Query 024860
Match_columns 261
No_of_seqs 283 out of 1878
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 07:57:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024860.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024860hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03212 Transcription repress 100.0 9.2E-39 2E-43 279.9 11.1 121 3-123 14-134 (249)
2 PLN03091 hypothetical protein; 100.0 1.1E-38 2.4E-43 297.6 12.2 123 1-123 1-123 (459)
3 KOG0048 Transcription factor, 100.0 3.2E-36 6.9E-41 267.7 10.2 111 10-120 5-115 (238)
4 KOG0048 Transcription factor, 99.8 3.1E-22 6.8E-27 178.0 0.3 92 63-154 5-115 (238)
5 KOG0049 Transcription factor, 99.8 4.8E-20 1E-24 178.2 6.6 109 1-110 347-456 (939)
6 KOG0049 Transcription factor, 99.8 1E-18 2.3E-23 169.0 7.0 114 12-126 303-420 (939)
7 PLN03212 Transcription repress 99.7 7.1E-19 1.5E-23 154.7 3.6 101 44-152 10-129 (249)
8 PF13921 Myb_DNA-bind_6: Myb-l 99.7 1.6E-17 3.4E-22 117.0 3.3 60 17-78 1-60 (60)
9 PLN03091 hypothetical protein; 99.7 1E-17 2.3E-22 157.3 0.7 88 63-150 10-116 (459)
10 COG5147 REB1 Myb superfamily p 99.6 4.5E-16 9.8E-21 150.2 6.1 109 8-117 14-122 (512)
11 KOG0050 mRNA splicing protein 99.6 6.2E-16 1.3E-20 146.9 2.2 107 12-120 5-111 (617)
12 KOG0051 RNA polymerase I termi 99.5 2.5E-14 5.3E-19 139.5 5.3 103 13-118 383-513 (607)
13 PF00249 Myb_DNA-binding: Myb- 99.5 5.7E-14 1.2E-18 94.7 5.1 46 67-112 1-48 (48)
14 PF13921 Myb_DNA-bind_6: Myb-l 99.4 1.2E-13 2.5E-18 97.2 5.3 56 70-125 1-56 (60)
15 PF00249 Myb_DNA-binding: Myb- 99.4 1.7E-14 3.7E-19 97.3 0.4 48 14-61 1-48 (48)
16 smart00717 SANT SANT SWI3, AD 99.3 9.5E-12 2.1E-16 82.2 5.5 47 67-113 1-48 (49)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 9.4E-11 2E-15 76.2 5.4 44 69-112 1-45 (45)
18 KOG0051 RNA polymerase I termi 99.1 2.1E-11 4.6E-16 119.2 2.9 114 13-128 307-446 (607)
19 smart00717 SANT SANT SWI3, AD 99.1 4.4E-11 9.6E-16 79.0 1.9 48 14-62 1-48 (49)
20 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 2.1E-10 4.4E-15 74.6 1.6 45 16-61 1-45 (45)
21 COG5147 REB1 Myb superfamily p 98.1 1.3E-06 2.7E-11 85.2 2.0 111 14-126 222-351 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.0 2.8E-06 6.1E-11 59.4 1.8 49 13-61 2-54 (57)
23 KOG0050 mRNA splicing protein 98.0 2.7E-06 5.9E-11 81.9 1.8 64 65-128 5-69 (617)
24 KOG0457 Histone acetyltransfer 97.9 3.6E-06 7.7E-11 79.7 1.3 50 11-61 69-118 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.7 7.9E-05 1.7E-09 52.1 5.6 47 67-113 3-55 (57)
26 KOG0457 Histone acetyltransfer 97.7 7.1E-05 1.5E-09 71.1 5.8 50 64-113 69-119 (438)
27 TIGR02894 DNA_bind_RsfA transc 97.5 0.00011 2.3E-09 61.5 4.1 53 66-119 3-62 (161)
28 PF08914 Myb_DNA-bind_2: Rap1 97.4 0.00027 5.9E-09 50.7 4.2 51 67-117 2-62 (65)
29 PF13325 MCRS_N: N-terminal re 97.3 0.00042 9.1E-09 60.1 5.9 100 16-117 1-131 (199)
30 COG5259 RSC8 RSC chromatin rem 97.3 7.3E-05 1.6E-09 71.5 1.0 46 13-60 278-323 (531)
31 KOG1279 Chromatin remodeling f 97.1 0.0002 4.4E-09 70.1 1.7 47 12-60 251-297 (506)
32 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.00044 9.5E-09 51.7 2.9 49 67-115 1-67 (90)
33 COG5259 RSC8 RSC chromatin rem 96.9 0.00096 2.1E-08 64.0 4.4 46 66-111 278-323 (531)
34 KOG1279 Chromatin remodeling f 96.9 0.0013 2.9E-08 64.4 5.1 46 66-111 252-297 (506)
35 PF08914 Myb_DNA-bind_2: Rap1 96.6 0.0006 1.3E-08 48.9 0.1 52 14-65 2-61 (65)
36 PRK13923 putative spore coat p 96.3 0.0044 9.5E-08 52.5 3.7 53 65-118 3-62 (170)
37 TIGR02894 DNA_bind_RsfA transc 96.3 0.0013 2.9E-08 55.0 0.5 50 12-63 2-57 (161)
38 PF13873 Myb_DNA-bind_5: Myb/S 96.1 0.014 3.1E-07 42.6 5.5 49 67-115 2-72 (78)
39 COG5114 Histone acetyltransfer 96.1 0.0058 1.3E-07 56.3 3.9 48 66-113 62-110 (432)
40 COG5114 Histone acetyltransfer 96.1 0.0014 3.1E-08 60.2 -0.2 48 14-62 63-110 (432)
41 PF13837 Myb_DNA-bind_4: Myb/S 96.0 0.0014 3.1E-08 48.8 -0.5 46 15-60 2-63 (90)
42 PLN03142 Probable chromatin-re 95.7 0.024 5.3E-07 60.3 6.7 102 16-118 826-990 (1033)
43 PRK13923 putative spore coat p 95.4 0.0033 7.2E-08 53.2 -0.5 50 11-62 2-57 (170)
44 PF13873 Myb_DNA-bind_5: Myb/S 95.1 0.0094 2E-07 43.5 1.1 49 13-61 1-69 (78)
45 PF09111 SLIDE: SLIDE; InterP 93.8 0.099 2.1E-06 41.9 4.4 54 64-117 46-115 (118)
46 KOG4282 Transcription factor G 93.3 0.14 3E-06 47.9 5.1 51 67-117 54-118 (345)
47 PF12776 Myb_DNA-bind_3: Myb/S 91.4 0.45 9.7E-06 35.7 5.0 46 69-114 1-64 (96)
48 KOG2656 DNA methyltransferase 90.2 0.37 8E-06 45.8 4.1 56 67-122 130-191 (445)
49 KOG4282 Transcription factor G 85.7 0.4 8.6E-06 44.8 1.4 46 15-60 55-112 (345)
50 PF09111 SLIDE: SLIDE; InterP 84.9 0.58 1.3E-05 37.4 1.8 34 11-44 46-82 (118)
51 COG5118 BDP1 Transcription ini 83.7 1.8 3.9E-05 41.2 4.7 47 68-114 366-412 (507)
52 PF08281 Sigma70_r4_2: Sigma-7 83.7 3.1 6.8E-05 27.6 4.9 41 72-113 12-52 (54)
53 COG5118 BDP1 Transcription ini 76.4 1.6 3.5E-05 41.5 1.9 65 13-79 364-436 (507)
54 PF11626 Rap1_C: TRF2-interact 74.5 2.8 6.1E-05 31.4 2.5 22 13-34 46-75 (87)
55 KOG1194 Predicted DNA-binding 73.6 6.9 0.00015 38.1 5.4 48 67-114 187-234 (534)
56 PRK11179 DNA-binding transcrip 68.7 7.8 0.00017 31.8 4.1 46 72-118 8-54 (153)
57 PF13404 HTH_AsnC-type: AsnC-t 68.1 13 0.00027 24.0 4.2 38 73-111 3-41 (42)
58 smart00595 MADF subfamily of S 66.6 5.1 0.00011 29.4 2.4 24 89-113 30-53 (89)
59 PF11626 Rap1_C: TRF2-interact 66.0 5.5 0.00012 29.8 2.4 17 63-79 43-59 (87)
60 PRK11169 leucine-responsive tr 63.7 9.9 0.00022 31.6 3.9 46 72-118 13-59 (164)
61 KOG4167 Predicted DNA-binding 63.7 3.1 6.8E-05 42.7 0.9 44 14-59 619-662 (907)
62 PF04545 Sigma70_r4: Sigma-70, 61.8 21 0.00046 23.2 4.5 41 73-114 7-47 (50)
63 PF13404 HTH_AsnC-type: AsnC-t 61.6 2.5 5.4E-05 27.4 -0.1 37 20-58 3-39 (42)
64 PF12776 Myb_DNA-bind_3: Myb/S 60.4 4.9 0.00011 29.9 1.3 44 16-59 1-60 (96)
65 PF13325 MCRS_N: N-terminal re 58.4 20 0.00043 31.3 4.8 43 69-112 1-46 (199)
66 cd08319 Death_RAIDD Death doma 58.3 13 0.00028 27.8 3.2 30 75-105 2-31 (83)
67 PRK11179 DNA-binding transcrip 57.0 3.9 8.3E-05 33.7 0.2 46 19-66 8-53 (153)
68 KOG0384 Chromodomain-helicase 56.1 11 0.00025 41.0 3.5 75 13-94 1132-1207(1373)
69 cd08803 Death_ank3 Death domai 56.1 17 0.00037 27.2 3.6 31 75-106 4-34 (84)
70 PRK11169 leucine-responsive tr 53.4 3.6 7.8E-05 34.3 -0.5 45 19-65 13-57 (164)
71 KOG4167 Predicted DNA-binding 52.3 24 0.00053 36.5 4.9 45 67-111 619-663 (907)
72 PF11035 SnAPC_2_like: Small n 52.3 49 0.0011 31.0 6.5 49 67-116 21-73 (344)
73 TIGR02985 Sig70_bacteroi1 RNA 51.8 31 0.00066 27.3 4.8 35 79-114 122-156 (161)
74 KOG4468 Polycomb-group transcr 51.8 11 0.00024 38.1 2.4 47 14-61 88-143 (782)
75 PF09420 Nop16: Ribosome bioge 50.4 36 0.00078 28.4 5.1 47 66-112 113-163 (164)
76 PF07750 GcrA: GcrA cell cycle 50.1 20 0.00043 30.1 3.5 42 69-111 2-43 (162)
77 KOG4468 Polycomb-group transcr 49.1 28 0.00061 35.3 4.8 51 67-117 88-148 (782)
78 cd08317 Death_ank Death domain 48.6 18 0.00039 26.7 2.7 29 75-104 4-32 (84)
79 PF01388 ARID: ARID/BRIGHT DNA 47.2 36 0.00078 25.1 4.2 38 77-114 40-90 (92)
80 smart00501 BRIGHT BRIGHT, ARID 46.2 39 0.00084 25.2 4.2 39 77-115 36-87 (93)
81 PF11035 SnAPC_2_like: Small n 46.0 43 0.00094 31.3 5.2 87 14-114 21-128 (344)
82 KOG4329 DNA-binding protein [G 44.0 1.9E+02 0.0041 27.8 9.1 44 68-111 278-322 (445)
83 smart00344 HTH_ASNC helix_turn 44.0 43 0.00093 25.2 4.3 44 73-117 3-47 (108)
84 PF10545 MADF_DNA_bdg: Alcohol 43.9 19 0.0004 25.6 2.1 25 89-113 29-54 (85)
85 cd08311 Death_p75NR Death doma 43.4 28 0.0006 25.6 2.9 34 72-107 2-35 (77)
86 cd08318 Death_NMPP84 Death dom 42.1 31 0.00068 25.6 3.1 27 78-105 10-36 (86)
87 TIGR02937 sigma70-ECF RNA poly 42.1 52 0.0011 25.2 4.6 34 80-114 120-153 (158)
88 cd08804 Death_ank2 Death domai 42.0 31 0.00067 25.6 3.0 31 75-106 4-34 (84)
89 smart00005 DEATH DEATH domain, 41.0 36 0.00078 24.6 3.3 30 74-104 4-34 (88)
90 PRK09413 IS2 repressor TnpA; R 39.9 40 0.00088 26.5 3.6 45 13-61 9-53 (121)
91 KOG2009 Transcription initiati 39.4 35 0.00077 34.4 3.8 50 65-114 407-456 (584)
92 KOG2656 DNA methyltransferase 38.6 19 0.00041 34.6 1.7 48 12-60 128-180 (445)
93 PF02954 HTH_8: Bacterial regu 37.3 67 0.0014 20.3 3.7 33 74-107 6-38 (42)
94 cd08777 Death_RIP1 Death Domai 36.6 37 0.00081 25.4 2.8 30 76-106 3-32 (86)
95 COG2197 CitB Response regulato 36.5 48 0.0011 28.6 3.9 45 68-115 147-191 (211)
96 cd08805 Death_ank1 Death domai 36.3 42 0.00091 25.1 3.0 26 75-101 4-29 (84)
97 PRK09652 RNA polymerase sigma 34.9 72 0.0016 25.7 4.5 29 85-114 143-171 (182)
98 PLN03142 Probable chromatin-re 34.3 29 0.00062 37.6 2.5 32 13-44 925-956 (1033)
99 cd08779 Death_PIDD Death Domai 34.1 44 0.00096 24.9 2.8 21 76-96 3-23 (86)
100 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 33.8 66 0.0014 21.8 3.3 34 73-107 7-40 (50)
101 PRK11924 RNA polymerase sigma 33.7 74 0.0016 25.6 4.4 29 85-114 140-168 (179)
102 KOG1194 Predicted DNA-binding 32.1 26 0.00057 34.3 1.6 46 12-59 185-230 (534)
103 PF07750 GcrA: GcrA cell cycle 31.9 31 0.00066 29.0 1.8 34 16-51 2-36 (162)
104 PRK04217 hypothetical protein; 31.8 1E+02 0.0022 24.3 4.6 46 68-115 41-86 (110)
105 PF09420 Nop16: Ribosome bioge 31.6 33 0.00072 28.6 2.0 46 12-58 112-160 (164)
106 COG1522 Lrp Transcriptional re 30.3 85 0.0018 25.0 4.2 47 72-119 7-54 (154)
107 smart00351 PAX Paired Box doma 30.0 86 0.0019 24.8 4.1 71 14-86 15-92 (125)
108 PRK09643 RNA polymerase sigma 29.8 98 0.0021 25.9 4.6 29 85-114 149-177 (192)
109 PRK09641 RNA polymerase sigma 29.7 92 0.002 25.5 4.4 29 85-114 151-179 (187)
110 cd06171 Sigma70_r4 Sigma70, re 29.3 1.4E+02 0.0031 18.3 4.4 40 70-111 11-50 (55)
111 KOG2009 Transcription initiati 28.5 40 0.00086 34.1 2.2 50 8-59 403-452 (584)
112 PF07638 Sigma70_ECF: ECF sigm 28.5 1.2E+02 0.0026 25.4 4.9 36 76-112 141-176 (185)
113 TIGR02939 RpoE_Sigma70 RNA pol 28.3 82 0.0018 25.9 3.9 29 85-114 153-181 (190)
114 PRK12515 RNA polymerase sigma 27.3 1.2E+02 0.0026 25.1 4.7 29 85-114 146-174 (189)
115 COG1522 Lrp Transcriptional re 27.1 21 0.00046 28.7 0.0 44 20-65 8-51 (154)
116 PF00196 GerE: Bacterial regul 26.6 70 0.0015 21.4 2.6 44 69-115 3-46 (58)
117 smart00344 HTH_ASNC helix_turn 26.4 26 0.00057 26.4 0.5 43 20-64 3-45 (108)
118 TIGR02948 SigW_bacill RNA poly 26.2 1.1E+02 0.0023 25.1 4.2 28 86-114 152-179 (187)
119 TIGR02954 Sig70_famx3 RNA poly 26.0 1.2E+02 0.0026 24.5 4.4 29 85-114 134-162 (169)
120 COG2963 Transposase and inacti 25.9 1.6E+02 0.0035 22.5 4.9 46 67-114 5-51 (116)
121 PRK12512 RNA polymerase sigma 25.7 1.3E+02 0.0029 24.6 4.7 30 85-115 146-175 (184)
122 PRK01905 DNA-binding protein F 25.7 1.6E+02 0.0035 21.2 4.5 35 72-107 36-70 (77)
123 PRK11923 algU RNA polymerase s 25.1 1.2E+02 0.0026 25.1 4.4 28 86-114 154-181 (193)
124 PRK09047 RNA polymerase factor 24.8 1.5E+02 0.0032 23.6 4.7 29 85-114 121-149 (161)
125 PRK12529 RNA polymerase sigma 24.5 1.8E+02 0.0039 23.9 5.2 33 85-118 142-174 (178)
126 PLN03162 golden-2 like transcr 24.2 5.7E+02 0.012 24.7 8.8 46 67-112 237-287 (526)
127 PF13936 HTH_38: Helix-turn-he 24.0 83 0.0018 20.2 2.5 36 69-106 4-39 (44)
128 PRK09637 RNA polymerase sigma 23.5 1.5E+02 0.0032 24.6 4.6 30 84-114 120-149 (181)
129 PRK12532 RNA polymerase sigma 23.1 1.8E+02 0.0039 24.2 5.1 34 85-119 151-187 (195)
130 PRK12523 RNA polymerase sigma 23.0 1.7E+02 0.0036 23.8 4.7 31 84-115 133-163 (172)
131 PF04504 DUF573: Protein of un 22.8 1.3E+02 0.0027 23.0 3.7 47 68-114 5-64 (98)
132 TIGR02943 Sig70_famx1 RNA poly 22.7 1.6E+02 0.0036 24.5 4.7 29 85-114 146-174 (188)
133 PF09905 DUF2132: Uncharacteri 22.7 50 0.0011 23.5 1.2 44 22-78 12-62 (64)
134 PF09197 Rap1-DNA-bind: Rap1, 22.6 74 0.0016 25.0 2.3 27 89-115 52-78 (105)
135 PRK09642 RNA polymerase sigma 22.2 1.7E+02 0.0038 23.2 4.6 29 85-114 121-149 (160)
136 PF10440 WIYLD: Ubiquitin-bind 21.9 61 0.0013 23.2 1.6 18 77-94 31-48 (65)
137 PRK09645 RNA polymerase sigma 21.7 1.8E+02 0.0039 23.5 4.7 29 85-114 133-161 (173)
138 cd08306 Death_FADD Fas-associa 21.5 1.2E+02 0.0026 22.5 3.2 27 79-106 6-32 (86)
139 PRK12531 RNA polymerase sigma 21.4 1.8E+02 0.0039 24.2 4.7 29 85-114 156-184 (194)
140 cd01670 Death Death Domain: a 21.3 92 0.002 21.9 2.5 25 78-103 2-26 (79)
141 PRK09648 RNA polymerase sigma 21.2 1.8E+02 0.004 23.9 4.7 30 85-115 154-183 (189)
142 PRK12524 RNA polymerase sigma 20.9 1.8E+02 0.004 24.2 4.7 29 85-114 151-179 (196)
143 PRK12530 RNA polymerase sigma 20.4 1.9E+02 0.0041 24.1 4.6 28 85-113 149-176 (189)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=9.2e-39 Score=279.86 Aligned_cols=121 Identities=63% Similarity=1.172 Sum_probs=116.4
Q ss_pred CCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCccCCCCHHHHHHHHHHH
Q 024860 3 RTPCCDKTGLKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIRLH 82 (261)
Q Consensus 3 r~p~~~k~~lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~~~ 82 (261)
++|||.|+++++++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.++|+|.+++++||.|||++|++++
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 67999999999999999999999999999999899999999977999999999999999999999999999999999999
Q ss_pred HhcCCchhHhhhcCCCCCHHHHHHHHHHhhhhhhhhCCCCC
Q 024860 83 ESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKKRLKRNSITN 123 (261)
Q Consensus 83 ~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~~~~s~ 123 (261)
.+||++|+.||+.|+|||+++||+||+.+|++++.+.....
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p 134 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDP 134 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCC
Confidence 99999999999999999999999999999999988876554
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=1.1e-38 Score=297.61 Aligned_cols=123 Identities=62% Similarity=1.158 Sum_probs=119.0
Q ss_pred CCCCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCccCCCCHHHHHHHHH
Q 024860 1 MVRTPCCDKTGLKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIR 80 (261)
Q Consensus 1 m~r~p~~~k~~lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~ 80 (261)
|||+|||+|++++|++||+|||++|+++|.+||..+|..||+.++.+|+++|||+||.++|+|.+++++||+|||++|++
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 99999999999999999999999999999999999999999999879999999999999999999999999999999999
Q ss_pred HHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhhhhhhCCCCC
Q 024860 81 LHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKKRLKRNSITN 123 (261)
Q Consensus 81 ~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~~~~s~ 123 (261)
++++||++|+.||+.|+|||+++||+||+.+|++++++.....
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p 123 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDP 123 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 9999999999999999999999999999999999988766554
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=3.2e-36 Score=267.67 Aligned_cols=111 Identities=62% Similarity=1.092 Sum_probs=107.1
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCccCCCCHHHHHHHHHHHHhcCCch
Q 024860 10 TGLKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIRLHESLGNRW 89 (261)
Q Consensus 10 ~~lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~~~~~~G~~W 89 (261)
+.+.||+||+|||.+|+++|.+||.++|..||+.+|++||+++||+||.|||+|+|++|.||+|||++|+++|+.+|++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 34558999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhhhcCCCCCHHHHHHHHHHhhhhhhhhCC
Q 024860 90 SAIAAQLPGRTDNEIKNHWHTSLKKRLKRNS 120 (261)
Q Consensus 90 ~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~~~ 120 (261)
+.||++|||||+++|||+|+.+||+++....
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 9999999999999999999999999998765
No 4
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.84 E-value=3.1e-22 Score=177.99 Aligned_cols=92 Identities=27% Similarity=0.356 Sum_probs=83.9
Q ss_pred CCCccCCCCHHHHHHHHHHHHhcC-CchhHhhhcCC-CCCHHHHHHHHHHhhhhhhhhCCCCC-----------------
Q 024860 63 PNIKRGNYTKEEEDTIIRLHESLG-NRWSAIAAQLP-GRTDNEIKNHWHTSLKKRLKRNSITN----------------- 123 (261)
Q Consensus 63 p~i~k~~WT~EED~~L~~~~~~~G-~~W~~Ia~~l~-gRt~~~~r~Rw~~~lk~~~k~~~~s~----------------- 123 (261)
+.+.||+||+|||++|+++|++|| ++|..||+.++ +|++++||.||.+||+|.++++.|+.
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 345579999999999999999999 77999999997 99999999999999999999999997
Q ss_pred CCCCCCCCCCCCccccCCCCCCCcccccccc
Q 024860 124 TNGAKDTPKRKDPEIYNHDDTEANPVQESNL 154 (261)
Q Consensus 124 ~~~~~~~~~r~~~~i~n~~~~~~~~~~~~~~ 154 (261)
+.||+++||||||+|||+|++.++++.....
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 6679999999999999999999887765443
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.80 E-value=4.8e-20 Score=178.17 Aligned_cols=109 Identities=25% Similarity=0.491 Sum_probs=101.0
Q ss_pred CCCCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCccCCCCHHHHHHHHH
Q 024860 1 MVRTPCCDKTGLKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIR 80 (261)
Q Consensus 1 m~r~p~~~k~~lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~ 80 (261)
++|..+.-.|++++|+||++||.+|+.+|.+||..+|..|-..++ +|+..|||+||.|.|+...|++.||-.||+.|+.
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 367888889999999999999999999999999999999999999 9999999999999999999999999999999999
Q ss_pred HHHhcC-CchhHhhhcCCCCCHHHHHHHHHH
Q 024860 81 LHESLG-NRWSAIAAQLPGRTDNEIKNHWHT 110 (261)
Q Consensus 81 ~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~ 110 (261)
+|++|| ++|.+||..||.||++|.+.|=..
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R 456 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRLR 456 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHHH
Confidence 999999 899999999999999655444333
No 6
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.75 E-value=1e-18 Score=169.00 Aligned_cols=114 Identities=25% Similarity=0.489 Sum_probs=106.5
Q ss_pred CCcCCCCHHHHHHHHHHHHHhC---CCCcccccccccccccccccccccccccCCCCccCCCCHHHHHHHHHHHHhcCC-
Q 024860 12 LKKGTWTPEEDRKLIAYVTKYG---YWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIRLHESLGN- 87 (261)
Q Consensus 12 lkk~~WT~eED~~L~~~V~~~g---~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~~~~~~G~- 87 (261)
++...||.|||.+|+++|++.. +.+|++|-..|+ +|+..|...||...|+|.+++|+||++||.+|+.+|.+||+
T Consensus 303 L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ymp-gr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~k 381 (939)
T KOG0049|consen 303 LSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMP-GRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAK 381 (939)
T ss_pred HHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcC-CcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCcc
Confidence 4567899999999999999874 468999999999 99999999999999999999999999999999999999995
Q ss_pred chhHhhhcCCCCCHHHHHHHHHHhhhhhhhhCCCCCCCC
Q 024860 88 RWSAIAAQLPGRTDNEIKNHWHTSLKKRLKRNSITNTNG 126 (261)
Q Consensus 88 ~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~~~~s~~~~ 126 (261)
.|-+|-..+|||++.|||.||++.|..+.|.+.|+..+.
T Consensus 382 dw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~ed 420 (939)
T KOG0049|consen 382 DWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVED 420 (939)
T ss_pred chhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecch
Confidence 599999999999999999999999999999999987433
No 7
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.74 E-value=7.1e-19 Score=154.70 Aligned_cols=101 Identities=25% Similarity=0.386 Sum_probs=87.1
Q ss_pred ccccccccccccccccccCCCCccCCCCHHHHHHHHHHHHhcC-CchhHhhhcC-CCCCHHHHHHHHHHhhhhhhhhCCC
Q 024860 44 AGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIRLHESLG-NRWSAIAAQL-PGRTDNEIKNHWHTSLKKRLKRNSI 121 (261)
Q Consensus 44 ~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~~~~~~G-~~W~~Ia~~l-~gRt~~~~r~Rw~~~lk~~~k~~~~ 121 (261)
++ +|+..-|-. +++++++||+|||++|+++|++|| ++|+.||+.+ ++||++|||.||.++|+|.++++.|
T Consensus 10 ~~-~~~~pcc~K-------~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpW 81 (249)
T PLN03212 10 VS-KKTTPCCTK-------MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGI 81 (249)
T ss_pred CC-CCCCCCccc-------CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCC
Confidence 44 565544432 578999999999999999999999 6899999998 6999999999999999999999999
Q ss_pred CC-----------------CCCCCCCCCCCCccccCCCCCCCcccccc
Q 024860 122 TN-----------------TNGAKDTPKRKDPEIYNHDDTEANPVQES 152 (261)
Q Consensus 122 s~-----------------~~~~~~~~~r~~~~i~n~~~~~~~~~~~~ 152 (261)
+. ..+++.+++|++++++|+|+..+++....
T Consensus 82 T~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r 129 (249)
T PLN03212 82 TSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLR 129 (249)
T ss_pred ChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHh
Confidence 87 45577999999999999999887776443
No 8
>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=99.68 E-value=1.6e-17 Score=116.99 Aligned_cols=60 Identities=48% Similarity=0.963 Sum_probs=55.4
Q ss_pred CCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCccCCCCHHHHHHH
Q 024860 17 WTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTI 78 (261)
Q Consensus 17 WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L 78 (261)
||+|||++|+.+|.+||. +|..||+.|| .|++.||+.||.++|++.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999997 9999999997 89999999999999999999999999999987
No 9
>PLN03091 hypothetical protein; Provisional
Probab=99.66 E-value=1e-17 Score=157.31 Aligned_cols=88 Identities=24% Similarity=0.421 Sum_probs=79.9
Q ss_pred CCCccCCCCHHHHHHHHHHHHhcC-CchhHhhhcC-CCCCHHHHHHHHHHhhhhhhhhCCCCC-----------------
Q 024860 63 PNIKRGNYTKEEEDTIIRLHESLG-NRWSAIAAQL-PGRTDNEIKNHWHTSLKKRLKRNSITN----------------- 123 (261)
Q Consensus 63 p~i~k~~WT~EED~~L~~~~~~~G-~~W~~Ia~~l-~gRt~~~~r~Rw~~~lk~~~k~~~~s~----------------- 123 (261)
..++++.||+|||++|+++|++|| ++|..||+.+ +||+++|||.||.++|++.++++.|+.
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnKW 89 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNRW 89 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcch
Confidence 578999999999999999999999 6899999988 599999999999999999999999997
Q ss_pred CCCCCCCCCCCCccccCCCCCCCcccc
Q 024860 124 TNGAKDTPKRKDPEIYNHDDTEANPVQ 150 (261)
Q Consensus 124 ~~~~~~~~~r~~~~i~n~~~~~~~~~~ 150 (261)
..+++.+++|++++|+|+|+..+++..
T Consensus 90 skIAk~LPGRTDnqIKNRWnslLKKkl 116 (459)
T PLN03091 90 SQIAAQLPGRTDNEIKNLWNSCLKKKL 116 (459)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence 445778999999999999998776643
No 10
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.61 E-value=4.5e-16 Score=150.18 Aligned_cols=109 Identities=32% Similarity=0.558 Sum_probs=104.3
Q ss_pred CCCCCCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCccCCCCHHHHHHHHHHHHhcCC
Q 024860 8 DKTGLKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIRLHESLGN 87 (261)
Q Consensus 8 ~k~~lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~~~~~~G~ 87 (261)
....++.|.|+..||+.|..+|++||.++|..||..++ .|+++||+.||.++++|.+++..|+.|||+.|+.+..++|.
T Consensus 14 ~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~ 92 (512)
T COG5147 14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT 92 (512)
T ss_pred ccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc
Confidence 45677889999999999999999999999999999998 69999999999999999999999999999999999999999
Q ss_pred chhHhhhcCCCCCHHHHHHHHHHhhhhhhh
Q 024860 88 RWSAIAAQLPGRTDNEIKNHWHTSLKKRLK 117 (261)
Q Consensus 88 ~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k 117 (261)
+|+.||..++||+..+|.+||...+....+
T Consensus 93 ~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 93 QWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 999999999999999999999999988776
No 11
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.57 E-value=6.2e-16 Score=146.86 Aligned_cols=107 Identities=27% Similarity=0.608 Sum_probs=100.7
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCccCCCCHHHHHHHHHHHHhcCCchhH
Q 024860 12 LKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIRLHESLGNRWSA 91 (261)
Q Consensus 12 lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~~~~~~G~~W~~ 91 (261)
++.|.|+.-||++|..+|.+||.+.|.+|++.+. -.+++||+.||..+|+|.|++..|+.|||++|+.+...+-..|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 5778999999999999999999999999999998 899999999999999999999999999999999999999999999
Q ss_pred hhhcCCCCCHHHHHHHHHHhhhhhhhhCC
Q 024860 92 IAAQLPGRTDNEIKNHWHTSLKKRLKRNS 120 (261)
Q Consensus 92 Ia~~l~gRt~~~~r~Rw~~~lk~~~k~~~ 120 (261)
||..| ||++++|-.||.++|-.......
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~~ 111 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYHY 111 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhhc
Confidence 99988 99999999999999877665443
No 12
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.48 E-value=2.5e-14 Score=139.55 Aligned_cols=103 Identities=27% Similarity=0.591 Sum_probs=93.2
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCC--CccCCCCHHHHHHHHHHHH-------
Q 024860 13 KKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPN--IKRGNYTKEEEDTIIRLHE------- 83 (261)
Q Consensus 13 kk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~--i~k~~WT~EED~~L~~~~~------- 83 (261)
.+|+||+||++.|..+|.++|. .|..|++.+| |.+..||+||++|...+ .+++.||.||+++|+++|+
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 7999999999999999999998 9999999997 99999999999999988 4899999999999999995
Q ss_pred hc-------------------CCchhHhhhcCCCCCHHHHHHHHHHhhhhhhhh
Q 024860 84 SL-------------------GNRWSAIAAQLPGRTDNEIKNHWHTSLKKRLKR 118 (261)
Q Consensus 84 ~~-------------------G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~ 118 (261)
++ +-.|+.|++.+..|+..+||.+|..++......
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n 513 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFN 513 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhh
Confidence 23 125999999888999999999999998766543
No 13
>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=99.47 E-value=5.7e-14 Score=94.75 Aligned_cols=46 Identities=30% Similarity=0.730 Sum_probs=41.9
Q ss_pred cCCCCHHHHHHHHHHHHhcCCc-hhHhhhcCC-CCCHHHHHHHHHHhh
Q 024860 67 RGNYTKEEEDTIIRLHESLGNR-WSAIAAQLP-GRTDNEIKNHWHTSL 112 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~G~~-W~~Ia~~l~-gRt~~~~r~Rw~~~l 112 (261)
|++||+|||++|++++.+||.+ |..||..|+ |||..||++||+++|
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 6899999999999999999977 999999999 999999999999875
No 14
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.45 E-value=1.2e-13 Score=97.16 Aligned_cols=56 Identities=32% Similarity=0.681 Sum_probs=49.0
Q ss_pred CCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhhhhhhCCCCCCC
Q 024860 70 YTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKKRLKRNSITNTN 125 (261)
Q Consensus 70 WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~~~~s~~~ 125 (261)
||+|||++|+++|..||++|..||+.|+.||+.+|++||.++|++.+++++|+..+
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eE 56 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEE 56 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHH
Confidence 99999999999999999999999999955999999999999999999998887543
No 15
>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=99.44 E-value=1.7e-14 Score=97.30 Aligned_cols=48 Identities=46% Similarity=0.818 Sum_probs=43.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccccc
Q 024860 14 KGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYL 61 (261)
Q Consensus 14 k~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L 61 (261)
|++||+|||++|+++|.+||..+|..||..++.+|++.||+.||.++|
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 688999999999999999999679999999998999999999999875
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.26 E-value=9.5e-12 Score=82.24 Aligned_cols=47 Identities=40% Similarity=0.879 Sum_probs=44.5
Q ss_pred cCCCCHHHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHhhh
Q 024860 67 RGNYTKEEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTSLK 113 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~lk 113 (261)
+++||++||.+|+.+++.|| .+|..||..|++||+.+|+.||..+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998765
No 17
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.14 E-value=9.4e-11 Score=76.23 Aligned_cols=44 Identities=34% Similarity=0.774 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHhh
Q 024860 69 NYTKEEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTSL 112 (261)
Q Consensus 69 ~WT~EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~l 112 (261)
+||.||+.+|++++..+| .+|..||+.+++|++.+|++||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999998763
No 18
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.13 E-value=2.1e-11 Score=119.21 Aligned_cols=114 Identities=27% Similarity=0.367 Sum_probs=94.2
Q ss_pred CcCCCCHHHHHHHHHHHHHhCC-----------------------CCcccccccccccccccccccccccccCCCC-ccC
Q 024860 13 KKGTWTPEEDRKLIAYVTKYGY-----------------------WNWRQLPKYAGLARCGKSCRLRWMNYLRPNI-KRG 68 (261)
Q Consensus 13 kk~~WT~eED~~L~~~V~~~g~-----------------------~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i-~k~ 68 (261)
+-+.|+.+||..|-..|..|-. +-|..|.+.++ .|+...++.+-++...|-- ++|
T Consensus 307 ~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~~rg 385 (607)
T KOG0051|consen 307 NLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFENKRG 385 (607)
T ss_pred hhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCccccccC
Confidence 3488999999999999998811 01677888888 5999988774334333332 999
Q ss_pred CCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhhhh--hhCCCCCCCCCC
Q 024860 69 NYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKKRL--KRNSITNTNGAK 128 (261)
Q Consensus 69 ~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~--k~~~~s~~~~~~ 128 (261)
.||+||++.|..+|.++|+.|..|++.| ||.+..|+.||+++.+..- +++.|+.++.++
T Consensus 386 ~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~ 446 (607)
T KOG0051|consen 386 KWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEK 446 (607)
T ss_pred CCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHH
Confidence 9999999999999999999999999999 9999999999999998884 889998755544
No 19
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.08 E-value=4.4e-11 Score=78.97 Aligned_cols=48 Identities=48% Similarity=0.884 Sum_probs=44.4
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccC
Q 024860 14 KGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLR 62 (261)
Q Consensus 14 k~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~ 62 (261)
++.||++||.+|+.+|.+||..+|..||..++ +|++.+|+.||.+++.
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 46899999999999999999669999999999 9999999999998764
No 20
>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=98.97 E-value=2.1e-10 Score=74.60 Aligned_cols=45 Identities=47% Similarity=0.830 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccccc
Q 024860 16 TWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYL 61 (261)
Q Consensus 16 ~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L 61 (261)
+||++||..|+.++.+||..+|..||+.++ +|++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHhC
Confidence 599999999999999999669999999999 899999999998753
No 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.09 E-value=1.3e-06 Score=85.22 Aligned_cols=111 Identities=28% Similarity=0.365 Sum_probs=91.8
Q ss_pred cCCCCHHHHHHHHHHHHHhCCC-----------------CcccccccccccccccccccccccccCCCCccCCCCHHHHH
Q 024860 14 KGTWTPEEDRKLIAYVTKYGYW-----------------NWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEED 76 (261)
Q Consensus 14 k~~WT~eED~~L~~~V~~~g~~-----------------~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~ 76 (261)
+.-|+...++.+-.+++++|-. .|.-|-+.+. .|+.+..+.+-.+.+++--.+|.||.||+.
T Consensus 222 ~~~~~~~~e~~i~~~~~~~~~sr~q~~~~Iws~~~~~~~f~~n~~~~l~-~R~~ksiy~~~rrky~~f~~~~~wt~e~~~ 300 (512)
T COG5147 222 KKGETLALEQEINEYKEKKGLSRKQFCERIWSTDRDEDKFWPNIYKKLP-YRDKKSIYKHLRRKYNIFEQRGKWTKEEEQ 300 (512)
T ss_pred chhHHHHHHHHHHHHHHHhcccHHHHHhhccccccccccccchhhcccc-cccccchHHHHHHhhhHHhhhccCcccccc
Confidence 4457777777777777777542 2444444554 788889888888888888899999999999
Q ss_pred HHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhh--hhhhCCCCCCCC
Q 024860 77 TIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKK--RLKRNSITNTNG 126 (261)
Q Consensus 77 ~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~--~~k~~~~s~~~~ 126 (261)
.|...+.++|+.|..|.+.+ +|-++.|++||.++.+. .+++++|+..+.
T Consensus 301 eL~~~~~~~~~~w~~ig~~~-~rmp~~crd~wr~~~~~g~t~~~~~ws~eee 351 (512)
T COG5147 301 ELAKLVVEHGGSWTEIGKLL-GRMPNDCRDRWRDYVKCGDTLKRNRWSIEEE 351 (512)
T ss_pred ccccccccccchhhHhhhhh-ccCcHHHHHHHhhhccccCccCCCCCchhhh
Confidence 99999999999999999988 99999999999999999 678888886443
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.00 E-value=2.8e-06 Score=59.43 Aligned_cols=49 Identities=14% Similarity=0.307 Sum_probs=43.4
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCc---ccccccccccc-ccccccccccccc
Q 024860 13 KKGTWTPEEDRKLIAYVTKYGYWNW---RQLPKYAGLAR-CGKSCRLRWMNYL 61 (261)
Q Consensus 13 kk~~WT~eED~~L~~~V~~~g~~~W---~~Ia~~~~~~R-~~~qcr~Rw~~~L 61 (261)
++-.||+||..+++.+|+.+|.++| ..|++.++..| +..||+.+++.|.
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 3557999999999999999999999 99999887667 9999999988764
No 23
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.97 E-value=2.7e-06 Score=81.89 Aligned_cols=64 Identities=25% Similarity=0.479 Sum_probs=58.6
Q ss_pred CccCCCCHHHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHhhhhhhhhCCCCCCCCCC
Q 024860 65 IKRGNYTKEEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTSLKKRLKRNSITNTNGAK 128 (261)
Q Consensus 65 i~k~~WT~EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~~~~s~~~~~~ 128 (261)
++.|-|+.-||++|-..|.+|| +.|+.|+..|...+..||++||..+|.+.+++..|+..+..+
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eeder 69 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDER 69 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHH
Confidence 5678899999999999999999 789999999999999999999999999999999998755543
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.91 E-value=3.6e-06 Score=79.73 Aligned_cols=50 Identities=20% Similarity=0.610 Sum_probs=46.0
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccccc
Q 024860 11 GLKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYL 61 (261)
Q Consensus 11 ~lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L 61 (261)
.+-...||++|+-+|+++++.||.|||..||.++| +|++.+|+++|.+++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 34556799999999999999999999999999999 999999999999864
No 25
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.75 E-value=7.9e-05 Score=52.10 Aligned_cols=47 Identities=19% Similarity=0.357 Sum_probs=41.3
Q ss_pred cCCCCHHHHHHHHHHHHhcC-Cch---hHhhhcCC-CC-CHHHHHHHHHHhhh
Q 024860 67 RGNYTKEEEDTIIRLHESLG-NRW---SAIAAQLP-GR-TDNEIKNHWHTSLK 113 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~G-~~W---~~Ia~~l~-gR-t~~~~r~Rw~~~lk 113 (261)
+-.||+||....+++++.+| ++| ..|+..|. .| |..+|+.+.+.+..
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 55799999999999999999 499 99999883 45 99999999988753
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.67 E-value=7.1e-05 Score=71.08 Aligned_cols=50 Identities=26% Similarity=0.471 Sum_probs=45.3
Q ss_pred CCccCCCCHHHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHhhh
Q 024860 64 NIKRGNYTKEEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTSLK 113 (261)
Q Consensus 64 ~i~k~~WT~EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~lk 113 (261)
.+-...||.+|+.+||+++..|| |+|..||.++..|++.+|+.+|.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 45567899999999999999999 999999999988999999999977653
No 27
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.51 E-value=0.00011 Score=61.46 Aligned_cols=53 Identities=17% Similarity=0.344 Sum_probs=45.4
Q ss_pred ccCCCCHHHHHHHHHHHHhc---CC----chhHhhhcCCCCCHHHHHHHHHHhhhhhhhhC
Q 024860 66 KRGNYTKEEEDTIIRLHESL---GN----RWSAIAAQLPGRTDNEIKNHWHTSLKKRLKRN 119 (261)
Q Consensus 66 ~k~~WT~EED~~L~~~~~~~---G~----~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~~ 119 (261)
+...||.|||.+|-+.|..| |+ -...++..| +||...|.-||+.++|+.....
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 46789999999999999887 43 278888888 9999999999999999986543
No 28
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.37 E-value=0.00027 Score=50.72 Aligned_cols=51 Identities=18% Similarity=0.448 Sum_probs=33.0
Q ss_pred cCCCCHHHHHHHHHHHHhc---C----Cc--hhHhhhcCC-CCCHHHHHHHHHHhhhhhhh
Q 024860 67 RGNYTKEEEDTIIRLHESL---G----NR--WSAIAAQLP-GRTDNEIKNHWHTSLKKRLK 117 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~---G----~~--W~~Ia~~l~-gRt~~~~r~Rw~~~lk~~~k 117 (261)
|.+||.|||.+|+++|..+ | |+ |..+++.-+ .+|-.+.|+||...|+++..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 4589999999999999654 2 22 999998877 89999999999999887654
No 29
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.34 E-value=0.00042 Score=60.13 Aligned_cols=100 Identities=23% Similarity=0.389 Sum_probs=71.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccc--cccccccccccccccc-CCCC--------------------ccCCCCH
Q 024860 16 TWTPEEDRKLIAYVTKYGYWNWRQLPKYAG--LARCGKSCRLRWMNYL-RPNI--------------------KRGNYTK 72 (261)
Q Consensus 16 ~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~--~~R~~~qcr~Rw~~~L-~p~i--------------------~k~~WT~ 72 (261)
+|++++|-.|+.+|.... +-+.|+..+. +.-|-..+.+||+..| +|.+ .+.+||.
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 699999999999999765 5555554333 2445567778999865 3322 3568999
Q ss_pred HHHHHHHHHHHhcCC---chhHhhh----cC-CCCCHHHHHHHHHHhhhhhhh
Q 024860 73 EEEDTIIRLHESLGN---RWSAIAA----QL-PGRTDNEIKNHWHTSLKKRLK 117 (261)
Q Consensus 73 EED~~L~~~~~~~G~---~W~~Ia~----~l-~gRt~~~~r~Rw~~~lk~~~k 117 (261)
+|+++|......... .+.+|-. .| ++||++++..+|..+.+-.+-
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchh
Confidence 999999997766542 4666632 24 789999999999865544443
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.32 E-value=7.3e-05 Score=71.53 Aligned_cols=46 Identities=20% Similarity=0.589 Sum_probs=43.3
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccc
Q 024860 13 KKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNY 60 (261)
Q Consensus 13 kk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~ 60 (261)
....||.+|..+|+++|+.||. +|.+||.++| +|+..||-.||.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 5568999999999999999999 9999999999 99999999999874
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.11 E-value=0.0002 Score=70.07 Aligned_cols=47 Identities=21% Similarity=0.608 Sum_probs=43.7
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccc
Q 024860 12 LKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNY 60 (261)
Q Consensus 12 lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~ 60 (261)
.-++.||.+|..+|+++|+.||. +|.+||.++| +|+..||-.++.+.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 45678999999999999999999 9999999999 99999999998874
No 32
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.07 E-value=0.00044 Score=51.68 Aligned_cols=49 Identities=35% Similarity=0.597 Sum_probs=34.3
Q ss_pred cCCCCHHHHHHHHHHHHh------cC--C------chhHhhhcC----CCCCHHHHHHHHHHhhhhh
Q 024860 67 RGNYTKEEEDTIIRLHES------LG--N------RWSAIAAQL----PGRTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~------~G--~------~W~~Ia~~l----~gRt~~~~r~Rw~~~lk~~ 115 (261)
|..||.+|...||+++.. ++ + .|..||..| ..||+.||+.+|.++.+.-
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 357999999999999876 21 1 399999987 3599999999998865554
No 33
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.93 E-value=0.00096 Score=64.03 Aligned_cols=46 Identities=17% Similarity=0.349 Sum_probs=43.0
Q ss_pred ccCCCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHh
Q 024860 66 KRGNYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTS 111 (261)
Q Consensus 66 ~k~~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~ 111 (261)
...+||.+|..+|++.++.||..|.+||.++..||..||-.|+.++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 3458999999999999999999999999999999999999999775
No 34
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.88 E-value=0.0013 Score=64.40 Aligned_cols=46 Identities=17% Similarity=0.358 Sum_probs=43.1
Q ss_pred ccCCCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHh
Q 024860 66 KRGNYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTS 111 (261)
Q Consensus 66 ~k~~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~ 111 (261)
-++.||.+|..+|++.++.||..|.+||.++.+||..+|-.++..+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 3678999999999999999999999999999999999999999765
No 35
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.56 E-value=0.0006 Score=48.92 Aligned_cols=52 Identities=25% Similarity=0.366 Sum_probs=32.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCC------C--CcccccccccccccccccccccccccCCCC
Q 024860 14 KGTWTPEEDRKLIAYVTKYGY------W--NWRQLPKYAGLARCGKSCRLRWMNYLRPNI 65 (261)
Q Consensus 14 k~~WT~eED~~L~~~V~~~g~------~--~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i 65 (261)
+.+||.|||++|+.+|..+.. + -|.++++.-+..++..+-|+||...|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 457999999999999976521 2 299999887667888889999999887653
No 36
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.28 E-value=0.0044 Score=52.51 Aligned_cols=53 Identities=13% Similarity=0.318 Sum_probs=42.1
Q ss_pred CccCCCCHHHHHHHHHHHHhcCC----c---hhHhhhcCCCCCHHHHHHHHHHhhhhhhhh
Q 024860 65 IKRGNYTKEEEDTIIRLHESLGN----R---WSAIAAQLPGRTDNEIKNHWHTSLKKRLKR 118 (261)
Q Consensus 65 i~k~~WT~EED~~L~~~~~~~G~----~---W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~ 118 (261)
.+...||.|+|.+|-+.|..|+. + -..++..| +||..+|..||+.++++....
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 45678999999999888888762 2 45555666 999999999999999986543
No 37
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.25 E-value=0.0013 Score=54.96 Aligned_cols=50 Identities=26% Similarity=0.497 Sum_probs=41.7
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCC------CCcccccccccccccccccccccccccCC
Q 024860 12 LKKGTWTPEEDRKLIAYVTKYGY------WNWRQLPKYAGLARCGKSCRLRWMNYLRP 63 (261)
Q Consensus 12 lkk~~WT~eED~~L~~~V~~~g~------~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p 63 (261)
.++..||.|||.+|.+.|-+|-. .-..++++.++ ||+.-|.-||..+++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 46678999999999999999832 13788888875 9999999999998763
No 38
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.14 E-value=0.014 Score=42.59 Aligned_cols=49 Identities=27% Similarity=0.562 Sum_probs=39.9
Q ss_pred cCCCCHHHHHHHHHHHHhc-----C--C----------chhHhhhcC-----CCCCHHHHHHHHHHhhhhh
Q 024860 67 RGNYTKEEEDTIIRLHESL-----G--N----------RWSAIAAQL-----PGRTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~-----G--~----------~W~~Ia~~l-----~gRt~~~~r~Rw~~~lk~~ 115 (261)
+..||.+|.++|++++.+| | . -|..|+..| +.|+..+|+.+|.++....
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 4689999999999999876 2 1 199999876 2499999999998876543
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.12 E-value=0.0058 Score=56.33 Aligned_cols=48 Identities=27% Similarity=0.496 Sum_probs=43.5
Q ss_pred ccCCCCHHHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHhhh
Q 024860 66 KRGNYTKEEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTSLK 113 (261)
Q Consensus 66 ~k~~WT~EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~lk 113 (261)
--..|+..|+.+|++....+| |+|..||.++..|+..+||.+|..+.-
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 345799999999999999999 999999999988999999999977654
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.08 E-value=0.0014 Score=60.21 Aligned_cols=48 Identities=21% Similarity=0.555 Sum_probs=44.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccC
Q 024860 14 KGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLR 62 (261)
Q Consensus 14 k~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~ 62 (261)
---|++.|+.+|+++.+-.|.+||..||..+| .|....|+++|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 34599999999999999999999999999999 9999999999998764
No 41
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.00 E-value=0.0014 Score=48.83 Aligned_cols=46 Identities=28% Similarity=0.602 Sum_probs=32.2
Q ss_pred CCCCHHHHHHHHHHHHH--hC-------C----CCcccccccc---cccccccccccccccc
Q 024860 15 GTWTPEEDRKLIAYVTK--YG-------Y----WNWRQLPKYA---GLARCGKSCRLRWMNY 60 (261)
Q Consensus 15 ~~WT~eED~~L~~~V~~--~g-------~----~~W~~Ia~~~---~~~R~~~qcr~Rw~~~ 60 (261)
..||.+|...|++++.. +. . .-|..||..| |..|++.||+.||.+.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 46999999999999987 21 1 1399999765 5579999999999874
No 42
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.66 E-value=0.024 Score=60.26 Aligned_cols=102 Identities=19% Similarity=0.318 Sum_probs=77.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccccccccccccc-------ccccc----------------------------
Q 024860 16 TWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRL-------RWMNY---------------------------- 60 (261)
Q Consensus 16 ~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~-------Rw~~~---------------------------- 60 (261)
-|+.-+=..++.+..+||..+-..||..++ +++...++. ||..+
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 488888888899999999888999999887 676665542 22211
Q ss_pred ---------------cCCCCccCCCCHHHHHHHHHHHHhcC-CchhHhhhc------------CCCCCHHHHHHHHHHhh
Q 024860 61 ---------------LRPNIKRGNYTKEEEDTIIRLHESLG-NRWSAIAAQ------------LPGRTDNEIKNHWHTSL 112 (261)
Q Consensus 61 ---------------L~p~i~k~~WT~EED~~L~~~~~~~G-~~W~~Ia~~------------l~gRt~~~~r~Rw~~~l 112 (261)
-.+..++..+|.|||..|+-++.+|| ++|..|-.. +..||+..|..|...++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 01233455699999999999999999 889998433 35799999999999988
Q ss_pred hhhhhh
Q 024860 113 KKRLKR 118 (261)
Q Consensus 113 k~~~k~ 118 (261)
+-..+.
T Consensus 985 ~~~~~e 990 (1033)
T PLN03142 985 RLIEKE 990 (1033)
T ss_pred HHHHHH
Confidence 776443
No 43
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.42 E-value=0.0033 Score=53.24 Aligned_cols=50 Identities=22% Similarity=0.419 Sum_probs=39.5
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCC------cccccccccccccccccccccccccC
Q 024860 11 GLKKGTWTPEEDRKLIAYVTKYGYWN------WRQLPKYAGLARCGKSCRLRWMNYLR 62 (261)
Q Consensus 11 ~lkk~~WT~eED~~L~~~V~~~g~~~------W~~Ia~~~~~~R~~~qcr~Rw~~~L~ 62 (261)
..++..||.|||.+|...|-+|+... ...++..+ +|++..|..||..+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHH
Confidence 45778899999999999999986533 45556666 4999999999976654
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.11 E-value=0.0094 Score=43.53 Aligned_cols=49 Identities=22% Similarity=0.341 Sum_probs=38.5
Q ss_pred CcCCCCHHHHHHHHHHHHHhCC----------------CCcccccccc----ccccccccccccccccc
Q 024860 13 KKGTWTPEEDRKLIAYVTKYGY----------------WNWRQLPKYA----GLARCGKSCRLRWMNYL 61 (261)
Q Consensus 13 kk~~WT~eED~~L~~~V~~~g~----------------~~W~~Ia~~~----~~~R~~~qcr~Rw~~~L 61 (261)
++..||.+|...|+++|.+|.. .-|.+|+..+ |..|+..||+.+|.++.
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 3567999999999999999821 1299998654 22699999999998754
No 45
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=93.85 E-value=0.099 Score=41.86 Aligned_cols=54 Identities=26% Similarity=0.421 Sum_probs=42.0
Q ss_pred CCccCCCCHHHHHHHHHHHHhcCC----chhHhhhc------------CCCCCHHHHHHHHHHhhhhhhh
Q 024860 64 NIKRGNYTKEEEDTIIRLHESLGN----RWSAIAAQ------------LPGRTDNEIKNHWHTSLKKRLK 117 (261)
Q Consensus 64 ~i~k~~WT~EED~~L~~~~~~~G~----~W~~Ia~~------------l~gRt~~~~r~Rw~~~lk~~~k 117 (261)
..++..||+|||..|+-++.+||- .|..|... +..||+..|..|...+++-..+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~K 115 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIEK 115 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHHC
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHHH
Confidence 566789999999999999999994 69888654 3569999999999988875443
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=93.28 E-value=0.14 Score=47.94 Aligned_cols=51 Identities=24% Similarity=0.384 Sum_probs=40.4
Q ss_pred cCCCCHHHHHHHHHHHHhc----------CCchhHhhhcC--C--CCCHHHHHHHHHHhhhhhhh
Q 024860 67 RGNYTKEEEDTIIRLHESL----------GNRWSAIAAQL--P--GRTDNEIKNHWHTSLKKRLK 117 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~----------G~~W~~Ia~~l--~--gRt~~~~r~Rw~~~lk~~~k 117 (261)
...|+.+|-..||++..+. +..|..||+.+ . -||+.+||.+|.++.++..+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~ 118 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKK 118 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence 4689999999999887542 23499999965 2 39999999999988776543
No 47
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=91.43 E-value=0.45 Score=35.65 Aligned_cols=46 Identities=33% Similarity=0.588 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhc---CC----------chhHhhhcC---CC--CCHHHHHHHHHHhhhh
Q 024860 69 NYTKEEEDTIIRLHESL---GN----------RWSAIAAQL---PG--RTDNEIKNHWHTSLKK 114 (261)
Q Consensus 69 ~WT~EED~~L~~~~~~~---G~----------~W~~Ia~~l---~g--Rt~~~~r~Rw~~~lk~ 114 (261)
.||+++++.|++++.+. |+ .|..|+..| .| .+..+|++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 49999999999988543 21 299999876 33 5789999998665443
No 48
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=90.20 E-value=0.37 Score=45.80 Aligned_cols=56 Identities=25% Similarity=0.385 Sum_probs=48.3
Q ss_pred cCCCCHHHHHHHHHHHHhcCCchhHhhhc-----CCC-CCHHHHHHHHHHhhhhhhhhCCCC
Q 024860 67 RGNYTKEEEDTIIRLHESLGNRWSAIAAQ-----LPG-RTDNEIKNHWHTSLKKRLKRNSIT 122 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~G~~W~~Ia~~-----l~g-Rt~~~~r~Rw~~~lk~~~k~~~~s 122 (261)
...||.||-+.|.++++.|.=+|-.||.. ++. ||-..+|.||...-++.++-...+
T Consensus 130 dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred cccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 35699999999999999999999999977 555 999999999999888877655544
No 49
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=85.68 E-value=0.4 Score=44.82 Aligned_cols=46 Identities=24% Similarity=0.419 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHHh---------CCCCccccccc---ccccccccccccccccc
Q 024860 15 GTWTPEEDRKLIAYVTKY---------GYWNWRQLPKY---AGLARCGKSCRLRWMNY 60 (261)
Q Consensus 15 ~~WT~eED~~L~~~V~~~---------g~~~W~~Ia~~---~~~~R~~~qcr~Rw~~~ 60 (261)
..|+.+|-..|+.+..+. ....|.+||+. .|.-|++.||+.||.|.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl 112 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENL 112 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 679999999999988753 22359999973 45579999999999874
No 50
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=84.90 E-value=0.58 Score=37.43 Aligned_cols=34 Identities=38% Similarity=0.683 Sum_probs=28.1
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCC---CCcccccccc
Q 024860 11 GLKKGTWTPEEDRKLIAYVTKYGY---WNWRQLPKYA 44 (261)
Q Consensus 11 ~lkk~~WT~eED~~L~~~V~~~g~---~~W~~Ia~~~ 44 (261)
.-++..||.+||.-|+-++.+||- +.|..|.+.+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 556788999999999999999998 8899887654
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=83.72 E-value=1.8 Score=41.19 Aligned_cols=47 Identities=21% Similarity=0.341 Sum_probs=43.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 68 GNYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 68 ~~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.+||.+|-++..++....|-..+.|+..+|.|..+||+..|.+--|.
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 37999999999999999999999999999999999999999776554
No 52
>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=83.69 E-value=3.1 Score=27.64 Aligned_cols=41 Identities=24% Similarity=0.336 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhh
Q 024860 72 KEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLK 113 (261)
Q Consensus 72 ~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk 113 (261)
++++..++.++-..|-.+.+||..+ |.+...|+.+.+..++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 4667788888888899999999999 9999999998876654
No 53
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=76.36 E-value=1.6 Score=41.46 Aligned_cols=65 Identities=12% Similarity=0.283 Sum_probs=51.0
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccc--cCCC------CccCCCCHHHHHHHH
Q 024860 13 KKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNY--LRPN------IKRGNYTKEEEDTII 79 (261)
Q Consensus 13 kk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~--L~p~------i~k~~WT~EED~~L~ 79 (261)
.--+||.+|-+++..+....|. ++.-|+.+++ +|..+|++.+|.+- .+|. ..+-++..+|--.|.
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP-~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~ 436 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGT-DFSLISSLFP-NRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLR 436 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcc-hHHHHHHhcC-chhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHH
Confidence 3457999999999999999999 9999999999 99999999998863 2221 124566666665443
No 54
>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=74.51 E-value=2.8 Score=31.40 Aligned_cols=22 Identities=41% Similarity=0.714 Sum_probs=12.8
Q ss_pred CcCCCCHHHHHHH--------HHHHHHhCC
Q 024860 13 KKGTWTPEEDRKL--------IAYVTKYGY 34 (261)
Q Consensus 13 kk~~WT~eED~~L--------~~~V~~~g~ 34 (261)
..|-||+|+|+.| ..++++||.
T Consensus 46 ~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 46 MPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp -TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 3678999999999 345667764
No 55
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=73.65 E-value=6.9 Score=38.15 Aligned_cols=48 Identities=17% Similarity=0.220 Sum_probs=42.8
Q ss_pred cCCCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 67 RGNYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
...||.||-.++-++...||.+..+|-+.||.|+-.+|...|...-|.
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~ 234 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKT 234 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHH
Confidence 557999999999999999999999999999999999999988665443
No 56
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=68.66 E-value=7.8 Score=31.82 Aligned_cols=46 Identities=11% Similarity=0.130 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHhhhhhhhh
Q 024860 72 KEEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTSLKKRLKR 118 (261)
Q Consensus 72 ~EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~ 118 (261)
.+-|.+|+.+..+-| -.|+.||+.+ |-+...|+.|+..+....+-+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 357889999888888 5799999999 999999999998887776544
No 57
>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=68.07 E-value=13 Score=24.05 Aligned_cols=38 Identities=21% Similarity=0.441 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHh
Q 024860 73 EEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTS 111 (261)
Q Consensus 73 EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~ 111 (261)
+=|..|+.+...-| -.+..||+.+ |=+...|..|+..+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 45788898888888 4699999999 99999999998653
No 58
>smart00595 MADF subfamily of SANT domain.
Probab=66.57 E-value=5.1 Score=29.42 Aligned_cols=24 Identities=33% Similarity=0.681 Sum_probs=20.7
Q ss_pred hhHhhhcCCCCCHHHHHHHHHHhhh
Q 024860 89 WSAIAAQLPGRTDNEIKNHWHTSLK 113 (261)
Q Consensus 89 W~~Ia~~l~gRt~~~~r~Rw~~~lk 113 (261)
|..||..| |-+..+|+.+|.++-.
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~ 53 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 99999999 5599999999977643
No 59
>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=65.96 E-value=5.5 Score=29.82 Aligned_cols=17 Identities=24% Similarity=0.511 Sum_probs=10.2
Q ss_pred CCCccCCCCHHHHHHHH
Q 024860 63 PNIKRGNYTKEEEDTII 79 (261)
Q Consensus 63 p~i~k~~WT~EED~~L~ 79 (261)
|....|-||+|+|+.|.
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 55668899999999984
No 60
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=63.70 E-value=9.9 Score=31.59 Aligned_cols=46 Identities=7% Similarity=0.061 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHhhhhhhhh
Q 024860 72 KEEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTSLKKRLKR 118 (261)
Q Consensus 72 ~EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~ 118 (261)
.+-|.+|+.+..+-| -.|+.||+.+ |=+...|+.|+..+.+..+-+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeE
Confidence 567888998888877 5699999999 999999999998888776544
No 61
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=63.65 E-value=3.1 Score=42.70 Aligned_cols=44 Identities=16% Similarity=0.319 Sum_probs=40.1
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccc
Q 024860 14 KGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMN 59 (261)
Q Consensus 14 k~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~ 59 (261)
...||+.|-.++.+++..|.. ++..|++.+. +++..||.+-|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K-DF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK-DFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc-cHHHHHHHhc-cccHHHHHHHHHH
Confidence 457999999999999999998 9999999999 9999999987654
No 62
>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=61.75 E-value=21 Score=23.24 Aligned_cols=41 Identities=29% Similarity=0.386 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 73 EEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 73 EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
+++..++.++--.|-.+..||..| |-+...|+.+-...+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 344455555555566799999999 88999998887776654
No 63
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=61.55 E-value=2.5 Score=27.38 Aligned_cols=37 Identities=24% Similarity=0.348 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccccccccccccccc
Q 024860 20 EEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWM 58 (261)
Q Consensus 20 eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~ 58 (261)
+=|.+|+.+.++.+...+.+||+.+| =+...|..|+.
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~ 39 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIR 39 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHH
Confidence 34889999999999889999999998 55566777654
No 64
>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=60.41 E-value=4.9 Score=29.88 Aligned_cols=44 Identities=25% Similarity=0.534 Sum_probs=29.2
Q ss_pred CCCHHHHHHHHHHHHHh---CC----C-----Cccccccccc----cccccccccccccc
Q 024860 16 TWTPEEDRKLIAYVTKY---GY----W-----NWRQLPKYAG----LARCGKSCRLRWMN 59 (261)
Q Consensus 16 ~WT~eED~~L~~~V~~~---g~----~-----~W~~Ia~~~~----~~R~~~qcr~Rw~~ 59 (261)
+||+++++.|++++... |. + .|..|++.+. ...+..||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999988654 21 1 2777775543 34455677777654
No 65
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=58.38 E-value=20 Score=31.32 Aligned_cols=43 Identities=21% Similarity=0.287 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHhcCCchhHhhhcC---CCCCHHHHHHHHHHhh
Q 024860 69 NYTKEEEDTIIRLHESLGNRWSAIAAQL---PGRTDNEIKNHWHTSL 112 (261)
Q Consensus 69 ~WT~EED~~L~~~~~~~G~~W~~Ia~~l---~gRt~~~~r~Rw~~~l 112 (261)
.|++++|-+|+..|.. |+.-..|+.-+ -.-|-.+|..||+.+|
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~ll 46 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALL 46 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHH
Confidence 4999999999998864 45555565433 3468899999999987
No 66
>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=58.32 E-value=13 Score=27.80 Aligned_cols=30 Identities=23% Similarity=0.560 Sum_probs=24.2
Q ss_pred HHHHHHHHHhcCCchhHhhhcCCCCCHHHHH
Q 024860 75 EDTIIRLHESLGNRWSAIAAQLPGRTDNEIK 105 (261)
Q Consensus 75 D~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r 105 (261)
|+.|..+...+|..|..+|.+| |=+..+|.
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~ 31 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIY 31 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 5678889999999999999998 65555443
No 67
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=57.01 E-value=3.9 Score=33.65 Aligned_cols=46 Identities=15% Similarity=0.151 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCc
Q 024860 19 PEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIK 66 (261)
Q Consensus 19 ~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~ 66 (261)
.+-|.+|+.+.++.|...|.+||+.+| -+...|+.|+.+....++-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 357999999999999889999999997 7778899998887665543
No 68
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=56.15 E-value=11 Score=40.99 Aligned_cols=75 Identities=16% Similarity=0.219 Sum_probs=46.0
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCCccCCCCHHHHHHHHHHHHhc-CCchhH
Q 024860 13 KKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIRLHESL-GNRWSA 91 (261)
Q Consensus 13 kk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~~~~~~-G~~W~~ 91 (261)
.-.-|..++|..|+-.|-+||-++|.+|-.- ......=...+...+..+.+=...-..|+.+...+ +.+|.+
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~D-------p~L~l~dKi~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLD-------PDLGLTDKIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccC-------ccccchhhhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 3456999999999999999999999998521 11111001112222445556666666677666666 455555
Q ss_pred hhh
Q 024860 92 IAA 94 (261)
Q Consensus 92 Ia~ 94 (261)
..+
T Consensus 1205 ~~~ 1207 (1373)
T KOG0384|consen 1205 KLK 1207 (1373)
T ss_pred hhh
Confidence 443
No 69
>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=56.08 E-value=17 Score=27.16 Aligned_cols=31 Identities=23% Similarity=0.453 Sum_probs=24.7
Q ss_pred HHHHHHHHHhcCCchhHhhhcCCCCCHHHHHH
Q 024860 75 EDTIIRLHESLGNRWSAIAAQLPGRTDNEIKN 106 (261)
Q Consensus 75 D~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~ 106 (261)
|..|..+...+|..|..+|..| |=+...|..
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 6678888999999999999999 656555443
No 70
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=53.43 E-value=3.6 Score=34.29 Aligned_cols=45 Identities=22% Similarity=0.236 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCC
Q 024860 19 PEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNI 65 (261)
Q Consensus 19 ~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i 65 (261)
.+-|.+|+.+.++.|.-.|.+||+.+| -+...|+.|+.+....++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 567999999999999989999999998 666788998888766554
No 71
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=52.31 E-value=24 Score=36.52 Aligned_cols=45 Identities=9% Similarity=0.061 Sum_probs=40.4
Q ss_pred cCCCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHh
Q 024860 67 RGNYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTS 111 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~ 111 (261)
...||+.|-.+.-+++-.|..+.-.|++.++++|-.+|-..|+..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 347999999999999999999999999999999999998876554
No 72
>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=52.30 E-value=49 Score=31.00 Aligned_cols=49 Identities=29% Similarity=0.577 Sum_probs=37.6
Q ss_pred cCCCCHHHHHHHHHHHHhc-CC---chhHhhhcCCCCCHHHHHHHHHHhhhhhh
Q 024860 67 RGNYTKEEEDTIIRLHESL-GN---RWSAIAAQLPGRTDNEIKNHWHTSLKKRL 116 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~-G~---~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~ 116 (261)
-..||.-|...|+++.... |. .-..|++.++||+..+|++-- +.||-++
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl-~~LK~rv 73 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFL-QQLKGRV 73 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHH-HHHHHHH
Confidence 3579999999999887765 43 366889999999999999854 4555543
No 73
>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=51.79 E-value=31 Score=27.30 Aligned_cols=35 Identities=26% Similarity=0.389 Sum_probs=26.6
Q ss_pred HHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 79 IRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 79 ~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
+.+.-..|-.+..||+.+ |.+...++.+.+..+++
T Consensus 122 l~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 122 FILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333333467899999988 99999999999876544
No 74
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=51.76 E-value=11 Score=38.06 Aligned_cols=47 Identities=13% Similarity=0.302 Sum_probs=34.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcccccccccc---------ccccccccccccccc
Q 024860 14 KGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGL---------ARCGKSCRLRWMNYL 61 (261)
Q Consensus 14 k~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~---------~R~~~qcr~Rw~~~L 61 (261)
|..||..|..-+..++..+|. ++++|-+++-. -++-.|.|.+|.+.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 667999999999999999999 99888433221 234456677666543
No 75
>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=50.43 E-value=36 Score=28.44 Aligned_cols=47 Identities=19% Similarity=0.215 Sum_probs=38.7
Q ss_pred ccCCCCHHHHHHHHHHHHhcCCchhHhhhcC----CCCCHHHHHHHHHHhh
Q 024860 66 KRGNYTKEEEDTIIRLHESLGNRWSAIAAQL----PGRTDNEIKNHWHTSL 112 (261)
Q Consensus 66 ~k~~WT~EED~~L~~~~~~~G~~W~~Ia~~l----~gRt~~~~r~Rw~~~l 112 (261)
....-|..|.+.|..|+++||.++..+|.-. --.|..+|+.+...+.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 4556889999999999999999999998643 2489999998876654
No 76
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=50.06 E-value=20 Score=30.15 Aligned_cols=42 Identities=29% Similarity=0.323 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHh
Q 024860 69 NYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTS 111 (261)
Q Consensus 69 ~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~ 111 (261)
.||+|..++|.+|.. -|-.=++||+.|.|.|.+.|--+-+.+
T Consensus 2 ~Wtde~~~~L~~lw~-~G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 2 SWTDERVERLRKLWA-EGLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CCCHHHHHHHHHHHH-cCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 599999999998884 476678999999768888887766543
No 77
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=49.13 E-value=28 Score=35.25 Aligned_cols=51 Identities=12% Similarity=0.371 Sum_probs=40.2
Q ss_pred cCCCCHHHHHHHHHHHHhcCCchhHhhhc----------CCCCCHHHHHHHHHHhhhhhhh
Q 024860 67 RGNYTKEEEDTIIRLHESLGNRWSAIAAQ----------LPGRTDNEIKNHWHTSLKKRLK 117 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~G~~W~~Ia~~----------l~gRt~~~~r~Rw~~~lk~~~k 117 (261)
|..||-+|.+-...+++++|.+..+|-+. ..-+|-.|+|.+|+..+++.-+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHh
Confidence 66899999999999999999999888332 2235667899998888776543
No 78
>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=48.63 E-value=18 Score=26.65 Aligned_cols=29 Identities=24% Similarity=0.618 Sum_probs=22.9
Q ss_pred HHHHHHHHHhcCCchhHhhhcCCCCCHHHH
Q 024860 75 EDTIIRLHESLGNRWSAIAAQLPGRTDNEI 104 (261)
Q Consensus 75 D~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~ 104 (261)
|..|..+.+.+|..|.++|..| |=+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4567888899999999999999 6555443
No 79
>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=47.24 E-value=36 Score=25.13 Aligned_cols=38 Identities=18% Similarity=0.394 Sum_probs=28.1
Q ss_pred HHHHHHHhcCC--------chhHhhhcCCC-C--C--HHHHHHHHHHhhhh
Q 024860 77 TIIRLHESLGN--------RWSAIAAQLPG-R--T--DNEIKNHWHTSLKK 114 (261)
Q Consensus 77 ~L~~~~~~~G~--------~W~~Ia~~l~g-R--t--~~~~r~Rw~~~lk~ 114 (261)
.|..+|..+|| +|..||..|.- . + ..++|..|..+|.+
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 57777888774 49999999822 1 2 46899999988865
No 80
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=46.18 E-value=39 Score=25.21 Aligned_cols=39 Identities=23% Similarity=0.443 Sum_probs=29.6
Q ss_pred HHHHHHHhcCC--------chhHhhhcCCC-----CCHHHHHHHHHHhhhhh
Q 024860 77 TIIRLHESLGN--------RWSAIAAQLPG-----RTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 77 ~L~~~~~~~G~--------~W~~Ia~~l~g-----Rt~~~~r~Rw~~~lk~~ 115 (261)
.|..+|.+.|| .|..||..|.- ....+++..|..+|.+-
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 46777877774 49999998822 34678899999998764
No 81
>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=45.96 E-value=43 Score=31.34 Aligned_cols=87 Identities=17% Similarity=0.313 Sum_probs=60.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCC---CcccccccccccccccccccccccccCCCCccCCCCHHHHHHHHHHHHh-c----
Q 024860 14 KGTWTPEEDRKLIAYVTKYGYW---NWRQLPKYAGLARCGKSCRLRWMNYLRPNIKRGNYTKEEEDTIIRLHES-L---- 85 (261)
Q Consensus 14 k~~WT~eED~~L~~~V~~~g~~---~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i~k~~WT~EED~~L~~~~~~-~---- 85 (261)
...||.-|.+.|+.+.+..... +-.+|++.+. +|+..+++. |.+.|+ +..+.+++.+ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHH-HHHHHH------------HHHHHHHHHHhccccc
Confidence 3569999999999999876322 4457778887 898887765 333332 2344444444 2
Q ss_pred -CCc------------hhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 86 -GNR------------WSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 86 -G~~------------W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
|.+ |..+|.++.|.-...+---|-..|.-
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~i 128 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLTI 128 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHHH
Confidence 211 99999999999999988888777643
No 82
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=44.04 E-value=1.9e+02 Score=27.82 Aligned_cols=44 Identities=16% Similarity=0.184 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCchhHhh-hcCCCCCHHHHHHHHHHh
Q 024860 68 GNYTKEEEDTIIRLHESLGNRWSAIA-AQLPGRTDNEIKNHWHTS 111 (261)
Q Consensus 68 ~~WT~EED~~L~~~~~~~G~~W~~Ia-~~l~gRt~~~~r~Rw~~~ 111 (261)
..|+++|-...-+-++.||.....|. .+++.|+--.|-..|...
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 46999999999999999999999995 578999999998876443
No 83
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=43.98 E-value=43 Score=25.22 Aligned_cols=44 Identities=11% Similarity=0.137 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHhhhhhhh
Q 024860 73 EEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTSLKKRLK 117 (261)
Q Consensus 73 EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k 117 (261)
+.|..|+.+....| -.++.||+.+ |-+...|+.|...+.+..+-
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i 47 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVI 47 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 56888888888887 4699999999 99999999999888776543
No 84
>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=43.88 E-value=19 Score=25.62 Aligned_cols=25 Identities=24% Similarity=0.514 Sum_probs=20.3
Q ss_pred hhHhhhcCCC-CCHHHHHHHHHHhhh
Q 024860 89 WSAIAAQLPG-RTDNEIKNHWHTSLK 113 (261)
Q Consensus 89 W~~Ia~~l~g-Rt~~~~r~Rw~~~lk 113 (261)
|..||..|.+ -+...|+.||.++-.
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHH
Confidence 9999999943 678899999987654
No 85
>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=43.43 E-value=28 Score=25.60 Aligned_cols=34 Identities=26% Similarity=0.568 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHH
Q 024860 72 KEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNH 107 (261)
Q Consensus 72 ~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~R 107 (261)
.||-++|+..- ..|.+|..+|.+| |=+...|++-
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHc-CCCHHHHHHH
Confidence 57888887322 4678999999999 7777777653
No 86
>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=42.14 E-value=31 Score=25.62 Aligned_cols=27 Identities=33% Similarity=0.665 Sum_probs=20.6
Q ss_pred HHHHHHhcCCchhHhhhcCCCCCHHHHH
Q 024860 78 IIRLHESLGNRWSAIAAQLPGRTDNEIK 105 (261)
Q Consensus 78 L~~~~~~~G~~W~~Ia~~l~gRt~~~~r 105 (261)
|..+....|..|..+|..| |=+..+|.
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 3346688899999999999 76766653
No 87
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=42.12 E-value=52 Score=25.18 Aligned_cols=34 Identities=26% Similarity=0.261 Sum_probs=26.0
Q ss_pred HHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 80 RLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 80 ~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.++-..|..+..||+.+ |-+...|+.+....+++
T Consensus 120 ~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 120 VLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33334577899999999 77999999988776554
No 88
>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=42.02 E-value=31 Score=25.64 Aligned_cols=31 Identities=26% Similarity=0.580 Sum_probs=24.9
Q ss_pred HHHHHHHHHhcCCchhHhhhcCCCCCHHHHHH
Q 024860 75 EDTIIRLHESLGNRWSAIAAQLPGRTDNEIKN 106 (261)
Q Consensus 75 D~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~ 106 (261)
|..|-.+...+|.+|..+|..| |=+...|..
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 5577788889999999999999 666666654
No 89
>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=40.97 E-value=36 Score=24.65 Aligned_cols=30 Identities=27% Similarity=0.654 Sum_probs=21.8
Q ss_pred HHHHHHHHHHh-cCCchhHhhhcCCCCCHHHH
Q 024860 74 EEDTIIRLHES-LGNRWSAIAAQLPGRTDNEI 104 (261)
Q Consensus 74 ED~~L~~~~~~-~G~~W~~Ia~~l~gRt~~~~ 104 (261)
-.+.|..++.. .|..|..+|..| |=+..+|
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 34566777777 899999999999 5444444
No 90
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=39.91 E-value=40 Score=26.49 Aligned_cols=45 Identities=18% Similarity=0.237 Sum_probs=31.4
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccccc
Q 024860 13 KKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYL 61 (261)
Q Consensus 13 kk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L 61 (261)
++.+||.|+-..++..+...|. .-.+||+.+|.+ .+-..+|.+.+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~-sv~evA~e~gIs---~~tl~~W~r~y 53 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM-TVSLVARQHGVA---ASQLFLWRKQY 53 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC-CHHHHHHHHCcC---HHHHHHHHHHH
Confidence 3577999998888887777665 677888888742 23345666543
No 91
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=39.38 E-value=35 Score=34.43 Aligned_cols=50 Identities=18% Similarity=0.360 Sum_probs=43.5
Q ss_pred CccCCCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 65 IKRGNYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 65 i~k~~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
...+.|+.+|-++--....+.|.+-+.|+..+++|..++||..+..-=++
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r 456 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKR 456 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhc
Confidence 34568999999999999999999999999999999999999988554333
No 92
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=38.62 E-value=19 Score=34.57 Aligned_cols=48 Identities=15% Similarity=0.320 Sum_probs=40.6
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccc-----ccccccccccccccccc
Q 024860 12 LKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKY-----AGLARCGKSCRLRWMNY 60 (261)
Q Consensus 12 lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~-----~~~~R~~~qcr~Rw~~~ 60 (261)
+.-..||.+|.+-|.++.++|.- .|--||.. .+..||....++||..+
T Consensus 128 l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 34467999999999999999998 88888865 66569999999999754
No 93
>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=37.28 E-value=67 Score=20.33 Aligned_cols=33 Identities=24% Similarity=0.238 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHH
Q 024860 74 EEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNH 107 (261)
Q Consensus 74 ED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~R 107 (261)
|.+.|.++.+.+|++-+..|+.| |=+...+..+
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~k 38 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHH
Confidence 67788999999999999999988 6555555443
No 94
>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=36.62 E-value=37 Score=25.36 Aligned_cols=30 Identities=37% Similarity=0.659 Sum_probs=23.0
Q ss_pred HHHHHHHHhcCCchhHhhhcCCCCCHHHHHH
Q 024860 76 DTIIRLHESLGNRWSAIAAQLPGRTDNEIKN 106 (261)
Q Consensus 76 ~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~ 106 (261)
+.|-.+....|.+|..+|..| |=+..+|..
T Consensus 3 ~~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 3 KHLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 345556688899999999999 777776655
No 95
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=36.51 E-value=48 Score=28.62 Aligned_cols=45 Identities=27% Similarity=0.287 Sum_probs=36.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhhh
Q 024860 68 GNYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 68 ~~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~ 115 (261)
...|+.|-+.|.-+.+ |-.=++||..| +.+.+-+|.+..++++|-
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 4789999988776554 43346999999 999999999999999884
No 96
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=36.32 E-value=42 Score=25.11 Aligned_cols=26 Identities=27% Similarity=0.445 Sum_probs=21.0
Q ss_pred HHHHHHHHHhcCCchhHhhhcCCCCCH
Q 024860 75 EDTIIRLHESLGNRWSAIAAQLPGRTD 101 (261)
Q Consensus 75 D~~L~~~~~~~G~~W~~Ia~~l~gRt~ 101 (261)
|..|..+.+.+|..|.++|..| |=+.
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~ 29 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSV 29 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCH
Confidence 5677788899999999999998 4333
No 97
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=34.87 E-value=72 Score=25.74 Aligned_cols=29 Identities=14% Similarity=0.210 Sum_probs=23.0
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-.+..||+.| |.+...++.+.+..+++
T Consensus 143 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 143 EGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466899999999 88999998887665443
No 98
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=34.32 E-value=29 Score=37.60 Aligned_cols=32 Identities=34% Similarity=0.532 Sum_probs=27.6
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCcccccccc
Q 024860 13 KKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYA 44 (261)
Q Consensus 13 kk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~ 44 (261)
++..+|.|||.-|+-++.+||-++|.+|-..+
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 45569999999999999999999999996544
No 99
>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=34.07 E-value=44 Score=24.87 Aligned_cols=21 Identities=29% Similarity=0.635 Sum_probs=19.0
Q ss_pred HHHHHHHHhcCCchhHhhhcC
Q 024860 76 DTIIRLHESLGNRWSAIAAQL 96 (261)
Q Consensus 76 ~~L~~~~~~~G~~W~~Ia~~l 96 (261)
..|..+...+|..|..+|.+|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L 23 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL 23 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc
Confidence 468889999999999999998
No 100
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=33.80 E-value=66 Score=21.75 Aligned_cols=34 Identities=24% Similarity=0.409 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHH
Q 024860 73 EEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNH 107 (261)
Q Consensus 73 EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~R 107 (261)
++|+-.+.++.+.|-.=.+||+.+ ||+...|++.
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~y 40 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRY 40 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHH
Confidence 345556778888998889999999 9999888764
No 101
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=33.66 E-value=74 Score=25.57 Aligned_cols=29 Identities=21% Similarity=0.242 Sum_probs=23.1
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-....||+.| |-+...|+.+.+...++
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466799999999 88899998888765443
No 102
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=32.14 E-value=26 Score=34.29 Aligned_cols=46 Identities=13% Similarity=0.130 Sum_probs=39.3
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccc
Q 024860 12 LKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMN 59 (261)
Q Consensus 12 lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~ 59 (261)
-....||.||--++-++...||. +..+|-+.|+ .|+-.++++-|..
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~LP-~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFGK-DFHKIRQALP-HRSLASLVQYYYS 230 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhcc-cHHHHHHHcc-CccHHHHHHHHHH
Confidence 34567999999999999999999 9999999998 9988887765543
No 103
>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=31.88 E-value=31 Score=29.03 Aligned_cols=34 Identities=24% Similarity=0.419 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccc-cccccc
Q 024860 16 TWTPEEDRKLIAYVTKYGYWNWRQLPKYAG-LARCGK 51 (261)
Q Consensus 16 ~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~-~~R~~~ 51 (261)
.||.|+.++|.++... |. .=.+||+.|| .+|++.
T Consensus 2 ~Wtde~~~~L~~lw~~-G~-SasqIA~~lg~vsRnAV 36 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GL-SASQIARQLGGVSRNAV 36 (162)
T ss_pred CCCHHHHHHHHHHHHc-CC-CHHHHHHHhCCcchhhh
Confidence 4999999999999965 44 6689999999 566654
No 104
>PRK04217 hypothetical protein; Provisional
Probab=31.83 E-value=1e+02 Score=24.32 Aligned_cols=46 Identities=20% Similarity=0.114 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhhh
Q 024860 68 GNYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 68 ~~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~ 115 (261)
..-|.+| ..++.+....|-.-.+||+.+ |-+...|+.+++...++-
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 3466666 566777777788899999999 999999999987755443
No 105
>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=31.60 E-value=33 Score=28.64 Aligned_cols=46 Identities=13% Similarity=0.114 Sum_probs=31.9
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCcccccccccc---cccccccccccc
Q 024860 12 LKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGL---ARCGKSCRLRWM 58 (261)
Q Consensus 12 lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~---~R~~~qcr~Rw~ 58 (261)
.+...-|..|..-|..||++||. ++.+.+.-..+ ..|..||+.+..
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHH
Confidence 45566899999999999999997 88877743321 245555554433
No 106
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=30.33 E-value=85 Score=25.03 Aligned_cols=47 Identities=11% Similarity=0.169 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHhcC-CchhHhhhcCCCCCHHHHHHHHHHhhhhhhhhC
Q 024860 72 KEEEDTIIRLHESLG-NRWSAIAAQLPGRTDNEIKNHWHTSLKKRLKRN 119 (261)
Q Consensus 72 ~EED~~L~~~~~~~G-~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~~ 119 (261)
.+-|.+|+++.+.-| -.+..||+.+ |-+...|+.|=..+.+..+.++
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~~ 54 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIKG 54 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCceee
Confidence 356788888888888 4699999999 9999999999988877765443
No 107
>smart00351 PAX Paired Box domain.
Probab=30.02 E-value=86 Score=24.83 Aligned_cols=71 Identities=13% Similarity=0.112 Sum_probs=45.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccccccc-cccccccccc--ccCCCC----ccCCCCHHHHHHHHHHHHhcC
Q 024860 14 KGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARC-GKSCRLRWMN--YLRPNI----KRGNYTKEEEDTIIRLHESLG 86 (261)
Q Consensus 14 k~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~-~~qcr~Rw~~--~L~p~i----~k~~WT~EED~~L~~~~~~~G 86 (261)
..+.+.++-.+++.++. -|. .-.+||+.+|..|. ...+..||.. .+.|.- +...-+.++++.|++++.++.
T Consensus 15 ~~~~s~~~R~riv~~~~-~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p 92 (125)
T smart00351 15 GRPLPDEERQRIVELAQ-NGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENP 92 (125)
T ss_pred CCCCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCC
Confidence 45588999999998886 454 77999999987654 3345556653 344432 222356666777776666544
No 108
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=29.84 E-value=98 Score=25.91 Aligned_cols=29 Identities=17% Similarity=0.233 Sum_probs=23.5
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-...+||..| |-+...++.|.+..+++
T Consensus 149 ~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 149 QGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 567799999999 99999999998655443
No 109
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=29.75 E-value=92 Score=25.47 Aligned_cols=29 Identities=14% Similarity=0.077 Sum_probs=23.3
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|.....||..| |-+...++++.+...++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456799999999 99999999888765544
No 110
>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=29.27 E-value=1.4e+02 Score=18.26 Aligned_cols=40 Identities=23% Similarity=0.366 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHh
Q 024860 70 YTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTS 111 (261)
Q Consensus 70 WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~ 111 (261)
.+++ +..++.++-..|-.+..||..+ |-+...|+.+....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3444 3444455445667899999998 77777776655443
No 111
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=28.55 E-value=40 Score=34.09 Aligned_cols=50 Identities=12% Similarity=0.251 Sum_probs=44.3
Q ss_pred CCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccccccccccccccccc
Q 024860 8 DKTGLKKGTWTPEEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMN 59 (261)
Q Consensus 8 ~k~~lkk~~WT~eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~ 59 (261)
..+....++|+.+|-.+...+....|. +..-|+...+ +|..+|++.++..
T Consensus 403 ~sk~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 403 YSKKLETDKWDASETELFYKALSERGS-DFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred ccCccccCcccchhhHHhhhHHhhhcc-cccccccccc-cccHHHHHHHHhh
Confidence 345677889999999999999999998 9999999998 9999999988764
No 112
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=28.49 E-value=1.2e+02 Score=25.44 Aligned_cols=36 Identities=17% Similarity=0.261 Sum_probs=27.3
Q ss_pred HHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhh
Q 024860 76 DTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSL 112 (261)
Q Consensus 76 ~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~l 112 (261)
..++.+..-.|-.+.+||+.| |-+...++.+|...-
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 334444444567899999999 999999999997654
No 113
>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=28.31 E-value=82 Score=25.86 Aligned_cols=29 Identities=10% Similarity=0.135 Sum_probs=23.2
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-....||..| |-+...|+.+.+..+++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 356689999998 88899999988766554
No 114
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=27.31 E-value=1.2e+02 Score=25.11 Aligned_cols=29 Identities=14% Similarity=0.192 Sum_probs=23.8
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-....||..| |-+...++.+.+..+++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 467799999999 88999999998776544
No 115
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=27.06 E-value=21 Score=28.66 Aligned_cols=44 Identities=11% Similarity=0.145 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCC
Q 024860 20 EEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNI 65 (261)
Q Consensus 20 eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i 65 (261)
+-|.+++++.++.+...+.+||+.+| -+...|+.|-.+..+.++
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 56889999999999889999999997 667778887776655443
No 116
>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=26.62 E-value=70 Score=21.41 Aligned_cols=44 Identities=27% Similarity=0.385 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHHHHHhhhhh
Q 024860 69 NYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 69 ~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~ 115 (261)
..|+.|-+.|.-+.. |..=.+||..+ |.+...++.+..+++++-
T Consensus 3 ~LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHHh
Confidence 356667666554443 55557999999 999999999988877663
No 117
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=26.36 E-value=26 Score=26.42 Aligned_cols=43 Identities=21% Similarity=0.179 Sum_probs=34.1
Q ss_pred HHHHHHHHHHHHhCCCCcccccccccccccccccccccccccCCC
Q 024860 20 EEDRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPN 64 (261)
Q Consensus 20 eED~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~ 64 (261)
+.|.+++.++.+.+...+.+||+.+| -+...|+.|..+....+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 56889999999988889999999997 66667777776655444
No 118
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=26.18 E-value=1.1e+02 Score=25.05 Aligned_cols=28 Identities=14% Similarity=0.113 Sum_probs=22.4
Q ss_pred CCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 86 GNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 86 G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
|-.-.+||..| |-+...++.+.+..+++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56689999988 88999999988765544
No 119
>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=25.98 E-value=1.2e+02 Score=24.47 Aligned_cols=29 Identities=24% Similarity=0.328 Sum_probs=22.8
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-....||..| |-+...|+.+.+..+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356788999888 88999999888776554
No 120
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.94 E-value=1.6e+02 Score=22.48 Aligned_cols=46 Identities=24% Similarity=0.398 Sum_probs=35.4
Q ss_pred cCCCCHHHHHHHHHHHHhcCCchhHhhhcCCCC-CHHHHHHHHHHhhhh
Q 024860 67 RGNYTKEEEDTIIRLHESLGNRWSAIAAQLPGR-TDNEIKNHWHTSLKK 114 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gR-t~~~~r~Rw~~~lk~ 114 (261)
+..||.|.-..+++++..-|..=+.||+.+ |- ..++++ +|...+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~-~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLY-KWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHH-HHHHHHHH
Confidence 568999999999999999888889999999 75 555544 45444443
No 121
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=25.70 E-value=1.3e+02 Score=24.64 Aligned_cols=30 Identities=20% Similarity=0.267 Sum_probs=24.2
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~ 115 (261)
.|-...+||..| |-+...++.+.+..+++-
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~L 175 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAAL 175 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 466789999999 999999999887766543
No 122
>PRK01905 DNA-binding protein Fis; Provisional
Probab=25.70 E-value=1.6e+02 Score=21.24 Aligned_cols=35 Identities=23% Similarity=0.228 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHHH
Q 024860 72 KEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKNH 107 (261)
Q Consensus 72 ~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~R 107 (261)
.-|.+.|++++...|++.++.|+.| |=+...++.+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 3467788999999999999999888 5555554443
No 123
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=25.08 E-value=1.2e+02 Score=25.08 Aligned_cols=28 Identities=11% Similarity=0.185 Sum_probs=21.9
Q ss_pred CCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 86 GNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 86 G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
|-....||..| |-+...|+.+.+..+++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55689999988 88899999887665443
No 124
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=24.77 E-value=1.5e+02 Score=23.55 Aligned_cols=29 Identities=17% Similarity=0.240 Sum_probs=23.0
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-.-..||..| |-+...|+.|.+..+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456689999999 88999999887665543
No 125
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.55 E-value=1.8e+02 Score=23.93 Aligned_cols=33 Identities=21% Similarity=0.121 Sum_probs=27.3
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhhhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKKRLKR 118 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~~k~ 118 (261)
.|-...+||..| |-+...++.|.+.-+..-+.+
T Consensus 142 ~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 142 DGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHh
Confidence 466799999999 999999999998877765544
No 126
>PLN03162 golden-2 like transcription factor; Provisional
Probab=24.23 E-value=5.7e+02 Score=24.75 Aligned_cols=46 Identities=22% Similarity=0.218 Sum_probs=35.9
Q ss_pred cCCCCHHHHHHHHHHHHhcCCc---hhHhhhcC--CCCCHHHHHHHHHHhh
Q 024860 67 RGNYTKEEEDTIIRLHESLGNR---WSAIAAQL--PGRTDNEIKNHWHTSL 112 (261)
Q Consensus 67 k~~WT~EED~~L~~~~~~~G~~---W~~Ia~~l--~gRt~~~~r~Rw~~~l 112 (261)
|-.||+|-.++.+++|.++|.. =+.|-+.| +|=|..+|+.+.+.|-
T Consensus 237 RLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYR 287 (526)
T PLN03162 237 KVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYR 287 (526)
T ss_pred cccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHH
Confidence 4579999999999999999932 34555555 7889999988876653
No 127
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=24.02 E-value=83 Score=20.16 Aligned_cols=36 Identities=31% Similarity=0.416 Sum_probs=17.6
Q ss_pred CCCHHHHHHHHHHHHhcCCchhHhhhcCCCCCHHHHHH
Q 024860 69 NYTKEEEDTIIRLHESLGNRWSAIAAQLPGRTDNEIKN 106 (261)
Q Consensus 69 ~WT~EED~~L~~~~~~~G~~W~~Ia~~l~gRt~~~~r~ 106 (261)
.+|.+|=..|..++ .-|-.=.+||+.| ||+...|..
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHH
Confidence 46677766666664 5677788999999 999887764
No 128
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.52 E-value=1.5e+02 Score=24.63 Aligned_cols=30 Identities=23% Similarity=0.133 Sum_probs=23.9
Q ss_pred hcCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 84 SLGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 84 ~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
..|-....||..| |-+...|+.+....+++
T Consensus 120 ~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 120 LEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3567799999999 89999999988765544
No 129
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=23.12 E-value=1.8e+02 Score=24.17 Aligned_cols=34 Identities=21% Similarity=0.267 Sum_probs=24.7
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHh---hhhhhhhC
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTS---LKKRLKRN 119 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~---lk~~~k~~ 119 (261)
.|-.-..||..| |-+...|+.|.+.. |++.+.+.
T Consensus 151 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~~l~~~ 187 (195)
T PRK12532 151 LGFSSDEIQQMC-GISTSNYHTIMHRARESLRQCLQIK 187 (195)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 466689999988 88888888887664 44555443
No 130
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=22.98 E-value=1.7e+02 Score=23.81 Aligned_cols=31 Identities=19% Similarity=0.251 Sum_probs=24.8
Q ss_pred hcCCchhHhhhcCCCCCHHHHHHHHHHhhhhh
Q 024860 84 SLGNRWSAIAAQLPGRTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 84 ~~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~ 115 (261)
..|-...+||+.| |-+...|+.+-+.-+++-
T Consensus 133 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 133 LDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3566799999999 999999999887766553
No 131
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=22.85 E-value=1.3e+02 Score=23.04 Aligned_cols=47 Identities=19% Similarity=0.175 Sum_probs=29.3
Q ss_pred CCCCHHHHHHHHHHHHhc----C----CchhHhhhc----C-CCCCHHHHHHHHHHhhhh
Q 024860 68 GNYTKEEEDTIIRLHESL----G----NRWSAIAAQ----L-PGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 68 ~~WT~EED~~L~~~~~~~----G----~~W~~Ia~~----l-~gRt~~~~r~Rw~~~lk~ 114 (261)
..||+|++..||+.+..| | ..|..+-.. | ..=+..|+.+.-+.+-++
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~K 64 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKK 64 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 469999999999887665 6 235444333 3 223667777766554433
No 132
>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=22.73 E-value=1.6e+02 Score=24.46 Aligned_cols=29 Identities=14% Similarity=0.053 Sum_probs=23.1
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-.-..||..| |-+...|+.|....+++
T Consensus 146 ~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 146 LGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466789999999 99999999887666443
No 133
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=22.67 E-value=50 Score=23.54 Aligned_cols=44 Identities=23% Similarity=0.569 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhCCCCcccccccccccccccccccccccccCCCC-------ccCCCCHHHHHHH
Q 024860 22 DRKLIAYVTKYGYWNWRQLPKYAGLARCGKSCRLRWMNYLRPNI-------KRGNYTKEEEDTI 78 (261)
Q Consensus 22 D~~L~~~V~~~g~~~W~~Ia~~~~~~R~~~qcr~Rw~~~L~p~i-------~k~~WT~EED~~L 78 (261)
+.+|.++|..|| |..+++.+. -| |.. .+|.+ +|.+|..+.-|.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~-i~----CF~-----~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERIN-IN----CFK-----NNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTT-SS----STT-----SS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcc-cc----cCC-----CCCchHHHHHHHhcCHhHHHHHHHh
Confidence 578899999997 899988776 33 322 35554 4778888776654
No 134
>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=22.64 E-value=74 Score=24.96 Aligned_cols=27 Identities=15% Similarity=0.370 Sum_probs=20.8
Q ss_pred hhHhhhcCCCCCHHHHHHHHHHhhhhh
Q 024860 89 WSAIAAQLPGRTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 89 W~~Ia~~l~gRt~~~~r~Rw~~~lk~~ 115 (261)
....+...|..|..+=|+|++..+...
T Consensus 52 F~~~~~~~p~HT~~sWRDR~RKfv~~~ 78 (105)
T PF09197_consen 52 FKDLARKNPRHTENSWRDRYRKFVSEY 78 (105)
T ss_dssp HHHHHHHTTTS-HHHHHHHHHHTHHHH
T ss_pred HHHHHHcCCccchhHHHHHHHHHHHHc
Confidence 456677889999999999998887653
No 135
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.22 E-value=1.7e+02 Score=23.24 Aligned_cols=29 Identities=14% Similarity=-0.011 Sum_probs=22.5
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-.-..||+.| |-+...|+.|-+..+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466688999998 99999998887665443
No 136
>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=21.92 E-value=61 Score=23.21 Aligned_cols=18 Identities=17% Similarity=0.375 Sum_probs=14.8
Q ss_pred HHHHHHHhcCCchhHhhh
Q 024860 77 TIIRLHESLGNRWSAIAA 94 (261)
Q Consensus 77 ~L~~~~~~~G~~W~~Ia~ 94 (261)
.|.++.+.||++|.-|-.
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 577888899988999864
No 137
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=21.73 E-value=1.8e+02 Score=23.52 Aligned_cols=29 Identities=31% Similarity=0.433 Sum_probs=22.5
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-.-.+||..| |.+...|+.|.+.-++.
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466688999988 88899998887665543
No 138
>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=21.46 E-value=1.2e+02 Score=22.48 Aligned_cols=27 Identities=26% Similarity=0.602 Sum_probs=19.4
Q ss_pred HHHHHhcCCchhHhhhcCCCCCHHHHHH
Q 024860 79 IRLHESLGNRWSAIAAQLPGRTDNEIKN 106 (261)
Q Consensus 79 ~~~~~~~G~~W~~Ia~~l~gRt~~~~r~ 106 (261)
--+.+..|..|..+|..| |=+..+|..
T Consensus 6 ~~i~~~lG~~Wk~laR~L-Glse~~Id~ 32 (86)
T cd08306 6 DVICENVGRDWRKLARKL-GLSETKIES 32 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 344566799999999998 666665543
No 139
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=21.44 E-value=1.8e+02 Score=24.22 Aligned_cols=29 Identities=10% Similarity=0.071 Sum_probs=22.9
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-...+||..| |-+...|+.|.+..+++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 466788999988 99999999887666554
No 140
>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=21.31 E-value=92 Score=21.87 Aligned_cols=25 Identities=36% Similarity=0.745 Sum_probs=17.7
Q ss_pred HHHHHHhcCCchhHhhhcCCCCCHHH
Q 024860 78 IIRLHESLGNRWSAIAAQLPGRTDNE 103 (261)
Q Consensus 78 L~~~~~~~G~~W~~Ia~~l~gRt~~~ 103 (261)
+..+...+|..|..+|..| |=+..+
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~ 26 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGE 26 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHH
Confidence 3456677899999999998 433333
No 141
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=21.23 E-value=1.8e+02 Score=23.91 Aligned_cols=30 Identities=20% Similarity=0.278 Sum_probs=23.5
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKKR 115 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~~ 115 (261)
.|-....||..| |-+...|+.+.+..+++-
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~L 183 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALARL 183 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 456799999998 888899988887665543
No 142
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=20.89 E-value=1.8e+02 Score=24.22 Aligned_cols=29 Identities=10% Similarity=-0.018 Sum_probs=22.1
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLKK 114 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk~ 114 (261)
.|-.+..||..| |=+...|+.+-+..+++
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466799999998 88888888877665443
No 143
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=20.43 E-value=1.9e+02 Score=24.06 Aligned_cols=28 Identities=7% Similarity=-0.054 Sum_probs=22.6
Q ss_pred cCCchhHhhhcCCCCCHHHHHHHHHHhhh
Q 024860 85 LGNRWSAIAAQLPGRTDNEIKNHWHTSLK 113 (261)
Q Consensus 85 ~G~~W~~Ia~~l~gRt~~~~r~Rw~~~lk 113 (261)
.|-....||..| |-+...|+.|.+..++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466799999999 9999999988765543
Done!