875
No 58
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=81.76 E-value=2.3 Score=33.57 Aligned_cols=48 Identities=15% Similarity=0.257 Sum_probs=37.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCC---------CCchhhHHHHHHhhhC
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGL---------LRCGKSCRLRWINYLR 62 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~---------~Rt~~qcr~Rw~~~l~ 62 (85)
|..||-.|..-+..+++++| ++...|...+-- .+|-.|.|..|++.+.
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 66899999999999999999 899888443210 2566789988887653
No 59
>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=81.64 E-value=2.2 Score=24.93 Aligned_cols=23 Identities=26% Similarity=0.319 Sum_probs=20.7
Q ss_pred HHHHHHHHHHhCCCCchhhhhhhC
Q 041165 22 DHKLMSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 22 D~~L~~~v~~~g~~~W~~Ia~~~~ 45 (85)
|+.|..+....| .+|+.+|..+|
T Consensus 2 ~~~L~~la~~LG-~~W~~Lar~Lg 24 (83)
T cd08319 2 DRELNQLAQRLG-PEWEQVLLDLG 24 (83)
T ss_pred HHHHHHHHHHHh-hhHHHHHHHcC
Confidence 577889999999 79999999998
No 60
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=81.03 E-value=2.5 Score=33.01 Aligned_cols=51 Identities=16% Similarity=0.266 Sum_probs=44.8
Q ss_pred CCCCCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 8 DKVGLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 8 ~k~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
+.+....++||..|-++........| .+.+.|+..+++ |+..|++..|..-
T Consensus 403 ~sk~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p~-R~rk~iK~K~~~e 453 (584)
T KOG2009|consen 403 YSKKLETDKWDASETELFYKALSERG-SDFSLISNLFPL-RDRKQIKAKFKKE 453 (584)
T ss_pred ccCccccCcccchhhHHhhhHHhhhc-cccccccccccc-ccHHHHHHHHhhh
Confidence 34566788999999999999999999 699999999995 9999999998753
No 61
>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=80.64 E-value=2.6 Score=27.55 Aligned_cols=37 Identities=19% Similarity=0.272 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhhhC-CCCchhhHH
Q 041165 16 PWTIEEDHKLMSFILNNGIHCWRMVPKLAG-LLRCGKSCR 54 (85)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~-~~Rt~~qcr 54 (85)
.||.|..+.|.++..+ | ..=+.||..|| .+|++..=+
T Consensus 2 ~Wtde~~~~L~~lw~~-G-~SasqIA~~lg~vsRnAViGk 39 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-G-LSASQIARQLGGVSRNAVIGK 39 (162)
T ss_pred CCCHHHHHHHHHHHHc-C-CCHHHHHHHhCCcchhhhhhh
Confidence 6999999999999855 6 57899999999 345554433
No 62
>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=80.29 E-value=2.8 Score=24.50 Aligned_cols=23 Identities=13% Similarity=0.248 Sum_probs=20.5
Q ss_pred HHHHHHHHHHhCCCCchhhhhhhC
Q 041165 22 DHKLMSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 22 D~~L~~~v~~~g~~~W~~Ia~~~~ 45 (85)
|..|..++...| .+|..+|..||
T Consensus 4 d~~l~~ia~~LG-~dW~~LA~eLg 26 (84)
T cd08803 4 DIRMAIVADHLG-LSWTELARELN 26 (84)
T ss_pred HHHHHHHHHHhh-ccHHHHHHHcC
Confidence 577888888999 79999999999
No 63
>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=79.38 E-value=1.9 Score=26.86 Aligned_cols=22 Identities=14% Similarity=0.312 Sum_probs=16.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHhC
Q 041165 64 DLKRGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 64 ~~~~~~wt~eEd~~L~~~v~~~ 85 (85)
..++..+|++||..|+-++.+|
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~ 67 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKY 67 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHh
Confidence 4456789999999999988764
No 64
>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=77.33 E-value=8.2 Score=23.65 Aligned_cols=46 Identities=15% Similarity=0.225 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHHHh--------CC----C------------------CchhhhhhhCCCCchhhHHHHHHhhhC
Q 041165 16 PWTIEEDHKLMSFILNN--------GI----H------------------CWRMVPKLAGLLRCGKSCRLRWINYLR 62 (85)
Q Consensus 16 ~WT~eED~~L~~~v~~~--------g~----~------------------~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 62 (85)
++|++||-.|-..|..+ +. . =....+...+ ++|...=|+||++++.
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p-~HT~~sWRDR~RKfv~ 76 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNP-RHTENSWRDRYRKFVS 76 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTT-TS-HHHHHHHHHHTHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCC-ccchhHHHHHHHHHHH
Confidence 48999999998888655 10 0 0334445556 5999999999998764
No 65
>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=75.73 E-value=7.4 Score=25.20 Aligned_cols=48 Identities=15% Similarity=0.113 Sum_probs=37.3
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCC---CCchhhHHHHHHhh
Q 041165 12 LKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGL---LRCGKSCRLRWINY 60 (85)
Q Consensus 12 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~---~Rt~~qcr~Rw~~~ 60 (85)
-+...=|..|..-+..+|.+|| .+...+|.-.-. ..|+.||+.+...+
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 4456678999999999999999 799888865321 27888888877665
No 66
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=75.44 E-value=1.3 Score=33.78 Aligned_cols=42 Identities=10% Similarity=0.223 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHh
Q 041165 15 GPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 15 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
-.||++|-. +++....|+ .+...||..++ +.++.|+..+|..
T Consensus 471 ~~wSp~e~s-~ircf~~y~-~~fe~ia~l~~-tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 471 YGWSPEEKS-AIRCFHWYK-DNFELIAELMA-TKTPEQIKKFYMD 512 (534)
T ss_pred CCCCCcccc-cccCchhhc-cchHHHHHHhc-CCCHHHHHHHhcC
Confidence 459999977 888888899 69999999999 5999999999853
No 67
>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=75.27 E-value=7.6 Score=23.73 Aligned_cols=25 Identities=12% Similarity=0.159 Sum_probs=21.2
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-....||+.+| .|...++.+....+
T Consensus 130 ~~~~eIA~~lg--is~~tv~~~~~ra~ 154 (161)
T TIGR02985 130 KSYKEIAEELG--ISVKTVEYHISKAL 154 (161)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 58999999999 89999988887654
No 68
>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=74.34 E-value=9.1 Score=19.02 Aligned_cols=30 Identities=17% Similarity=0.120 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhhCCCCch
Q 041165 20 EEDHKLMSFILNNGIHCWRMVPKLAGLLRCG 50 (85)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~ 50 (85)
-|.+.|.++...++ ++....|+.+|.+|+.
T Consensus 5 ~E~~~i~~aL~~~~-gn~~~aA~~Lgisr~t 34 (42)
T PF02954_consen 5 FEKQLIRQALERCG-GNVSKAARLLGISRRT 34 (42)
T ss_dssp HHHHHHHHHHHHTT-T-HHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHHhC-CCHHHHHHHHCCCHHH
Confidence 36778888888988 8999999999954443
No 69
>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=73.46 E-value=3.7 Score=23.57 Aligned_cols=23 Identities=22% Similarity=0.322 Sum_probs=19.8
Q ss_pred HHHHHHHHHHhCCCCchhhhhhhC
Q 041165 22 DHKLMSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 22 D~~L~~~v~~~g~~~W~~Ia~~~~ 45 (85)
|..|..+....| .+|..+|..+|
T Consensus 4 ~~~l~~ia~~lG-~dW~~LAr~Lg 26 (84)
T cd08317 4 DIRLADISNLLG-SDWPQLARELG 26 (84)
T ss_pred cchHHHHHHHHh-hHHHHHHHHcC
Confidence 566778888889 89999999988
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=69.63 E-value=6.2 Score=22.86 Aligned_cols=29 Identities=10% Similarity=0.206 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhCCCCchhhhhhhCCCCchhhH
Q 041165 22 DHKLMSFILNNGIHCWRMVPKLAGLLRCGKSC 53 (85)
Q Consensus 22 D~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc 53 (85)
|..|..+....| .+|..+|..+| =+...+
T Consensus 4 ~~~l~~ia~~LG-~dWk~LAr~Lg--~se~dI 32 (84)
T cd08804 4 EERLAVIADHLG-FSWTELARELD--FTEEQI 32 (84)
T ss_pred hhHHHHHHHHHh-hhHHHHHHHcC--CCHHHH
Confidence 467778888889 68999999998 444444
No 71
>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=66.38 E-value=7.2 Score=22.76 Aligned_cols=28 Identities=18% Similarity=0.220 Sum_probs=20.0
Q ss_pred HHHHHHHHHhCCCCchhhhhhhCCCCchhhH
Q 041165 23 HKLMSFILNNGIHCWRMVPKLAGLLRCGKSC 53 (85)
Q Consensus 23 ~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc 53 (85)
+.|-.+....| .+|+.+|..+| =+..++
T Consensus 3 ~~l~~l~~~lG-~~Wk~lar~LG--~s~~eI 30 (86)
T cd08777 3 KHLDLLRENLG-KKWKRCARKLG--FTESEI 30 (86)
T ss_pred HHHHHHHHHHH-HHHHHHHHHcC--CCHHHH
Confidence 44556667778 79999999998 444443
No 72
>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=66.08 E-value=8.6 Score=22.27 Aligned_cols=27 Identities=15% Similarity=0.240 Sum_probs=19.2
Q ss_pred HHHHHHHHhCCCCchhhhhhhCCCCchhhH
Q 041165 24 KLMSFILNNGIHCWRMVPKLAGLLRCGKSC 53 (85)
Q Consensus 24 ~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc 53 (85)
.|..+....| .+|..+|..+| -+..++
T Consensus 9 ~l~~ia~~iG-~~Wk~Lar~LG--ls~~dI 35 (86)
T cd08318 9 QITVFANKLG-EDWKTLAPHLE--MKDKEI 35 (86)
T ss_pred HHHHHHHHHh-hhHHHHHHHcC--CCHHHH
Confidence 3445667778 79999999998 444443
No 73
>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=65.26 E-value=8.3 Score=21.32 Aligned_cols=23 Identities=22% Similarity=0.450 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCCchhhhhhhCC
Q 041165 24 KLMSFILNNGIHCWRMVPKLAGL 46 (85)
Q Consensus 24 ~L~~~v~~~g~~~W~~Ia~~~~~ 46 (85)
.|..++......+|+.+|..+|-
T Consensus 2 ~l~~~l~~~~~~~Wk~La~~Lg~ 24 (83)
T PF00531_consen 2 KLFDLLAEDLGSDWKRLARKLGL 24 (83)
T ss_dssp HHHHHHHHSHSTCHHHHHHHTTS
T ss_pred hHHHHHhhcchhhHHHHHHHhCc
Confidence 45566655544899999999984
No 74
>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=64.58 E-value=19 Score=20.34 Aligned_cols=36 Identities=14% Similarity=0.264 Sum_probs=25.0
Q ss_pred chhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHH
Q 041165 37 WRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQ 80 (85)
Q Consensus 37 W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~ 80 (85)
-..||..+.| +|+.++|.-|. + ...+|++|+..|.+
T Consensus 36 ~~~iA~~i~g-ks~eeir~~fg------i-~~d~t~eee~~i~~ 71 (78)
T PF01466_consen 36 CKYIANMIKG-KSPEEIRKYFG------I-ENDLTPEEEEEIRK 71 (78)
T ss_dssp HHHHHHHHTT-S-HHHHHHHHT----------TSSHHHHHHHHH
T ss_pred HHHHHHHhcC-CCHHHHHHHcC------C-CCCCCHHHHHHHHH
Confidence 4778888884 99999999872 2 23599988877543
No 75
>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=61.38 E-value=19 Score=21.30 Aligned_cols=28 Identities=11% Similarity=0.162 Sum_probs=21.7
Q ss_pred HhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 31 NNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 31 ~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
..| .++..||+.+| -|...++.+....+
T Consensus 124 ~~g-~s~~eIA~~l~--~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 124 LEG-LSYKEIAEILG--ISVGTVKRRLKRAR 151 (158)
T ss_pred hcC-CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 345 68999999999 68888888777654
No 76
>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=61.03 E-value=11 Score=22.04 Aligned_cols=23 Identities=13% Similarity=0.232 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhCCCCchhhhhhhC
Q 041165 22 DHKLMSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 22 D~~L~~~v~~~g~~~W~~Ia~~~~ 45 (85)
|-+|..+++..| .+|..+|..+|
T Consensus 4 ~~~l~~Ia~~LG-~dW~~Lar~L~ 26 (84)
T cd08805 4 EMKMAVIREHLG-LSWAELARELQ 26 (84)
T ss_pred hhHHHHHHHHhc-chHHHHHHHcC
Confidence 456778888889 79999999988
No 77
>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=60.48 E-value=8.9 Score=21.98 Aligned_cols=26 Identities=31% Similarity=0.388 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhhCC
Q 041165 19 IEEDHKLMSFILNNGIHCWRMVPKLAGL 46 (85)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~ 46 (85)
.||-++|+..= ..| .+|..+|..+|-
T Consensus 2 ~~~v~~ll~~~-nlG-~dW~~LA~~LG~ 27 (77)
T cd08311 2 QEEVEKLLESG-RPG-RDWRSLAGELGY 27 (77)
T ss_pred hHHHHHHHhCC-CCc-cCHHHHHHHcCC
Confidence 57878877422 224 799999999983
No 78
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=60.43 E-value=13 Score=23.96 Aligned_cols=36 Identities=19% Similarity=0.291 Sum_probs=27.5
Q ss_pred chhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHH
Q 041165 37 WRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQ 80 (85)
Q Consensus 37 W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~ 80 (85)
=+.||..+.| +|+..++.-|. .-..||+||+..+.+
T Consensus 115 CKivaemirg-kSpeeir~tfn-------i~ndfTpEEe~~irk 150 (158)
T COG5201 115 CKIVAEMIRG-KSPEEIRETFN-------IENDFTPEEERRIRK 150 (158)
T ss_pred HHHHHHHHcc-CCHHHHHHHhC-------CCCCCCHHHHHHHHH
Confidence 3778888885 99999987753 234699999988754
No 79
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=59.70 E-value=22 Score=23.10 Aligned_cols=35 Identities=11% Similarity=0.173 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 23 HKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 23 ~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
..++.+....| -.+..||..+| -|...++.+|...
T Consensus 141 ~~~v~l~~~~G-ls~~EIA~~lg--iS~~tV~r~l~~a 175 (185)
T PF07638_consen 141 RRVVELRFFEG-LSVEEIAERLG--ISERTVRRRLRRA 175 (185)
T ss_pred HHHHHHHHHCC-CCHHHHHHHHC--cCHHHHHHHHHHH
Confidence 34444444456 58999999999 8888888888754
No 80
>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=59.41 E-value=11 Score=21.88 Aligned_cols=23 Identities=26% Similarity=0.379 Sum_probs=20.1
Q ss_pred HHHHHHHHHhCCCCchhhhhhhCC
Q 041165 23 HKLMSFILNNGIHCWRMVPKLAGL 46 (85)
Q Consensus 23 ~~L~~~v~~~g~~~W~~Ia~~~~~ 46 (85)
+.|..+....| .+|..+|..+|-
T Consensus 3 ~~l~~ia~~LG-~~Wk~lar~LGl 25 (86)
T cd08779 3 SNLLSIAGRLG-LDWQAIGLHLGL 25 (86)
T ss_pred hHHHHHHHHHh-HHHHHHHHHcCC
Confidence 56888999999 799999999884
No 81
>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=57.58 E-value=61 Score=22.44 Aligned_cols=46 Identities=13% Similarity=0.211 Sum_probs=30.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh---CCCCCCCCCCHHHHHHHHHHH
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL---RPDLKRGAFTEDEEDQIIQLH 82 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l---~~~~~~~~wt~eEd~~L~~~v 82 (85)
-+-..||+.+| .|...|+.+.++.. ..........+++...|++.+
T Consensus 125 ~s~~EIA~~lg--~s~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~f 173 (281)
T TIGR02957 125 YPYEEIASIVG--KSEANCRQLVSRARRHLDARRPRFEVSREESRQLLERF 173 (281)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHHH
Confidence 45689999999 89999998877643 322223335566666555543
No 82
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=57.37 E-value=9.5 Score=29.42 Aligned_cols=19 Identities=21% Similarity=0.321 Sum_probs=17.0
Q ss_pred CCCCCHHHHHHHHHHHHhC
Q 041165 67 RGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 67 ~~~wt~eEd~~L~~~v~~~ 85 (85)
+..||.+|..+|++++..|
T Consensus 253 ~~~WT~qE~lLLLE~ie~y 271 (506)
T KOG1279|consen 253 RPNWTEQETLLLLEAIEMY 271 (506)
T ss_pred CCCccHHHHHHHHHHHHHh
Confidence 5689999999999999876
No 83
>PF09356 Phage_BR0599: Phage conserved hypothetical protein BR0599; InterPro: IPR018964 This entry describes the C-terminal region of a family of proteins found almost exclusively in phage or in prophage regions of bacterial genomes, including the phage-like Rhodobacter capsulatus (Rhodopseudomonas capsulata) gene transfer agent, which packages DNA. An apparent exception is Wolbachia pipientis wMel, a bacterial endosymbiont of the fruit fly, which has several candidate phage-related genes physically separate from obvious prophage regions.
Probab=57.29 E-value=6 Score=22.81 Aligned_cols=19 Identities=26% Similarity=0.420 Sum_probs=16.6
Q ss_pred hCCCCchhhHHHHHHhhhC
Q 041165 44 AGLLRCGKSCRLRWINYLR 62 (85)
Q Consensus 44 ~~~~Rt~~qcr~Rw~~~l~ 62 (85)
.|..++...|+.||.|.++
T Consensus 51 ~GCDkt~~tC~~kF~N~~N 69 (80)
T PF09356_consen 51 PGCDKTFATCRAKFNNALN 69 (80)
T ss_pred eCCCCCHHHHHHHhCCccc
Confidence 4677999999999999886
No 84
>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=56.98 E-value=19 Score=19.55 Aligned_cols=45 Identities=20% Similarity=0.242 Sum_probs=30.9
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 13 KRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
++..||+|+-..++..+..-| ..-..||..+|. ++ +.-.+|....
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g-~sv~~va~~~gi--~~-~~l~~W~~~~ 47 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESG-ESVSEVAREYGI--SP-STLYNWRKQY 47 (76)
T ss_dssp SS----HHHHHHHHHHHHHHH-CHHHHHHHHHTS---H-HHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCC-CceEeeeccccc--cc-ccccHHHHHH
Confidence 356899999999999996667 689999999994 44 4455677755
No 85
>PF04435 SPK: Domain of unknown function (DUF545) ; InterPro: IPR006570 SPK is a domain of unknown function found in SET and PHD domain containing proteins and protein kinases.
Probab=56.84 E-value=12 Score=21.99 Aligned_cols=43 Identities=26% Similarity=0.462 Sum_probs=32.6
Q ss_pred chhhhhhhCCCCchhhHHHHHHhhhCCCCC-CCCCCHHHHHHHH
Q 041165 37 WRMVPKLAGLLRCGKSCRLRWINYLRPDLK-RGAFTEDEEDQII 79 (85)
Q Consensus 37 W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~-~~~wt~eEd~~L~ 79 (85)
|....+..|..++....+.||.+.+.|.+. ..+++.+.-..|+
T Consensus 25 ~~~f~~~~~~~~~~~~l~~~~~~~l~~~i~~~~~~d~~tk~~m~ 68 (109)
T PF04435_consen 25 WEEFKKKSGSKRSPKSLRKRFRRKLAPNIHKLSDFDLETKAKML 68 (109)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHH
Confidence 666667777679999999999998887776 6677776655543
No 86
>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=56.50 E-value=14 Score=20.82 Aligned_cols=24 Identities=29% Similarity=0.504 Sum_probs=18.3
Q ss_pred HHHHHHHHHH-hCCCCchhhhhhhCC
Q 041165 22 DHKLMSFILN-NGIHCWRMVPKLAGL 46 (85)
Q Consensus 22 D~~L~~~v~~-~g~~~W~~Ia~~~~~ 46 (85)
++.|..++.. .| .+|..+|..+|.
T Consensus 5 ~~~~~~l~~~~~g-~~W~~la~~Lg~ 29 (88)
T smart00005 5 REKLAKLLDHPLG-LDWRELARKLGL 29 (88)
T ss_pred HHHHHHHHcCccc-hHHHHHHHHcCC
Confidence 4556666666 56 799999999984
No 87
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=55.50 E-value=27 Score=21.70 Aligned_cols=25 Identities=12% Similarity=0.108 Sum_probs=19.4
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.....||..+| -|...++.+.....
T Consensus 142 ~~~~eIA~~lg--is~~tv~~~~~ra~ 166 (179)
T PRK11924 142 LSYREIAEILG--VPVGTVKSRLRRAR 166 (179)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 57899999999 77888877766543
No 88
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=55.00 E-value=10 Score=19.07 Aligned_cols=36 Identities=22% Similarity=0.337 Sum_probs=16.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHH
Q 041165 15 GPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCR 54 (85)
Q Consensus 15 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr 54 (85)
..+|++|-..+..+. .-| .+=..||+.|| |+...+.
T Consensus 3 ~~Lt~~eR~~I~~l~-~~G-~s~~~IA~~lg--~s~sTV~ 38 (44)
T PF13936_consen 3 KHLTPEERNQIEALL-EQG-MSIREIAKRLG--RSRSTVS 38 (44)
T ss_dssp ---------HHHHHH-CS----HHHHHHHTT----HHHHH
T ss_pred cchhhhHHHHHHHHH-HcC-CCHHHHHHHHC--cCcHHHH
Confidence 357888877766664 346 57899999999 8877664
No 89
>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=54.81 E-value=24 Score=16.94 Aligned_cols=39 Identities=10% Similarity=0.261 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHh
Q 041165 17 WTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 17 WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
.+++ +..++.+....| .....||..+| -+...++.+...
T Consensus 11 l~~~-~~~~~~~~~~~~-~~~~~ia~~~~--~s~~~i~~~~~~ 49 (55)
T cd06171 11 LPER-EREVILLRFGEG-LSYEEIAEILG--ISRSTVRQRLHR 49 (55)
T ss_pred CCHH-HHHHHHHHHhcC-CCHHHHHHHHC--cCHHHHHHHHHH
Confidence 3444 344555544455 68999999999 677777655444
No 90
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=54.76 E-value=27 Score=22.05 Aligned_cols=25 Identities=4% Similarity=-0.096 Sum_probs=19.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+...||..+| -|...++.+..+..
T Consensus 153 ~s~~eIA~~lg--is~~~v~~~l~Rar 177 (187)
T PRK09641 153 LSLKEISEILD--LPVGTVKTRIHRGR 177 (187)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 57899999999 77888887766543
No 91
>smart00351 PAX Paired Box domain.
Probab=53.58 E-value=50 Score=20.25 Aligned_cols=70 Identities=14% Similarity=0.095 Sum_probs=45.4
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCc-hhhHHHHHHh--hhCCCCC----CCCCCHHHHHHHHHHHHh
Q 041165 13 KRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRC-GKSCRLRWIN--YLRPDLK----RGAFTEDEEDQIIQLHSL 84 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt-~~qcr~Rw~~--~l~~~~~----~~~wt~eEd~~L~~~v~~ 84 (85)
...+.|.++-++++.++. -| ..-..||+.+|.+++ ...+..||.. .+.|.-. ...-+++.+..|++++.+
T Consensus 14 ~~~~~s~~~R~riv~~~~-~G-~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~ 90 (125)
T smart00351 14 NGRPLPDEERQRIVELAQ-NG-VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQE 90 (125)
T ss_pred CCCCCCHHHHHHHHHHHH-cC-CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHH
Confidence 345689999999988886 46 578999999986543 4455677764 3444221 123556666667766543
No 92
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=53.51 E-value=32 Score=21.38 Aligned_cols=24 Identities=13% Similarity=0.130 Sum_probs=18.2
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+...||..+| .+...++.+....
T Consensus 145 ~s~~eIA~~lg--is~~tV~~~l~ra 168 (182)
T PRK09652 145 LSYEEIAEIMG--CPIGTVRSRIFRA 168 (182)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHH
Confidence 58999999999 6777776665543
No 93
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=53.30 E-value=32 Score=22.26 Aligned_cols=24 Identities=8% Similarity=0.015 Sum_probs=19.7
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.+...||..+| -|...++.|..+.
T Consensus 151 ~s~~EIA~~lg--~s~~tV~~rl~ra 174 (192)
T PRK09643 151 YSVADAARMLG--VAEGTVKSRCARG 174 (192)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHH
Confidence 68899999999 7888888887553
No 94
>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=53.14 E-value=12 Score=21.01 Aligned_cols=19 Identities=11% Similarity=0.302 Sum_probs=14.6
Q ss_pred HHHHHHHHHhCCCCchhhhh
Q 041165 23 HKLMSFILNNGIHCWRMVPK 42 (85)
Q Consensus 23 ~~L~~~v~~~g~~~W~~Ia~ 42 (85)
..|.++.+.|| +||..|..
T Consensus 30 ~vl~~LL~lY~-~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYD-GNWELIEE 48 (65)
T ss_pred HHHHHHHHHHc-CCchhhhc
Confidence 35677888999 67999874
No 95
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=53.02 E-value=47 Score=19.73 Aligned_cols=42 Identities=17% Similarity=0.236 Sum_probs=32.4
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCC-chhhHHHHHHh
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLR-CGKSCRLRWIN 59 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~R-t~~qcr~Rw~~ 59 (85)
+..||+|.-..++.++..-| ..=+.||..+| - ++.+.+ +|..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g-~sv~~vAr~~g--v~~~~~l~-~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGG-DTVSEVAREFG--IVSATQLY-KWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcC-ccHHHHHHHhC--CCChHHHH-HHHH
Confidence 67899999999999988888 57899999999 4 444444 4444
No 96
>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=52.13 E-value=14 Score=22.61 Aligned_cols=18 Identities=28% Similarity=0.392 Sum_probs=14.7
Q ss_pred cCCCCHHHHHHHHHHHHH
Q 041165 14 RGPWTIEEDHKLMSFILN 31 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~ 31 (85)
-+-|||+|+.+|++.-..
T Consensus 26 E~GLtPeEe~~LIE~TM~ 43 (104)
T PF09846_consen 26 EEGLTPEEESKLIEMTMT 43 (104)
T ss_pred cCCCChHHHHHHHHHHHH
Confidence 356999999999997643
No 97
>PRK02866 cyanate hydratase; Validated
Probab=51.44 E-value=65 Score=20.88 Aligned_cols=50 Identities=12% Similarity=0.264 Sum_probs=33.6
Q ss_pred HHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHHHH
Q 041165 23 HKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQLH 82 (85)
Q Consensus 23 ~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~~v 82 (85)
+.|+.+-.+.| -.|..||+.+| +|..-+..-.+. ....++++-+.|.++.
T Consensus 8 e~Ll~AK~~kG-LTw~~IA~~iG--~S~v~vaaa~lG-------Q~~ls~e~A~kla~~L 57 (147)
T PRK02866 8 EKILAAKKEKG-LTWADIAEAIG--LSEVWVTAALLG-------QMTLPAEEAEKVAELL 57 (147)
T ss_pred HHHHHHHHHcC-CCHHHHHHHhC--CCHHHHHHHHhC-------CCCCCHHHHHHHHHHh
Confidence 45666767777 69999999998 888755544332 2345666666665543
No 98
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=50.19 E-value=35 Score=21.85 Aligned_cols=25 Identities=8% Similarity=-0.031 Sum_probs=20.2
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+...||+.+| -|...++.+..+.+
T Consensus 155 ~s~~eIA~~lg--is~~tv~~~l~Rar 179 (193)
T PRK11923 155 LSYEDIASVMQ--CPVGTVRSRIFRAR 179 (193)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 56899999999 78888888877654
No 99
>PRK01905 DNA-binding protein Fis; Provisional
Probab=49.76 E-value=46 Score=18.69 Aligned_cols=32 Identities=16% Similarity=0.132 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHHHHhCCCCchhhhhhhCCCCch
Q 041165 18 TIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCG 50 (85)
Q Consensus 18 T~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~ 50 (85)
..-|...+..++..++ ++....|+.+|.+|+.
T Consensus 35 ~~~E~~~i~~aL~~~~-gn~s~aAr~LGIsrst 66 (77)
T PRK01905 35 SCVEKPLLEVVMEQAG-GNQSLAAEYLGINRNT 66 (77)
T ss_pred HHHHHHHHHHHHHHcC-CCHHHHHHHHCCCHHH
Confidence 3446677888888888 7999999999954443
No 100
>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=48.90 E-value=25 Score=20.30 Aligned_cols=20 Identities=25% Similarity=0.439 Sum_probs=14.7
Q ss_pred HHHHHHHhCCCCchhhhhhhC
Q 041165 25 LMSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 25 L~~~v~~~g~~~W~~Ia~~~~ 45 (85)
+--++...| .+|..+|..+|
T Consensus 5 f~~i~~~lG-~~Wk~laR~LG 24 (86)
T cd08306 5 FDVICENVG-RDWRKLARKLG 24 (86)
T ss_pred HHHHHHHHh-hhHHHHHHHcC
Confidence 333445557 79999999998
No 101
>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=48.78 E-value=29 Score=21.97 Aligned_cols=25 Identities=8% Similarity=0.032 Sum_probs=19.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+...||..+| -|...++.+.++.+
T Consensus 155 ~s~~EIA~~lg--is~~tv~~~l~rar 179 (190)
T TIGR02939 155 LSYEDIARIMD--CPVGTVRSRIFRAR 179 (190)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHH
Confidence 57899999999 67888888776543
No 102
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=48.73 E-value=53 Score=19.05 Aligned_cols=40 Identities=13% Similarity=0.019 Sum_probs=30.0
Q ss_pred CHHHHHHHHHHHHHhCC----CCchhhhhhhCCCCchhhHHHHHHh
Q 041165 18 TIEEDHKLMSFILNNGI----HCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 18 T~eED~~L~~~v~~~g~----~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
|+-.-+.|..+|+.|-. -.=+.||+.++ +++..||+--..
T Consensus 3 t~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~--~s~aTIRN~M~~ 46 (78)
T PF03444_consen 3 TERQREILKALVELYIETGEPVGSKTIAEELG--RSPATIRNEMAD 46 (78)
T ss_pred CHHHHHHHHHHHHHHHhcCCCcCHHHHHHHHC--CChHHHHHHHHH
Confidence 56677888889988842 23588999888 899999886443
No 103
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=48.63 E-value=44 Score=21.35 Aligned_cols=25 Identities=12% Similarity=0.013 Sum_probs=19.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+...||..+| -+...++.+..+.+
T Consensus 156 ~s~~EIA~~lg--is~~tV~~~l~Ra~ 180 (189)
T PRK09648 156 LSAEETAEAVG--STPGAVRVAQHRAL 180 (189)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 57899999999 67777877766543
No 104
>PRK04217 hypothetical protein; Provisional
Probab=48.31 E-value=50 Score=20.22 Aligned_cols=43 Identities=14% Similarity=-0.015 Sum_probs=31.0
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-..-|++| ..++.+....| -+-..||+.+| -|...++.++...
T Consensus 40 ~~~Lt~ee-reai~l~~~eG-lS~~EIAk~LG--IS~sTV~r~L~RA 82 (110)
T PRK04217 40 PIFMTYEE-FEALRLVDYEG-LTQEEAGKRMG--VSRGTVWRALTSA 82 (110)
T ss_pred cccCCHHH-HHHHHHHHHcC-CCHHHHHHHHC--cCHHHHHHHHHHH
Confidence 34456666 56666666667 58999999999 7777777777654
No 105
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=47.81 E-value=42 Score=21.55 Aligned_cols=24 Identities=8% Similarity=-0.057 Sum_probs=17.4
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+...||..|| -|...++.+....
T Consensus 123 ~~~~EIA~~lg--is~~tV~~~l~Ra 146 (181)
T PRK09637 123 LSQKEIAEKLG--LSLSGAKSRVQRG 146 (181)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHH
Confidence 57899999999 6666666665443
No 106
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=47.52 E-value=46 Score=21.45 Aligned_cols=25 Identities=8% Similarity=-0.137 Sum_probs=19.8
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||..+| -|...++.|..+.+
T Consensus 158 ~s~~EIA~~lg--is~~tVk~rl~ra~ 182 (194)
T PRK12531 158 LPHQQVAEMFD--IPLGTVKSRLRLAV 182 (194)
T ss_pred CCHHHHHHHhC--cCHHHHHHHHHHHH
Confidence 46799999999 78888888876543
No 107
>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=47.14 E-value=41 Score=24.69 Aligned_cols=43 Identities=14% Similarity=0.093 Sum_probs=31.8
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCc---hhhhhhhCCCCchhhHHHHH
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCW---RMVPKLAGLLRCGKSCRLRW 57 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W---~~Ia~~~~~~Rt~~qcr~Rw 57 (85)
-..||.-|...|+.+.+....... ..|++.+.+ |+..+|++--
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~-Rs~aEI~~fl 66 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPG-RSEAEIRDFL 66 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccC-cCHHHHHHHH
Confidence 346999999999999876632444 456667885 9999888643
No 108
>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=47.05 E-value=45 Score=20.82 Aligned_cols=25 Identities=4% Similarity=0.011 Sum_probs=20.0
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||..+| -|...++.+....+
T Consensus 136 ~s~~eiA~~lg--is~~tv~~~l~Ra~ 160 (169)
T TIGR02954 136 LTIKEIAEVMN--KPEGTVKTYLHRAL 160 (169)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 57899999999 78888888877654
No 109
>PF00674 DUP: DUP family; InterPro: IPR001142 A number of uncharacterised integral membrane proteins from yeast contain an internal duplication due to duplicated genes. Duplicated copies of genes may be classified in two types of cluster organisation. The first type includes genes sharing a significant level of identity in the amino acid sequences of their predicted protein product. They are recovered on two different chromosomes, transcribed in the same orientation and the distance between them is conserved. The second type of cluster is based on one gene unit tandemly repeated. This duplication is itself repeated elsewhere in the genome. The basic gene unit is recovered many times in the genome and is a component of a multigene family of unknown function. These organisations in clusters of genes suggest a 'Lego organisation' of the yeast chromosomes []. The proteins belonging to this family are of unknown function.
Probab=46.91 E-value=62 Score=19.34 Aligned_cols=42 Identities=14% Similarity=0.233 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCC----CCchhhhhhhCC-------CC------chhhHHHHHHhhhCCC
Q 041165 23 HKLMSFILNNGI----HCWRMVPKLAGL-------LR------CGKSCRLRWINYLRPD 64 (85)
Q Consensus 23 ~~L~~~v~~~g~----~~W~~Ia~~~~~-------~R------t~~qcr~Rw~~~l~~~ 64 (85)
.+|+.-|-...+ ..|..||..|+. -+ .+.+|..-|.+.+.+.
T Consensus 44 ~kfl~eIi~~~P~~d~~~Wd~IA~~mN~yly~~~~w~t~~~FyDG~~C~~~Fr~~v~~p 102 (108)
T PF00674_consen 44 MKFLKEIIEVKPGVDMKKWDIIASRMNQYLYEEGLWNTPYFFYDGKDCYRFFRRLVLKP 102 (108)
T ss_pred HHHHHHHHhcCCCCCcccHHHHHHHHHHHHHhCCCCCCcCcccCcHHHHHHHHHHhccc
Confidence 445555544433 479999999851 12 4568988888866543
No 110
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=46.88 E-value=48 Score=21.02 Aligned_cols=25 Identities=8% Similarity=-0.049 Sum_probs=19.9
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+-..||..+| -|...++.+..+.+
T Consensus 148 ~s~~eIA~~l~--is~~tV~~~l~ra~ 172 (184)
T PRK12512 148 ASIKETAAKLS--MSEGAVRVALHRGL 172 (184)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHHH
Confidence 57899999999 78888888876644
No 111
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=46.86 E-value=39 Score=21.32 Aligned_cols=25 Identities=4% Similarity=-0.096 Sum_probs=19.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+-..||..+| -|...++.+..+.+
T Consensus 153 ~s~~eIA~~lg--is~~~v~~~l~Rar 177 (187)
T TIGR02948 153 LSLKEISEILD--LPVGTVKTRIHRGR 177 (187)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 56789999999 77888888776543
No 112
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=46.85 E-value=38 Score=16.81 Aligned_cols=39 Identities=8% Similarity=0.081 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 21 EDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 21 ED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+..++.++...|.-.-..||+.+| -|...+..+.....
T Consensus 4 ~~~~Il~~l~~~~~~t~~ela~~~~--is~~tv~~~l~~L~ 42 (48)
T PF13412_consen 4 TQRKILNYLRENPRITQKELAEKLG--ISRSTVNRYLKKLE 42 (48)
T ss_dssp HHHHHHHHHHHCTTS-HHHHHHHHT--S-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHhC--CCHHHHHHHHHHHH
Confidence 3566778888888789999999999 56666666655544
No 113
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=46.80 E-value=41 Score=25.32 Aligned_cols=43 Identities=12% Similarity=0.067 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCchhhhhh-hCCCCchhhHHHHHHh
Q 041165 15 GPWTIEEDHKLMSFILNNGIHCWRMVPKL-AGLLRCGKSCRLRWIN 59 (85)
Q Consensus 15 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~-~~~~Rt~~qcr~Rw~~ 59 (85)
..||.+|=..+-+.++.|| +++..|-.. +. +|+-..|-.-|+-
T Consensus 278 ~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvr-tRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYG-KDFHLIRANKVR-TRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHhcccc-cchHHHHHHHHHH
Confidence 4699999999999999999 899999766 77 5999999876643
No 114
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=46.75 E-value=56 Score=20.32 Aligned_cols=63 Identities=13% Similarity=0.092 Sum_probs=41.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCC---chhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHhC
Q 041165 15 GPWTIEEDHKLMSFILNNGIHC---WRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 15 g~WT~eED~~L~~~v~~~g~~~---W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~~v~~~ 85 (85)
+.|.||.=..|.+=....+..+ =.+|+..++ +|...+|.-|-..-. .-|.|+-..|+..+.+|
T Consensus 46 akldpe~a~e~veEL~~i~~~~e~~avkIadI~P--~t~~ElRsIla~e~~------~~s~E~l~~Ildiv~Ky 111 (114)
T COG1460 46 AKLDPEKARELVEELLSIVKMSEKIAVKIADIMP--RTPDELRSILAKERV------MLSDEELDKILDIVDKY 111 (114)
T ss_pred hcCCHHHHHHHHHHHHhhccccHHHHHHHHHhCC--CCHHHHHHHHHHccC------CCCHHHHHHHHHHHHHH
Confidence 3456666555544333333111 356777788 999999998876522 33999999999998875
No 115
>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=46.68 E-value=43 Score=21.20 Aligned_cols=23 Identities=9% Similarity=0.134 Sum_probs=16.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
..|..||..+. -+..+|+..+..
T Consensus 100 ~TW~~IA~~l~--i~erta~r~~~~ 122 (130)
T PF05263_consen 100 RTWYQIAQKLH--ISERTARRWRDR 122 (130)
T ss_pred chHHHHHHHhC--ccHHHHHHHHHH
Confidence 57999999987 666677654443
No 116
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=46.32 E-value=55 Score=20.07 Aligned_cols=25 Identities=8% Similarity=-0.142 Sum_probs=19.8
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||..+| -|...++.|....+
T Consensus 123 ~s~~EIA~~lg--is~~tV~~~l~ra~ 147 (161)
T PRK09047 123 MDVAETAAAMG--CSEGSVKTHCSRAT 147 (161)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 46799999999 78888888776654
No 117
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=45.68 E-value=54 Score=20.62 Aligned_cols=25 Identities=12% Similarity=-0.047 Sum_probs=19.7
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+...||+.+| -+...++.+-.+-+
T Consensus 136 ~s~~EIA~~lg--is~~tV~~~l~ra~ 160 (172)
T PRK12523 136 MGHAEIAERLG--VSVSRVRQYLAQGL 160 (172)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 57899999999 78888887766543
No 118
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=45.48 E-value=50 Score=21.31 Aligned_cols=24 Identities=0% Similarity=-0.284 Sum_probs=18.5
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+...||+.+| -+...++.+....
T Consensus 153 ~s~~eIA~~lg--is~~tV~~~l~Ra 176 (196)
T PRK12524 153 LSNPEIAEVME--IGVEAVESLTARG 176 (196)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHH
Confidence 57999999999 6777777766553
No 119
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=45.34 E-value=56 Score=20.15 Aligned_cols=25 Identities=4% Similarity=-0.007 Sum_probs=19.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||+.+| -|...++.|....+
T Consensus 123 ~s~~EIA~~lg--is~~tV~~~l~Rar 147 (160)
T PRK09642 123 KSYQEIALQEK--IEVKTVEMKLYRAR 147 (160)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 46789999999 88888888776543
No 120
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=45.24 E-value=64 Score=19.05 Aligned_cols=30 Identities=13% Similarity=-0.031 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhhCCCCch
Q 041165 20 EEDHKLMSFILNNGIHCWRMVPKLAGLLRCG 50 (85)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~ 50 (85)
-|...|..++..++ ++....|+.+|.+|+.
T Consensus 55 ~Er~~i~~aL~~~~-gn~s~AAr~LGIsRsT 84 (95)
T PRK00430 55 VEAPLLDMVMQYTR-GNQTRAALMLGINRGT 84 (95)
T ss_pred HHHHHHHHHHHHcC-CCHHHHHHHhCCCHHH
Confidence 46667777888888 7999999999965553
No 121
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=45.19 E-value=55 Score=20.82 Aligned_cols=25 Identities=0% Similarity=-0.218 Sum_probs=20.2
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+...||..+| -|...++.|..+-+
T Consensus 144 ~s~~EIA~~lg--is~~tVk~~l~rAl 168 (178)
T PRK12529 144 MKQKDIAQALD--IALPTVKKYIHQAY 168 (178)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 57899999999 78888888876644
No 122
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=44.81 E-value=27 Score=26.47 Aligned_cols=21 Identities=19% Similarity=0.267 Sum_probs=17.6
Q ss_pred CCCCCCCHHHHHHHHHHHHhC
Q 041165 65 LKRGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 65 ~~~~~wt~eEd~~L~~~v~~~ 85 (85)
+-...||.+|+-+|++++..|
T Consensus 70 i~~~~WtadEEilLLea~~t~ 90 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETY 90 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHh
Confidence 445679999999999998765
No 123
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=44.21 E-value=58 Score=20.37 Aligned_cols=25 Identities=12% Similarity=-0.057 Sum_probs=19.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||+.+| .+...++.|...-+
T Consensus 135 ~s~~EIA~~lg--is~~tV~~~l~ra~ 159 (173)
T PRK09645 135 WSTAQIAADLG--IPEGTVKSRLHYAL 159 (173)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHH
Confidence 46799999999 78888888776643
No 124
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=43.93 E-value=58 Score=20.80 Aligned_cols=25 Identities=12% Similarity=0.064 Sum_probs=20.4
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||..+| -|...++.+..+.+
T Consensus 148 ~s~~eIA~~lg--is~~tV~~~l~Rar 172 (189)
T PRK12515 148 KSVEEVGEIVG--IPESTVKTRMFYAR 172 (189)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHH
Confidence 57899999999 78888888877654
No 125
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=43.68 E-value=84 Score=19.93 Aligned_cols=61 Identities=15% Similarity=0.259 Sum_probs=44.2
Q ss_pred CCCHHHHHHH----HHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCC-C----CCCCCCHHHHHHH
Q 041165 16 PWTIEEDHKL----MSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPD-L----KRGAFTEDEEDQI 78 (85)
Q Consensus 16 ~WT~eED~~L----~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~-~----~~~~wt~eEd~~L 78 (85)
++|+||-+.| +++|.++|.---..++...| =|-.+++..+....... + ..|-|++|...+-
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TG--asR~Tvk~~lreLVa~G~l~~~G~~GvF~seqA~~d 73 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRITIKQLVAKTG--ASRNTVKRYLRELVARGDLYRHGRSGVFPSEQARKD 73 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHC--CCHHHHHHHHHHHHHcCCeEeCCCccccccHHHHHH
Confidence 6899998766 56788889878888888888 56667787777765442 1 2267888776653
No 126
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=43.67 E-value=56 Score=17.92 Aligned_cols=43 Identities=16% Similarity=0.224 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHH-----HHHHhhhCC
Q 041165 19 IEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCR-----LRWINYLRP 63 (85)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr-----~Rw~~~l~~ 63 (85)
|.-|+...-.....|...=..||+.+| -+..+++ ++|..-|+.
T Consensus 7 p~rdkA~e~y~~~~g~i~lkdIA~~Lg--vs~~tIr~WK~~dkW~~~~~~ 54 (60)
T PF10668_consen 7 PNRDKAFEIYKESNGKIKLKDIAEKLG--VSESTIRKWKSRDKWDEKLKG 54 (60)
T ss_pred cCHHHHHHHHHHhCCCccHHHHHHHHC--CCHHHHHHHhhhcchhhHhcc
Confidence 344444433333345567899999999 7788876 355544443
No 127
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=43.10 E-value=60 Score=20.90 Aligned_cols=25 Identities=4% Similarity=-0.107 Sum_probs=19.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+-..||+.+| -|...++.|....+
T Consensus 148 ~s~~EIA~~lg--is~~tvk~rl~Rar 172 (188)
T TIGR02943 148 FESDEICQELE--ISTSNCHVLLYRAR 172 (188)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHHH
Confidence 57899999999 78887887766653
No 128
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=43.07 E-value=1.1e+02 Score=21.18 Aligned_cols=44 Identities=16% Similarity=0.237 Sum_probs=27.9
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh---CCCCCCCCCCHHHHHHHHH
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL---RPDLKRGAFTEDEEDQIIQ 80 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l---~~~~~~~~wt~eEd~~L~~ 80 (85)
-+-..||+.+| .|...|+.+.++-. ........-..++...+++
T Consensus 132 ~s~~EIA~~lg--~s~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~v~ 178 (293)
T PRK09636 132 VPFDEIASTLG--RSPAACRQLASRARKHVRAARPRFPVSDEEGAELVE 178 (293)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHHHHHHhhCCCCCCCchHHHHHHH
Confidence 45699999999 89999998877643 3333323344445444443
No 129
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=41.48 E-value=39 Score=25.32 Aligned_cols=21 Identities=33% Similarity=0.575 Sum_probs=18.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCC
Q 041165 14 RGPWTIEEDHKLMSFILNNGI 34 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~ 34 (85)
..-||+||=.+|.+++.+||.
T Consensus 172 Grvwt~eeL~~i~elc~kh~v 192 (388)
T COG1168 172 GRVWTKEELRKIAELCLRHGV 192 (388)
T ss_pred CccccHHHHHHHHHHHHHcCC
Confidence 345999999999999999973
No 130
>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=41.39 E-value=30 Score=18.90 Aligned_cols=19 Identities=16% Similarity=0.380 Sum_probs=14.9
Q ss_pred HHHHHHhCCCCchhhhhhhC
Q 041165 26 MSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 26 ~~~v~~~g~~~W~~Ia~~~~ 45 (85)
..++...| .+|..+|..+|
T Consensus 3 ~~ia~~lg-~~W~~la~~Lg 21 (79)
T cd01670 3 DKLAKKLG-KDWKKLARKLG 21 (79)
T ss_pred HHHHHHHh-hHHHHHHHHhC
Confidence 34556667 89999999988
No 131
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 a
Probab=41.19 E-value=19 Score=20.80 Aligned_cols=28 Identities=11% Similarity=0.175 Sum_probs=20.8
Q ss_pred HHHHHHHhCCCCchhhhhhhCCCCchhhHH
Q 041165 25 LMSFILNNGIHCWRMVPKLAGLLRCGKSCR 54 (85)
Q Consensus 25 L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr 54 (85)
|..++...+..+|+.++..+| =|..++.
T Consensus 2 ~y~v~d~v~~~~wk~~~R~LG--lse~~Id 29 (80)
T cd08313 2 LYTVLDEVPPRRWKEFVRRLG--LSDNEIE 29 (80)
T ss_pred HHHHHHhCCHHHHHHHHHHcC--CCHHHHH
Confidence 566777778789999999998 4444443
No 132
>PLN03079 Uncharacterized protein At4g33100; Provisional
Probab=41.18 E-value=40 Score=20.17 Aligned_cols=27 Identities=15% Similarity=0.420 Sum_probs=14.8
Q ss_pred hhHHHHHHhhhCCCCCCCCCCHHHHHHHHH
Q 041165 51 KSCRLRWINYLRPDLKRGAFTEDEEDQIIQ 80 (85)
Q Consensus 51 ~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~ 80 (85)
.+|.++|..- .+-+|.|+.+|=.-+.+
T Consensus 26 D~CFN~WYsE---kFLKG~~~~~eC~~~w~ 52 (91)
T PLN03079 26 HNCFNRWYSE---KFVKGQWDKEDCVAEWH 52 (91)
T ss_pred HHHHHHHHHH---hhhcCCcccchHHHHHH
Confidence 3677777642 23356676555444443
No 133
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=40.61 E-value=67 Score=20.67 Aligned_cols=25 Identities=0% Similarity=-0.205 Sum_probs=20.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+...||..+| -|...++.|..+.+
T Consensus 151 ~s~~EIA~~lg--is~~tVk~~l~RAr 175 (189)
T PRK12530 151 LSSEQICQECD--ISTSNLHVLLYRAR 175 (189)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 57899999999 88888888876543
No 134
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=40.47 E-value=75 Score=19.57 Aligned_cols=25 Identities=8% Similarity=0.073 Sum_probs=18.0
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+=..||..|| -|...++.|..+.+
T Consensus 122 ~s~~eIA~~lg--is~~tv~~~l~ra~ 146 (159)
T PRK12527 122 LSHQQIAEHLG--ISRSLVEKHIVNAM 146 (159)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHHH
Confidence 45688999998 67777777765543
No 135
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=40.35 E-value=82 Score=22.14 Aligned_cols=45 Identities=7% Similarity=0.068 Sum_probs=28.7
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh---CCCCCCCCCCHHHHHHHHHH
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL---RPDLKRGAFTEDEEDQIIQL 81 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l---~~~~~~~~wt~eEd~~L~~~ 81 (85)
-+-..||+.+| .|...|+.+.+.-. .........++++...|++.
T Consensus 135 ~s~~EIA~~Lg--is~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~ 182 (290)
T PRK09635 135 LPYQQIATTIG--SQASTCRQLAHRARRKINESRIAASVEPAQHRVVTRA 182 (290)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHH
Confidence 45699999999 89999998876543 22111223555665555544
No 136
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=40.22 E-value=34 Score=19.14 Aligned_cols=49 Identities=10% Similarity=0.359 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhCCCCchhhhhhhCCC--CchhhHHHHHHhhhCCCCCCCCCCHHHHHHH
Q 041165 22 DHKLMSFILNNGIHCWRMVPKLAGLL--RCGKSCRLRWINYLRPDLKRGAFTEDEEDQI 78 (85)
Q Consensus 22 D~~L~~~v~~~g~~~W~~Ia~~~~~~--Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L 78 (85)
+..|.++|..|| |..+++.+..+ .+.-+++.-- .+ +++.||..+..+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i~CF~~~PsikSSL-kF----LRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERININCFKNNPSIKSSL-KF----LRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTSSSTTSS--HHHHH-HH----HHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcccccCCCCCchHHHH-HH----HhcCHhHHHHHHHh
Confidence 467888999997 99999987642 2222222211 11 13557777665554
No 137
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=39.60 E-value=51 Score=20.79 Aligned_cols=25 Identities=8% Similarity=-0.043 Sum_probs=20.1
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+-..||+.+| -|...++.|..+.+
T Consensus 136 ~s~~EIA~~lg--is~~tV~~~l~Ra~ 160 (172)
T PRK09651 136 LTYSEIAHKLG--VSVSSVKKYVAKAT 160 (172)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHHH
Confidence 46799999999 78888888877654
No 138
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=38.93 E-value=1.1e+02 Score=20.08 Aligned_cols=57 Identities=25% Similarity=0.369 Sum_probs=36.7
Q ss_pred HHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCC---CCCHHHHHHHHHHH
Q 041165 22 DHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRG---AFTEDEEDQIIQLH 82 (85)
Q Consensus 22 D~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~---~wt~eEd~~L~~~v 82 (85)
+..+++-.-.+| .+...+..+|| -|...|..| +.+|.-....| .-|++++..|-..-
T Consensus 76 ~~~~idr~L~lG-AS~~mm~~~FG--ls~~ev~~r-R~llgi~~~~GR~~~~~ee~~~~iW~~W 135 (180)
T PF11198_consen 76 EQQLIDRALRLG-ASIEMMQRLFG--LSSAEVAAR-RRLLGIPVRKGRPPALSEEEEAAIWRRW 135 (180)
T ss_pred HHHHHHHHHHcC-CCHHHHHHHHC--CCHHHHHHH-HHHhCCCCCCCCCCCcCHHHHHHHHHHH
Confidence 344555555668 79999999999 677777665 45554333333 35677776665544
No 139
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=38.88 E-value=1.1e+02 Score=19.90 Aligned_cols=50 Identities=12% Similarity=0.024 Sum_probs=32.4
Q ss_pred HHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHHHH
Q 041165 23 HKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQLH 82 (85)
Q Consensus 23 ~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~~v 82 (85)
+.|+.+-...| -.|..||+.+| ++..-+-.-... ....++++-.+|.++.
T Consensus 11 ~~Ll~AK~~KG-LTwe~IAe~iG--~sevwvaaa~lG-------Q~~ls~e~A~kla~lL 60 (150)
T TIGR00673 11 DALLESKKKKG-LTFADIADGLG--LAEVFVAAALYG-------QAAAPADEARLVGAKL 60 (150)
T ss_pred HHHHHHHHHcC-CCHHHHHHHHC--CCHHHHHHHHhC-------CCCCCHHHHHHHHHHh
Confidence 56677777778 69999999999 777644333322 2345666666665543
No 140
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=38.64 E-value=82 Score=19.43 Aligned_cols=24 Identities=4% Similarity=-0.115 Sum_probs=19.2
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+-..||..+| -+...++.|..+.
T Consensus 130 ~s~~EIA~~l~--is~~tV~~~l~ra 153 (161)
T PRK12528 130 LGYGEIATELG--ISLATVKRYLNKA 153 (161)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHH
Confidence 57899999999 7888888776654
No 141
>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=37.62 E-value=30 Score=18.96 Aligned_cols=16 Identities=25% Similarity=0.225 Sum_probs=12.1
Q ss_pred cCCCCHHHHHHHHHHH
Q 041165 14 RGPWTIEEDHKLMSFI 29 (85)
Q Consensus 14 kg~WT~eED~~L~~~v 29 (85)
..--|||||..+.+..
T Consensus 42 ~~CitpEE~~~I~e~~ 57 (60)
T PF10892_consen 42 GDCITPEEDREILEAT 57 (60)
T ss_pred hccCCHHHHHHHHHHH
Confidence 3446999999988763
No 142
>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=37.58 E-value=82 Score=19.80 Aligned_cols=25 Identities=12% Similarity=0.117 Sum_probs=20.0
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||..+| -+...++.|.++.+
T Consensus 151 ~s~~EIA~~lg--is~~tVk~~l~Rar 175 (183)
T TIGR02999 151 LTVEEIAELLG--VSVRTVERDWRFAR 175 (183)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHHH
Confidence 46899999999 88888888876643
No 143
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=37.54 E-value=97 Score=19.49 Aligned_cols=50 Identities=10% Similarity=0.270 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhCCCCchhhhhhhCCC--CchhhHHHHHHhhhCCCCCCCCCCHHHHHHHH
Q 041165 22 DHKLMSFILNNGIHCWRMVPKLAGLL--RCGKSCRLRWINYLRPDLKRGAFTEDEEDQII 79 (85)
Q Consensus 22 D~~L~~~v~~~g~~~W~~Ia~~~~~~--Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~ 79 (85)
+..|..+|..|| |..++..+..+ -+.-++..-- ++ +++.||..|-.+.+.
T Consensus 21 E~llt~Lvd~YG---Wd~L~~ri~inCF~ndPSi~SSl-Kf----LrkT~WARekvEa~Y 72 (136)
T COG4628 21 ETLLTELVDFYG---WDGLATRIRINCFHNDPSIKSSL-KF----LRKTPWAREKVEALY 72 (136)
T ss_pred HHHHHHHHHHhC---hHHHHhhceeccccCCccHHHHH-HH----HhcCHhHHHHHHHHH
Confidence 467788888888 98888876532 2333333221 12 246788877666543
No 144
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=37.27 E-value=59 Score=16.37 Aligned_cols=45 Identities=20% Similarity=0.176 Sum_probs=33.7
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCc---hhhhhhhCCCCchhhHHHHHHh
Q 041165 13 KRGPWTIEEDHKLMSFILNNGIHCW---RMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~g~~~W---~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
.+..+|++....|......++..+- ..||..+| -+..|+..=|.+
T Consensus 3 ~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~--l~~~qV~~WF~n 50 (59)
T cd00086 3 KRTRFTPEQLEELEKEFEKNPYPSREEREELAKELG--LTERQVKIWFQN 50 (59)
T ss_pred CCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHC--cCHHHHHHHHHH
Confidence 4678999999999999988775554 55666677 788888765544
No 145
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=37.24 E-value=91 Score=18.48 Aligned_cols=69 Identities=12% Similarity=0.254 Sum_probs=43.8
Q ss_pred CCCCHHHHHHHHHHHHHh----CC---CCchhhhhh----hCCCCchhhH-------HHHHHhhhCCCCCCC---CCCHH
Q 041165 15 GPWTIEEDHKLMSFILNN----GI---HCWRMVPKL----AGLLRCGKSC-------RLRWINYLRPDLKRG---AFTED 73 (85)
Q Consensus 15 g~WT~eED~~L~~~v~~~----g~---~~W~~Ia~~----~~~~Rt~~qc-------r~Rw~~~l~~~~~~~---~wt~e 73 (85)
..||++++-.|++++..| |. .++..+-.. +...=|..|. +.||.+.... ...| +++..
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k-~~~g~~~~~~~~ 83 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK-SKNGKDPSFSKP 83 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh-cccCcCCCCCCH
Confidence 469999999999988766 53 345444333 3322344554 4566666554 2223 68889
Q ss_pred HHHHHHHHHHh
Q 041165 74 EEDQIIQLHSL 84 (85)
Q Consensus 74 Ed~~L~~~v~~ 84 (85)
-|..+.++-..
T Consensus 84 hd~~~f~Lsk~ 94 (98)
T PF04504_consen 84 HDRRLFELSKK 94 (98)
T ss_pred hHHHHHHHHHH
Confidence 99998887653
No 146
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=37.00 E-value=88 Score=18.99 Aligned_cols=25 Identities=8% Similarity=-0.102 Sum_probs=19.5
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+-..||..+| -|...++.+-.+.+
T Consensus 123 ~s~~EIA~~l~--is~~tV~~~~~ra~ 147 (154)
T PRK06759 123 KTMGEIALETE--MTYYQVRWIYRQAL 147 (154)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 46789999998 88888888766544
No 147
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=36.94 E-value=85 Score=19.91 Aligned_cols=24 Identities=8% Similarity=0.004 Sum_probs=19.1
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+-..||..|| .+...++.+-...
T Consensus 146 ~s~~EIA~~l~--is~~tV~~~l~ra 169 (181)
T PRK12536 146 LSVAETAQLTG--LSESAVKVGIHRG 169 (181)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHH
Confidence 57899999999 8888888776654
No 148
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=36.87 E-value=87 Score=19.28 Aligned_cols=25 Identities=8% Similarity=0.123 Sum_probs=18.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||+.+| -|...++.+-...+
T Consensus 139 ~s~~eIA~~l~--is~~tv~~~l~ra~ 163 (170)
T TIGR02952 139 LPIAEVARILG--KTEGAVKILQFRAI 163 (170)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 46789999998 77777877765543
No 149
>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=36.76 E-value=86 Score=19.68 Aligned_cols=25 Identities=16% Similarity=0.312 Sum_probs=19.0
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+-..||..+| -|...++.+..+.+
T Consensus 157 ~s~~eIA~~lg--is~~~v~~~l~Ra~ 181 (189)
T TIGR02984 157 LSFAEVAERMD--RSEGAVSMLWVRGL 181 (189)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHH
Confidence 47789999999 77788877766543
No 150
>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=36.50 E-value=21 Score=21.85 Aligned_cols=25 Identities=4% Similarity=0.041 Sum_probs=19.8
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+...||..+| -|...++.+.....
T Consensus 122 ~s~~eIA~~lg--is~~tv~~~l~Ra~ 146 (154)
T TIGR02950 122 FSYKEIAELLN--LSLAKVKSNLFRAR 146 (154)
T ss_pred CcHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 46899999999 77888888876643
No 151
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=36.49 E-value=88 Score=19.66 Aligned_cols=25 Identities=8% Similarity=-0.045 Sum_probs=19.9
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+=..||..|| .|...++.+..+.+
T Consensus 146 ~s~~eIA~~lg--is~~tV~~~l~Rar 170 (179)
T PRK12514 146 LSYKELAERHD--VPLNTMRTWLRRSL 170 (179)
T ss_pred CCHHHHHHHHC--CChHHHHHHHHHHH
Confidence 46789999999 88888888876643
No 152
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=36.37 E-value=89 Score=19.46 Aligned_cols=24 Identities=8% Similarity=0.068 Sum_probs=18.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+-..||..+| -|...++.+-.+.
T Consensus 129 ~s~~eIA~~lg--is~~tV~~~l~Ra 152 (164)
T PRK12547 129 FSYEDAAAICG--CAVGTIKSRVSRA 152 (164)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHH
Confidence 56789999999 7788887776654
No 153
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=36.21 E-value=74 Score=20.64 Aligned_cols=24 Identities=8% Similarity=0.094 Sum_probs=18.4
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+...||..+| -|...++.+....
T Consensus 130 ~s~~EIA~~Lg--iS~~tVk~~l~Ra 153 (188)
T PRK12546 130 FSYEEAAEMCG--VAVGTVKSRANRA 153 (188)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHH
Confidence 57899999999 6777777766554
No 154
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=35.88 E-value=36 Score=22.79 Aligned_cols=24 Identities=8% Similarity=-0.026 Sum_probs=18.7
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.+-..||+.+| -|..+++.+....
T Consensus 166 ~s~~EIAe~lg--is~~tVk~~l~Ra 189 (231)
T PRK11922 166 LSVEETAQALG--LPEETVKTRLHRA 189 (231)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHH
Confidence 56799999999 7788777776643
No 155
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=35.74 E-value=81 Score=20.20 Aligned_cols=25 Identities=12% Similarity=-0.023 Sum_probs=19.9
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-.-..||..+| -|...++.|....+
T Consensus 147 ~s~~EIA~~lg--is~~tVk~~l~Rar 171 (185)
T PRK09649 147 LSYADAAAVCG--CPVGTIRSRVARAR 171 (185)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 46799999999 78888888876643
No 156
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=34.86 E-value=86 Score=20.09 Aligned_cols=24 Identities=4% Similarity=-0.031 Sum_probs=19.2
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.+-..||+.+| -|...++.|..+.
T Consensus 153 ~s~~EIA~~lg--is~~tVk~~l~Ra 176 (195)
T PRK12532 153 FSSDEIQQMCG--ISTSNYHTIMHRA 176 (195)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHH
Confidence 46799999999 7888888877654
No 157
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=34.63 E-value=95 Score=20.02 Aligned_cols=23 Identities=9% Similarity=0.131 Sum_probs=17.7
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
-+...||+.|| -|...++.|-.+
T Consensus 133 ~s~~EIA~~Lg--is~~tVk~~l~R 155 (187)
T PRK12516 133 FAYEEAAEICG--CAVGTIKSRVNR 155 (187)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHH
Confidence 57899999999 677777766554
No 158
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=34.48 E-value=84 Score=19.93 Aligned_cols=24 Identities=0% Similarity=-0.319 Sum_probs=18.0
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.+-..||+.+| -|...++.+.+..
T Consensus 145 ~s~~EIA~~lg--is~~tV~~~l~Ra 168 (186)
T PRK05602 145 LSNIEAAAVMD--ISVDALESLLARG 168 (186)
T ss_pred CCHHHHHHHhC--cCHHHHHHHHHHH
Confidence 57889999998 6777777665554
No 159
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=34.44 E-value=94 Score=20.21 Aligned_cols=24 Identities=4% Similarity=-0.097 Sum_probs=19.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.+-..||..+| .|...++.|..+.
T Consensus 156 ~s~~EIA~~lg--is~~tVk~~l~RA 179 (201)
T PRK12545 156 FEIDDICTELT--LTANHCSVLLYRA 179 (201)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHH
Confidence 46799999999 7888888876654
No 160
>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=34.37 E-value=91 Score=19.16 Aligned_cols=25 Identities=16% Similarity=0.017 Sum_probs=19.7
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+=..||..+| -|...++.+..+.+
T Consensus 127 ~s~~eIA~~lg--is~~tV~~~l~ra~ 151 (162)
T TIGR02983 127 LSEAQVAEALG--ISVGTVKSRLSRAL 151 (162)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHHH
Confidence 46789999999 77888888776654
No 161
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=34.25 E-value=55 Score=24.79 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=20.3
Q ss_pred HHHHhhhCCCCCCCCCCHHHHHHHHHHHHhC
Q 041165 55 LRWINYLRPDLKRGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 55 ~Rw~~~l~~~~~~~~wt~eEd~~L~~~v~~~ 85 (85)
+-|..+|+ ...||.+|-..|+.+...|
T Consensus 122 eEYe~~l~----dn~WskeETD~LF~lck~f 148 (445)
T KOG2656|consen 122 EEYEAHLN----DNSWSKEETDYLFDLCKRF 148 (445)
T ss_pred HHHHHhhc----cccccHHHHHHHHHHHHhc
Confidence 34555554 3679999999999998765
No 162
>smart00583 SPK domain in SET and PHD domain containing proteins and protein kinases.
Probab=34.22 E-value=69 Score=19.59 Aligned_cols=34 Identities=18% Similarity=0.314 Sum_probs=27.1
Q ss_pred CCCchhhHHHHHHhhhCCCCCC-CCCCHHHHHHHH
Q 041165 46 LLRCGKSCRLRWINYLRPDLKR-GAFTEDEEDQII 79 (85)
Q Consensus 46 ~~Rt~~qcr~Rw~~~l~~~~~~-~~wt~eEd~~L~ 79 (85)
..++....+.||++.|.|++.. ..++.++-..++
T Consensus 37 ~~~s~~~~~~rf~~~Lap~i~~~~~y~~~~kirm~ 71 (114)
T smart00583 37 SLLSYETYYKRFHNKLAPNMIKLNNYSIEERIRMM 71 (114)
T ss_pred CcccHHHHHHHHHHHHHhhHhhccCCCHHHHHHHH
Confidence 4589999999999999998776 678877766554
No 163
>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=34.10 E-value=12 Score=21.29 Aligned_cols=15 Identities=13% Similarity=0.308 Sum_probs=12.2
Q ss_pred HhCCCCchhhhhhhCC
Q 041165 31 NNGIHCWRMVPKLAGL 46 (85)
Q Consensus 31 ~~g~~~W~~Ia~~~~~ 46 (85)
..| ++|..+|..+|-
T Consensus 14 ~~g-~DWr~LA~~Lg~ 28 (79)
T cd08312 14 VVA-ADWTALAEEMGF 28 (79)
T ss_pred Ccc-cCHHHHHHHcCC
Confidence 345 799999999993
No 164
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=34.03 E-value=97 Score=19.66 Aligned_cols=25 Identities=8% Similarity=0.138 Sum_probs=19.5
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||..+| -|...++.|..+.+
T Consensus 139 ~s~~EIA~~lg--is~~tVk~~l~Rar 163 (185)
T PRK12542 139 LTYQEISSVMG--ITEANVRKQFERAR 163 (185)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 56799999999 78888888766543
No 165
>PRK00118 putative DNA-binding protein; Validated
Probab=33.87 E-value=1.1e+02 Score=18.50 Aligned_cols=38 Identities=5% Similarity=-0.030 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHh
Q 041165 19 IEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
++.+..++.+....| .....||+.+| -|...++.+...
T Consensus 19 ~ekqRevl~L~y~eg-~S~~EIAe~lG--IS~~TV~r~L~R 56 (104)
T PRK00118 19 TEKQRNYMELYYLDD-YSLGEIAEEFN--VSRQAVYDNIKR 56 (104)
T ss_pred CHHHHHHHHHHHHcC-CCHHHHHHHHC--cCHHHHHHHHHH
Confidence 445566666666666 68999999999 666666655443
No 166
>PF15603 Imm45: Immunity protein 45
Probab=33.59 E-value=58 Score=18.97 Aligned_cols=24 Identities=21% Similarity=0.238 Sum_probs=19.6
Q ss_pred hCCCCCCCCCCHHHHHHHHHHHHh
Q 041165 61 LRPDLKRGAFTEDEEDQIIQLHSL 84 (85)
Q Consensus 61 l~~~~~~~~wt~eEd~~L~~~v~~ 84 (85)
..|.....|.|..|-+.+++++..
T Consensus 47 We~P~e~~~it~~e~q~II~aI~~ 70 (82)
T PF15603_consen 47 WEPPHENEPITIAERQKIIEAIEK 70 (82)
T ss_pred ccCCCCCcccCHHHHHHHHHHHHH
Confidence 345566779999999999999875
No 167
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=33.25 E-value=80 Score=16.64 Aligned_cols=35 Identities=17% Similarity=0.403 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHH
Q 041165 19 IEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRW 57 (85)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw 57 (85)
..+++..+.+..+.| -.=..||..++ |+-. |-.+|
T Consensus 6 t~~Eqaqid~m~qlG-~s~~~isr~i~--RSr~-~Ir~y 40 (50)
T PF11427_consen 6 TDAEQAQIDVMHQLG-MSLREISRRIG--RSRT-CIRRY 40 (50)
T ss_dssp -HHHHHHHHHHHHTT---HHHHHHHHT----HH-HHHHH
T ss_pred CHHHHHHHHHHHHhc-hhHHHHHHHhC--ccHH-HHHHH
Confidence 345566777777778 58899999999 7764 33444
No 168
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=33.21 E-value=1.1e+02 Score=19.36 Aligned_cols=25 Identities=20% Similarity=0.028 Sum_probs=18.7
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+=..||..+| -|...++.+.++.+
T Consensus 152 ~s~~eIA~~lg--is~~~V~~~l~ra~ 176 (186)
T PRK13919 152 YTHREAAQLLG--LPLGTLKTRARRAL 176 (186)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHH
Confidence 45688999999 77788877766543
No 169
>PF11216 DUF3012: Protein of unknown function (DUF3012); InterPro: IPR021379 This family of proteins with unknown function is restricted to Gammaproteobacteria.
Probab=33.17 E-value=24 Score=17.03 Aligned_cols=14 Identities=29% Similarity=0.594 Sum_probs=10.2
Q ss_pred CCCcCCCCHHHHHH
Q 041165 11 GLKRGPWTIEEDHK 24 (85)
Q Consensus 11 ~~~kg~WT~eED~~ 24 (85)
...||.||.+|-.-
T Consensus 12 ~kpK~dWtanea~~ 25 (32)
T PF11216_consen 12 EKPKGDWTANEAAD 25 (32)
T ss_pred hCCcccCcHhHHHH
Confidence 34589999998553
No 170
>COG2901 Fis Factor for inversion stimulation Fis, transcriptional activator [Transcription / DNA replication, recombination, and repair]
Probab=32.52 E-value=56 Score=19.64 Aligned_cols=31 Identities=13% Similarity=0.171 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhhCCCCch
Q 041165 20 EEDHKLMSFILNNGIHCWRMVPKLAGLLRCG 50 (85)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~ 50 (85)
|=++=|+..|.+|-.+|-+.-|.++|.+|..
T Consensus 57 evE~PLL~~vM~~~~gNQtrAa~mLGinR~T 87 (98)
T COG2901 57 EVEQPLLDMVMQYTRGNQTRAALMLGINRGT 87 (98)
T ss_pred HHHhHHHHHHHHHhcccHHHHHHHHcccHHH
Confidence 3456678888888778999999999977754
No 171
>PF06892 Phage_CP76: Phage regulatory protein CII (CP76); InterPro: IPR009679 This entry is represented by Bacteriophage 186, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several phage regulatory protein CII (CP76) sequences which are thought to be DNA binding proteins which are involved in the establishment of lysogeny [].
Probab=32.01 E-value=1.5e+02 Score=19.29 Aligned_cols=50 Identities=20% Similarity=0.145 Sum_probs=33.3
Q ss_pred HHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHHHH
Q 041165 23 HKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQLH 82 (85)
Q Consensus 23 ~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~~v 82 (85)
+.....+..| +=..||..+| -+.. -.+|.|+|+. .-..|..|-..|.++-
T Consensus 12 ~Ac~~fa~~h---~~~~lA~~lG--m~~~----~LrNKLNP~q-~H~Lt~~el~~i~~~T 61 (162)
T PF06892_consen 12 EACRAFAKNH---NMAALAERLG--MNPQ----TLRNKLNPEQ-PHKLTVDELIAITDAT 61 (162)
T ss_pred HHHHHHHHhc---CHHHHHHHhC--CCHH----HHHHHcCCCC-CCCCCHHHHHHHHHHh
Confidence 3334444444 4589999999 5553 4566689984 4578998887777653
No 172
>KOG3493 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=31.37 E-value=52 Score=18.62 Aligned_cols=28 Identities=14% Similarity=0.406 Sum_probs=22.6
Q ss_pred hhhhhhhCCCCchhhHHHHHHhhhCCCCC
Q 041165 38 RMVPKLAGLLRCGKSCRLRWINYLRPDLK 66 (85)
Q Consensus 38 ~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~ 66 (85)
+.||...| ++-.+..-.+|..+++..+.
T Consensus 29 KliaaQtG-T~~~kivl~k~~~i~kd~I~ 56 (73)
T KOG3493|consen 29 KLIAAQTG-TRPEKIVLKKWYTIFKDHIT 56 (73)
T ss_pred HHHHHhhC-CChhHhHHHhhhhhhhcccc
Confidence 56777788 59999999999999877654
No 173
>PF11084 DUF2621: Protein of unknown function (DUF2621); InterPro: IPR020203 This entry represents a group of uncharacterised proteins.
Probab=30.73 E-value=44 Score=21.41 Aligned_cols=27 Identities=26% Similarity=0.313 Sum_probs=20.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhh
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVP 41 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia 41 (85)
+.-||.|+-+.|-++|.-.+ .-...||
T Consensus 56 rhlW~de~K~lL~eLV~PVP-elFRdvA 82 (141)
T PF11084_consen 56 RHLWTDEQKALLEELVSPVP-ELFRDVA 82 (141)
T ss_pred HhhcCHHHHHHHHHHhhcCc-HHHHHHH
Confidence 56799999999999998776 3444433
No 174
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=30.03 E-value=89 Score=19.92 Aligned_cols=25 Identities=16% Similarity=-0.071 Sum_probs=18.5
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+=..||..+| -|...++.+..+.+
T Consensus 158 ~s~~EIA~~lg--is~~tV~~~l~Ra~ 182 (194)
T PRK12519 158 LSQSEIAKRLG--IPLGTVKARARQGL 182 (194)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHHH
Confidence 46688999999 67777777766544
No 175
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=29.90 E-value=1.1e+02 Score=19.44 Aligned_cols=25 Identities=8% Similarity=0.112 Sum_probs=19.1
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+=..||..+| -+...++.|....+
T Consensus 144 ~s~~EIA~~l~--is~~tv~~~l~Ra~ 168 (179)
T PRK09415 144 LSIKEIAEVTG--VNENTVKTRLKKAK 168 (179)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 45688888888 68888888876654
No 176
>PF07325 Curto_V2: Curtovirus V2 protein; InterPro: IPR009931 This family consists of several Curtovirus V2 proteins. The exact function of V2 is unclear but it is known that the protein is required for a successful host infection process [].
Probab=29.69 E-value=84 Score=19.54 Aligned_cols=35 Identities=20% Similarity=0.347 Sum_probs=24.7
Q ss_pred hhhHHHHHHhhhCCCC--CCCCCCHHHHHHHHHHHHh
Q 041165 50 GKSCRLRWINYLRPDL--KRGAFTEDEEDQIIQLHSL 84 (85)
Q Consensus 50 ~~qcr~Rw~~~l~~~~--~~~~wt~eEd~~L~~~v~~ 84 (85)
..+|.-||++-.--.+ .-.|.|-||-+..++.+.+
T Consensus 20 sTSCflrYNkwCilGi~~eie~LtlEeGE~FLqFQKe 56 (126)
T PF07325_consen 20 STSCFLRYNKWCILGIHPEIEPLTLEEGEVFLQFQKE 56 (126)
T ss_pred HhHHHHhhchhheecccccccccchhhhHHHHHHHHH
Confidence 3589999888432222 2379999999888887654
No 177
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=29.50 E-value=1.3e+02 Score=19.16 Aligned_cols=24 Identities=13% Similarity=-0.057 Sum_probs=18.4
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+=..||+.+| -|...++.|-...
T Consensus 148 ~s~~EIAe~lg--is~~~V~~~l~Ra 171 (189)
T PRK06811 148 EKIEEIAKKLG--LTRSAIDNRLSRG 171 (189)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHH
Confidence 46688999999 7778888776654
No 178
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=29.31 E-value=50 Score=25.58 Aligned_cols=19 Identities=5% Similarity=0.066 Sum_probs=16.6
Q ss_pred CCCCCHHHHHHHHHHHHhC
Q 041165 67 RGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 67 ~~~wt~eEd~~L~~~v~~~ 85 (85)
..+||.+|..+|++.++.|
T Consensus 279 dk~WS~qE~~LLLEGIe~y 297 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMY 297 (531)
T ss_pred cccccHHHHHHHHHHHHHh
Confidence 4489999999999998865
No 179
>KOG1724 consensus SCF ubiquitin ligase, Skp1 component [Posttranslational modification, protein turnover, chaperones]
Probab=28.98 E-value=83 Score=20.61 Aligned_cols=33 Identities=21% Similarity=0.256 Sum_probs=23.2
Q ss_pred hhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHH
Q 041165 38 RMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQI 78 (85)
Q Consensus 38 ~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L 78 (85)
+.||.++-| +|+.++|.-| ++ ...+|++|+..+
T Consensus 121 k~va~mikg-ktpeEir~~f-~I------~~d~t~eE~~~~ 153 (162)
T KOG1724|consen 121 KTVANMIKG-KTPEEIREIF-NI------ENDETPEEEEAI 153 (162)
T ss_pred HHHHHHHcc-CCHHHHHHHc-CC------CCCCChhHHHHH
Confidence 678888874 9999999984 33 334777776443
No 180
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=28.79 E-value=84 Score=15.49 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=15.1
Q ss_pred HHHHHHHHhCCCCchhhhhhhCCCCchhhH
Q 041165 24 KLMSFILNNGIHCWRMVPKLAGLLRCGKSC 53 (85)
Q Consensus 24 ~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc 53 (85)
.++.++.. | .....||+.+| -|...+
T Consensus 9 ~ii~l~~~-G-~s~~~ia~~lg--vs~~Tv 34 (50)
T PF13384_consen 9 QIIRLLRE-G-WSIREIAKRLG--VSRSTV 34 (50)
T ss_dssp -HHHHHHH-T---HHHHHHHHT--S-HHHH
T ss_pred HHHHHHHC-C-CCHHHHHHHHC--cCHHHH
Confidence 34555555 7 68999999999 444433
No 181
>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=28.68 E-value=1.1e+02 Score=21.25 Aligned_cols=24 Identities=13% Similarity=-0.061 Sum_probs=19.2
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+-..||+.+| .|...++.|..+.
T Consensus 159 ~s~~EIA~~lg--is~~tV~~~l~Ra 182 (324)
T TIGR02960 159 WRAAETAELLG--TSTASVNSALQRA 182 (324)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHH
Confidence 46799999999 8888888876653
No 182
>PF11784 DUF3320: Protein of unknown function (DUF3320); InterPro: IPR021754 This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins.
Probab=28.65 E-value=77 Score=16.52 Aligned_cols=32 Identities=25% Similarity=0.288 Sum_probs=20.1
Q ss_pred HHHHHHHhCCCCc----hhhhhhhCCCCchhhHHHH
Q 041165 25 LMSFILNNGIHCW----RMVPKLAGLLRCGKSCRLR 56 (85)
Q Consensus 25 L~~~v~~~g~~~W----~~Ia~~~~~~Rt~~qcr~R 56 (85)
+.++|..-|+-.. ..|+...|-.|++..+++|
T Consensus 17 i~~Iv~~EgPI~~~~L~~Ri~~a~G~~R~G~rI~~r 52 (52)
T PF11784_consen 17 IRQIVEVEGPIHEDELARRIARAWGLSRAGSRIRER 52 (52)
T ss_pred HHHHHHHcCCccHHHHHHHHHHHcCcccchHHHhcC
Confidence 3445555576555 4555556777888887764
No 183
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=28.53 E-value=1.4e+02 Score=19.15 Aligned_cols=24 Identities=13% Similarity=-0.022 Sum_probs=17.8
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+-..||+.+| -+...++.+-.+.
T Consensus 159 ~s~~EIA~~Lg--is~~tVk~~l~ra 182 (194)
T PRK09646 159 LTYREVAERLA--VPLGTVKTRMRDG 182 (194)
T ss_pred CCHHHHHHHhC--CChHhHHHHHHHH
Confidence 46788999998 6777777765554
No 184
>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=28.40 E-value=1.2e+02 Score=18.11 Aligned_cols=18 Identities=22% Similarity=0.403 Sum_probs=14.1
Q ss_pred HHHHHhCCCCchhhhhhhC
Q 041165 27 SFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 27 ~~v~~~g~~~W~~Ia~~~~ 45 (85)
......| .+|+.++..+|
T Consensus 7 ~~~~nvG-r~WK~laR~Lg 24 (90)
T cd08780 7 HFAKSVG-KKWKPVGRSLQ 24 (90)
T ss_pred HHHHHHh-HHHHHHHHHHc
Confidence 3445557 79999999999
No 185
>PHA00442 host recBCD nuclease inhibitor
Probab=28.23 E-value=49 Score=18.00 Aligned_cols=37 Identities=22% Similarity=0.532 Sum_probs=26.9
Q ss_pred CCCCCCcCCC--------CHHHHHHHHHHHHHhCCCCchhhhhhh
Q 041165 8 DKVGLKRGPW--------TIEEDHKLMSFILNNGIHCWRMVPKLA 44 (85)
Q Consensus 8 ~k~~~~kg~W--------T~eED~~L~~~v~~~g~~~W~~Ia~~~ 44 (85)
+...+.+-.| +-|-+...+.+....|..||.-+...+
T Consensus 6 d~VtitRd~wnd~q~yidsLek~~~~L~~Lea~GVDNW~Gy~eA~ 50 (59)
T PHA00442 6 DLVTITRDAWNDMQGYIDSLEKDNEFLKALRACGVDNWDGYMDAV 50 (59)
T ss_pred cceeecHHHHHHHHHHHHHHHHhhHHHHHHHHcCCcchhhHHHHH
Confidence 4445566667 556677788888999999998877653
No 186
>PRK10365 transcriptional regulatory protein ZraR; Provisional
Probab=28.19 E-value=58 Score=23.62 Aligned_cols=30 Identities=13% Similarity=0.152 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhCCCCchhhhhhhCCCCch
Q 041165 20 EEDHKLMSFILNNGIHCWRMVPKLAGLLRCG 50 (85)
Q Consensus 20 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~ 50 (85)
-|.+.+..+...++ +|....|+.+|.+|+.
T Consensus 405 ~e~~~i~~~l~~~~-gn~~~aa~~Lgisr~t 434 (441)
T PRK10365 405 VEKEVILAALEKTG-GNKTEAARQLGITRKT 434 (441)
T ss_pred HHHHHHHHHHHHhC-CCHHHHHHHhCCCHHH
Confidence 35566777888888 7999999999977765
No 187
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.13 E-value=1.5e+02 Score=18.80 Aligned_cols=25 Identities=8% Similarity=-0.074 Sum_probs=19.1
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+=..||+.+| -|...++.+..+.+
T Consensus 150 ~s~~eIA~~lg--is~~tV~~~l~ra~ 174 (182)
T PRK12537 150 CSHAEIAQRLG--APLGTVKAWIKRSL 174 (182)
T ss_pred CCHHHHHHHHC--CChhhHHHHHHHHH
Confidence 46688998888 77778888777654
No 188
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=28.01 E-value=49 Score=20.73 Aligned_cols=24 Identities=8% Similarity=0.005 Sum_probs=17.4
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+-..||..+| -+...++.+..+.
T Consensus 143 ~s~~eIA~~l~--is~~~V~~~l~ra 166 (176)
T PRK09638 143 YTYEEIAKMLN--IPEGTVKSRVHHG 166 (176)
T ss_pred CCHHHHHHHHC--CChhHHHHHHHHH
Confidence 46789999999 5777676665543
No 189
>PF15586 Imm47: Immunity protein 47
Probab=28.01 E-value=52 Score=20.28 Aligned_cols=22 Identities=9% Similarity=0.116 Sum_probs=16.7
Q ss_pred HHHHHHHHhCCCCchhhhhhhC
Q 041165 24 KLMSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 24 ~L~~~v~~~g~~~W~~Ia~~~~ 45 (85)
.|-+++..+...+|..||+.++
T Consensus 84 ~i~~~i~~c~~~~W~~~~~kLs 105 (116)
T PF15586_consen 84 TIERIIESCEGDDWDEIAEKLS 105 (116)
T ss_pred HHHHHHHHccCCCHHHHHHHHH
Confidence 4455667776689999998887
No 190
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=27.97 E-value=1.5e+02 Score=19.51 Aligned_cols=25 Identities=12% Similarity=-0.045 Sum_probs=18.7
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+=..||+.|| -+...++.+....+
T Consensus 155 ~s~~EIA~~Lg--is~~tV~~~l~RAr 179 (203)
T PRK09647 155 LSYEEIAATLG--VKLGTVRSRIHRGR 179 (203)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 46789999999 77777777766543
No 191
>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=27.94 E-value=37 Score=22.60 Aligned_cols=28 Identities=21% Similarity=0.405 Sum_probs=24.0
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhh
Q 041165 16 PWTIEEDHKLMSFILNNGIHCWRMVPKL 43 (85)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~ 43 (85)
-|-..-|--|+..|..||...|..|..-
T Consensus 5 iw~r~hdywll~gi~~hgy~rwqdi~nd 32 (173)
T PF08074_consen 5 IWHRRHDYWLLAGIVKHGYGRWQDIQND 32 (173)
T ss_pred hhhhhhhHHHHhHHhhccchhHHHHhcC
Confidence 3777888999999999999999988754
No 192
>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=27.77 E-value=1.4e+02 Score=19.68 Aligned_cols=25 Identities=8% Similarity=-0.097 Sum_probs=18.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
..-..||+.+| -|...++.+....+
T Consensus 195 ~s~~eIA~~lg--is~~~v~~~~~ra~ 219 (227)
T TIGR02980 195 KTQSEIAERLG--ISQMHVSRLLRRAL 219 (227)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHH
Confidence 46789999998 77777777765543
No 193
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=27.75 E-value=1.9e+02 Score=20.39 Aligned_cols=25 Identities=8% Similarity=-0.142 Sum_probs=20.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||..+| -|...++.|..+-+
T Consensus 170 ~s~~EIA~~lg--is~~tVk~~l~RAr 194 (339)
T PRK08241 170 WSAAEVAELLD--TSVAAVNSALQRAR 194 (339)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHHH
Confidence 46799999999 88899988877644
No 194
>cd08310 Death_NFkB-like Death domain of Nuclear Factor-KappaB precursor proteins. Death Domain (DD) of Nuclear Factor-KappaB (NF-kB) precursor proteins. The NF-kB family of transcription factors play a central role in cardiovascular growth, stress response, and inflammation by controlling the expression of a network of different genes. There are five NF-kB proteins, all containing an N-terminal REL Homology Domain (RHD). Two of these, NF-kB1 and NF-kB2 are produced from the processing of the precursor proteins p105 and p100, respectively. In addition to RHD, p105 and p100 contain ANK repeats and a C-terminal DD. NF-kBs are regulated by the Inhibitor of NF-kB (IkB) Kinase (IKK) complex through classical and non-canonical pathways, which differ in the IKK subunits involved and downstream targets. IKKs facilitate the release of NF-kB dimers from an inactive state, allowing them to migrate to the nucleus where they regulate gene transcription. The precursor proteins p105 and p100 function
Probab=27.59 E-value=43 Score=18.80 Aligned_cols=13 Identities=38% Similarity=0.756 Sum_probs=11.4
Q ss_pred CCCCchhhhhhhCC
Q 041165 33 GIHCWRMVPKLAGL 46 (85)
Q Consensus 33 g~~~W~~Ia~~~~~ 46 (85)
| .+|..+|+.+|.
T Consensus 12 ~-~dWr~LA~~L~~ 24 (72)
T cd08310 12 G-CDWRELAQLLDL 24 (72)
T ss_pred C-CCHHHHHHHcCc
Confidence 5 799999999984
No 195
>PF09019 EcoRII-C: EcoRII C terminal; InterPro: IPR015109 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the C-terminal catalytic domain of the type II restriction endonuclease EcoRII, which has a restriction endonuclease-like fold with a central five-stranded mixed beta-sheet surrounded on both sides by alpha-helices. EcoRII cleaves DNA specifically at single 5' CCWGG sites []. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 3HQG_A 1NA6_A 2GB7_C 2FQZ_A 3BM3_B.
Probab=27.57 E-value=9.4 Score=25.19 Aligned_cols=12 Identities=25% Similarity=0.534 Sum_probs=9.1
Q ss_pred hhHHHHHHhhhC
Q 041165 51 KSCRLRWINYLR 62 (85)
Q Consensus 51 ~qcr~Rw~~~l~ 62 (85)
..||+||+.+++
T Consensus 96 TTlkdRWrQVl~ 107 (164)
T PF09019_consen 96 TTLKDRWRQVLN 107 (164)
T ss_dssp SS-TTGCGHHHH
T ss_pred ccHHHHHHHHHH
Confidence 479999999874
No 196
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=27.13 E-value=1.5e+02 Score=18.69 Aligned_cols=24 Identities=0% Similarity=-0.223 Sum_probs=16.9
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+-..||..+| =|...++.+-.+.
T Consensus 154 ~s~~eIA~~lg--is~~~v~~~l~Ra 177 (187)
T PRK12534 154 ITYEELAARTD--TPIGTVKSWIRRG 177 (187)
T ss_pred CCHHHHHHHhC--CChhHHHHHHHHH
Confidence 46788888888 6666776665543
No 197
>PF05546 She9_MDM33: She9 / Mdm33 family; InterPro: IPR008839 Members of this family are mitochondrial inner membrane proteins with a role in inner mitochondrial membrane organisation and biogenesis []. The yeast Mdm33 protein assembles into an oligomeric complex in the inner membrane where it performs homotypic protein-protein interactions. It has been suggested that Mdm33 plays a distinct role, possibly involved in fission of the mitochondrial inner membrane [].
Probab=27.09 E-value=68 Score=21.99 Aligned_cols=20 Identities=10% Similarity=0.434 Sum_probs=17.2
Q ss_pred CcCCCCHHHHHHHHHHHHHh
Q 041165 13 KRGPWTIEEDHKLMSFILNN 32 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~ 32 (85)
+|..|||.+.+++..++..-
T Consensus 82 RK~sWs~~DleRFT~Lyr~d 101 (207)
T PF05546_consen 82 RKHSWSPADLERFTELYRND 101 (207)
T ss_pred cccCCChHHHHHHHHHHHhh
Confidence 57899999999999998643
No 198
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=26.95 E-value=1e+02 Score=15.87 Aligned_cols=41 Identities=15% Similarity=0.075 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 16 PWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 16 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
..|+.|-+.|.-+.. | .+=..||..++ .+...++.+..+.+
T Consensus 3 ~LT~~E~~vl~~l~~--G-~~~~eIA~~l~--is~~tV~~~~~~i~ 43 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--G-MSNKEIAEELG--ISEKTVKSHRRRIM 43 (58)
T ss_dssp SS-HHHHHHHHHHHT--T-S-HHHHHHHHT--SHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--c-CCcchhHHhcC--cchhhHHHHHHHHH
Confidence 356777665554433 4 46789999999 88888888777654
No 199
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=26.82 E-value=1.5e+02 Score=17.86 Aligned_cols=46 Identities=17% Similarity=0.262 Sum_probs=32.9
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 12 LKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 12 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.++..||+|+-...+..+...| .+=..||..+|. +..+ -.+|.+..
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI--s~~t-l~~W~r~y 53 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV--AASQ-LFLWRKQY 53 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc--CHHH-HHHHHHHH
Confidence 3457899999887777777767 577899999994 4444 45676654
No 200
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=26.78 E-value=1.4e+02 Score=20.22 Aligned_cols=25 Identities=4% Similarity=-0.129 Sum_probs=19.8
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
..-..||..+| -|...++.+....+
T Consensus 218 ~s~~EIA~~lg--is~~tV~~~~~ra~ 242 (251)
T PRK07670 218 LTLTEIGQVLN--LSTSRISQIHSKAL 242 (251)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHH
Confidence 56799999999 78888888776544
No 201
>PF05373 Pro_3_hydrox_C: L-proline 3-hydroxylase, C-terminal; InterPro: IPR008035 Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes. Proline 3-hydroxylase hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure contains conserved motifs present in other 2-OG oxygenases including a jelly roll strand core and residues binding iron and 2-oxoglutarate, consistent with divergent evolution within the extended family. The structure differs significantly from many other 2-OG oxygenases in possessing a discrete C-terminal helical domain.; GO: 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process; PDB: 1E5S_A 1E5R_B.
Probab=26.67 E-value=27 Score=21.29 Aligned_cols=35 Identities=23% Similarity=0.224 Sum_probs=23.1
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCchhhhhhhC
Q 041165 11 GLKRGPWTIEEDHKLMSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 11 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~ 45 (85)
-+.+.+||.++-+.|+.+-.-.+..+|..|...+.
T Consensus 19 i~~R~~~t~e~~e~Ll~ls~vis~~n~r~i~~~La 53 (101)
T PF05373_consen 19 IISRPPLTEEERERLLALSAVISRENFRDIVFLLA 53 (101)
T ss_dssp ----EE--HHHHHHHHGGGGT--TTTHHHHHHHHC
T ss_pred ccCCCCCCHHHHHHHHHHHHHhhHHHHHHHHHHHH
Confidence 45578899999999999777777788988887765
No 202
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=26.61 E-value=1.4e+02 Score=18.30 Aligned_cols=25 Identities=4% Similarity=0.131 Sum_probs=18.6
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||..+| -|...++.+-...+
T Consensus 129 ~s~~eIA~~lg--is~~tv~~~l~Rar 153 (161)
T PRK12541 129 FSYKEIAEMTG--LSLAKVKIELHRGR 153 (161)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 45688999999 67777887766543
No 203
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=26.58 E-value=62 Score=16.09 Aligned_cols=18 Identities=28% Similarity=0.484 Sum_probs=13.9
Q ss_pred CCCCCCCCCHHHHHHHHH
Q 041165 63 PDLKRGAFTEDEEDQIIQ 80 (85)
Q Consensus 63 ~~~~~~~wt~eEd~~L~~ 80 (85)
..-+.||+|.+|-..|++
T Consensus 7 ~g~~~GP~s~~el~~l~~ 24 (45)
T PF14237_consen 7 NGQQQGPFSLEELRQLIS 24 (45)
T ss_pred CCeEECCcCHHHHHHHHH
Confidence 345679999999887765
No 204
>PRK11388 DNA-binding transcriptional regulator DhaR; Provisional
Probab=26.28 E-value=1e+02 Score=24.01 Aligned_cols=34 Identities=15% Similarity=0.071 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchh
Q 041165 17 WTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGK 51 (85)
Q Consensus 17 WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~ 51 (85)
...-|-+.+..+...++ +|-++.|+.+|.+|+.-
T Consensus 588 l~~~E~~~i~~al~~~~-gn~~~aA~~LGisR~TL 621 (638)
T PRK11388 588 LAELEKEAIINAAQVCG-GRIQEMAALLGIGRTTL 621 (638)
T ss_pred HHHHHHHHHHHHHHHhC-CCHHHHHHHHCCCHHHH
Confidence 34456677888888888 79999999999777664
No 205
>KOG3200 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.25 E-value=64 Score=21.93 Aligned_cols=27 Identities=30% Similarity=0.377 Sum_probs=18.7
Q ss_pred CCHHHHHHHHHHHHHhCCCCchhhhhh
Q 041165 17 WTIEEDHKLMSFILNNGIHCWRMVPKL 43 (85)
Q Consensus 17 WT~eED~~L~~~v~~~g~~~W~~Ia~~ 43 (85)
=|.||+..++..+..-+...|..++..
T Consensus 21 It~EEe~~~lshIe~ap~pkW~~L~NR 47 (224)
T KOG3200|consen 21 ITEEEENLYLSHIENAPQPKWRVLANR 47 (224)
T ss_pred cChHHHHHHHHHHhcCCCchhHHHHhh
Confidence 366777777777766666789887754
No 206
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=26.18 E-value=1.3e+02 Score=22.72 Aligned_cols=49 Identities=12% Similarity=0.117 Sum_probs=28.7
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCch-------------hhhhh----hCCCCchhhHHHHHHhh
Q 041165 12 LKRGPWTIEEDHKLMSFILNNGIHCWR-------------MVPKL----AGLLRCGKSCRLRWINY 60 (85)
Q Consensus 12 ~~kg~WT~eED~~L~~~v~~~g~~~W~-------------~Ia~~----~~~~Rt~~qcr~Rw~~~ 60 (85)
-..+.|+++=++.++++...|...... .||.+ -|..||.+|+..|-+-+
T Consensus 47 ~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 47 DGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 456789999999999999988654443 34433 25569999999886543
No 207
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=26.06 E-value=1.7e+02 Score=18.67 Aligned_cols=24 Identities=0% Similarity=-0.270 Sum_probs=18.5
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.+=..||..+| -|...++.|..+.
T Consensus 148 ~s~~EIA~~lg--is~~tV~~~l~Ra 171 (191)
T PRK12520 148 LETEEICQELQ--ITATNAWVLLYRA 171 (191)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHH
Confidence 45689999999 7888888776654
No 208
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=26.00 E-value=1.6e+02 Score=18.05 Aligned_cols=25 Identities=8% Similarity=-0.000 Sum_probs=18.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+=..||..+| -|...++.+..+.+
T Consensus 128 ~s~~eIA~~lg--is~~tV~~~i~ra~ 152 (166)
T PRK09639 128 YSYKEIAEALG--IKESSVGTTLARAK 152 (166)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 45688888888 77777777766543
No 209
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. 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=25.59 E-value=52 Score=18.59 Aligned_cols=20 Identities=5% Similarity=-0.014 Sum_probs=14.8
Q ss_pred HHHHHHhCCCCchhhhhhhC
Q 041165 26 MSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 26 ~~~v~~~g~~~W~~Ia~~~~ 45 (85)
..++...+...|+.++..+|
T Consensus 3 ~~v~~~v~~~~Wk~laR~LG 22 (79)
T cd08784 3 FDVFEEVPFDQHKRFFRKLG 22 (79)
T ss_pred HHHHHHCCHHHHHHHHHHcC
Confidence 45566667677999988887
No 210
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=25.52 E-value=95 Score=16.57 Aligned_cols=22 Identities=18% Similarity=0.199 Sum_probs=16.3
Q ss_pred HHHHHHHHHhCCCCchhhhhhhC
Q 041165 23 HKLMSFILNNGIHCWRMVPKLAG 45 (85)
Q Consensus 23 ~~L~~~v~~~g~~~W~~Ia~~~~ 45 (85)
+.|..+|...| ++=..|..+++
T Consensus 35 ~~L~~AV~~vG-~~~~~V~~~L~ 56 (57)
T PF12244_consen 35 EQLREAVRAVG-NSRAAVRAYLG 56 (57)
T ss_pred HHHHHHHHHHC-cCHHHHHHHHc
Confidence 56888888888 56777776665
No 211
>cd08799 Death_UNC5C Death domain found in Uncoordinated-5C. Death Domain (DD) found in Uncoordinated-5C (UNC5C). UNC5C is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5C plays a critical role in the development of spinal accesory motor neurons. Methylation of the UNC5C gene is associated with early stages of colorectal carcinogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN.
Probab=25.24 E-value=35 Score=19.95 Aligned_cols=12 Identities=33% Similarity=0.695 Sum_probs=10.9
Q ss_pred CCchhhhhhhCC
Q 041165 35 HCWRMVPKLAGL 46 (85)
Q Consensus 35 ~~W~~Ia~~~~~ 46 (85)
++|..+|+.||-
T Consensus 21 ~DWr~LAekLgl 32 (84)
T cd08799 21 NDWRMLAHKLNL 32 (84)
T ss_pred CCHHHHHHHcCC
Confidence 699999999995
No 212
>cd08801 Death_UNC5D Death domain found in Uncoordinated-5D. Death Domain (DD) found in Uncoordinated-5D (UNC5D). UNC5D is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=25.05 E-value=31 Score=20.82 Aligned_cols=22 Identities=23% Similarity=0.594 Sum_probs=16.1
Q ss_pred hCCCCchhhhhhhCCCCchhhHHHHHHhhhC
Q 041165 32 NGIHCWRMVPKLAGLLRCGKSCRLRWINYLR 62 (85)
Q Consensus 32 ~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 62 (85)
.| ++|..+|+.++. +||.+|+.
T Consensus 19 kg-~DWR~LA~kL~i--------DRyl~yFa 40 (98)
T cd08801 19 KG-KDWQMLAQKNSI--------DRNLSYFA 40 (98)
T ss_pred CC-ccHHHHHHHhcc--------hhHHHHHh
Confidence 45 799999999885 45555553
No 213
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=24.85 E-value=1.5e+02 Score=19.80 Aligned_cols=25 Identities=4% Similarity=-0.047 Sum_probs=19.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-.-..||..+| -|...++.+..+.+
T Consensus 201 ~s~~EIA~~lg--is~~tV~~~~~ra~ 225 (236)
T PRK06986 201 LNLKEIGAVLG--VSESRVSQIHSQAI 225 (236)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 46799999999 78888887766544
No 214
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=24.79 E-value=1.8e+02 Score=17.98 Aligned_cols=42 Identities=14% Similarity=0.148 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhhCC
Q 041165 19 IEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYLRP 63 (85)
Q Consensus 19 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~ 63 (85)
..||..++.+.-+.. ++-+.+++.+| =|=-.+|.|...++..
T Consensus 35 ~~E~~~Fi~~Fi~~r-GnlKe~e~~lg--iSYPTvR~rLd~ii~~ 76 (113)
T PF09862_consen 35 SPEQLEFIKLFIKNR-GNLKEMEKELG--ISYPTVRNRLDKIIEK 76 (113)
T ss_pred CHHHHHHHHHHHHhc-CCHHHHHHHHC--CCcHHHHHHHHHHHHH
Confidence 356666666666666 69999999999 5666889998887753
No 215
>COG3795 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.74 E-value=40 Score=21.28 Aligned_cols=59 Identities=22% Similarity=0.311 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHHHhCC-----CCchhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHH
Q 041165 15 GPWTIEEDHKLMSFILNNGI-----HCWRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQ 77 (85)
Q Consensus 15 g~WT~eED~~L~~~v~~~g~-----~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~ 77 (85)
..||+++|+.|+.....|.. +.+--.+.+.+ +.++...+-+ -=.+....|||.+--|++
T Consensus 15 ~a~~~e~daalm~~~~~y~e~L~~aG~l~~~~~L~p-t~~a~tlr~~---~G~~~viDGPFaEtKEql 78 (123)
T COG3795 15 AAWSVEEDAALMAALGKYNERLAKAGVLGPGARLHP-TTAATTLRFR---GGKRTVIDGPFAETKEQL 78 (123)
T ss_pred hcCCcCccHHHHHHHHHHHHHHHHcCCccccccccC-CccceEEEec---CCcceecCCCchhHHHHh
Confidence 57999999999998876631 34555555555 3555433211 012234567887766654
No 216
>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=24.65 E-value=1.1e+02 Score=15.47 Aligned_cols=45 Identities=20% Similarity=0.171 Sum_probs=34.0
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCC---CchhhhhhhCCCCchhhHHHHHHh
Q 041165 13 KRGPWTIEEDHKLMSFILNNGIH---CWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~g~~---~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
++..+|+++-..|.......+.. .-..||..+| -+..|+..=|.|
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~--l~~~~V~~WF~n 50 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELG--LTERQVKNWFQN 50 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHT--SSHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhcccccccccccccccc--ccccccccCHHH
Confidence 56789999999999999885532 2577888888 788888765544
No 217
>cd08802 Death_UNC5B Death domain found in Uncoordinated-5B. Death Domain (DD) found in Uncoordinated-5B (UNC5B). UNC5B is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5B signaling is involved in the netrin-1-induced proliferation and migration of renal proximal tubular cells. It is also required for vascular patterning during embryonic development, and its activation inhibits sprouting angiogenesis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activatio
Probab=24.59 E-value=36 Score=19.93 Aligned_cols=12 Identities=17% Similarity=0.645 Sum_probs=10.9
Q ss_pred CCchhhhhhhCC
Q 041165 35 HCWRMVPKLAGL 46 (85)
Q Consensus 35 ~~W~~Ia~~~~~ 46 (85)
++|..+|+.||-
T Consensus 21 ~DW~~LAekL~l 32 (84)
T cd08802 21 NDWRLLAQKLSM 32 (84)
T ss_pred CcHHHHHHHcCc
Confidence 689999999995
No 218
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=24.40 E-value=2.1e+02 Score=18.54 Aligned_cols=52 Identities=15% Similarity=0.228 Sum_probs=32.8
Q ss_pred HHHHHHHHHhCCCC---chhhhhhhCCCCchhhHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHH
Q 041165 23 HKLMSFILNNGIHC---WRMVPKLAGLLRCGKSCRLRWINYLRPDLKRGAFTEDEEDQIIQLHS 83 (85)
Q Consensus 23 ~~L~~~v~~~g~~~---W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~~v~ 83 (85)
+++..++...|... =..||..+|.+++. .. +.|+ -+.+||-+|-..|.+...
T Consensus 8 erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ss--a~----RKL~---G~~~ftl~EI~~Ia~~fg 62 (147)
T PF08667_consen 8 ERVRELLDRKGIPKRKHASELADILGISYSS--AY----RKLN---GKSPFTLEEIKKIAKHFG 62 (147)
T ss_pred HHHHHHHHHcCCcchhhHHHHHHHHCCCHHH--HH----HHhc---CCCCCCHHHHHHHHHHhC
Confidence 35566777777433 25677778843333 32 2243 367999999999887653
No 219
>TIGR02915 PEP_resp_reg putative PEP-CTERM system response regulator. Members of this protein family share full-length homology with (but do not include) the acetoacetate metabolism regulatory protein AtoC. These proteins have a Fis family DNA binding sequence (pfam02954), a response regulator receiver domain (pfam00072), and sigma-54 interaction domain (pfam00158).
Probab=24.40 E-value=75 Score=23.16 Aligned_cols=29 Identities=17% Similarity=0.093 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhCCCCchhhhhhhCCCCch
Q 041165 21 EDHKLMSFILNNGIHCWRMVPKLAGLLRCG 50 (85)
Q Consensus 21 ED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~ 50 (85)
|-+.+..+...++ +|-...|+.+|.+|+.
T Consensus 406 E~~~i~~al~~~~-gn~~~aA~~Lgisr~t 434 (445)
T TIGR02915 406 EREAVRKAIARVD-GNIARAAELLGITRPT 434 (445)
T ss_pred HHHHHHHHHHHhC-CCHHHHHHHhCCCHHH
Confidence 5567778888888 7999999999976665
No 220
>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=24.27 E-value=1.8e+02 Score=17.93 Aligned_cols=19 Identities=0% Similarity=-0.323 Sum_probs=14.7
Q ss_pred CchhhhhhhCCCCchhhHHHH
Q 041165 36 CWRMVPKLAGLLRCGKSCRLR 56 (85)
Q Consensus 36 ~W~~Ia~~~~~~Rt~~qcr~R 56 (85)
.|..||..+| =|..+|..+
T Consensus 102 t~~~Ia~~l~--iS~~t~~r~ 120 (134)
T TIGR01636 102 TLVGLAQQLF--ISKSTAYRL 120 (134)
T ss_pred CHHHHHHHhC--CCHHHHHHH
Confidence 7999999988 677777543
No 221
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=24.24 E-value=1.1e+02 Score=24.82 Aligned_cols=45 Identities=18% Similarity=0.096 Sum_probs=36.3
Q ss_pred CCCCcC---CCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHh
Q 041165 10 VGLKRG---PWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 10 ~~~~kg---~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
.+.+++ .|+..|+.....++..+| .+--.||..+++ +.|+..|..
T Consensus 402 ~~~~~~~~~ew~~~ek~~fr~~~~~~~-~n~c~Iar~l~~----ktC~~v~~~ 449 (739)
T KOG1079|consen 402 VHGKKDTNVEWNGAEKVLFRVGSTLYG-TNRCSIARNLLT----KTCRQVYEY 449 (739)
T ss_pred ccccCCcccccchhhhHHHHhcccccc-chhhHHHHHhcc----hHHHHHHHH
Confidence 345555 899999999999999999 688899999883 667777654
No 222
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=24.12 E-value=1.8e+02 Score=18.62 Aligned_cols=24 Identities=8% Similarity=-0.128 Sum_probs=18.0
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.+-..||..+| -|...++.+....
T Consensus 128 ~s~~EIA~~lg--is~~tV~~~l~Ra 151 (182)
T PRK12511 128 LSYQEAAAVLG--IPIGTLMSRIGRA 151 (182)
T ss_pred CCHHHHHHHhC--cCHHHHHHHHHHH
Confidence 56799999999 7777777776543
No 223
>cd08781 Death_UNC5-like Death domain found in Uncoordinated-5 homolog family. Death Domain (DD) found in Uncoordinated-5 (UNC-5) homolog family, which includes Unc5A, B, C and D in vertebrates. UNC5 proteins are receptors for secreted netrins (netrin-1, -3 and -4) that are involved in diverse processes like axonal guidance, neuronal migration, blood vessel patterning, and apoptosis. They are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit
Probab=23.99 E-value=40 Score=19.38 Aligned_cols=12 Identities=25% Similarity=0.664 Sum_probs=10.6
Q ss_pred CCchhhhhhhCC
Q 041165 35 HCWRMVPKLAGL 46 (85)
Q Consensus 35 ~~W~~Ia~~~~~ 46 (85)
++|..+|+.+|.
T Consensus 21 ~dWr~LA~~Lgl 32 (83)
T cd08781 21 NDWRLLAKKLSV 32 (83)
T ss_pred CCHHHHHHHhCc
Confidence 689999999994
No 224
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=23.95 E-value=1.8e+02 Score=18.10 Aligned_cols=24 Identities=4% Similarity=-0.017 Sum_probs=17.5
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.+=..||+.+| .+...++.|..+.
T Consensus 136 ~s~~EIA~~lg--is~~tV~~~l~Ra 159 (173)
T PRK12522 136 YSYKEMSEILN--IPIGTVKYRLNYA 159 (173)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHH
Confidence 45688888888 7777777776543
No 225
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.58 E-value=2e+02 Score=18.77 Aligned_cols=24 Identities=4% Similarity=-0.219 Sum_probs=18.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-+=..||..+| .|...++.+..+.
T Consensus 170 ~s~~EIA~~lg--is~~tV~~~l~Ra 193 (206)
T PRK12526 170 LSQEQLAQQLN--VPLGTVKSRLRLA 193 (206)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHH
Confidence 45688999999 7788888776654
No 226
>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=23.55 E-value=1.8e+02 Score=17.61 Aligned_cols=24 Identities=8% Similarity=-0.002 Sum_probs=16.2
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
.+=..||+.+| -|...++.+....
T Consensus 128 ~~~~eIA~~l~--is~~tv~~~l~Ra 151 (159)
T TIGR02989 128 VSLTALAEQLG--RTVNAVYKALSRL 151 (159)
T ss_pred CCHHHHHHHhC--CCHHHHHHHHHHH
Confidence 45678888888 6667777665543
No 227
>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=23.46 E-value=1.9e+02 Score=19.78 Aligned_cols=24 Identities=0% Similarity=-0.215 Sum_probs=17.2
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINY 60 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 60 (85)
-....||..+| -|...++.|..+.
T Consensus 178 ~S~~EIA~~Lg--is~~TVk~rl~RA 201 (244)
T TIGR03001 178 LSMDRIGAMYQ--VHRSTVSRWVAQA 201 (244)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHH
Confidence 57899999999 5666666655543
No 228
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=23.36 E-value=29 Score=24.67 Aligned_cols=43 Identities=12% Similarity=-0.046 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 17 WTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 17 WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
||+++..++.+++..++ ..|..|-.+.+ .....+.+..+..++
T Consensus 56 ~t~~~~~~~~~~l~~~~-~~~~~~~~~~~-~~~~v~~~~~~~~~~ 98 (335)
T KOG0724|consen 56 RTPDSWDKFAEALPLEK-RLEDKIEEYIG-LVFDVNIRESGQKPF 98 (335)
T ss_pred cchhhhhHHHhcCcccc-ccchhHHhhhh-hHHHHhhhhccCCCc
Confidence 66666665555555553 46666666655 366666666655443
No 229
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=23.26 E-value=2e+02 Score=17.92 Aligned_cols=25 Identities=4% Similarity=-0.049 Sum_probs=17.8
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
-+-..||..+| -+...++.+-.+.+
T Consensus 135 ~s~~EIA~~l~--is~~tV~~~l~ra~ 159 (168)
T PRK12525 135 LTYVEIGERLG--VSLSRIHQYMVEAF 159 (168)
T ss_pred CCHHHHHHHHC--CCHHHHHHHHHHHH
Confidence 57889999998 66666766655543
No 230
>cd00131 PAX Paired Box domain
Probab=23.18 E-value=1.9e+02 Score=17.77 Aligned_cols=68 Identities=12% Similarity=0.082 Sum_probs=44.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCchhhhhhhCCCCc-hhhHHHHHHhh--hCCCCCCC----CCCHHHHHHHHHHHH
Q 041165 14 RGPWTIEEDHKLMSFILNNGIHCWRMVPKLAGLLRC-GKSCRLRWINY--LRPDLKRG----AFTEDEEDQIIQLHS 83 (85)
Q Consensus 14 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt-~~qcr~Rw~~~--l~~~~~~~----~wt~eEd~~L~~~v~ 83 (85)
-.+.|.+.=++++.++. .| ..-..||..++.+++ -.-+..||... +.|....+ .-+++.+..|+.++.
T Consensus 15 ~~~lS~d~R~rIv~~~~-~G-~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~ 89 (128)
T cd00131 15 GRPLPDSIRQRIVELAQ-SG-IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQ 89 (128)
T ss_pred CCcCCHHHHHHHHHHHH-cC-CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHH
Confidence 35788888899998886 56 689999999985443 33456777642 44432222 246666666666654
No 231
>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=23.17 E-value=98 Score=18.85 Aligned_cols=27 Identities=15% Similarity=0.100 Sum_probs=14.1
Q ss_pred hHHHHHHhhhCCCCCCCCCCHHHHHHHHH
Q 041165 52 SCRLRWINYLRPDLKRGAFTEDEEDQIIQ 80 (85)
Q Consensus 52 qcr~Rw~~~l~~~~~~~~wt~eEd~~L~~ 80 (85)
.|-+-=+......+ ..+|+|||.+|=.
T Consensus 59 ~Ci~~ir~i~~~pL--~~lTpEEDFiLG~ 85 (101)
T PF09633_consen 59 ECIEVIRSIVTRPL--NELTPEEDFILGI 85 (101)
T ss_dssp HHHHHHHHHHTS-G--GG--HHHHHHHHH
T ss_pred HHHHHHHHHhCCch--hhCCcHHHHHHHH
Confidence 45554444444333 3599999998743
No 232
>PRK15328 invasion protein IagB; Provisional
Probab=22.42 E-value=1.3e+02 Score=19.53 Aligned_cols=34 Identities=24% Similarity=0.292 Sum_probs=20.0
Q ss_pred HHHHHHHHhCCCCchhhhhh-hCCCCchhhHHHHHH
Q 041165 24 KLMSFILNNGIHCWRMVPKL-AGLLRCGKSCRLRWI 58 (85)
Q Consensus 24 ~L~~~v~~~g~~~W~~Ia~~-~~~~Rt~~qcr~Rw~ 58 (85)
.|..+...+| +.|..|+.. .|..+....-+.+|.
T Consensus 98 ~L~~~~~~~g-~~~~alaaYNaG~~~~~~~~~~~Y~ 132 (160)
T PRK15328 98 ILSDMMKIYG-YSWEAVGAYNAGTSPKRSDIRKRYA 132 (160)
T ss_pred HHHHHHHHcC-ChHHhhhhccCCCCCCCCHHHHHHH
Confidence 3456677888 689999987 332233333344443
No 233
>PRK09458 pspB phage shock protein B; Provisional
Probab=22.37 E-value=1.7e+02 Score=16.84 Aligned_cols=18 Identities=17% Similarity=0.416 Sum_probs=13.8
Q ss_pred CCCCCCHHHHHHHHHHHH
Q 041165 66 KRGAFTEDEEDQIIQLHS 83 (85)
Q Consensus 66 ~~~~wt~eEd~~L~~~v~ 83 (85)
.....|.+|.+.|-++.+
T Consensus 32 ~~~~Ls~~d~~~L~~L~~ 49 (75)
T PRK09458 32 GSQGLSQEEQQRLAQLTE 49 (75)
T ss_pred CCCCCCHHHHHHHHHHHH
Confidence 345689999888888765
No 234
>PRK11608 pspF phage shock protein operon transcriptional activator; Provisional
Probab=21.37 E-value=96 Score=22.09 Aligned_cols=29 Identities=17% Similarity=0.105 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHhCCCCchhhhhhhCCCCch
Q 041165 21 EDHKLMSFILNNGIHCWRMVPKLAGLLRCG 50 (85)
Q Consensus 21 ED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~ 50 (85)
|-+.+..+.+.++ +|-.+.|+.+|.+|+.
T Consensus 287 Er~~I~~aL~~~~-gn~~~aA~~LGIsR~t 315 (326)
T PRK11608 287 EKELLQRSLQQAK-FNQKRAAELLGLTYHQ 315 (326)
T ss_pred HHHHHHHHHHHhC-CCHHHHHHHhCCCHHH
Confidence 5566777888888 7999999999966665
No 235
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=21.02 E-value=1.3e+02 Score=14.96 Aligned_cols=45 Identities=18% Similarity=0.170 Sum_probs=32.2
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCc---hhhhhhhCCCCchhhHHHHHHh
Q 041165 13 KRGPWTIEEDHKLMSFILNNGIHCW---RMVPKLAGLLRCGKSCRLRWIN 59 (85)
Q Consensus 13 ~kg~WT~eED~~L~~~v~~~g~~~W---~~Ia~~~~~~Rt~~qcr~Rw~~ 59 (85)
.++.+|++.-..|..........+- ..||..+| -+..|+..=|.+
T Consensus 3 ~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~--l~~~qV~~WF~n 50 (56)
T smart00389 3 KRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLG--LSERQVKVWFQN 50 (56)
T ss_pred CCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHC--cCHHHHHHhHHH
Confidence 3566999999999998887765444 56666677 777777765544
No 236
>cd08782 Death_DAPK1 Death domain found in death-associated protein kinase 1. Death domain (DD) found in death-associated protein kinase 1 (DAPK1). DAPK1 is composed of several functional domains, including a kinase domain, a CaM regulatory domain, ankyrin repeats, a cytoskeletal binding domain and a C-terminal DD. It plays important roles in a diverse range of signal transduction pathways including apoptosis, growth factor signalling, and autophagy. Loss of DAPK1 expression, usually because of DNA methylation, is implicated in many tumor types. DAPK1 is highly abundant in the brain and has also been associated with neurodegeneration. 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 ad
Probab=20.55 E-value=29 Score=20.06 Aligned_cols=14 Identities=21% Similarity=0.442 Sum_probs=11.7
Q ss_pred HhCCCCchhhhhhhC
Q 041165 31 NNGIHCWRMVPKLAG 45 (85)
Q Consensus 31 ~~g~~~W~~Ia~~~~ 45 (85)
..| ++|..+|..+|
T Consensus 15 ~~g-~DW~~LA~~Lg 28 (82)
T cd08782 15 PMG-RDWCLLAVNLG 28 (82)
T ss_pred CCC-CCHHHHHHHcC
Confidence 345 69999999999
No 237
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. 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, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=20.49 E-value=1e+02 Score=16.55 Aligned_cols=37 Identities=16% Similarity=0.197 Sum_probs=12.2
Q ss_pred HHHHHHHHHHhCCCCchhhhhhh---CCCCchhhHHHHHH
Q 041165 22 DHKLMSFILNNGIHCWRMVPKLA---GLLRCGKSCRLRWI 58 (85)
Q Consensus 22 D~~L~~~v~~~g~~~W~~Ia~~~---~~~Rt~~qcr~Rw~ 58 (85)
|..|+.+|...+...|..|+..+ |.+=|..-++.+-.
T Consensus 1 ~r~I~~~v~~~p~~s~~~i~~~l~~~~~~vS~~TI~r~L~ 40 (72)
T PF01498_consen 1 DRRIVRMVRRNPRISAREIAQELQEAGISVSKSTIRRRLR 40 (72)
T ss_dssp ---------------HHHHHHHT---T--S-HHHHHHHHH
T ss_pred CcHHHHHHHHCCCCCHHHHHHHHHHccCCcCHHHHHHHHH
Confidence 34577788888778899999888 54344444444433
No 238
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.41 E-value=1.8e+02 Score=19.56 Aligned_cols=25 Identities=0% Similarity=-0.235 Sum_probs=19.3
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
.+-..||..|| -+...++.|..+.+
T Consensus 188 ~s~~EIA~~Lg--is~~tVk~~l~RAr 212 (233)
T PRK12538 188 MSNGEIAEVMD--TTVAAVESLLKRGR 212 (233)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHH
Confidence 46789999999 78888877766644
No 239
>PF05176 ATP-synt_10: ATP10 protein; InterPro: IPR007849 This entry represents the ATPase assembly factor ATP10 found in mitochondria, which is essential for the assembly of the mitochondrial F1-F0 complex. A yeast nuclear gene (ATP10) encodes a product that is essential for the assembly of a functional mitochondrial ATPase complex. Mutations in ATP10 induce a loss of rutamycin sensitivity in the mitochondrial ATPase, but do not affect the respiratory enzymes. ATP10 has an Mr of 30,293 and its primary structure is not related to any known subunit of the yeast or mammalian mitochondrial ATPase complexes. ATP10 is associated with the mitochondrial membrane. It is suggested that the ATP10 product is not a subunit of the ATPase complex but rather a protein required for the assembly of the F0 sector of the complex [].; GO: 0033615 mitochondrial proton-transporting ATP synthase complex assembly, 0005743 mitochondrial inner membrane
Probab=20.38 E-value=47 Score=23.20 Aligned_cols=20 Identities=20% Similarity=0.175 Sum_probs=16.6
Q ss_pred CCCCCCHHHHHHHHHHHHhC
Q 041165 66 KRGAFTEDEEDQIIQLHSLL 85 (85)
Q Consensus 66 ~~~~wt~eEd~~L~~~v~~~ 85 (85)
..|.-|++|-+.|...++.+
T Consensus 233 gsG~At~~E~~~L~k~~~~L 252 (252)
T PF05176_consen 233 GSGPATPEELESLWKCVKGL 252 (252)
T ss_pred ccCCCCHHHHHHHHHHHhcC
Confidence 46889999999999988753
No 240
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=20.21 E-value=2.3e+02 Score=19.35 Aligned_cols=25 Identities=12% Similarity=-0.068 Sum_probs=19.0
Q ss_pred CCchhhhhhhCCCCchhhHHHHHHhhh
Q 041165 35 HCWRMVPKLAGLLRCGKSCRLRWINYL 61 (85)
Q Consensus 35 ~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 61 (85)
..-..||..+| -|...++.+....+
T Consensus 220 ~s~~eIA~~lg--vs~~~V~~~~~ra~ 244 (256)
T PRK07408 220 LTQKEAAERLG--ISPVTVSRRVKKGL 244 (256)
T ss_pred CCHHHHHHHHC--cCHHHHHHHHHHHH
Confidence 46788999998 77778877766544
Done!