Query 028843
Match_columns 203
No_of_seqs 202 out of 1824
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 03:24:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028843.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028843hhsearch_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 3.1E-36 6.7E-41 248.2 10.8 124 15-138 17-140 (249)
2 KOG0048 Transcription factor, 100.0 2.3E-34 5.1E-39 240.9 9.7 112 18-129 4-115 (238)
3 PLN03091 hypothetical protein; 100.0 4.6E-34 1E-38 250.9 11.3 113 15-127 6-118 (459)
4 KOG0049 Transcription factor, 99.9 5.8E-24 1.3E-28 193.2 6.8 143 13-155 243-441 (939)
5 PLN03212 Transcription repress 99.8 1.8E-20 3.8E-25 154.9 4.9 98 53-158 10-109 (249)
6 KOG0049 Transcription factor, 99.8 5.3E-20 1.2E-24 167.6 6.7 117 1-118 338-458 (939)
7 KOG0048 Transcription factor, 99.8 3.3E-19 7.1E-24 149.4 3.0 87 72-158 5-93 (238)
8 PLN03091 hypothetical protein; 99.7 5.9E-19 1.3E-23 155.8 4.0 89 70-158 8-98 (459)
9 PF13921 Myb_DNA-bind_6: Myb-l 99.7 1.8E-18 4E-23 114.9 5.1 60 26-87 1-60 (60)
10 COG5147 REB1 Myb superfamily p 99.7 2.4E-17 5.2E-22 149.5 7.4 134 17-152 14-147 (512)
11 KOG0050 mRNA splicing protein 99.7 2.6E-17 5.7E-22 146.9 4.4 107 20-128 4-110 (617)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.6 2.2E-16 4.7E-21 104.9 2.7 60 79-138 1-60 (60)
13 PF00249 Myb_DNA-binding: Myb- 99.5 2.7E-15 5.8E-20 95.4 2.8 48 23-70 1-48 (48)
14 KOG0051 RNA polymerase I termi 99.5 1.2E-14 2.7E-19 133.2 6.7 108 22-132 383-519 (607)
15 PF00249 Myb_DNA-binding: Myb- 99.5 1.1E-14 2.4E-19 92.5 4.4 46 76-121 1-48 (48)
16 smart00717 SANT SANT SWI3, AD 99.3 2.6E-12 5.6E-17 80.4 5.6 47 76-122 1-48 (49)
17 KOG0051 RNA polymerase I termi 99.3 1.6E-12 3.4E-17 119.5 5.8 122 20-143 305-452 (607)
18 smart00717 SANT SANT SWI3, AD 99.2 7.7E-12 1.7E-16 78.2 3.7 48 23-71 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.2 2.4E-11 5.3E-16 74.7 5.3 44 78-121 1-45 (45)
20 COG5147 REB1 Myb superfamily p 99.1 9.2E-12 2E-16 113.4 0.4 121 73-193 17-139 (512)
21 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 5.6E-11 1.2E-15 73.1 3.4 44 25-69 1-44 (45)
22 KOG0050 mRNA splicing protein 99.1 1.9E-11 4.1E-16 109.8 0.8 96 74-169 5-101 (617)
23 TIGR01557 myb_SHAQKYF myb-like 98.2 1.1E-06 2.4E-11 57.7 3.5 49 22-70 2-54 (57)
24 KOG0457 Histone acetyltransfer 98.1 1.7E-06 3.7E-11 77.0 3.5 51 19-70 68-118 (438)
25 TIGR01557 myb_SHAQKYF myb-like 98.0 2.2E-05 4.8E-10 51.5 5.4 47 76-122 3-55 (57)
26 KOG0457 Histone acetyltransfer 97.8 2.3E-05 5.1E-10 69.9 5.1 49 74-122 70-119 (438)
27 TIGR02894 DNA_bind_RsfA transc 97.8 1.3E-05 2.8E-10 62.8 3.0 50 75-125 3-59 (161)
28 PF13325 MCRS_N: N-terminal re 97.5 0.00032 6.9E-09 57.2 7.0 96 25-122 1-127 (199)
29 COG5259 RSC8 RSC chromatin rem 97.5 5.5E-05 1.2E-09 68.1 2.7 46 22-69 278-323 (531)
30 TIGR02894 DNA_bind_RsfA transc 97.4 9.2E-05 2E-09 58.1 2.5 49 21-71 2-56 (161)
31 COG5259 RSC8 RSC chromatin rem 97.4 0.00017 3.7E-09 65.0 4.1 43 77-119 280-322 (531)
32 KOG1279 Chromatin remodeling f 97.3 0.00014 3E-09 66.9 3.1 49 19-69 249-297 (506)
33 KOG1279 Chromatin remodeling f 97.3 0.00033 7.3E-09 64.5 5.1 46 75-120 252-297 (506)
34 PF08914 Myb_DNA-bind_2: Rap1 97.2 0.00036 7.7E-09 47.0 3.0 52 23-74 2-61 (65)
35 PF08914 Myb_DNA-bind_2: Rap1 97.2 0.00069 1.5E-08 45.6 4.2 50 76-125 2-61 (65)
36 PF13837 Myb_DNA-bind_4: Myb/S 97.1 0.00043 9.3E-09 48.8 2.7 52 77-128 2-71 (90)
37 PF13837 Myb_DNA-bind_4: Myb/S 97.0 0.00041 8.9E-09 48.9 1.9 48 23-70 1-64 (90)
38 PRK13923 putative spore coat p 96.9 0.00063 1.4E-08 54.1 2.4 50 75-125 4-60 (170)
39 COG5114 Histone acetyltransfer 96.8 0.00062 1.4E-08 58.9 2.2 48 23-71 63-110 (432)
40 PRK13923 putative spore coat p 96.7 0.00067 1.4E-08 54.0 1.4 49 21-71 3-57 (170)
41 PLN03142 Probable chromatin-re 96.5 0.0077 1.7E-07 60.2 7.6 100 24-124 825-987 (1033)
42 COG5114 Histone acetyltransfer 96.3 0.0038 8.3E-08 54.1 3.4 46 77-122 64-110 (432)
43 PF13873 Myb_DNA-bind_5: Myb/S 96.1 0.0035 7.6E-08 43.2 1.7 49 22-70 1-69 (78)
44 PF13873 Myb_DNA-bind_5: Myb/S 95.6 0.019 4E-07 39.5 4.0 48 76-123 2-71 (78)
45 PF09111 SLIDE: SLIDE; InterP 94.5 0.11 2.4E-06 39.0 5.6 36 19-54 45-83 (118)
46 KOG2656 DNA methyltransferase 93.7 0.067 1.5E-06 47.6 3.5 84 45-129 75-189 (445)
47 KOG4282 Transcription factor G 92.8 0.14 3E-06 45.1 4.2 50 76-125 54-117 (345)
48 COG5118 BDP1 Transcription ini 92.8 0.17 3.6E-06 45.1 4.5 42 78-119 367-408 (507)
49 KOG1194 Predicted DNA-binding 90.7 1.1 2.3E-05 41.0 7.4 46 75-120 186-231 (534)
50 PF12776 Myb_DNA-bind_3: Myb/S 90.0 0.64 1.4E-05 32.7 4.5 45 78-122 1-63 (96)
51 PF11626 Rap1_C: TRF2-interact 89.6 0.46 1E-05 33.5 3.4 31 19-52 43-81 (87)
52 COG5118 BDP1 Transcription ini 89.2 0.35 7.5E-06 43.1 3.0 49 19-69 361-409 (507)
53 PF12776 Myb_DNA-bind_3: Myb/S 83.9 1.4 2.9E-05 31.0 3.2 45 25-69 1-61 (96)
54 PF09111 SLIDE: SLIDE; InterP 83.7 1.5 3.3E-05 32.9 3.5 51 73-123 46-112 (118)
55 KOG4282 Transcription factor G 83.6 0.94 2E-05 39.8 2.8 47 24-70 55-113 (345)
56 PF08281 Sigma70_r4_2: Sigma-7 83.5 2 4.3E-05 26.9 3.6 41 81-122 12-52 (54)
57 PF13404 HTH_AsnC-type: AsnC-t 83.4 1 2.2E-05 27.4 2.0 38 29-68 3-40 (42)
58 smart00595 MADF subfamily of S 77.8 2.8 6.1E-05 29.0 3.1 25 98-123 30-54 (89)
59 KOG4167 Predicted DNA-binding 77.2 1.7 3.8E-05 41.9 2.3 50 11-69 614-663 (907)
60 PF13404 HTH_AsnC-type: AsnC-t 76.2 4.8 0.0001 24.4 3.4 38 82-120 3-41 (42)
61 PRK11179 DNA-binding transcrip 75.4 2.4 5.2E-05 32.8 2.4 45 29-75 9-53 (153)
62 KOG4167 Predicted DNA-binding 75.1 4.6 0.0001 39.1 4.5 44 76-119 619-662 (907)
63 PF13325 MCRS_N: N-terminal re 73.4 7.5 0.00016 31.9 4.8 44 78-122 1-47 (199)
64 PF11626 Rap1_C: TRF2-interact 72.5 3.9 8.5E-05 28.7 2.7 17 72-88 43-59 (87)
65 PRK11169 leucine-responsive tr 70.8 2.6 5.6E-05 33.1 1.6 47 28-76 13-59 (164)
66 KOG4329 DNA-binding protein [G 70.5 8.1 0.00017 34.6 4.7 43 77-119 278-321 (445)
67 PRK11179 DNA-binding transcrip 69.8 7.6 0.00016 30.0 4.1 45 82-127 9-54 (153)
68 KOG2009 Transcription initiati 68.8 6.8 0.00015 37.1 4.1 45 75-119 408-452 (584)
69 KOG4468 Polycomb-group transcr 67.5 7.2 0.00016 37.0 3.9 51 76-126 88-148 (782)
70 KOG1194 Predicted DNA-binding 67.3 5.6 0.00012 36.5 3.1 49 19-69 183-231 (534)
71 PF04545 Sigma70_r4: Sigma-70, 65.1 10 0.00022 23.3 3.2 41 82-123 7-47 (50)
72 PF11035 SnAPC_2_like: Small n 64.5 23 0.00051 31.1 6.2 89 20-122 18-127 (344)
73 PRK09413 IS2 repressor TnpA; R 64.2 27 0.00058 25.8 5.9 46 21-70 8-53 (121)
74 PRK11169 leucine-responsive tr 62.2 11 0.00023 29.6 3.5 46 81-127 13-59 (164)
75 PF02954 HTH_8: Bacterial regu 58.0 11 0.00024 22.5 2.4 29 29-58 5-33 (42)
76 cd08319 Death_RAIDD Death doma 54.6 16 0.00034 25.6 3.0 30 84-114 2-31 (83)
77 PF10545 MADF_DNA_bdg: Alcohol 52.5 5.1 0.00011 26.9 0.2 25 45-69 28-52 (85)
78 cd08803 Death_ank3 Death domai 51.8 21 0.00046 25.0 3.3 31 84-115 4-34 (84)
79 TIGR02985 Sig70_bacteroi1 RNA 51.5 25 0.00053 26.2 3.9 29 94-123 128-156 (161)
80 KOG0384 Chromodomain-helicase 50.9 21 0.00045 36.9 4.2 77 22-105 1132-1209(1373)
81 PLN03142 Probable chromatin-re 50.1 20 0.00043 36.5 4.0 33 21-53 924-956 (1033)
82 PF01388 ARID: ARID/BRIGHT DNA 50.0 26 0.00057 24.3 3.6 38 86-123 40-90 (92)
83 COG1522 Lrp Transcriptional re 49.8 13 0.00029 28.1 2.2 46 29-76 8-53 (154)
84 smart00344 HTH_ASNC helix_turn 47.9 19 0.00041 25.6 2.7 44 29-74 3-46 (108)
85 KOG4468 Polycomb-group transcr 47.6 13 0.00028 35.4 2.1 47 23-70 88-143 (782)
86 PF07750 GcrA: GcrA cell cycle 47.6 23 0.0005 28.0 3.2 38 25-65 2-39 (162)
87 PF07750 GcrA: GcrA cell cycle 46.4 21 0.00045 28.2 2.8 41 78-119 2-42 (162)
88 PF09905 DUF2132: Uncharacteri 46.0 28 0.0006 23.2 2.9 21 31-54 12-32 (64)
89 cd08317 Death_ank Death domain 43.6 24 0.00051 24.4 2.5 30 84-114 4-33 (84)
90 PF11035 SnAPC_2_like: Small n 43.6 60 0.0013 28.6 5.3 44 76-119 21-68 (344)
91 smart00501 BRIGHT BRIGHT, ARID 43.5 35 0.00077 23.9 3.4 39 86-124 36-87 (93)
92 KOG2656 DNA methyltransferase 42.5 11 0.00024 34.0 0.8 50 19-69 126-180 (445)
93 PF09420 Nop16: Ribosome bioge 42.3 70 0.0015 25.0 5.3 46 75-120 113-162 (164)
94 smart00344 HTH_ASNC helix_turn 41.6 51 0.0011 23.3 4.1 45 82-127 3-48 (108)
95 PF10440 WIYLD: Ubiquitin-bind 37.1 25 0.00055 23.6 1.7 18 85-102 30-47 (65)
96 cd08804 Death_ank2 Death domai 36.7 42 0.0009 23.4 2.9 31 84-115 4-34 (84)
97 KOG2009 Transcription initiati 36.6 25 0.00055 33.4 2.2 52 15-68 401-452 (584)
98 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 34.4 60 0.0013 20.5 3.0 34 82-116 7-40 (50)
99 TIGR02937 sigma70-ECF RNA poly 33.3 60 0.0013 23.4 3.5 30 93-123 124-153 (158)
100 PF07638 Sigma70_ECF: ECF sigm 32.7 69 0.0015 25.3 3.9 33 87-120 143-175 (185)
101 PF09420 Nop16: Ribosome bioge 31.8 58 0.0013 25.5 3.3 48 21-69 112-162 (164)
102 cd08318 Death_NMPP84 Death dom 31.8 57 0.0012 22.7 2.9 26 88-114 11-36 (86)
103 cd08805 Death_ank1 Death domai 31.8 53 0.0011 23.0 2.7 26 84-110 4-29 (84)
104 KOG4329 DNA-binding protein [G 31.7 44 0.00096 30.0 2.8 44 24-69 278-322 (445)
105 PRK09652 RNA polymerase sigma 30.8 71 0.0015 24.3 3.6 28 94-122 143-170 (182)
106 smart00351 PAX Paired Box doma 30.7 2.2E+02 0.0049 21.0 7.6 87 19-118 11-104 (125)
107 COG1522 Lrp Transcriptional re 30.0 87 0.0019 23.5 4.0 45 82-127 8-53 (154)
108 PRK09645 RNA polymerase sigma 28.5 96 0.0021 23.7 4.0 27 95-122 134-160 (173)
109 PF01710 HTH_Tnp_IS630: Transp 28.5 1.5E+02 0.0032 21.8 4.8 57 28-87 56-112 (119)
110 smart00005 DEATH DEATH domain, 28.4 62 0.0013 21.9 2.7 29 84-113 5-34 (88)
111 PRK11924 RNA polymerase sigma 28.1 81 0.0018 23.8 3.5 28 94-122 140-167 (179)
112 PF04504 DUF573: Protein of un 28.1 49 0.0011 23.8 2.1 18 77-94 5-22 (98)
113 KOG0384 Chromodomain-helicase 27.4 39 0.00084 35.0 1.9 25 78-102 1135-1160(1373)
114 cd08777 Death_RIP1 Death Domai 26.8 68 0.0015 22.4 2.6 29 86-115 4-32 (86)
115 PRK09643 RNA polymerase sigma 26.7 94 0.002 24.5 3.8 28 94-122 149-176 (192)
116 cd06171 Sigma70_r4 Sigma70, re 26.0 1.3E+02 0.0028 17.2 3.6 36 84-120 15-50 (55)
117 PRK04217 hypothetical protein; 25.9 1.1E+02 0.0024 22.5 3.7 43 78-122 42-84 (110)
118 PRK09641 RNA polymerase sigma 25.2 99 0.0022 23.8 3.6 27 95-122 152-178 (187)
119 cd08779 Death_PIDD Death Domai 25.2 81 0.0018 22.0 2.7 25 85-110 3-27 (86)
120 cd08311 Death_p75NR Death doma 24.1 71 0.0015 21.9 2.2 33 81-115 2-34 (77)
121 PF00531 Death: Death domain; 23.8 63 0.0014 21.4 2.0 23 33-55 2-24 (83)
122 PRK12523 RNA polymerase sigma 23.6 1.3E+02 0.0027 23.1 3.9 30 94-124 134-163 (172)
123 PRK09637 RNA polymerase sigma 22.4 1.3E+02 0.0027 23.6 3.7 28 94-122 121-148 (181)
124 TIGR02954 Sig70_famx3 RNA poly 22.4 1.2E+02 0.0027 23.0 3.6 27 95-122 135-161 (169)
125 TIGR02948 SigW_bacill RNA poly 22.2 1.1E+02 0.0024 23.5 3.4 27 95-122 152-178 (187)
126 PRK09047 RNA polymerase factor 22.2 1.5E+02 0.0031 22.2 3.9 27 95-122 122-148 (161)
127 PRK12515 RNA polymerase sigma 21.8 1.4E+02 0.003 23.2 3.9 28 95-123 147-174 (189)
128 PF13936 HTH_38: Helix-turn-he 21.5 80 0.0017 18.9 1.9 36 78-115 4-39 (44)
129 PRK12512 RNA polymerase sigma 21.3 1.4E+02 0.0031 23.0 3.8 28 95-123 147-174 (184)
130 TIGR02939 RpoE_Sigma70 RNA pol 21.2 1E+02 0.0022 23.8 2.9 28 95-123 154-181 (190)
131 COG1168 MalY Bifunctional PLP- 21.2 1.1E+02 0.0024 27.7 3.3 28 16-43 165-192 (388)
132 PRK09642 RNA polymerase sigma 20.8 1.6E+02 0.0034 22.1 3.9 27 95-122 122-148 (160)
133 PF05029 TIMELESS_C: Timeless 20.7 3E+02 0.0066 26.2 6.4 91 24-116 93-212 (566)
134 KOG0385 Chromatin remodeling c 20.5 1.1E+02 0.0024 30.4 3.5 47 75-121 894-956 (971)
135 PRK11923 algU RNA polymerase s 20.4 1.3E+02 0.0029 23.3 3.5 27 95-122 154-180 (193)
136 PF09197 Rap1-DNA-bind: Rap1, 20.3 95 0.002 22.8 2.3 25 99-123 53-77 (105)
137 PRK09648 RNA polymerase sigma 20.2 1.6E+02 0.0034 22.9 3.9 27 95-122 155-181 (189)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=3.1e-36 Score=248.16 Aligned_cols=124 Identities=60% Similarity=1.114 Sum_probs=115.4
Q ss_pred CCCCCCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCChHHHHHHHHHHHHh
Q 028843 15 ASGKNVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLILRLHKLL 94 (203)
Q Consensus 15 ~~~~~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~Ll~~v~~~ 94 (203)
-|.|+.+++++||+|||++|+++|++||..+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++++..|
T Consensus 17 cc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~ 96 (249)
T PLN03212 17 CCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLL 96 (249)
T ss_pred CcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhc
Confidence 38899999999999999999999999998899999999966999999999999999999999999999999999999999
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhcccccCCCCCCCCCCch
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLSKKINHKHKTPQQPQQP 138 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~~~~t~~e~~~l 138 (203)
|++|+.||+.|||||+++||+||+.++++.+......++...++
T Consensus 97 GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~ 140 (249)
T PLN03212 97 GNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPL 140 (249)
T ss_pred cccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCC
Confidence 99999999999999999999999999999877766665554443
No 2
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=2.3e-34 Score=240.87 Aligned_cols=112 Identities=58% Similarity=1.033 Sum_probs=106.9
Q ss_pred CCCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCChHHHHHHHHHHHHhCCc
Q 028843 18 KNVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLILRLHKLLGSR 97 (203)
Q Consensus 18 ~~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~Ll~~v~~~G~~ 97 (203)
++.+.||+||+|||++|+++|++||.++|..||+.+|++|++++||.||.|||+|++++|.||+|||.+|++++..+|++
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 44566899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhccCCCCCHHHHHHHHHHhhcccccCCC
Q 028843 98 WSLIAGRLPGRTDNEIKNYWNSHLSKKINHKH 129 (203)
Q Consensus 98 W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~~~ 129 (203)
|+.||++|||||++.|||+|+..+++++....
T Consensus 84 Ws~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 84 WSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999998887654
No 3
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=4.6e-34 Score=250.88 Aligned_cols=113 Identities=56% Similarity=1.041 Sum_probs=108.3
Q ss_pred CCCCCCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCChHHHHHHHHHHHHh
Q 028843 15 ASGKNVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLILRLHKLL 94 (203)
Q Consensus 15 ~~~~~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~Ll~~v~~~ 94 (203)
-|.|..+++|+||+|||++|+++|.+||..+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++++++|
T Consensus 6 Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~ 85 (459)
T PLN03091 6 CCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVL 85 (459)
T ss_pred cCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHh
Confidence 37889999999999999999999999999999999999877999999999999999999999999999999999999999
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhcccccC
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLSKKINH 127 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~ 127 (203)
|++|+.||+.|||||+++||+||+.++++++..
T Consensus 86 GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~ 118 (459)
T PLN03091 86 GNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQ 118 (459)
T ss_pred CcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 999999999999999999999999999887653
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.89 E-value=5.8e-24 Score=193.16 Aligned_cols=143 Identities=21% Similarity=0.312 Sum_probs=129.1
Q ss_pred CCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchh---------------------------
Q 028843 13 NDASGKNVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLR--------------------------- 65 (203)
Q Consensus 13 ~~~~~~~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R--------------------------- 65 (203)
+..+..|.++|.-|++|||++|..+...+|..+|..||..+|++|+..||..|
T Consensus 243 W~n~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~ 322 (939)
T KOG0049|consen 243 WYNELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKI 322 (939)
T ss_pred HhhhcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHH
Confidence 34567899999999999999999999999988999999999877888888744
Q ss_pred ---------------------------hhhcccCCCCCCCCChHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHH
Q 028843 66 ---------------------------WLNYLRPNIKRGNISDDEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYW 117 (203)
Q Consensus 66 ---------------------------w~~~l~~~~~~~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw 117 (203)
|...|+|.+++|+||++||.+|+.+|.+|| ..|.+|...+|||++.|||.||
T Consensus 323 ~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY 402 (939)
T KOG0049|consen 323 TSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERY 402 (939)
T ss_pred hhccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHH
Confidence 445566999999999999999999999999 5699999999999999999999
Q ss_pred HHhhcccccCCCCCCCCCCchhhhhhhCCC-CCCccccc
Q 028843 118 NSHLSKKINHKHKTPQQPQQPATTRLKVPE-NTSEIAPV 155 (203)
Q Consensus 118 ~~~l~~~~~~~~~t~~e~~~l~~~~~~~~~-~~s~i~~~ 155 (203)
.+.|....+.+.|+-.++.+|+..+..||. +|..+|..
T Consensus 403 ~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~ 441 (939)
T KOG0049|consen 403 TNVLNRSAKVERWTLVEDEQLLYAVKVYGKGNWAKCAML 441 (939)
T ss_pred HHHHHHhhccCceeecchHHHHHHHHHHccchHHHHHHH
Confidence 999999999999999999999999999996 88887754
No 5
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.81 E-value=1.8e-20 Score=154.92 Aligned_cols=98 Identities=17% Similarity=0.244 Sum_probs=88.4
Q ss_pred hccCcCCcccchhhhhcccCCCCCCCCChHHHHHHHHHHHHhC-CchhhhhccC-CCCCHHHHHHHHHHhhcccccCCCC
Q 028843 53 SGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLILRLHKLLG-SRWSLIAGRL-PGRTDNEIKNYWNSHLSKKINHKHK 130 (203)
Q Consensus 53 ~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l-~~Rt~~q~k~Rw~~~l~~~~~~~~~ 130 (203)
++ .|+..-| .++.+++++||+|||++|+++|++|| .+|..||+.+ ++||+.||+.||.++|+|.+++++|
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-KKTTPCC-------TKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGI 81 (249)
T ss_pred CC-CCCCCCc-------ccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCC
Confidence 44 5666655 34688999999999999999999999 6899999998 6999999999999999999999999
Q ss_pred CCCCCCchhhhhhhCCCCCCcccccCCc
Q 028843 131 TPQQPQQPATTRLKVPENTSEIAPVNEE 158 (203)
Q Consensus 131 t~~e~~~l~~~~~~~~~~~s~i~~~~~~ 158 (203)
|.+|+..|+..+..+|++|+.||....+
T Consensus 82 T~EED~lLlel~~~~GnKWs~IAk~LpG 109 (249)
T PLN03212 82 TSDEEDLILRLHRLLGNRWSLIAGRIPG 109 (249)
T ss_pred ChHHHHHHHHHHHhccccHHHHHhhcCC
Confidence 9999999999999999999999987533
No 6
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.80 E-value=5.3e-20 Score=167.55 Aligned_cols=117 Identities=26% Similarity=0.336 Sum_probs=104.6
Q ss_pred CCCCCCCCCCCCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCC
Q 028843 1 MAPTKSNNNNNNNDASGKNVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNIS 80 (203)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT 80 (203)
|..++++..-+.+.-.-.|.+++|.||.+||.+|+.+|.+||.++|-+|-+.+| ||+..|||+||.+.|+...+.+.||
T Consensus 338 mpgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~ 416 (939)
T KOG0049|consen 338 MPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWT 416 (939)
T ss_pred cCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCcee
Confidence 444555555566666778999999999999999999999999999999999999 9999999999999999999999999
Q ss_pred hHHHHHHHHHHHHhC-CchhhhhccCCCCCHH---HHHHHHH
Q 028843 81 DDEEDLILRLHKLLG-SRWSLIAGRLPGRTDN---EIKNYWN 118 (203)
Q Consensus 81 ~eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~---q~k~Rw~ 118 (203)
-.||+.|+.+|.+|| ++|.+||..||+||.. .||-|+.
T Consensus 417 l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~ 458 (939)
T KOG0049|consen 417 LVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLI 458 (939)
T ss_pred ecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHH
Confidence 999999999999999 8899999999999994 4555554
No 7
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.75 E-value=3.3e-19 Score=149.41 Aligned_cols=87 Identities=14% Similarity=0.145 Sum_probs=81.5
Q ss_pred CCCCCCCCChHHHHHHHHHHHHhC-CchhhhhccCC-CCCHHHHHHHHHHhhcccccCCCCCCCCCCchhhhhhhCCCCC
Q 028843 72 PNIKRGNISDDEEDLILRLHKLLG-SRWSLIAGRLP-GRTDNEIKNYWNSHLSKKINHKHKTPQQPQQPATTRLKVPENT 149 (203)
Q Consensus 72 ~~~~~~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~-~Rt~~q~k~Rw~~~l~~~~~~~~~t~~e~~~l~~~~~~~~~~~ 149 (203)
+.+.+||||+|||.+|+++|++|| .+|..||+.++ +|++++||-||.++|+|.++++.||.+|+..++.++..+|++|
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 66999999998 9999999999999999999999999999999999999999999
Q ss_pred CcccccCCc
Q 028843 150 SEIAPVNEE 158 (203)
Q Consensus 150 s~i~~~~~~ 158 (203)
+.||..-.+
T Consensus 85 s~IA~~LPG 93 (238)
T KOG0048|consen 85 SLIAGRLPG 93 (238)
T ss_pred HHHHhhCCC
Confidence 999987443
No 8
>PLN03091 hypothetical protein; Provisional
Probab=99.75 E-value=5.9e-19 Score=155.83 Aligned_cols=89 Identities=17% Similarity=0.240 Sum_probs=83.0
Q ss_pred ccCCCCCCCCChHHHHHHHHHHHHhC-CchhhhhccC-CCCCHHHHHHHHHHhhcccccCCCCCCCCCCchhhhhhhCCC
Q 028843 70 LRPNIKRGNISDDEEDLILRLHKLLG-SRWSLIAGRL-PGRTDNEIKNYWNSHLSKKINHKHKTPQQPQQPATTRLKVPE 147 (203)
Q Consensus 70 l~~~~~~~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l-~~Rt~~q~k~Rw~~~l~~~~~~~~~t~~e~~~l~~~~~~~~~ 147 (203)
.++.+++++||+|||++|+++|.+|| .+|..||+.+ ++|+++|||.||.++|++.+++++|+++|+..|+.++..+|.
T Consensus 8 ~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~Gn 87 (459)
T PLN03091 8 YKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGN 87 (459)
T ss_pred cCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCc
Confidence 34678999999999999999999999 5799999988 599999999999999999999999999999999999999999
Q ss_pred CCCcccccCCc
Q 028843 148 NTSEIAPVNEE 158 (203)
Q Consensus 148 ~~s~i~~~~~~ 158 (203)
+|+.|+....+
T Consensus 88 KWskIAk~LPG 98 (459)
T PLN03091 88 RWSQIAAQLPG 98 (459)
T ss_pred chHHHHHhcCC
Confidence 99999986533
No 9
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.74 E-value=1.8e-18 Score=114.90 Aligned_cols=60 Identities=45% Similarity=0.844 Sum_probs=55.2
Q ss_pred CCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCChHHHHHH
Q 028843 26 WTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLI 87 (203)
Q Consensus 26 WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~L 87 (203)
||++||++|+.+|..|| .+|..||..|| +|++.+|+.||.++|.|.+++++||++||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 68999999997 89999999999999999999999999999987
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=99.70 E-value=2.4e-17 Score=149.46 Aligned_cols=134 Identities=26% Similarity=0.422 Sum_probs=115.8
Q ss_pred CCCCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCChHHHHHHHHHHHHhCC
Q 028843 17 GKNVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLILRLHKLLGS 96 (203)
Q Consensus 17 ~~~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~Ll~~v~~~G~ 96 (203)
.....+.|.|+..||+.|..+|+.+|+.+|..||..+. .|+++||+.||.++++|.++++.|+.+||..|+.+..++|.
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 chhhhhccCCCCCHHHHHHHHHHhhcccccCCCCCCCCCCchhhhhhhCCCCCCcc
Q 028843 97 RWSLIAGRLPGRTDNEIKNYWNSHLSKKINHKHKTPQQPQQPATTRLKVPENTSEI 152 (203)
Q Consensus 97 ~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~~~~t~~e~~~l~~~~~~~~~~~s~i 152 (203)
.|+.||..+++|++.+|.+||...+..... ..++..+..........+...++..
T Consensus 93 ~wstia~~~d~rt~~~~~ery~~~~~~~~s-~~~s~~~~~~~f~k~d~f~~~~~~~ 147 (512)
T COG5147 93 QWSTIADYKDRRTAQQCVERYVNTLEDLSS-THDSKLQRRNEFDKIDPFNENSARR 147 (512)
T ss_pred hhhhhccccCccchHHHHHHHHHHhhhhhc-cccccccchhhccccCchhhhhhhh
Confidence 999999999999999999999998887766 5555555544444444444444433
No 11
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.67 E-value=2.6e-17 Score=146.92 Aligned_cols=107 Identities=27% Similarity=0.566 Sum_probs=100.8
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCChHHHHHHHHHHHHhCCchh
Q 028843 20 VVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLILRLHKLLGSRWS 99 (203)
Q Consensus 20 ~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~Ll~~v~~~G~~W~ 99 (203)
.++.|.|+.-||+.|..+|.+||.+.|.+||+.+. -.+++||+.||..+++|.+++..|+.+||.+|+.+.+.+...|.
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwr 82 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWR 82 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccc
Confidence 35789999999999999999999999999999998 88999999999999999999999999999999999999999999
Q ss_pred hhhccCCCCCHHHHHHHHHHhhcccccCC
Q 028843 100 LIAGRLPGRTDNEIKNYWNSHLSKKINHK 128 (203)
Q Consensus 100 ~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~~ 128 (203)
.||..| ||+++||-.||++++.......
T Consensus 83 tIa~i~-gr~~~qc~eRy~~ll~~~~s~~ 110 (617)
T KOG0050|consen 83 TIADIM-GRTSQQCLERYNNLLDVYVSYH 110 (617)
T ss_pred hHHHHh-hhhHHHHHHHHHHHHHHHHhhh
Confidence 999998 9999999999999988765443
No 12
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.61 E-value=2.2e-16 Score=104.88 Aligned_cols=60 Identities=33% Similarity=0.564 Sum_probs=53.3
Q ss_pred CChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhcccccCCCCCCCCCCch
Q 028843 79 ISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNSHLSKKINHKHKTPQQPQQP 138 (203)
Q Consensus 79 WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~~~~t~~e~~~l 138 (203)
||++||++|+++|..||.+|..||+.|+.||+.+|++||...|.+.++.++|+++|+..|
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999999999999999669999999999999999999999999887643
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=99.54 E-value=2.7e-15 Score=95.43 Aligned_cols=48 Identities=44% Similarity=0.759 Sum_probs=43.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcc
Q 028843 23 RGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYL 70 (203)
Q Consensus 23 k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 70 (203)
|++||++||++|+++|.+||..+|..||..||.+||+.||+.||.+++
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 689999999999999999997779999999988999999999999875
No 14
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.53 E-value=1.2e-14 Score=133.23 Aligned_cols=108 Identities=28% Similarity=0.589 Sum_probs=94.9
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCC--CCCCCChHHHHHHHHHHH-------
Q 028843 22 NRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNI--KRGNISDDEEDLILRLHK------- 92 (203)
Q Consensus 22 ~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~--~~~~WT~eEd~~Ll~~v~------- 92 (203)
.+|+||+||++.|..+|..+| ++|.+|+..|| |.+..|++||.++...+- +++.||.||++.|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 899999999999999999999 78999999995 999999999999998874 999999999999999995
Q ss_pred Hh-------------------CCchhhhhccCCCCCHHHHHHHHHHhhccc-ccCCCCCC
Q 028843 93 LL-------------------GSRWSLIAGRLPGRTDNEIKNYWNSHLSKK-INHKHKTP 132 (203)
Q Consensus 93 ~~-------------------G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~-~~~~~~t~ 132 (203)
++ +-+|+.|++.+..|+..||+-+|+.++... .+...+..
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~~~~~ 519 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKRQESK 519 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhcccccc
Confidence 33 124999999999999999999999877654 45555554
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=99.52 E-value=1.1e-14 Score=92.53 Aligned_cols=46 Identities=33% Similarity=0.660 Sum_probs=41.8
Q ss_pred CCCCChHHHHHHHHHHHHhCCc-hhhhhccCC-CCCHHHHHHHHHHhh
Q 028843 76 RGNISDDEEDLILRLHKLLGSR-WSLIAGRLP-GRTDNEIKNYWNSHL 121 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~G~~-W~~Ia~~l~-~Rt~~q~k~Rw~~~l 121 (203)
+++||++||.+|+++|.+||.. |..||..|| +||..||++||++++
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 5799999999999999999987 999999999 999999999999874
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.33 E-value=2.6e-12 Score=80.37 Aligned_cols=47 Identities=36% Similarity=0.799 Sum_probs=44.4
Q ss_pred CCCCChHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 76 RGNISDDEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
+++||++||.+|+.++..|| .+|..||..|++||+.+|++||..+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998764
No 17
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.32 E-value=1.6e-12 Score=119.52 Aligned_cols=122 Identities=21% Similarity=0.244 Sum_probs=105.4
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCC-----------------------CChhhhhhhhccCcCCcccchhhhhcccCCC-C
Q 028843 20 VVNRGAWTAEEDRKLTEYIEIHGA-----------------------KRWKNVATESGLNRCGKSCRLRWLNYLRPNI-K 75 (203)
Q Consensus 20 ~~~k~~WT~eED~~L~~~v~~~g~-----------------------~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~-~ 75 (203)
.++.+.|+++||..|-+.|..|-. +-|..|...|| -|+...++++-++...|-- .
T Consensus 305 e~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~~ 383 (607)
T KOG0051|consen 305 EINLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFENK 383 (607)
T ss_pred hhhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCccccc
Confidence 566799999999999999977721 12788888899 5999999885554444433 9
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhccc--ccCCCCCCCCCCchhhhhh
Q 028843 76 RGNISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNSHLSKK--INHKHKTPQQPQQPATTRL 143 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~--~~~~~~t~~e~~~l~~~~~ 143 (203)
+|.||++|++.|..+|.++|+.|..|++.| ||.+..|+.||.+++... .+.+.|+.+|...|+.++.
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~ 452 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVN 452 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHH
Confidence 999999999999999999999999999999 999999999999999877 4899999999999999884
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.23 E-value=7.7e-12 Score=78.18 Aligned_cols=48 Identities=40% Similarity=0.823 Sum_probs=44.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhccc
Q 028843 23 RGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLR 71 (203)
Q Consensus 23 k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 71 (203)
++.||++||.+|+.++..||..+|..||..|+ +|++.+|+.||.+++.
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 47899999999999999999778999999999 9999999999998764
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.22 E-value=2.4e-11 Score=74.71 Aligned_cols=44 Identities=34% Similarity=0.709 Sum_probs=41.7
Q ss_pred CCChHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhh
Q 028843 78 NISDDEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHL 121 (203)
Q Consensus 78 ~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l 121 (203)
+||++|+..|+.++..|| .+|..||..|++||+.+|++||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999998753
No 20
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.13 E-value=9.2e-12 Score=113.36 Aligned_cols=121 Identities=26% Similarity=0.325 Sum_probs=98.7
Q ss_pred CCCCCCCChHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhcccccCCCCCCCCCCchhhhhhhCCCCCCc
Q 028843 73 NIKRGNISDDEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHLSKKINHKHKTPQQPQQPATTRLKVPENTSE 151 (203)
Q Consensus 73 ~~~~~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~~~~t~~e~~~l~~~~~~~~~~~s~ 151 (203)
..+.|.|+..||..|..+|+.|| ++|+.||..|..+++++|++||++++.+.++++.|+.+++.+++.+...+|..|+.
T Consensus 17 ~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~wst 96 (512)
T COG5147 17 KRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWST 96 (512)
T ss_pred eecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchhhh
Confidence 45788999999999999999999 67999999998899999999999999999999999999999999999999999999
Q ss_pred ccccCC-cCCccccCCCCCccccccCCCCCCchhhccccccCc
Q 028843 152 IAPVNE-EGGRQIANSEVNLDFDFSTEGLCGLDWVNKFLQLDD 193 (203)
Q Consensus 152 i~~~~~-~~~~~~~~~~~~~~~d~~~~~~~~~e~~~~f~~~d~ 193 (203)
|+.... ....++.+-.++..=+++.........++.|..+|+
T Consensus 97 ia~~~d~rt~~~~~ery~~~~~~~~s~~~s~~~~~~~f~k~d~ 139 (512)
T COG5147 97 IADYKDRRTAQQCVERYVNTLEDLSSTHDSKLQRRNEFDKIDP 139 (512)
T ss_pred hccccCccchHHHHHHHHHHhhhhhccccccccchhhccccCc
Confidence 999877 455555544444433333333344455555655554
No 21
>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=99.12 E-value=5.6e-11 Score=73.06 Aligned_cols=44 Identities=41% Similarity=0.762 Sum_probs=41.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhc
Q 028843 25 AWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNY 69 (203)
Q Consensus 25 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 69 (203)
+||++||..|+.++..+|..+|..||..++ +|++.+|+.||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHh
Confidence 599999999999999999778999999999 89999999999875
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.09 E-value=1.9e-11 Score=109.76 Aligned_cols=96 Identities=21% Similarity=0.274 Sum_probs=88.9
Q ss_pred CCCCCCChHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhcccccCCCCCCCCCCchhhhhhhCCCCCCcc
Q 028843 74 IKRGNISDDEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHLSKKINHKHKTPQQPQQPATTRLKVPENTSEI 152 (203)
Q Consensus 74 ~~~~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~~~~t~~e~~~l~~~~~~~~~~~s~i 152 (203)
++.|.|+.-||++|..+|.+|| +.|+.||..++..|+.||++||...+++.+++..|+.+++..++++....+++|..|
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrtI 84 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRTI 84 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccchH
Confidence 4678999999999999999999 679999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCcCCccccCCCCC
Q 028843 153 APVNEEGGRQIANSEVN 169 (203)
Q Consensus 153 ~~~~~~~~~~~~~~~~~ 169 (203)
++++...+++|..-..+
T Consensus 85 a~i~gr~~~qc~eRy~~ 101 (617)
T KOG0050|consen 85 ADIMGRTSQQCLERYNN 101 (617)
T ss_pred HHHhhhhHHHHHHHHHH
Confidence 99998888777654443
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.24 E-value=1.1e-06 Score=57.69 Aligned_cols=49 Identities=14% Similarity=0.297 Sum_probs=43.6
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCh---hhhhhhhccCc-CCcccchhhhhcc
Q 028843 22 NRGAWTAEEDRKLTEYIEIHGAKRW---KNVATESGLNR-CGKSCRLRWLNYL 70 (203)
Q Consensus 22 ~k~~WT~eED~~L~~~v~~~g~~~W---~~Ia~~~~~~R-t~~qcr~Rw~~~l 70 (203)
.+-.||+||..+++.+|+.+|.++| ..|+..|+..| |..||+.|++.|.
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 3568999999999999999998799 99999987566 9999999998864
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.14 E-value=1.7e-06 Score=77.02 Aligned_cols=51 Identities=25% Similarity=0.510 Sum_probs=46.9
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcc
Q 028843 19 NVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYL 70 (203)
Q Consensus 19 ~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 70 (203)
-++-...||++|+-+|++++..||.+||..||.++| .|++.+|+++|.+++
T Consensus 68 ~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 68 FPILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 345568899999999999999999999999999999 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=97.96 E-value=2.2e-05 Score=51.53 Aligned_cols=47 Identities=19% Similarity=0.235 Sum_probs=41.0
Q ss_pred CCCCChHHHHHHHHHHHHhCC-ch---hhhhccCC-CC-CHHHHHHHHHHhhc
Q 028843 76 RGNISDDEEDLILRLHKLLGS-RW---SLIAGRLP-GR-TDNEIKNYWNSHLS 122 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~G~-~W---~~Ia~~l~-~R-t~~q~k~Rw~~~l~ 122 (203)
+-.||+||...+++++..+|. +| ..|+..|. .| |..||+.+.+.+..
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 457999999999999999995 99 99999883 45 99999999987653
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.84 E-value=2.3e-05 Score=69.87 Aligned_cols=49 Identities=29% Similarity=0.420 Sum_probs=44.4
Q ss_pred CCCCCCChHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 74 IKRGNISDDEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 74 ~~~~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
+-...||.+|+-+|++++..|| ++|..||.++..|+..+|+.+|.+++-
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 4456799999999999999999 999999999999999999999997543
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=97.83 E-value=1.3e-05 Score=62.81 Aligned_cols=50 Identities=20% Similarity=0.292 Sum_probs=44.2
Q ss_pred CCCCCChHHHHHHHHHHHHh---CCc----hhhhhccCCCCCHHHHHHHHHHhhcccc
Q 028843 75 KRGNISDDEEDLILRLHKLL---GSR----WSLIAGRLPGRTDNEIKNYWNSHLSKKI 125 (203)
Q Consensus 75 ~~~~WT~eEd~~Ll~~v~~~---G~~----W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~ 125 (203)
....||.|||.+|.+.|..| |+. ...++..| +||+.+|.-||+.++++.+
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY 59 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQY 59 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHH
Confidence 45789999999999999988 432 89999999 9999999999999999765
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.53 E-value=0.00032 Score=57.22 Aligned_cols=96 Identities=19% Similarity=0.341 Sum_probs=70.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhhhhhhhccC--cCCcccchhhhhccc----------------CCC-----CCCCCCh
Q 028843 25 AWTAEEDRKLTEYIEIHGAKRWKNVATESGLN--RCGKSCRLRWLNYLR----------------PNI-----KRGNISD 81 (203)
Q Consensus 25 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~--Rt~~qcr~Rw~~~l~----------------~~~-----~~~~WT~ 81 (203)
+|++++|-+|+.+|..-. +-..|+..+... -|...+.+||+..|- |.. .+.+||.
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 699999999999998876 677887765433 356778899997653 221 3458999
Q ss_pred HHHHHHHHHHHHhCC---chhhhh----ccC-CCCCHHHHHHHHHHhhc
Q 028843 82 DEEDLILRLHKLLGS---RWSLIA----GRL-PGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 82 eEd~~Ll~~v~~~G~---~W~~Ia----~~l-~~Rt~~q~k~Rw~~~l~ 122 (203)
+|+++|........+ .+.+|- ..| ++||+.++.++|..+..
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkq 127 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQ 127 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHH
Confidence 999999997765542 366662 223 78999999999995433
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.52 E-value=5.5e-05 Score=68.07 Aligned_cols=46 Identities=30% Similarity=0.579 Sum_probs=42.6
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhc
Q 028843 22 NRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNY 69 (203)
Q Consensus 22 ~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 69 (203)
....||.+|..+|++.|+.|| .+|.+||.++| +|+..||..||.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 556899999999999999999 57999999999 99999999999864
No 30
>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=97.42 E-value=9.2e-05 Score=58.09 Aligned_cols=49 Identities=35% Similarity=0.629 Sum_probs=42.7
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCC------ChhhhhhhhccCcCCcccchhhhhccc
Q 028843 21 VNRGAWTAEEDRKLTEYIEIHGAK------RWKNVATESGLNRCGKSCRLRWLNYLR 71 (203)
Q Consensus 21 ~~k~~WT~eED~~L~~~v~~~g~~------~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 71 (203)
.+...||.|||.+|...|.+|-.. ...+|+..+ +||+..|.-||+.+++
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L--~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL--NRTAAACGFRWNAYVR 56 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH--cccHHHhcchHHHHHH
Confidence 467899999999999999988421 489999998 5999999999999877
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.39 E-value=0.00017 Score=65.00 Aligned_cols=43 Identities=21% Similarity=0.261 Sum_probs=41.4
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHH
Q 028843 77 GNISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNS 119 (203)
Q Consensus 77 ~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~ 119 (203)
.+||.+|..+|++.+..||..|.+||.++.+||..||--||.+
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHc
Confidence 4899999999999999999999999999999999999999985
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.34 E-value=0.00014 Score=66.92 Aligned_cols=49 Identities=33% Similarity=0.623 Sum_probs=44.3
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhc
Q 028843 19 NVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNY 69 (203)
Q Consensus 19 ~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 69 (203)
....++.||.+|.-+|+++|+.|| .+|.+||.+++ +|+..||..++.+.
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccC-CCCHHHHHHHHHhc
Confidence 345578999999999999999999 67999999999 99999999998764
No 33
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.30 E-value=0.00033 Score=64.48 Aligned_cols=46 Identities=17% Similarity=0.321 Sum_probs=43.1
Q ss_pred CCCCCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHh
Q 028843 75 KRGNISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNSH 120 (203)
Q Consensus 75 ~~~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~ 120 (203)
.++.||.+|..+|++++..||..|.+||.++.+||..||--++..+
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 4568999999999999999999999999999999999999999864
No 34
>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=97.18 E-value=0.00036 Score=47.02 Aligned_cols=52 Identities=27% Similarity=0.436 Sum_probs=33.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCC--------ChhhhhhhhccCcCCcccchhhhhcccCCC
Q 028843 23 RGAWTAEEDRKLTEYIEIHGAK--------RWKNVATESGLNRCGKSCRLRWLNYLRPNI 74 (203)
Q Consensus 23 k~~WT~eED~~L~~~v~~~g~~--------~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~ 74 (203)
+.+||.+||+.|+..|..+... -|.+++..-++.+|..+-|+||.+.|.+..
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 5689999999999999766321 299999998768899999999999887643
No 35
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.16 E-value=0.00069 Score=45.63 Aligned_cols=50 Identities=16% Similarity=0.336 Sum_probs=32.8
Q ss_pred CCCCChHHHHHHHHHHHHhC--------Cc-hhhhhccCC-CCCHHHHHHHHHHhhcccc
Q 028843 76 RGNISDDEEDLILRLHKLLG--------SR-WSLIAGRLP-GRTDNEIKNYWNSHLSKKI 125 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~G--------~~-W~~Ia~~l~-~Rt~~q~k~Rw~~~l~~~~ 125 (203)
+.++|.+||+.|++.|..+. +. |..++..-| .+|-.+.|+||...|.+..
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 45899999999999997652 11 999998887 8999999999999887654
No 36
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.07 E-value=0.00043 Score=48.76 Aligned_cols=52 Identities=31% Similarity=0.463 Sum_probs=36.9
Q ss_pred CCCChHHHHHHHHHHHH------hC--C------chhhhhccC----CCCCHHHHHHHHHHhhcccccCC
Q 028843 77 GNISDDEEDLILRLHKL------LG--S------RWSLIAGRL----PGRTDNEIKNYWNSHLSKKINHK 128 (203)
Q Consensus 77 ~~WT~eEd~~Ll~~v~~------~G--~------~W~~Ia~~l----~~Rt~~q~k~Rw~~~l~~~~~~~ 128 (203)
..||.+|...|++++.. ++ + -|..||..| ..||+.||+++|.++.+......
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~~k 71 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKKIK 71 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHCSS
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999877 21 1 399999887 36999999999999777654433
No 37
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.98 E-value=0.00041 Score=48.86 Aligned_cols=48 Identities=40% Similarity=0.702 Sum_probs=33.1
Q ss_pred cCCCCHHHHHHHHHHHHH--h----C--CC-----Chhhhhhhh---ccCcCCcccchhhhhcc
Q 028843 23 RGAWTAEEDRKLTEYIEI--H----G--AK-----RWKNVATES---GLNRCGKSCRLRWLNYL 70 (203)
Q Consensus 23 k~~WT~eED~~L~~~v~~--~----g--~~-----~W~~Ia~~~---~~~Rt~~qcr~Rw~~~l 70 (203)
+..||.+|-..|+.++.. + + .. -|..||..| |..|++.||+.+|.+..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 458999999999999877 1 1 11 399999997 45799999999998753
No 38
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.90 E-value=0.00063 Score=54.11 Aligned_cols=50 Identities=16% Similarity=0.242 Sum_probs=42.4
Q ss_pred CCCCCChHHHHHHHHHHHHhCCc-------hhhhhccCCCCCHHHHHHHHHHhhcccc
Q 028843 75 KRGNISDDEEDLILRLHKLLGSR-------WSLIAGRLPGRTDNEIKNYWNSHLSKKI 125 (203)
Q Consensus 75 ~~~~WT~eEd~~Ll~~v~~~G~~-------W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~ 125 (203)
+++.||.|+|.+|.+.|..|+.. ...++..| +||+.+|..||+.++++.+
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Y 60 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQY 60 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHH
Confidence 56789999999999999988632 67777888 9999999999999888654
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.85 E-value=0.00062 Score=58.85 Aligned_cols=48 Identities=23% Similarity=0.518 Sum_probs=44.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhccc
Q 028843 23 RGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLR 71 (203)
Q Consensus 23 k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 71 (203)
---|+..|+-+|+++....|-++|..||..+| .|+...|+.+|.+++.
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 35699999999999999999999999999999 9999999999998755
No 40
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.73 E-value=0.00067 Score=53.95 Aligned_cols=49 Identities=29% Similarity=0.554 Sum_probs=41.3
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCC------ChhhhhhhhccCcCCcccchhhhhccc
Q 028843 21 VNRGAWTAEEDRKLTEYIEIHGAK------RWKNVATESGLNRCGKSCRLRWLNYLR 71 (203)
Q Consensus 21 ~~k~~WT~eED~~L~~~v~~~g~~------~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~ 71 (203)
.++..||.|+|.+|.+.|..|+.. ....++..| +|++.+|..||+.+++
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHH
Confidence 567899999999999999888743 377778877 5999999999977766
No 41
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=96.53 E-value=0.0077 Score=60.15 Aligned_cols=100 Identities=15% Similarity=0.281 Sum_probs=75.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccch-------hhhh------ccc-------------------
Q 028843 24 GAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRL-------RWLN------YLR------------------- 71 (203)
Q Consensus 24 ~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~-------Rw~~------~l~------------------- 71 (203)
..||.-+=..++.+..+||..+-..||..|. +++...++. ||.. ++.
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~ 903 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAI 903 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3477777777788889999888999999997 788877752 2111 000
Q ss_pred ------------------CCCCCCCCChHHHHHHHHHHHHhC-Cchhhhhc------------cCCCCCHHHHHHHHHHh
Q 028843 72 ------------------PNIKRGNISDDEEDLILRLHKLLG-SRWSLIAG------------RLPGRTDNEIKNYWNSH 120 (203)
Q Consensus 72 ------------------~~~~~~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~------------~l~~Rt~~q~k~Rw~~~ 120 (203)
+..++..+|.+||..|+-++.+|| .+|..|-. ++..||+..+..|...+
T Consensus 904 ~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 904 GKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred HHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 233445699999999999999999 78998832 23579999999999987
Q ss_pred hccc
Q 028843 121 LSKK 124 (203)
Q Consensus 121 l~~~ 124 (203)
+.-.
T Consensus 984 ~~~~ 987 (1033)
T PLN03142 984 IRLI 987 (1033)
T ss_pred HHHH
Confidence 7654
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.28 E-value=0.0038 Score=54.07 Aligned_cols=46 Identities=28% Similarity=0.408 Sum_probs=42.9
Q ss_pred CCCChHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 77 GNISDDEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 77 ~~WT~eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
..|+..|+.+|+++..-.| ++|..||.++..|+...||.+|..+..
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 3699999999999999999 999999999999999999999987665
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.06 E-value=0.0035 Score=43.16 Aligned_cols=49 Identities=29% Similarity=0.473 Sum_probs=39.9
Q ss_pred ccCCCCHHHHHHHHHHHHHhCC----------------CChhhhhhhh----ccCcCCcccchhhhhcc
Q 028843 22 NRGAWTAEEDRKLTEYIEIHGA----------------KRWKNVATES----GLNRCGKSCRLRWLNYL 70 (203)
Q Consensus 22 ~k~~WT~eED~~L~~~v~~~g~----------------~~W~~Ia~~~----~~~Rt~~qcr~Rw~~~l 70 (203)
++..||++|.+.|+++|.+|.. ..|..|+..| |..|+..||+.+|.++.
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 4578999999999999988831 1399999987 22699999999998764
No 44
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.64 E-value=0.019 Score=39.46 Aligned_cols=48 Identities=27% Similarity=0.498 Sum_probs=39.0
Q ss_pred CCCCChHHHHHHHHHHHHhC----C-------------chhhhhccC-----CCCCHHHHHHHHHHhhcc
Q 028843 76 RGNISDDEEDLILRLHKLLG----S-------------RWSLIAGRL-----PGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~G----~-------------~W~~Ia~~l-----~~Rt~~q~k~Rw~~~l~~ 123 (203)
...||.+|..+|+++|.+|. + -|..|+..| +.||..+|+.+|.++...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 35799999999999998872 1 199998776 359999999999987543
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=94.50 E-value=0.11 Score=39.01 Aligned_cols=36 Identities=22% Similarity=0.323 Sum_probs=30.5
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCC---CChhhhhhhhc
Q 028843 19 NVVNRGAWTAEEDRKLTEYIEIHGA---KRWKNVATESG 54 (203)
Q Consensus 19 ~~~~k~~WT~eED~~L~~~v~~~g~---~~W~~Ia~~~~ 54 (203)
+..++..||.+||.-|+-++.+||. +.|..|...+.
T Consensus 45 ~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir 83 (118)
T PF09111_consen 45 PNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIR 83 (118)
T ss_dssp STSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHH
T ss_pred CCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHH
Confidence 4677899999999999999999998 78999998874
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=93.73 E-value=0.067 Score=47.64 Aligned_cols=84 Identities=23% Similarity=0.351 Sum_probs=62.7
Q ss_pred ChhhhhhhhccCcCCcccchhhhhcccC-------------------------CCCCCCCChHHHHHHHHHHHHhCCchh
Q 028843 45 RWKNVATESGLNRCGKSCRLRWLNYLRP-------------------------NIKRGNISDDEEDLILRLHKLLGSRWS 99 (203)
Q Consensus 45 ~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~-------------------------~~~~~~WT~eEd~~Ll~~v~~~G~~W~ 99 (203)
.|..+.-..+ .|...-...||.....+ .+....||.+|-+-|.++++.|.-+|-
T Consensus 75 ~W~w~pFtn~-aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~ 153 (445)
T KOG2656|consen 75 PWKWVPFTNS-ARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCCc-cccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 5766665544 67677777777665221 223346999999999999999999999
Q ss_pred hhhcc-----CCC-CCHHHHHHHHHHhhcccccCCC
Q 028843 100 LIAGR-----LPG-RTDNEIKNYWNSHLSKKINHKH 129 (203)
Q Consensus 100 ~Ia~~-----l~~-Rt~~q~k~Rw~~~l~~~~~~~~ 129 (203)
.||.. ++. ||-..+|+||+.+.+..++-..
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 99977 555 9999999999987766554443
No 47
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.84 E-value=0.14 Score=45.10 Aligned_cols=50 Identities=16% Similarity=0.241 Sum_probs=40.7
Q ss_pred CCCCChHHHHHHHHHHHHh----------CCchhhhhccC----CCCCHHHHHHHHHHhhcccc
Q 028843 76 RGNISDDEEDLILRLHKLL----------GSRWSLIAGRL----PGRTDNEIKNYWNSHLSKKI 125 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~----------G~~W~~Ia~~l----~~Rt~~q~k~Rw~~~l~~~~ 125 (203)
...|+.+|-..||++.... +..|..||..+ .-||+.+|+++|.++.+...
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk 117 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYK 117 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence 4689999999999988653 34499999865 34999999999998877654
No 48
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=92.78 E-value=0.17 Score=45.11 Aligned_cols=42 Identities=24% Similarity=0.393 Sum_probs=40.7
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHH
Q 028843 78 NISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNS 119 (203)
Q Consensus 78 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~ 119 (203)
+||.+|-.+...+....|...+.||..+|.|...||+..|.+
T Consensus 367 ~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 367 RWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred cccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHH
Confidence 799999999999999999999999999999999999999975
No 49
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=90.75 E-value=1.1 Score=40.96 Aligned_cols=46 Identities=17% Similarity=0.287 Sum_probs=41.9
Q ss_pred CCCCCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHh
Q 028843 75 KRGNISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNSH 120 (203)
Q Consensus 75 ~~~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~ 120 (203)
-...||.||-.++-++...||.+..+|.+.||.|+-..+...|+..
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSW 231 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHH
Confidence 3457999999999999999999999999999999999999988754
No 50
>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=90.03 E-value=0.64 Score=32.75 Aligned_cols=45 Identities=24% Similarity=0.457 Sum_probs=34.0
Q ss_pred CCChHHHHHHHHHHHHh---CC----------chhhhhccC---CC--CCHHHHHHHHHHhhc
Q 028843 78 NISDDEEDLILRLHKLL---GS----------RWSLIAGRL---PG--RTDNEIKNYWNSHLS 122 (203)
Q Consensus 78 ~WT~eEd~~Ll~~v~~~---G~----------~W~~Ia~~l---~~--Rt~~q~k~Rw~~~l~ 122 (203)
.||++++..|++++.+. |+ .|..|+..| +| .+..||++||..+-+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 49999999999988654 21 288898776 23 478899999986544
No 51
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=89.65 E-value=0.46 Score=33.52 Aligned_cols=31 Identities=29% Similarity=0.476 Sum_probs=18.5
Q ss_pred CCCccCCCCHHHHHHH--------HHHHHHhCCCChhhhhhh
Q 028843 19 NVVNRGAWTAEEDRKL--------TEYIEIHGAKRWKNVATE 52 (203)
Q Consensus 19 ~~~~k~~WT~eED~~L--------~~~v~~~g~~~W~~Ia~~ 52 (203)
|.-..|.||+++|+.| ..++++|| +..|+..
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~R 81 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIERR 81 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHHH
Confidence 5566899999999999 45678887 5666643
No 52
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.17 E-value=0.35 Score=43.14 Aligned_cols=49 Identities=16% Similarity=0.264 Sum_probs=43.6
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhc
Q 028843 19 NVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNY 69 (203)
Q Consensus 19 ~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 69 (203)
....--+||.+|-+++.+++...| .++.-|+..+| +|..+|+..+|.+-
T Consensus 361 ~~~~~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP-~R~RkqIKaKfi~E 409 (507)
T COG5118 361 KKKGALRWSKKEIEKFYKALSIWG-TDFSLISSLFP-NRERKQIKAKFIKE 409 (507)
T ss_pred CCCCCCcccHHHHHHHHHHHHHhc-chHHHHHHhcC-chhHHHHHHHHHHH
Confidence 444557899999999999999999 67999999999 99999999999863
No 53
>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=83.93 E-value=1.4 Score=31.02 Aligned_cols=45 Identities=31% Similarity=0.592 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------Chhhhhhhhc----cCcCCcccchhhhhc
Q 028843 25 AWTAEEDRKLTEYIEIH---GAK---------RWKNVATESG----LNRCGKSCRLRWLNY 69 (203)
Q Consensus 25 ~WT~eED~~L~~~v~~~---g~~---------~W~~Ia~~~~----~~Rt~~qcr~Rw~~~ 69 (203)
+||+++++.|++++... |.. .|..|+..|. ...+..||..||...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999987444 111 3999998874 234557777777643
No 54
>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=83.71 E-value=1.5 Score=32.90 Aligned_cols=51 Identities=24% Similarity=0.385 Sum_probs=39.7
Q ss_pred CCCCCCCChHHHHHHHHHHHHhCC----chhhhhcc------------CCCCCHHHHHHHHHHhhcc
Q 028843 73 NIKRGNISDDEEDLILRLHKLLGS----RWSLIAGR------------LPGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 73 ~~~~~~WT~eEd~~Ll~~v~~~G~----~W~~Ia~~------------l~~Rt~~q~k~Rw~~~l~~ 123 (203)
+.++..+|++||.-|+-++.+||- .|..|... +..||+..+..|...+++-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 556779999999999999999995 69888532 2569999999999987764
No 55
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=83.61 E-value=0.94 Score=39.85 Aligned_cols=47 Identities=28% Similarity=0.443 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHHhC---------CCChhhhhhhh---ccCcCCcccchhhhhcc
Q 028843 24 GAWTAEEDRKLTEYIEIHG---------AKRWKNVATES---GLNRCGKSCRLRWLNYL 70 (203)
Q Consensus 24 ~~WT~eED~~L~~~v~~~g---------~~~W~~Ia~~~---~~~Rt~~qcr~Rw~~~l 70 (203)
..|+.+|=..|+.+..+.. ...|..||..+ |..|++.||+.+|.+..
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 7899999999999874331 13599999954 45699999999998754
No 56
>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=83.50 E-value=2 Score=26.89 Aligned_cols=41 Identities=20% Similarity=0.268 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 81 DDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 81 ~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
++++..++.++-..|-.+..||..+ |.|...|+.+....++
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 3567777888888899999999999 9999999998876543
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=83.35 E-value=1 Score=27.40 Aligned_cols=38 Identities=26% Similarity=0.396 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhh
Q 028843 29 EEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLN 68 (203)
Q Consensus 29 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 68 (203)
+=|.+|+.++...+...+.+||..+| =+...|..|+..
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 34788999999999889999999996 888888888754
No 58
>smart00595 MADF subfamily of SANT domain.
Probab=77.78 E-value=2.8 Score=29.00 Aligned_cols=25 Identities=32% Similarity=0.603 Sum_probs=21.3
Q ss_pred hhhhhccCCCCCHHHHHHHHHHhhcc
Q 028843 98 WSLIAGRLPGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 98 W~~Ia~~l~~Rt~~q~k~Rw~~~l~~ 123 (203)
|..||..| |-+...|+.+|.++-..
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~ 54 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 99999999 55999999999976443
No 59
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=77.18 E-value=1.7 Score=41.91 Aligned_cols=50 Identities=14% Similarity=0.212 Sum_probs=43.1
Q ss_pred CCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhc
Q 028843 11 NNNDASGKNVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNY 69 (203)
Q Consensus 11 ~~~~~~~~~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 69 (203)
++++.++ .||+.|-.++.+++-.|. +++-.|++.+. ++|..||-+-|+..
T Consensus 614 Y~Y~gSd-------~WTp~E~~lF~kA~y~~~-KDF~~v~km~~-~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 614 YHYAGSD-------KWTPLERKLFNKALYTYS-KDFIFVQKMVK-SKTVAQCVEYYYTW 663 (907)
T ss_pred eeecCcc-------cccHHHHHHHHHHHHHhc-ccHHHHHHHhc-cccHHHHHHHHHHH
Confidence 5666654 799999999999999998 78999999998 99999997766543
No 60
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=76.20 E-value=4.8 Score=24.36 Aligned_cols=38 Identities=21% Similarity=0.328 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHh
Q 028843 82 DEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSH 120 (203)
Q Consensus 82 eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~ 120 (203)
+=|..|+.+...-| ..+..||+.+ |=|...|..|...+
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 45788888888888 5699999999 99999999998753
No 61
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=75.38 E-value=2.4 Score=32.81 Aligned_cols=45 Identities=16% Similarity=0.167 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCC
Q 028843 29 EEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIK 75 (203)
Q Consensus 29 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~ 75 (203)
+-|.+|+.+..+.|...|.+||..+| -+...|+.|+.+....++.
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 57999999999999889999999995 9999999999987666554
No 62
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=75.08 E-value=4.6 Score=39.14 Aligned_cols=44 Identities=9% Similarity=0.138 Sum_probs=40.9
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHH
Q 028843 76 RGNISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNS 119 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~ 119 (203)
...||+.|-.+.-+++-.|......|++.++++|-.+|-+.|+.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 45799999999999999999999999999999999999998874
No 63
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=73.35 E-value=7.5 Score=31.86 Aligned_cols=44 Identities=14% Similarity=0.136 Sum_probs=34.0
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhccC---CCCCHHHHHHHHHHhhc
Q 028843 78 NISDDEEDLILRLHKLLGSRWSLIAGRL---PGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 78 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l---~~Rt~~q~k~Rw~~~l~ 122 (203)
.|++++|-.|+.+|.. |+.-..|+..+ -.-|-..+..||+.+|-
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 4999999999999865 66666666544 33488999999997664
No 64
>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=72.51 E-value=3.9 Score=28.73 Aligned_cols=17 Identities=12% Similarity=0.427 Sum_probs=10.2
Q ss_pred CCCCCCCCChHHHHHHH
Q 028843 72 PNIKRGNISDDEEDLIL 88 (203)
Q Consensus 72 ~~~~~~~WT~eEd~~Ll 88 (203)
|....|-||+++|..|.
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 55678999999999994
No 65
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=70.77 E-value=2.6 Score=33.07 Aligned_cols=47 Identities=15% Similarity=0.175 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCC
Q 028843 28 AEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKR 76 (203)
Q Consensus 28 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~ 76 (203)
.+-|.+|+.+..+.|.-.|.+||+.+| -+...|+.|+.+....++.+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCeE
Confidence 567899999999999889999999995 89999999999887766543
No 66
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=70.52 E-value=8.1 Score=34.59 Aligned_cols=43 Identities=23% Similarity=0.329 Sum_probs=38.6
Q ss_pred CCCChHHHHHHHHHHHHhCCchhhh-hccCCCCCHHHHHHHHHH
Q 028843 77 GNISDDEEDLILRLHKLLGSRWSLI-AGRLPGRTDNEIKNYWNS 119 (203)
Q Consensus 77 ~~WT~eEd~~Ll~~v~~~G~~W~~I-a~~l~~Rt~~q~k~Rw~~ 119 (203)
..|+++|-...-+.++.||.+...| +..++.|+--.|-..|+.
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH
Confidence 3799999999999999999999999 566899999999888764
No 67
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=69.83 E-value=7.6 Score=29.96 Aligned_cols=45 Identities=13% Similarity=0.058 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhcccccC
Q 028843 82 DEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHLSKKINH 127 (203)
Q Consensus 82 eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~ 127 (203)
+-|..|+.+..+-| ..|+.||+.+ |-|...|+.|+..+....+-.
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 56888888888888 6799999999 999999999999887765433
No 68
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=68.82 E-value=6.8 Score=37.05 Aligned_cols=45 Identities=24% Similarity=0.369 Sum_probs=41.9
Q ss_pred CCCCCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHH
Q 028843 75 KRGNISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNS 119 (203)
Q Consensus 75 ~~~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~ 119 (203)
..++|+.+|-.+...+....|.+.+.||..+|+|...|||..|..
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 445899999999999999999999999999999999999999974
No 69
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=67.51 E-value=7.2 Score=37.03 Aligned_cols=51 Identities=12% Similarity=0.367 Sum_probs=41.7
Q ss_pred CCCCChHHHHHHHHHHHHhCCchhhhh----------ccCCCCCHHHHHHHHHHhhccccc
Q 028843 76 RGNISDDEEDLILRLHKLLGSRWSLIA----------GRLPGRTDNEIKNYWNSHLSKKIN 126 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~G~~W~~Ia----------~~l~~Rt~~q~k~Rw~~~l~~~~~ 126 (203)
+..||-.|..-...+++++|.+..+|- ....-+|..|++.+|+..+.+..+
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 668999999999999999999999882 233447788999999988776543
No 70
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=67.31 E-value=5.6 Score=36.46 Aligned_cols=49 Identities=16% Similarity=0.246 Sum_probs=41.9
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhc
Q 028843 19 NVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNY 69 (203)
Q Consensus 19 ~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 69 (203)
.......||.||--++.++..-|| .+..+|-+.|| .|+-..+..-|...
T Consensus 183 r~~~~d~WT~Ed~vlFe~aF~~~G-K~F~kIrq~LP-~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 183 RTEFPDEWTAEDIVLFEQAFQFFG-KDFHKIRQALP-HRSLASLVQYYYSW 231 (534)
T ss_pred cCCCcccchHHHHHHHHHHHHHhc-ccHHHHHHHcc-CccHHHHHHHHHHH
Confidence 455678899999999999999999 77999999999 99998887766543
No 71
>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=65.06 E-value=10 Score=23.28 Aligned_cols=41 Identities=27% Similarity=0.374 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhcc
Q 028843 82 DEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 82 eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~ 123 (203)
+++..++.++-..|-.+..||..+ |-|...|+.+....+.+
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 445555555555567899999999 88999999988876653
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=64.48 E-value=23 Score=31.08 Aligned_cols=89 Identities=20% Similarity=0.348 Sum_probs=65.3
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCC---ChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCChHHHHHHHHHHHH-h-
Q 028843 20 VVNRGAWTAEEDRKLTEYIEIHGAK---RWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLILRLHKL-L- 94 (203)
Q Consensus 20 ~~~k~~WT~eED~~L~~~v~~~g~~---~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~Ll~~v~~-~- 94 (203)
+.....||.-|...|+.+....... +-.+|++.++ +|+..++++ |.+.|+ +..+.+++++ |
T Consensus 18 ~~gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~ 83 (344)
T PF11035_consen 18 VTGPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRD-FLQQLK------------GRVAREAIQKVHP 83 (344)
T ss_pred CCCcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHH-HHHHHH------------HHHHHHHHHHhcc
Confidence 3445789999999999988766433 5678899998 999988876 334443 3345555555 2
Q ss_pred ----CC------------chhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 95 ----GS------------RWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 95 ----G~------------~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
|. -|..+|+.+.|.-...+-.-|.++|.
T Consensus 84 ~g~~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 84 GGLKGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred cccccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 21 19999999999999999998887765
No 73
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=64.25 E-value=27 Score=25.83 Aligned_cols=46 Identities=17% Similarity=0.163 Sum_probs=33.0
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcc
Q 028843 21 VNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYL 70 (203)
Q Consensus 21 ~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l 70 (203)
.++.+||.|+-..++..+...| ..=..||..++. +.. -..+|.+.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI--s~~-tl~~W~r~y 53 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV--AAS-QLFLWRKQY 53 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc--CHH-HHHHHHHHH
Confidence 4568899999888888777777 457899999873 433 345566644
No 74
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=62.23 E-value=11 Score=29.56 Aligned_cols=46 Identities=13% Similarity=0.003 Sum_probs=38.6
Q ss_pred hHHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhcccccC
Q 028843 81 DDEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHLSKKINH 127 (203)
Q Consensus 81 ~eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~ 127 (203)
.+-|.+|+.+.++-| -.|+.||+.+ |=|...|+.|+..+....+-.
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 456888888888877 6799999999 999999999999887766543
No 75
>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=57.95 E-value=11 Score=22.47 Aligned_cols=29 Identities=21% Similarity=0.217 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHhCCCChhhhhhhhccCcC
Q 028843 29 EEDRKLTEYIEIHGAKRWKNVATESGLNRC 58 (203)
Q Consensus 29 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt 58 (203)
-|.+.|.+++..++ ++-...|..+|.+|+
T Consensus 5 ~E~~~i~~aL~~~~-gn~~~aA~~Lgisr~ 33 (42)
T PF02954_consen 5 FEKQLIRQALERCG-GNVSKAARLLGISRR 33 (42)
T ss_dssp HHHHHHHHHHHHTT-T-HHHHHHHHTS-HH
T ss_pred HHHHHHHHHHHHhC-CCHHHHHHHHCCCHH
Confidence 47788889999998 779999999985443
No 76
>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=54.64 E-value=16 Score=25.59 Aligned_cols=30 Identities=23% Similarity=0.453 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCHHHHH
Q 028843 84 EDLILRLHKLLGSRWSLIAGRLPGRTDNEIK 114 (203)
Q Consensus 84 d~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k 114 (203)
|+.|..+....|..|..+|..| |=|..+|.
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 65655443
No 77
>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=52.46 E-value=5.1 Score=26.94 Aligned_cols=25 Identities=32% Similarity=0.740 Sum_probs=20.7
Q ss_pred ChhhhhhhhccCcCCcccchhhhhc
Q 028843 45 RWKNVATESGLNRCGKSCRLRWLNY 69 (203)
Q Consensus 45 ~W~~Ia~~~~~~Rt~~qcr~Rw~~~ 69 (203)
.|..||..++..-++..|+.||.+.
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~L 52 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNL 52 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHH
Confidence 4999999998556778899999874
No 78
>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=51.83 E-value=21 Score=24.96 Aligned_cols=31 Identities=23% Similarity=0.347 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCHHHHHH
Q 028843 84 EDLILRLHKLLGSRWSLIAGRLPGRTDNEIKN 115 (203)
Q Consensus 84 d~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~ 115 (203)
|..|..+....|..|..+|..| |=+...|..
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 6678888899999999999999 666655443
No 79
>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=51.47 E-value=25 Score=26.24 Aligned_cols=29 Identities=21% Similarity=0.266 Sum_probs=24.2
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhcc
Q 028843 94 LGSRWSLIAGRLPGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 94 ~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~ 123 (203)
.|-.+..||+.+ |.|...++.+......+
T Consensus 128 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 128 EGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467899999998 99999999999876543
No 80
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=50.93 E-value=21 Score=36.85 Aligned_cols=77 Identities=17% Similarity=0.170 Sum_probs=50.7
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCChHHHHHHHHHHHHh-CCchhh
Q 028843 22 NRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLILRLHKLL-GSRWSL 100 (203)
Q Consensus 22 ~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~Ll~~v~~~-G~~W~~ 100 (203)
.---|..++|..|+-.|-+||.++|..|-.- +.-|... ...+......+.+=..+-..|+.++..+ +.+|..
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~D------p~L~l~d-Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLD------PDLGLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccC------ccccchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 3457999999999999999999999988532 1111111 0112222455667777778888888777 566766
Q ss_pred hhccC
Q 028843 101 IAGRL 105 (203)
Q Consensus 101 Ia~~l 105 (203)
.++.-
T Consensus 1205 ~~~~~ 1209 (1373)
T KOG0384|consen 1205 KLKRE 1209 (1373)
T ss_pred hhhcc
Confidence 55443
No 81
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=50.11 E-value=20 Score=36.52 Aligned_cols=33 Identities=15% Similarity=0.232 Sum_probs=29.3
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCChhhhhhhh
Q 028843 21 VNRGAWTAEEDRKLTEYIEIHGAKRWKNVATES 53 (203)
Q Consensus 21 ~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~ 53 (203)
-++..+|.+||.-|+-++.+||.++|.+|-..+
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 345669999999999999999999999998776
No 82
>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=49.95 E-value=26 Score=24.27 Aligned_cols=38 Identities=16% Similarity=0.286 Sum_probs=27.4
Q ss_pred HHHHHHHHhCC--------chhhhhccCCC---CC--HHHHHHHHHHhhcc
Q 028843 86 LILRLHKLLGS--------RWSLIAGRLPG---RT--DNEIKNYWNSHLSK 123 (203)
Q Consensus 86 ~Ll~~v~~~G~--------~W~~Ia~~l~~---Rt--~~q~k~Rw~~~l~~ 123 (203)
.|-.+|...|+ .|..||..|.- -+ +.+++..|..+|.+
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 46677777773 49999999822 12 36899999988754
No 83
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=49.78 E-value=13 Score=28.10 Aligned_cols=46 Identities=11% Similarity=0.122 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCC
Q 028843 29 EEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKR 76 (203)
Q Consensus 29 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~ 76 (203)
+-|.+++++.+..+...+.+||+.++ -+...|+.|-.+....++.+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCcee
Confidence 56889999999999889999999995 89999999988776655433
No 84
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=47.90 E-value=19 Score=25.58 Aligned_cols=44 Identities=18% Similarity=0.181 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCC
Q 028843 29 EEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNI 74 (203)
Q Consensus 29 eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~ 74 (203)
+.|..++.++...+.-.+..||..++ -+...|+.|.......++
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 46888999999988778999999985 888899998887766554
No 85
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=47.55 E-value=13 Score=35.39 Aligned_cols=47 Identities=17% Similarity=0.354 Sum_probs=36.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCChhhhhhhhcc---------CcCCcccchhhhhcc
Q 028843 23 RGAWTAEEDRKLTEYIEIHGAKRWKNVATESGL---------NRCGKSCRLRWLNYL 70 (203)
Q Consensus 23 k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~---------~Rt~~qcr~Rw~~~l 70 (203)
|..||-.|.+-+..+++.+| +++..|-..+-. -++..|+|++|++.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 66899999999999999999 789998433321 356678888888754
No 86
>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=47.55 E-value=23 Score=27.97 Aligned_cols=38 Identities=16% Similarity=0.179 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchh
Q 028843 25 AWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLR 65 (203)
Q Consensus 25 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~R 65 (203)
.||.|+.+.|.++...-- .=.+||..|| +.|...+.-+
T Consensus 2 ~Wtde~~~~L~~lw~~G~--SasqIA~~lg-~vsRnAViGk 39 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGL--SASQIARQLG-GVSRNAVIGK 39 (162)
T ss_pred CCCHHHHHHHHHHHHcCC--CHHHHHHHhC-Ccchhhhhhh
Confidence 599999999999995543 5789999998 5555555443
No 87
>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=46.37 E-value=21 Score=28.20 Aligned_cols=41 Identities=22% Similarity=0.223 Sum_probs=33.7
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHH
Q 028843 78 NISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNS 119 (203)
Q Consensus 78 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~ 119 (203)
.||+|..++|.++..+ |-.=++||..|.+.|.++|--+-+.
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhhc
Confidence 5999999999888744 8888999999976888888766654
No 88
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=45.99 E-value=28 Score=23.22 Aligned_cols=21 Identities=29% Similarity=0.586 Sum_probs=17.3
Q ss_pred HHHHHHHHHHhCCCChhhhhhhhc
Q 028843 31 DRKLTEYIEIHGAKRWKNVATESG 54 (203)
Q Consensus 31 D~~L~~~v~~~g~~~W~~Ia~~~~ 54 (203)
+.+|.++|..|| |..++..+.
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~ 32 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERIN 32 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTT
T ss_pred HHHHHHHHHHhC---HHHHHhhcc
Confidence 567889999999 999998876
No 89
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=43.55 E-value=24 Score=24.40 Aligned_cols=30 Identities=30% Similarity=0.623 Sum_probs=23.3
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCHHHHH
Q 028843 84 EDLILRLHKLLGSRWSLIAGRLPGRTDNEIK 114 (203)
Q Consensus 84 d~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k 114 (203)
|..|..+....|..|..+|..| |=+...|.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~ 33 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDID 33 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHH
Confidence 4567788889999999999998 65555443
No 90
>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=43.55 E-value=60 Score=28.62 Aligned_cols=44 Identities=30% Similarity=0.486 Sum_probs=35.6
Q ss_pred CCCCChHHHHHHHHHHHHh-CC---chhhhhccCCCCCHHHHHHHHHH
Q 028843 76 RGNISDDEEDLILRLHKLL-GS---RWSLIAGRLPGRTDNEIKNYWNS 119 (203)
Q Consensus 76 ~~~WT~eEd~~Ll~~v~~~-G~---~W~~Ia~~l~~Rt~~q~k~Rw~~ 119 (203)
-..||.-|...|+.+.+.. |. .-..|++.++||+..+|++.-..
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~ 68 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQ 68 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHH
Confidence 4579999999999988765 43 35688999999999999886654
No 91
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=43.50 E-value=35 Score=23.85 Aligned_cols=39 Identities=21% Similarity=0.297 Sum_probs=28.0
Q ss_pred HHHHHHHHhCC--------chhhhhccCCC-----CCHHHHHHHHHHhhccc
Q 028843 86 LILRLHKLLGS--------RWSLIAGRLPG-----RTDNEIKNYWNSHLSKK 124 (203)
Q Consensus 86 ~Ll~~v~~~G~--------~W~~Ia~~l~~-----Rt~~q~k~Rw~~~l~~~ 124 (203)
.|..+|...|+ .|..||..|.- ....+++..|..+|.+.
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 36677777764 59999999822 23568899998887653
No 92
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=42.46 E-value=11 Score=33.96 Aligned_cols=50 Identities=18% Similarity=0.260 Sum_probs=42.1
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhh-----hccCcCCcccchhhhhc
Q 028843 19 NVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATE-----SGLNRCGKSCRLRWLNY 69 (203)
Q Consensus 19 ~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~-----~~~~Rt~~qcr~Rw~~~ 69 (203)
..++-..||.+|-+-|..+.+.|. -.|--||.. ++..||.....+||...
T Consensus 126 ~~l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 126 AHLNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred HhhccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 345568899999999999999998 568888877 67559999999999865
No 93
>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=42.30 E-value=70 Score=25.03 Aligned_cols=46 Identities=17% Similarity=0.185 Sum_probs=38.0
Q ss_pred CCCCCChHHHHHHHHHHHHhCCchhhhhccCC----CCCHHHHHHHHHHh
Q 028843 75 KRGNISDDEEDLILRLHKLLGSRWSLIAGRLP----GRTDNEIKNYWNSH 120 (203)
Q Consensus 75 ~~~~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~----~Rt~~q~k~Rw~~~ 120 (203)
....-|..|...|..++.+||.++...|.-.. -.|..||+.+...+
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 44568899999999999999999999986542 27999999887765
No 94
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=41.58 E-value=51 Score=23.28 Aligned_cols=45 Identities=11% Similarity=0.079 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhcccccC
Q 028843 82 DEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHLSKKINH 127 (203)
Q Consensus 82 eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~ 127 (203)
+.|..|+.+....| -.++.||+.+ |-+...|+.+...+....+-.
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 56888888888877 5799999999 999999999999887765433
No 95
>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=37.07 E-value=25 Score=23.55 Aligned_cols=18 Identities=33% Similarity=0.641 Sum_probs=14.4
Q ss_pred HHHHHHHHHhCCchhhhh
Q 028843 85 DLILRLHKLLGSRWSLIA 102 (203)
Q Consensus 85 ~~Ll~~v~~~G~~W~~Ia 102 (203)
..|.++.+.||++|.-|-
T Consensus 30 ~vl~~LL~lY~~nW~lIE 47 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIE 47 (65)
T ss_pred HHHHHHHHHHcCCchhhh
Confidence 346678889999999885
No 96
>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=36.65 E-value=42 Score=23.36 Aligned_cols=31 Identities=26% Similarity=0.468 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCHHHHHH
Q 028843 84 EDLILRLHKLLGSRWSLIAGRLPGRTDNEIKN 115 (203)
Q Consensus 84 d~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~ 115 (203)
|..|..+....|.+|..+|..| |=+...|..
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 4567778889999999999998 666665544
No 97
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=36.62 E-value=25 Score=33.37 Aligned_cols=52 Identities=13% Similarity=0.200 Sum_probs=45.7
Q ss_pred CCCCCCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhh
Q 028843 15 ASGKNVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLN 68 (203)
Q Consensus 15 ~~~~~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~ 68 (203)
....+....++||.+|-++...+....| .+.+.|+..++ +|..+|++.+|..
T Consensus 401 ~t~sk~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 401 ATYSKKLETDKWDASETELFYKALSERG-SDFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred hhccCccccCcccchhhHHhhhHHhhhc-ccccccccccc-cccHHHHHHHHhh
Confidence 3455677789999999999999999999 67999999999 9999999998864
No 98
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=34.39 E-value=60 Score=20.51 Aligned_cols=34 Identities=29% Similarity=0.489 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHH
Q 028843 82 DEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNY 116 (203)
Q Consensus 82 eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~R 116 (203)
+.|+-.+.++.+.|-.=..||+.+ ||+-..|++.
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 456667788899999999999999 9999888764
No 99
>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=33.31 E-value=60 Score=23.39 Aligned_cols=30 Identities=27% Similarity=0.248 Sum_probs=23.9
Q ss_pred HhCCchhhhhccCCCCCHHHHHHHHHHhhcc
Q 028843 93 LLGSRWSLIAGRLPGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 93 ~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~ 123 (203)
..|..+..||+.+ |=+...++.+....+.+
T Consensus 124 ~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 124 LEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3477899999998 77888898888876543
No 100
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=32.74 E-value=69 Score=25.28 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=25.8
Q ss_pred HHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHh
Q 028843 87 ILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNSH 120 (203)
Q Consensus 87 Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~ 120 (203)
++.+..-.|-.+..||..+ |-|...++.+|...
T Consensus 143 ~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~a 175 (185)
T PF07638_consen 143 VVELRFFEGLSVEEIAERL-GISERTVRRRLRRA 175 (185)
T ss_pred HHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3333334577899999999 99999999999864
No 101
>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=31.82 E-value=58 Score=25.50 Aligned_cols=48 Identities=21% Similarity=0.259 Sum_probs=34.2
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhcc---CcCCcccchhhhhc
Q 028843 21 VNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGL---NRCGKSCRLRWLNY 69 (203)
Q Consensus 21 ~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~---~Rt~~qcr~Rw~~~ 69 (203)
.....-|..|-.-|..+|++|| .++..+|.-.-+ -.|+.||+.+...|
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhG-dDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHG-DDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHC-ccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 5667889999999999999999 678777754321 24566666555443
No 102
>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=31.77 E-value=57 Score=22.67 Aligned_cols=26 Identities=31% Similarity=0.535 Sum_probs=20.1
Q ss_pred HHHHHHhCCchhhhhccCCCCCHHHHH
Q 028843 88 LRLHKLLGSRWSLIAGRLPGRTDNEIK 114 (203)
Q Consensus 88 l~~v~~~G~~W~~Ia~~l~~Rt~~q~k 114 (203)
..+....|..|..+|..| |=+..+|.
T Consensus 11 ~~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 11 TVFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 335677899999999999 77776663
No 103
>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=31.75 E-value=53 Score=23.01 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCH
Q 028843 84 EDLILRLHKLLGSRWSLIAGRLPGRTD 110 (203)
Q Consensus 84 d~~Ll~~v~~~G~~W~~Ia~~l~~Rt~ 110 (203)
|..|..+....|..|..+|..| |=+.
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 5567778889999999999998 4444
No 104
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=31.66 E-value=44 Score=30.05 Aligned_cols=44 Identities=20% Similarity=0.346 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCCChhhhhhh-hccCcCCcccchhhhhc
Q 028843 24 GAWTAEEDRKLTEYIEIHGAKRWKNVATE-SGLNRCGKSCRLRWLNY 69 (203)
Q Consensus 24 ~~WT~eED~~L~~~v~~~g~~~W~~Ia~~-~~~~Rt~~qcr~Rw~~~ 69 (203)
-.||.+|-..+.+.++.|| +++..|-+. ++ .|+...|-+-|+-.
T Consensus 278 ~~wsEeEcr~FEegl~~yG-KDF~lIr~nkvr-tRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYG-KDFHLIRANKVR-TRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhc-ccHHHHHhcccc-cchHHHHHHHHHHh
Confidence 4699999999999999999 778888665 55 89999998766543
No 105
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=30.81 E-value=71 Score=24.26 Aligned_cols=28 Identities=14% Similarity=0.086 Sum_probs=22.3
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 94 LGSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 94 ~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
.|-....||+.| |-+...++.+....++
T Consensus 143 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~ 170 (182)
T PRK09652 143 EGLSYEEIAEIM-GCPIGTVRSRIFRARE 170 (182)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 467899999999 8899999888765444
No 106
>smart00351 PAX Paired Box domain.
Probab=30.68 E-value=2.2e+02 Score=21.02 Aligned_cols=87 Identities=20% Similarity=0.231 Sum_probs=54.6
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCChhhhhhhhccCc-CCcccchhhhhc--ccCCC----CCCCCChHHHHHHHHHH
Q 028843 19 NVVNRGAWTAEEDRKLTEYIEIHGAKRWKNVATESGLNR-CGKSCRLRWLNY--LRPNI----KRGNISDDEEDLILRLH 91 (203)
Q Consensus 19 ~~~~k~~WT~eED~~L~~~v~~~g~~~W~~Ia~~~~~~R-t~~qcr~Rw~~~--l~~~~----~~~~WT~eEd~~Ll~~v 91 (203)
.-++..+.+.++-.+++.++. -| ..-..||+.++..| +...+..||... +.|.. ....-+...+..|++++
T Consensus 11 ~~~~~~~~s~~~R~riv~~~~-~G-~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~ 88 (125)
T smart00351 11 VFVNGRPLPDEERQRIVELAQ-NG-VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYK 88 (125)
T ss_pred eecCCCCCCHHHHHHHHHHHH-cC-CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHH
Confidence 445556799999999998886 45 46799999998555 345566666542 44422 12234556666666666
Q ss_pred HHhCCchhhhhccCCCCCHHHHHHHHH
Q 028843 92 KLLGSRWSLIAGRLPGRTDNEIKNYWN 118 (203)
Q Consensus 92 ~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~ 118 (203)
.+. |..|..+++..+.
T Consensus 89 ~~~-----------p~~t~~el~~~L~ 104 (125)
T smart00351 89 QEN-----------PGIFAWEIRDRLL 104 (125)
T ss_pred HHC-----------CCCCHHHHHHHHH
Confidence 654 4555555655553
No 107
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=30.02 E-value=87 Score=23.46 Aligned_cols=45 Identities=18% Similarity=0.125 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHhC-CchhhhhccCCCCCHHHHHHHHHHhhcccccC
Q 028843 82 DEEDLILRLHKLLG-SRWSLIAGRLPGRTDNEIKNYWNSHLSKKINH 127 (203)
Q Consensus 82 eEd~~Ll~~v~~~G-~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~~~~ 127 (203)
+-|.+|+++.+.-| ..+..||+.+ |-|...|..|-..+.+.-+.+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCcee
Confidence 45778888887777 6799999999 999999999999887765433
No 108
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=28.51 E-value=96 Score=23.67 Aligned_cols=27 Identities=26% Similarity=0.298 Sum_probs=21.6
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
|-.-..||..| |.+...|+.|....++
T Consensus 134 g~s~~EIA~~l-gis~~tV~~~l~ra~~ 160 (173)
T PRK09645 134 GWSTAQIAADL-GIPEGTVKSRLHYALR 160 (173)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 55679999998 8999999988875443
No 109
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.45 E-value=1.5e+02 Score=21.76 Aligned_cols=57 Identities=16% Similarity=0.186 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHhCCCChhhhhhhhccCcCCcccchhhhhcccCCCCCCCCChHHHHHH
Q 028843 28 AEEDRKLTEYIEIHGAKRWKNVATESGLNRCGKSCRLRWLNYLRPNIKRGNISDDEEDLI 87 (203)
Q Consensus 28 ~eED~~L~~~v~~~g~~~W~~Ia~~~~~~Rt~~qcr~Rw~~~l~~~~~~~~WT~eEd~~L 87 (203)
+-+.+.|..+|..+++..=.++|..++. ..+...++.+.+.-..++..|..+++..-
T Consensus 56 Kid~~~L~~~v~~~pd~tl~Ela~~l~V---s~~ti~~~Lkrlg~t~KK~~~~~~~~~~~ 112 (119)
T PF01710_consen 56 KIDRDELKALVEENPDATLRELAERLGV---SPSTIWRALKRLGITRKKKTLHSEKDREK 112 (119)
T ss_pred cccHHHHHHHHHHCCCcCHHHHHHHcCC---CHHHHHHHHHHcCchhccCcccchhHHHH
Confidence 3356679999999998778899999862 44445566666676778888777655543
No 110
>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=28.44 E-value=62 Score=21.92 Aligned_cols=29 Identities=28% Similarity=0.590 Sum_probs=20.5
Q ss_pred HHHHHHHHHH-hCCchhhhhccCCCCCHHHH
Q 028843 84 EDLILRLHKL-LGSRWSLIAGRLPGRTDNEI 113 (203)
Q Consensus 84 d~~Ll~~v~~-~G~~W~~Ia~~l~~Rt~~q~ 113 (203)
.+.|..++.. .|..|..+|..| |=+...|
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 4556666666 799999999999 4444444
No 111
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=28.12 E-value=81 Score=23.84 Aligned_cols=28 Identities=21% Similarity=0.167 Sum_probs=22.4
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 94 LGSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 94 ~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
.|-....||..| |-|...|+.+......
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 167 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRARQ 167 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 366789999999 8889999888876444
No 112
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=28.11 E-value=49 Score=23.78 Aligned_cols=18 Identities=22% Similarity=0.099 Sum_probs=16.2
Q ss_pred CCCChHHHHHHHHHHHHh
Q 028843 77 GNISDDEEDLILRLHKLL 94 (203)
Q Consensus 77 ~~WT~eEd~~Ll~~v~~~ 94 (203)
..||++++..||+++..|
T Consensus 5 R~WS~eDEi~iL~gl~~~ 22 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDF 22 (98)
T ss_pred CCCCchHHHHHHHHHHHH
Confidence 469999999999999877
No 113
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=27.42 E-value=39 Score=35.03 Aligned_cols=25 Identities=16% Similarity=0.356 Sum_probs=23.2
Q ss_pred CCChHHHHHHHHHHHHhC-Cchhhhh
Q 028843 78 NISDDEEDLILRLHKLLG-SRWSLIA 102 (203)
Q Consensus 78 ~WT~eEd~~Ll~~v~~~G-~~W~~Ia 102 (203)
.|..++|..||-.|-+|| ++|..|-
T Consensus 1135 ~W~~e~Ds~LLiGI~khGygswe~Ir 1160 (1373)
T KOG0384|consen 1135 DWGSEDDSMLLIGIFKHGYGSWEAIR 1160 (1373)
T ss_pred CCCchhhhhHhhhhhhcccccHHHhc
Confidence 599999999999999999 9998884
No 114
>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=26.82 E-value=68 Score=22.41 Aligned_cols=29 Identities=34% Similarity=0.566 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCchhhhhccCCCCCHHHHHH
Q 028843 86 LILRLHKLLGSRWSLIAGRLPGRTDNEIKN 115 (203)
Q Consensus 86 ~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~ 115 (203)
.|-.+....|..|..+|..| |=++.+|..
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 34455677899999999999 777776655
No 115
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=26.69 E-value=94 Score=24.46 Aligned_cols=28 Identities=18% Similarity=0.120 Sum_probs=22.9
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 94 LGSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 94 ~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
.|-....||..| |-+...++.|.....+
T Consensus 149 ~g~s~~EIA~~l-g~s~~tV~~rl~rar~ 176 (192)
T PRK09643 149 QGYSVADAARML-GVAEGTVKSRCARGRA 176 (192)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 467799999999 9999999999865443
No 116
>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=25.98 E-value=1.3e+02 Score=17.24 Aligned_cols=36 Identities=19% Similarity=0.203 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHh
Q 028843 84 EDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNSH 120 (203)
Q Consensus 84 d~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~ 120 (203)
+..++.++-..|-.+..||..+ |=+...|+.+....
T Consensus 15 ~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 15 EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 4445555545678899999998 77777776665543
No 117
>PRK04217 hypothetical protein; Provisional
Probab=25.90 E-value=1.1e+02 Score=22.52 Aligned_cols=43 Identities=19% Similarity=0.101 Sum_probs=33.5
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 78 NISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 78 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
.-|.++ ..++.++...|-.-..||+.+ |-+...|+.++.....
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArk 84 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARK 84 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 355555 566677766788999999999 9999999999886444
No 118
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=25.20 E-value=99 Score=23.78 Aligned_cols=27 Identities=11% Similarity=-0.040 Sum_probs=21.9
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
|.....||..+ |-|...++++......
T Consensus 152 ~~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T PRK09641 152 DLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56789999998 8899999888775544
No 119
>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=25.17 E-value=81 Score=21.96 Aligned_cols=25 Identities=28% Similarity=0.428 Sum_probs=20.1
Q ss_pred HHHHHHHHHhCCchhhhhccCCCCCH
Q 028843 85 DLILRLHKLLGSRWSLIAGRLPGRTD 110 (203)
Q Consensus 85 ~~Ll~~v~~~G~~W~~Ia~~l~~Rt~ 110 (203)
.-|..+....|..|..+|..| |=+.
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse 27 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSY 27 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCH
Confidence 457788899999999999998 4333
No 120
>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=24.12 E-value=71 Score=21.92 Aligned_cols=33 Identities=30% Similarity=0.555 Sum_probs=24.1
Q ss_pred hHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHH
Q 028843 81 DDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKN 115 (203)
Q Consensus 81 ~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~ 115 (203)
.||-++|+.. -..|.+|..+|..| |=+...|.+
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5677777732 25678999999999 777776655
No 121
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=23.81 E-value=63 Score=21.43 Aligned_cols=23 Identities=30% Similarity=0.515 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCChhhhhhhhcc
Q 028843 33 KLTEYIEIHGAKRWKNVATESGL 55 (203)
Q Consensus 33 ~L~~~v~~~g~~~W~~Ia~~~~~ 55 (203)
.|..++......+|..+|..+|.
T Consensus 2 ~l~~~l~~~~~~~Wk~La~~Lg~ 24 (83)
T PF00531_consen 2 KLFDLLAEDLGSDWKRLARKLGL 24 (83)
T ss_dssp HHHHHHHHSHSTCHHHHHHHTTS
T ss_pred hHHHHHhhcchhhHHHHHHHhCc
Confidence 45666666655889999999974
No 122
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.57 E-value=1.3e+02 Score=23.10 Aligned_cols=30 Identities=27% Similarity=0.347 Sum_probs=24.3
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhccc
Q 028843 94 LGSRWSLIAGRLPGRTDNEIKNYWNSHLSKK 124 (203)
Q Consensus 94 ~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~~ 124 (203)
.|-....||..+ |-+...|+.+....++..
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 134 DGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 466789999999 999999999988765543
No 123
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=22.41 E-value=1.3e+02 Score=23.56 Aligned_cols=28 Identities=21% Similarity=0.064 Sum_probs=22.7
Q ss_pred hCCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 94 LGSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 94 ~G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
.|-....||..| |-+...|+.+......
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar~ 148 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGRV 148 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 366789999999 8999999998876544
No 124
>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=22.38 E-value=1.2e+02 Score=22.97 Aligned_cols=27 Identities=19% Similarity=0.299 Sum_probs=21.6
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
|-....||..+ |-|...|+.+....+.
T Consensus 135 g~s~~eiA~~l-gis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 135 DLTIKEIAEVM-NKPEGTVKTYLHRALK 161 (169)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56688999888 8899999988876554
No 125
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.24 E-value=1.1e+02 Score=23.49 Aligned_cols=27 Identities=11% Similarity=-0.040 Sum_probs=21.4
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
|-.-..||..| |-+...|+.+......
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 55688999998 8899999988876544
No 126
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.24 E-value=1.5e+02 Score=22.18 Aligned_cols=27 Identities=11% Similarity=0.123 Sum_probs=22.3
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
|-.-..||..| |-+...|+.|....++
T Consensus 122 g~s~~EIA~~l-gis~~tV~~~l~ra~~ 148 (161)
T PRK09047 122 DMDVAETAAAM-GCSEGSVKTHCSRATH 148 (161)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56689999999 8899999998876544
No 127
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=21.85 E-value=1.4e+02 Score=23.25 Aligned_cols=28 Identities=11% Similarity=0.041 Sum_probs=22.8
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhcc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~ 123 (203)
|-....||..| |-|...++.+.......
T Consensus 147 ~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 147 EKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 56789999999 88999999998765543
No 128
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=21.49 E-value=80 Score=18.90 Aligned_cols=36 Identities=28% Similarity=0.383 Sum_probs=17.3
Q ss_pred CCChHHHHHHHHHHHHhCCchhhhhccCCCCCHHHHHH
Q 028843 78 NISDDEEDLILRLHKLLGSRWSLIAGRLPGRTDNEIKN 115 (203)
Q Consensus 78 ~WT~eEd~~Ll~~v~~~G~~W~~Ia~~l~~Rt~~q~k~ 115 (203)
.+|.+|-..|..+ ..-|..=..||+.| ||+...|..
T Consensus 4 ~Lt~~eR~~I~~l-~~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEAL-LEQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHH-HCS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHH-HHcCCCHHHHHHHH-CcCcHHHHH
Confidence 4566666666555 45678889999999 999887765
No 129
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.35 E-value=1.4e+02 Score=22.96 Aligned_cols=28 Identities=14% Similarity=0.243 Sum_probs=22.7
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhcc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~ 123 (203)
|-....||..| |-+...|+.+....++.
T Consensus 147 g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 147 GASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 56789999998 99999999988865543
No 130
>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=21.18 E-value=1e+02 Score=23.78 Aligned_cols=28 Identities=11% Similarity=0.031 Sum_probs=22.1
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhcc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~~ 123 (203)
|-....||..+ |=|...|+.+.....+.
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 55689999998 88899999888765543
No 131
>COG1168 MalY Bifunctional PLP-dependent enzyme with beta-cystathionase and maltose regulon repressor activities [Amino acid transport and metabolism]
Probab=21.15 E-value=1.1e+02 Score=27.69 Aligned_cols=28 Identities=32% Similarity=0.436 Sum_probs=24.8
Q ss_pred CCCCCCccCCCCHHHHHHHHHHHHHhCC
Q 028843 16 SGKNVVNRGAWTAEEDRKLTEYIEIHGA 43 (203)
Q Consensus 16 ~~~~~~~k~~WT~eED~~L~~~v~~~g~ 43 (203)
|.+.+-.+.-||+||=.+|.++..+||.
T Consensus 165 CnPHNP~Grvwt~eeL~~i~elc~kh~v 192 (388)
T COG1168 165 CNPHNPTGRVWTKEELRKIAELCLRHGV 192 (388)
T ss_pred eCCCCCCCccccHHHHHHHHHHHHHcCC
Confidence 6667777889999999999999999984
No 132
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=20.77 E-value=1.6e+02 Score=22.10 Aligned_cols=27 Identities=7% Similarity=-0.117 Sum_probs=21.8
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
|-.-..||..+ |-+...|+.|......
T Consensus 122 g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 122 EKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56689999998 9999999988875443
No 133
>PF05029 TIMELESS_C: Timeless protein C terminal region; InterPro: IPR007725 The timeless (tim) gene is essential for circadian function in Drosophila. Putative homologues of Drosophila tim have been identified in both mice and humans (mTim and hTIM, respectively). Mammalian TIM is not the true orthologue of Drosophila TIM, but is the likely orthologue of a fly gene, timeout (also called tim-2) []. mTim has been shown to be essential for embryonic development, but does not have substantiated circadian function []. Some family members contain a SANT domain in this region.
Probab=20.74 E-value=3e+02 Score=26.16 Aligned_cols=91 Identities=19% Similarity=0.285 Sum_probs=50.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCC--------Chhhhhhhhc-cCcCCcccchhhhhc--c----------cCCCCCC----C
Q 028843 24 GAWTAEEDRKLTEYIEIHGAK--------RWKNVATESG-LNRCGKSCRLRWLNY--L----------RPNIKRG----N 78 (203)
Q Consensus 24 ~~WT~eED~~L~~~v~~~g~~--------~W~~Ia~~~~-~~Rt~~qcr~Rw~~~--l----------~~~~~~~----~ 78 (203)
..||+++...|.++...|+.. +| |...|. ..|+..+....-... . ....+++ .
T Consensus 93 ~~~~~~~~~e~~~l~i~~~~~~~~~~D~vdw--i~~~L~~~~r~Rr~~~~~l~~~Gl~~~~~~~~~~k~a~~kk~~~rll 170 (566)
T PF05029_consen 93 EVWTEEEEEELRQLYIEVKDLDEEDQDLVDW--ILDNLSDATRTRRQWEKKLVEMGLADSAKDLIETKSAMFKKGRLRLL 170 (566)
T ss_pred ccccchhHHHHHHHHHHHhhhcccchhHHHH--HHHHhccchhhhHHHHHHHHHcccccccccccccccccccCCccccc
Confidence 589999999888877766633 23 333332 134444433222110 0 0112344 6
Q ss_pred CChHHHHHHHHHHHHhCCc---hhhhhccC-CCCCHHHHHHH
Q 028843 79 ISDDEEDLILRLHKLLGSR---WSLIAGRL-PGRTDNEIKNY 116 (203)
Q Consensus 79 WT~eEd~~Ll~~v~~~G~~---W~~Ia~~l-~~Rt~~q~k~R 116 (203)
||++++..|-.++..|... -..|.+.+ ..|+..++..+
T Consensus 171 ~t~e~e~~l~~L~e~~~~~~d~l~~i~~~~~~k~s~~~i~~k 212 (566)
T PF05029_consen 171 WTEEEEEELKDLYEEFKDSDDCLGRIMKELTGKRSKAEIVEK 212 (566)
T ss_pred cChHHHHHHHHHhhhccCcHHHHHHHHhhhccccChhhhccc
Confidence 9999999999888776522 34444444 34566555443
No 134
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=20.52 E-value=1.1e+02 Score=30.45 Aligned_cols=47 Identities=21% Similarity=0.310 Sum_probs=31.9
Q ss_pred CCCCCChHHHHHHHHHHHHhCC----chhhhhcc------------CCCCCHHHHHHHHHHhh
Q 028843 75 KRGNISDDEEDLILRLHKLLGS----RWSLIAGR------------LPGRTDNEIKNYWNSHL 121 (203)
Q Consensus 75 ~~~~WT~eEd~~Ll~~v~~~G~----~W~~Ia~~------------l~~Rt~~q~k~Rw~~~l 121 (203)
+..+.|.+||.-|+.++.++|- .|..+-.. +..||...+..|++.++
T Consensus 894 k~~~ys~~edrfL~~~l~K~g~~~~~~~e~lr~~~~~~~~frfdw~~~sRt~~el~Rr~ntli 956 (971)
T KOG0385|consen 894 KGKNYSEEEDRFLECMLHKLGFDAENVYEELRQPIRNSPQFRFDWFIKSRTAMELQRRCNTLI 956 (971)
T ss_pred cCCCCchhhHHHHHHHHHHhccCchhHHHHHHHHHhcCcccccceeeehhhHHHHHhcCCeeE
Confidence 6678999999999999999982 24444322 23466666666665443
No 135
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=20.36 E-value=1.3e+02 Score=23.34 Aligned_cols=27 Identities=11% Similarity=0.046 Sum_probs=21.3
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
|-....||..+ |-|...|+.+....++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~ 180 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRARE 180 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 55688999998 8889999988875544
No 136
>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=20.31 E-value=95 Score=22.82 Aligned_cols=25 Identities=20% Similarity=0.365 Sum_probs=18.5
Q ss_pred hhhhccCCCCCHHHHHHHHHHhhcc
Q 028843 99 SLIAGRLPGRTDNEIKNYWNSHLSK 123 (203)
Q Consensus 99 ~~Ia~~l~~Rt~~q~k~Rw~~~l~~ 123 (203)
...+...|..|..+=|+||++.+..
T Consensus 53 ~~~~~~~p~HT~~sWRDR~RKfv~~ 77 (105)
T PF09197_consen 53 KDLARKNPRHTENSWRDRYRKFVSE 77 (105)
T ss_dssp HHHHHHTTTS-HHHHHHHHHHTHHH
T ss_pred HHHHHcCCccchhHHHHHHHHHHHH
Confidence 4446677899999999999877664
No 137
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=20.16 E-value=1.6e+02 Score=22.88 Aligned_cols=27 Identities=19% Similarity=0.161 Sum_probs=21.9
Q ss_pred CCchhhhhccCCCCCHHHHHHHHHHhhc
Q 028843 95 GSRWSLIAGRLPGRTDNEIKNYWNSHLS 122 (203)
Q Consensus 95 G~~W~~Ia~~l~~Rt~~q~k~Rw~~~l~ 122 (203)
|.....||..| |=+...|+.+....+.
T Consensus 155 g~s~~EIA~~l-gis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 155 GLSAEETAEAV-GSTPGAVRVAQHRALA 181 (189)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56789999998 8888889888876554
Done!