Query 046419
Match_columns 505
No_of_seqs 187 out of 1442
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 11:55:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046419.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046419hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 100.0 1.9E-31 4.2E-36 262.5 10.9 110 31-140 6-115 (238)
2 PLN03212 Transcription repress 100.0 8.4E-31 1.8E-35 257.1 14.3 113 27-139 18-130 (249)
3 PLN03091 hypothetical protein; 100.0 1.9E-29 4.2E-34 263.1 23.3 112 28-139 8-119 (459)
4 KOG0049 Transcription factor, 99.7 1.2E-17 2.6E-22 180.0 5.7 127 6-133 329-462 (939)
5 KOG0049 Transcription factor, 99.6 1.9E-16 4.2E-21 170.8 7.3 148 4-152 272-426 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 1.3E-15 2.8E-20 119.3 3.4 60 37-98 1-60 (60)
7 KOG0050 mRNA splicing protein 99.4 2.8E-14 6E-19 151.5 3.1 107 31-139 4-110 (617)
8 COG5147 REB1 Myb superfamily p 99.4 1.1E-13 2.4E-18 149.2 6.2 109 28-137 14-122 (512)
9 KOG0051 RNA polymerase I termi 99.4 4.3E-13 9.3E-18 146.1 6.0 108 33-143 383-518 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.3 3.7E-13 8E-18 101.6 0.4 48 34-81 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.2 1.3E-11 2.9E-16 93.1 5.6 46 87-132 1-48 (48)
12 PLN03212 Transcription repress 99.1 2.7E-11 5.8E-16 120.1 4.6 89 64-160 10-100 (249)
13 PF13921 Myb_DNA-bind_6: Myb-l 99.1 7.5E-11 1.6E-15 92.3 5.8 53 90-142 1-53 (60)
14 PLN03091 hypothetical protein; 99.1 5.9E-11 1.3E-15 125.4 3.4 71 83-153 10-82 (459)
15 smart00717 SANT SANT SWI3, AD 99.0 4E-10 8.6E-15 82.2 6.1 47 87-133 1-48 (49)
16 KOG0048 Transcription factor, 99.0 1.6E-10 3.6E-15 114.3 3.0 71 84-154 6-78 (238)
17 smart00717 SANT SANT SWI3, AD 98.9 3.2E-10 7E-15 82.7 2.0 48 34-82 1-48 (49)
18 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 2.6E-09 5.7E-14 76.9 6.0 44 89-132 1-45 (45)
19 KOG0051 RNA polymerase I termi 98.8 2.9E-09 6.4E-14 116.6 5.1 118 30-151 304-449 (607)
20 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 2E-09 4.4E-14 77.4 1.7 44 36-80 1-44 (45)
21 COG5147 REB1 Myb superfamily p 98.1 1.2E-06 2.7E-11 95.3 1.6 131 2-135 37-170 (512)
22 TIGR01557 myb_SHAQKYF myb-like 97.9 7.2E-06 1.6E-10 65.0 2.1 49 33-81 2-54 (57)
23 TIGR01557 myb_SHAQKYF myb-like 97.7 0.00011 2.5E-09 58.2 6.0 48 87-134 3-56 (57)
24 KOG0050 mRNA splicing protein 97.6 4.3E-05 9.3E-10 82.7 3.0 76 85-160 5-81 (617)
25 KOG0457 Histone acetyltransfer 97.5 3.7E-05 8.1E-10 81.8 1.3 53 29-82 67-119 (438)
26 KOG0457 Histone acetyltransfer 97.4 0.00027 5.8E-09 75.4 6.4 51 85-135 70-121 (438)
27 COG5259 RSC8 RSC chromatin rem 96.9 0.00035 7.6E-09 75.1 1.2 47 33-81 278-324 (531)
28 TIGR02894 DNA_bind_RsfA transc 96.8 0.0019 4E-08 61.2 4.8 53 86-139 3-62 (161)
29 KOG1279 Chromatin remodeling f 96.7 0.0019 4E-08 71.0 5.4 47 86-132 252-298 (506)
30 PF13325 MCRS_N: N-terminal re 96.7 0.003 6.5E-08 61.9 6.1 99 36-136 1-130 (199)
31 COG5259 RSC8 RSC chromatin rem 96.7 0.0018 3.9E-08 69.8 4.8 45 87-131 279-323 (531)
32 KOG1279 Chromatin remodeling f 96.7 0.00071 1.5E-08 74.2 1.8 49 31-81 250-298 (506)
33 PF13837 Myb_DNA-bind_4: Myb/S 96.5 0.0024 5.2E-08 53.1 3.4 49 88-136 2-68 (90)
34 PF08914 Myb_DNA-bind_2: Rap1 96.1 0.0085 1.8E-07 48.8 4.6 51 87-137 2-62 (65)
35 TIGR02894 DNA_bind_RsfA transc 96.1 0.0015 3.3E-08 61.7 0.1 50 32-83 2-57 (161)
36 PF13837 Myb_DNA-bind_4: Myb/S 96.1 0.0013 2.9E-08 54.7 -0.5 48 34-81 1-64 (90)
37 PF13873 Myb_DNA-bind_5: Myb/S 96.0 0.013 2.8E-07 48.1 5.1 51 87-137 2-74 (78)
38 PRK13923 putative spore coat p 95.8 0.011 2.3E-07 56.8 4.4 53 85-138 3-62 (170)
39 PF08914 Myb_DNA-bind_2: Rap1 95.4 0.0043 9.3E-08 50.6 0.1 51 34-84 2-60 (65)
40 COG5114 Histone acetyltransfer 95.3 0.019 4.2E-07 59.6 4.3 48 88-135 64-112 (432)
41 COG5114 Histone acetyltransfer 95.2 0.0053 1.2E-07 63.6 -0.0 50 32-82 61-110 (432)
42 PF13873 Myb_DNA-bind_5: Myb/S 95.0 0.0059 1.3E-07 50.1 -0.3 49 33-81 1-69 (78)
43 PLN03142 Probable chromatin-re 94.9 0.066 1.4E-06 63.8 7.9 102 36-138 826-990 (1033)
44 PRK13923 putative spore coat p 93.2 0.015 3.3E-07 55.6 -1.4 50 31-82 2-57 (170)
45 PF12776 Myb_DNA-bind_3: Myb/S 91.8 0.43 9.4E-06 40.1 5.8 47 89-135 1-65 (96)
46 KOG4282 Transcription factor G 91.5 0.34 7.3E-06 50.6 5.8 52 87-138 54-119 (345)
47 PF09111 SLIDE: SLIDE; InterP 91.4 0.37 7.9E-06 43.7 5.2 54 84-137 46-115 (118)
48 COG5118 BDP1 Transcription ini 90.3 0.43 9.3E-06 50.9 5.2 46 89-134 367-412 (507)
49 KOG4282 Transcription factor G 88.3 0.39 8.4E-06 50.1 3.2 48 34-81 54-113 (345)
50 KOG2656 DNA methyltransferase 88.1 0.64 1.4E-05 49.8 4.6 86 56-142 75-191 (445)
51 KOG1194 Predicted DNA-binding 84.6 2.6 5.6E-05 46.2 7.0 52 86-137 186-237 (534)
52 PF08281 Sigma70_r4_2: Sigma-7 83.2 2.9 6.3E-05 31.6 5.0 42 92-134 12-53 (54)
53 COG5118 BDP1 Transcription ini 82.0 1.8 3.8E-05 46.5 4.5 65 33-99 364-436 (507)
54 KOG4329 DNA-binding protein [G 80.2 14 0.0003 39.8 10.2 43 89-131 279-322 (445)
55 KOG4167 Predicted DNA-binding 77.7 5.7 0.00012 45.9 6.9 44 88-131 620-663 (907)
56 PF09111 SLIDE: SLIDE; InterP 76.8 1.8 4E-05 39.2 2.4 34 31-64 46-82 (118)
57 smart00595 MADF subfamily of S 76.6 3.4 7.3E-05 34.3 3.8 26 109-135 30-55 (89)
58 PF13404 HTH_AsnC-type: AsnC-t 75.7 7.2 0.00016 29.0 4.9 38 93-131 3-41 (42)
59 PF12776 Myb_DNA-bind_3: Myb/S 75.5 1.4 3E-05 37.1 1.1 44 36-79 1-60 (96)
60 KOG4468 Polycomb-group transcr 75.1 4.5 9.7E-05 45.8 5.1 53 86-138 87-149 (782)
61 PF11035 SnAPC_2_like: Small n 73.7 11 0.00023 39.9 7.2 51 87-137 21-75 (344)
62 PF07750 GcrA: GcrA cell cycle 73.4 3.8 8.2E-05 39.0 3.7 41 89-130 2-42 (162)
63 KOG4167 Predicted DNA-binding 73.4 1.5 3.2E-05 50.4 1.0 42 35-78 620-661 (907)
64 PRK11179 DNA-binding transcrip 73.3 6.4 0.00014 36.4 5.1 46 92-138 8-54 (153)
65 PF04545 Sigma70_r4: Sigma-70, 69.8 12 0.00026 28.0 5.0 42 93-135 7-48 (50)
66 PF11035 SnAPC_2_like: Small n 69.4 58 0.0013 34.6 11.4 87 35-135 22-129 (344)
67 PRK11169 leucine-responsive tr 69.2 7.6 0.00017 36.4 4.7 46 92-138 13-59 (164)
68 KOG3841 TEF-1 and related tran 68.9 71 0.0015 34.8 12.0 72 31-139 73-149 (455)
69 KOG4468 Polycomb-group transcr 68.8 2.7 5.8E-05 47.4 1.7 49 33-83 87-145 (782)
70 PF11626 Rap1_C: TRF2-interact 66.9 4.8 0.0001 34.2 2.5 23 32-54 45-75 (87)
71 PF11626 Rap1_C: TRF2-interact 64.5 8.6 0.00019 32.7 3.6 17 83-99 43-59 (87)
72 TIGR02985 Sig70_bacteroi1 RNA 58.1 24 0.00053 31.2 5.6 37 98-135 121-157 (161)
73 PF04504 DUF573: Protein of un 57.9 17 0.00037 31.8 4.4 49 87-135 4-65 (98)
74 KOG0260 RNA polymerase II, lar 57.1 4.1E+02 0.0089 33.4 16.4 9 41-49 1234-1242(1605)
75 PLN03162 golden-2 like transcr 55.4 81 0.0018 34.3 9.6 49 87-135 237-290 (526)
76 PF01388 ARID: ARID/BRIGHT DNA 54.7 27 0.00059 29.3 5.0 37 98-134 41-90 (92)
77 KOG2656 DNA methyltransferase 54.5 5.7 0.00012 42.9 1.0 50 31-81 127-181 (445)
78 PF13404 HTH_AsnC-type: AsnC-t 53.2 4 8.7E-05 30.4 -0.2 38 40-79 3-40 (42)
79 KOG0384 Chromodomain-helicase 53.2 15 0.00032 45.0 4.2 72 33-111 1132-1204(1373)
80 smart00344 HTH_ASNC helix_turn 49.7 33 0.00072 29.3 4.9 45 93-138 3-48 (108)
81 smart00351 PAX Paired Box doma 48.6 47 0.001 30.0 5.9 80 26-107 7-93 (125)
82 KOG2009 Transcription initiati 48.2 18 0.00038 41.1 3.6 50 86-135 408-457 (584)
83 PF13325 MCRS_N: N-terminal re 47.9 35 0.00077 33.8 5.3 45 89-134 1-48 (199)
84 TIGR02937 sigma70-ECF RNA poly 47.8 45 0.00096 28.6 5.4 35 100-135 120-154 (158)
85 PF09420 Nop16: Ribosome bioge 47.1 39 0.00085 31.9 5.3 46 87-132 114-163 (164)
86 smart00501 BRIGHT BRIGHT, ARID 46.5 43 0.00094 28.4 5.0 38 98-135 37-87 (93)
87 PRK11179 DNA-binding transcrip 44.4 8.6 0.00019 35.6 0.4 45 39-85 8-52 (153)
88 cd06171 Sigma70_r4 Sigma70, re 43.0 66 0.0014 22.6 4.9 42 90-133 11-52 (55)
89 PRK09652 RNA polymerase sigma 41.6 62 0.0013 29.3 5.7 31 104-135 142-172 (182)
90 PF01388 ARID: ARID/BRIGHT DNA 41.5 7.9 0.00017 32.5 -0.3 39 43-81 39-88 (92)
91 PF07638 Sigma70_ECF: ECF sigm 41.1 55 0.0012 31.1 5.4 39 96-135 141-179 (185)
92 cd08319 Death_RAIDD Death doma 40.7 40 0.00086 28.8 3.9 28 95-123 2-29 (83)
93 PRK11169 leucine-responsive tr 39.9 8.3 0.00018 36.1 -0.4 45 39-85 13-57 (164)
94 PRK11924 RNA polymerase sigma 39.8 61 0.0013 29.3 5.3 30 105-135 140-169 (179)
95 PF02954 HTH_8: Bacterial regu 39.8 60 0.0013 23.7 4.2 35 94-129 6-40 (42)
96 COG1522 Lrp Transcriptional re 39.3 53 0.0012 29.6 4.8 46 92-138 7-53 (154)
97 PF10545 MADF_DNA_bdg: Alcohol 38.3 37 0.0008 27.2 3.2 28 109-136 29-57 (85)
98 PRK04217 hypothetical protein; 35.8 89 0.0019 28.2 5.5 45 89-135 42-86 (110)
99 KOG1194 Predicted DNA-binding 35.7 20 0.00043 39.6 1.6 47 29-77 182-228 (534)
100 KOG2009 Transcription initiati 35.1 22 0.00048 40.4 1.9 49 29-79 404-452 (584)
101 PRK09643 RNA polymerase sigma 34.8 83 0.0018 29.7 5.5 30 105-135 149-178 (192)
102 COG2963 Transposase and inacti 33.2 1.1E+02 0.0025 26.6 5.7 48 87-135 5-53 (116)
103 cd08803 Death_ank3 Death domai 32.8 69 0.0015 27.4 4.1 29 95-124 4-32 (84)
104 PF09905 DUF2132: Uncharacteri 32.3 56 0.0012 26.9 3.2 23 95-119 12-34 (64)
105 PF02954 HTH_8: Bacterial regu 32.1 26 0.00055 25.7 1.2 30 40-70 5-34 (42)
106 TIGR02954 Sig70_famx3 RNA poly 31.9 98 0.0021 28.3 5.3 30 106-136 135-164 (169)
107 cd01852 AIG1 AIG1 (avrRpt2-ind 31.4 74 0.0016 30.0 4.5 67 36-114 95-161 (196)
108 smart00501 BRIGHT BRIGHT, ARID 31.3 12 0.00027 31.7 -0.7 39 43-81 35-84 (93)
109 PRK09641 RNA polymerase sigma 31.1 1E+02 0.0022 28.4 5.3 29 106-135 152-180 (187)
110 TIGR02939 RpoE_Sigma70 RNA pol 30.9 81 0.0018 29.1 4.7 30 106-136 154-183 (190)
111 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 30.9 97 0.0021 24.3 4.3 34 94-128 8-41 (50)
112 cd08317 Death_ank Death domain 30.6 58 0.0013 27.3 3.3 29 95-124 4-32 (84)
113 KOG1878 Nuclear receptor coreg 29.2 15 0.00033 45.4 -0.6 32 104-135 371-402 (1672)
114 cd08318 Death_NMPP84 Death dom 29.1 75 0.0016 26.9 3.7 25 99-124 11-35 (86)
115 PF00046 Homeobox: Homeobox do 29.0 2.5E+02 0.0054 21.0 6.4 48 86-134 3-54 (57)
116 PF09197 Rap1-DNA-bind: Rap1, 28.5 20 0.00043 32.2 0.1 17 36-52 1-17 (105)
117 PRK09637 RNA polymerase sigma 28.4 1.2E+02 0.0026 28.4 5.4 30 105-135 121-150 (181)
118 PRK09648 RNA polymerase sigma 28.2 1.3E+02 0.0028 28.0 5.6 31 105-136 154-184 (189)
119 PRK09047 RNA polymerase factor 28.1 1.4E+02 0.0031 26.7 5.7 29 106-135 122-150 (161)
120 KOG4786 Ubinuclein, nuclear pr 27.9 3.1E+02 0.0066 32.6 9.1 63 272-344 1005-1067(1136)
121 PRK01905 DNA-binding protein F 27.6 1.4E+02 0.003 24.7 5.0 37 92-129 36-72 (77)
122 KOG4329 DNA-binding protein [G 27.5 33 0.00072 37.1 1.5 41 36-78 279-320 (445)
123 PF13384 HTH_23: Homeodomain-l 27.1 72 0.0016 23.5 2.9 35 92-128 4-38 (50)
124 PF07750 GcrA: GcrA cell cycle 27.0 47 0.001 31.7 2.3 35 36-73 2-36 (162)
125 TIGR02943 Sig70_famx1 RNA poly 26.9 1.4E+02 0.0031 28.1 5.7 30 105-135 146-175 (188)
126 PRK11923 algU RNA polymerase s 26.4 1.3E+02 0.0028 28.1 5.2 29 106-135 154-182 (193)
127 cd08777 Death_RIP1 Death Domai 26.3 79 0.0017 27.0 3.4 30 96-126 3-32 (86)
128 TIGR02948 SigW_bacill RNA poly 25.9 1.3E+02 0.0028 27.7 5.1 29 106-135 152-180 (187)
129 cd08804 Death_ank2 Death domai 25.9 91 0.002 26.4 3.7 31 95-126 4-34 (84)
130 PF09420 Nop16: Ribosome bioge 25.5 39 0.00085 32.0 1.5 30 32-62 112-141 (164)
131 PRK12524 RNA polymerase sigma 25.4 1.5E+02 0.0033 27.9 5.5 30 105-135 151-180 (196)
132 PRK12512 RNA polymerase sigma 25.3 1.5E+02 0.0033 27.4 5.4 30 106-136 147-176 (184)
133 PRK12531 RNA polymerase sigma 25.3 1.6E+02 0.0034 27.8 5.6 30 106-136 157-186 (194)
134 PRK09645 RNA polymerase sigma 25.1 1.6E+02 0.0035 26.8 5.5 29 106-135 134-162 (173)
135 PRK12515 RNA polymerase sigma 25.1 1.6E+02 0.0035 27.4 5.6 29 106-135 147-175 (189)
136 PF05263 DUF722: Protein of un 24.8 1.4E+02 0.0031 27.7 5.0 40 93-134 84-125 (130)
137 PRK09642 RNA polymerase sigma 24.7 1.7E+02 0.0038 26.3 5.6 29 106-135 122-150 (160)
138 smart00005 DEATH DEATH domain, 24.6 89 0.0019 25.6 3.4 30 94-124 4-34 (88)
139 PRK06759 RNA polymerase factor 24.1 1.9E+02 0.004 25.8 5.6 29 106-135 122-150 (154)
140 KOG3554 Histone deacetylase co 24.1 1.1E+02 0.0023 34.3 4.6 42 88-129 286-328 (693)
141 PRK12530 RNA polymerase sigma 24.1 1.7E+02 0.0036 27.6 5.5 28 106-134 150-177 (189)
142 PRK12529 RNA polymerase sigma 24.1 1.7E+02 0.0038 27.1 5.6 32 105-137 142-173 (178)
143 PRK12523 RNA polymerase sigma 23.9 1.8E+02 0.0039 26.7 5.6 31 104-135 133-163 (172)
144 PRK00430 fis global DNA-bindin 23.2 1.8E+02 0.004 25.3 5.1 36 93-129 55-90 (95)
145 PF05029 TIMELESS_C: Timeless 22.9 2.2E+02 0.0048 32.5 7.0 91 35-127 93-212 (566)
146 PRK10100 DNA-binding transcrip 22.9 1.6E+02 0.0034 29.0 5.2 46 89-137 155-200 (216)
147 cd08311 Death_p75NR Death doma 22.8 89 0.0019 26.3 3.0 33 92-126 2-34 (77)
148 PLN03142 Probable chromatin-re 22.8 1.3E+02 0.0029 36.7 5.5 41 89-129 826-867 (1033)
149 PRK06811 RNA polymerase factor 22.8 2.2E+02 0.0047 26.7 6.0 33 107-140 148-180 (189)
150 COG5352 Uncharacterized protei 22.8 94 0.002 29.6 3.4 40 89-129 2-41 (169)
151 PRK09413 IS2 repressor TnpA; R 22.7 1E+02 0.0023 27.4 3.6 81 33-118 9-118 (121)
152 cd00131 PAX Paired Box domain 22.4 2.2E+02 0.0047 25.9 5.7 87 28-116 9-103 (128)
153 TIGR02999 Sig-70_X6 RNA polyme 22.4 2E+02 0.0043 26.4 5.6 29 106-135 150-178 (183)
154 TIGR02952 Sig70_famx2 RNA poly 22.3 1.9E+02 0.0042 26.0 5.4 29 106-135 138-166 (170)
155 PF13936 HTH_38: Helix-turn-he 21.8 1.2E+02 0.0027 22.4 3.3 37 89-127 4-40 (44)
156 smart00344 HTH_ASNC helix_turn 21.3 38 0.00082 28.9 0.5 42 40-83 3-44 (108)
157 PRK12532 RNA polymerase sigma 21.2 1.9E+02 0.0042 27.0 5.4 29 106-135 152-180 (195)
158 TIGR02950 SigM_subfam RNA poly 20.9 80 0.0017 28.1 2.6 28 108-136 123-150 (154)
159 cd08805 Death_ank1 Death domai 20.8 1.2E+02 0.0027 25.9 3.5 22 95-116 4-25 (84)
160 PRK09649 RNA polymerase sigma 20.6 2E+02 0.0044 26.9 5.3 31 106-137 146-176 (185)
161 TIGR02984 Sig-70_plancto1 RNA 20.6 2.2E+02 0.0047 26.1 5.5 30 105-135 155-184 (189)
162 PRK00118 putative DNA-binding 20.5 2.5E+02 0.0054 25.1 5.5 42 92-134 19-60 (104)
163 PRK12516 RNA polymerase sigma 20.3 2.2E+02 0.0048 26.9 5.5 30 105-135 131-160 (187)
164 COG2197 CitB Response regulato 20.1 2E+02 0.0043 28.0 5.3 47 88-137 147-193 (211)
165 PRK05602 RNA polymerase sigma 20.1 2.1E+02 0.0046 26.5 5.3 29 106-135 144-172 (186)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.97 E-value=1.9e-31 Score=262.53 Aligned_cols=110 Identities=54% Similarity=0.963 Sum_probs=106.1
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCHH
Q 046419 31 QLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQLGNKWA 110 (505)
Q Consensus 31 ~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~kyG~kWs 110 (505)
.+.||+||+|||++|+++|++||.++|..|++.+|++|++|+||+||.|||+|.++++.||+|||++|++|+++||++|+
T Consensus 6 ~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrWs 85 (238)
T KOG0048|consen 6 ELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRWS 85 (238)
T ss_pred cccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHHH
Confidence 45679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHHhhhhhhcCC
Q 046419 111 RMAAQLPGRTDNEIKNYWNTRVKRRHRQGL 140 (505)
Q Consensus 111 kIAk~LpgRT~~qcKnRW~~llkk~~r~~~ 140 (505)
.||++|||||+++|||+|+..+||+.+...
T Consensus 86 ~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 86 LIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 999999999999999999999999987654
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.97 E-value=8.4e-31 Score=257.09 Aligned_cols=113 Identities=50% Similarity=1.067 Sum_probs=107.7
Q ss_pred CCCCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhC
Q 046419 27 EGGVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQLG 106 (505)
Q Consensus 27 ~~~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~kyG 106 (505)
-.+.+++|++||+|||++|+++|++||..+|.+||+.++.+|+++|||+||.++|+|.+++++||+|||++|++++.+||
T Consensus 18 c~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~G 97 (249)
T PLN03212 18 CTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLG 97 (249)
T ss_pred cccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhcc
Confidence 35789999999999999999999999998999999999669999999999999999999999999999999999999999
Q ss_pred CCHHHHHhhCCCCCHHHHHHHHHHHhhhhhhcC
Q 046419 107 NKWARMAAQLPGRTDNEIKNYWNTRVKRRHRQG 139 (505)
Q Consensus 107 ~kWskIAk~LpgRT~~qcKnRW~~llkk~~r~~ 139 (505)
++|+.||+.|+|||+++||+||+.+++++..+.
T Consensus 98 nKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~ 130 (249)
T PLN03212 98 NRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQ 130 (249)
T ss_pred ccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhc
Confidence 999999999999999999999999999887654
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.97 E-value=1.9e-29 Score=263.11 Aligned_cols=112 Identities=58% Similarity=1.058 Sum_probs=107.1
Q ss_pred CCCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCC
Q 046419 28 GGVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQLGN 107 (505)
Q Consensus 28 ~~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~kyG~ 107 (505)
.+++++||+||+|||++|+++|++||..+|.+||+.++.+|+++|||+||.++|+|.+++++||+|||++|++++++||.
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 36789999999999999999999999999999999997799999999999999999999999999999999999999999
Q ss_pred CHHHHHhhCCCCCHHHHHHHHHHHhhhhhhcC
Q 046419 108 KWARMAAQLPGRTDNEIKNYWNTRVKRRHRQG 139 (505)
Q Consensus 108 kWskIAk~LpgRT~~qcKnRW~~llkk~~r~~ 139 (505)
+|++||+.|+|||+++||+||+.+++++.++.
T Consensus 88 KWskIAk~LPGRTDnqIKNRWnslLKKklr~~ 119 (459)
T PLN03091 88 RWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQR 119 (459)
T ss_pred chHHHHHhcCCCCHHHHHHHHHHHHHHHHHHc
Confidence 99999999999999999999999999887653
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.69 E-value=1.2e-17 Score=179.97 Aligned_cols=127 Identities=21% Similarity=0.318 Sum_probs=109.2
Q ss_pred CCcceecccCCCCCCCCCCCC---CCCCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccC
Q 046419 6 SNGEQLESGVGGLNVSDGSGG---EGGVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLR 82 (505)
Q Consensus 6 ~~~~~~~s~~gg~~~~~~s~~---~~~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~ 82 (505)
++|.+|---+.|++.....++ .-.+.+|+|+||.+||.+|..+|.+||..+|.+|-..++ +|+..|||+||.+.|.
T Consensus 329 I~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~ 407 (939)
T KOG0049|consen 329 IQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLN 407 (939)
T ss_pred cchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHH
Confidence 456666666677765544443 567899999999999999999999999999999999999 9999999999999999
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHH---HHHHHHHHhh
Q 046419 83 PNLKKGTFSPEEERLIVELHAQLG-NKWARMAAQLPGRTDNE---IKNYWNTRVK 133 (505)
Q Consensus 83 p~lkkg~WT~EED~lLlelV~kyG-~kWskIAk~LpgRT~~q---cKnRW~~llk 133 (505)
...|++.|+-.||++|+.+|++|| +.|.+||..|+.||+.| ||.|+..+..
T Consensus 408 ~s~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k~ 462 (939)
T KOG0049|consen 408 RSAKVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAKL 462 (939)
T ss_pred HhhccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHHHHHH
Confidence 999999999999999999999999 57999999999999954 5555544433
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.64 E-value=1.9e-16 Score=170.82 Aligned_cols=148 Identities=20% Similarity=0.295 Sum_probs=123.7
Q ss_pred cCCCcceecccCCCCCCCCCCCC---CCCCCCccCCCCHHHHHHHHHHHHHhCC---CCcchhccccCCccccccccccc
Q 046419 4 GNSNGEQLESGVGGLNVSDGSGG---EGGVQLKKGPWTAAEDAILTEYVRKHGE---GNWNAVQRNTGLARCGKSCRLRW 77 (505)
Q Consensus 4 g~~~~~~~~s~~gg~~~~~~s~~---~~~~~lkKG~WT~EEDelL~~lV~k~G~---~nW~~IAk~m~~gRT~kQCR~Rw 77 (505)
|-++|+.++...|-..-+..+=. .+...+++..||+|||.+|+.+|+.-.. .+|++|-..|+ +|+..|...||
T Consensus 272 ~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ymp-gr~~~qLI~R~ 350 (939)
T KOG0049|consen 272 KFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMP-GRTRQQLITRF 350 (939)
T ss_pred ccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcC-Ccchhhhhhhh
Confidence 34567777766654221111100 1234667799999999999999998854 48999999999 99999999999
Q ss_pred ccccCCCCCCCCCCHHHHHHHHHHHHHhCCC-HHHHHhhCCCCCHHHHHHHHHHHhhhhhhcCCCCCCCCCCchhh
Q 046419 78 ANHLRPNLKKGTFSPEEERLIVELHAQLGNK-WARMAAQLPGRTDNEIKNYWNTRVKRRHRQGLPLYPPEIQPQHQ 152 (505)
Q Consensus 78 ~n~L~p~lkkg~WT~EED~lLlelV~kyG~k-WskIAk~LpgRT~~qcKnRW~~llkk~~r~~~~~~~~e~q~~~~ 152 (505)
...|+|.+++|.||.+||.+|+.+|.+||.+ |.+|...+|||++.|||.||.+.+.++.+.+.|...++.+....
T Consensus 351 ~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~ 426 (939)
T KOG0049|consen 351 SHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYA 426 (939)
T ss_pred eeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHH
Confidence 9999999999999999999999999999965 99999999999999999999999999999999998887665443
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.57 E-value=1.3e-15 Score=119.30 Aligned_cols=60 Identities=42% Similarity=0.932 Sum_probs=55.2
Q ss_pred CCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHH
Q 046419 37 WTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLI 98 (505)
Q Consensus 37 WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lL 98 (505)
||+|||++|+++|++||. +|.+||+.|| .|++.||+.||.++|.+.+++++||+|||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999997 9999999997 89999999999999999999999999999987
No 7
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.45 E-value=2.8e-14 Score=151.54 Aligned_cols=107 Identities=25% Similarity=0.523 Sum_probs=101.5
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCHH
Q 046419 31 QLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQLGNKWA 110 (505)
Q Consensus 31 ~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~kyG~kWs 110 (505)
-++.|.|+.-||++|..+|++||...|.+|++.+. .++++||+.||..+|+|.+++..|+.|||++|+.+...+...|.
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 46789999999999999999999999999999998 88999999999999999999999999999999999999999999
Q ss_pred HHHhhCCCCCHHHHHHHHHHHhhhhhhcC
Q 046419 111 RMAAQLPGRTDNEIKNYWNTRVKRRHRQG 139 (505)
Q Consensus 111 kIAk~LpgRT~~qcKnRW~~llkk~~r~~ 139 (505)
.||..| ||+.+||-.||+.++.......
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 999999 9999999999999998776543
No 8
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.43 E-value=1.1e-13 Score=149.23 Aligned_cols=109 Identities=30% Similarity=0.534 Sum_probs=103.4
Q ss_pred CCCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCC
Q 046419 28 GGVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQLGN 107 (505)
Q Consensus 28 ~~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~kyG~ 107 (505)
...+++.|.|+..||+.|..+|++||..+|.+||..+. -|+++||+.||.+++.+.+++..|+.|||.+|+.+..++|.
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 46688899999999999999999999999999999998 68999999999999999999999999999999999999999
Q ss_pred CHHHHHhhCCCCCHHHHHHHHHHHhhhhhh
Q 046419 108 KWARMAAQLPGRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 108 kWskIAk~LpgRT~~qcKnRW~~llkk~~r 137 (505)
.|+.||..+++|+..+|.+||...+.....
T Consensus 93 ~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 93 QWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 999999999999999999999988776654
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.37 E-value=4.3e-13 Score=146.11 Aligned_cols=108 Identities=24% Similarity=0.477 Sum_probs=95.9
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCC--CCCCCCCHHHHHHHHHHHH-------
Q 046419 33 KKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPN--LKKGTFSPEEERLIVELHA------- 103 (505)
Q Consensus 33 kKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~--lkkg~WT~EED~lLlelV~------- 103 (505)
+||+||+||++.|+.+|.++|. .|.+|++.|| |.+..||+||+++.... .+++.||.||+++|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 8999999999999999999999 9999999995 99999999999999886 4889999999999999995
Q ss_pred HhC------------C-------CHHHHHhhCCCCCHHHHHHHHHHHhhhhhhcCCCCC
Q 046419 104 QLG------------N-------KWARMAAQLPGRTDNEIKNYWNTRVKRRHRQGLPLY 143 (505)
Q Consensus 104 kyG------------~-------kWskIAk~LpgRT~~qcKnRW~~llkk~~r~~~~~~ 143 (505)
++. . .|..|++.+.+|+..|||-+|..++.+....+...+
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~~~~ 518 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKRQES 518 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhccccc
Confidence 341 1 399999999999999999999998888765554333
No 10
>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=99.30 E-value=3.7e-13 Score=101.60 Aligned_cols=48 Identities=42% Similarity=0.790 Sum_probs=43.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcchhccccCCccccccccccccccc
Q 046419 34 KGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHL 81 (505)
Q Consensus 34 KG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L 81 (505)
|++||+|||++|+++|.+||.++|.+||+.|+.+||..||+.||.++|
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 689999999999999999999669999999988999999999998865
No 11
>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=99.23 E-value=1.3e-11 Score=93.10 Aligned_cols=46 Identities=24% Similarity=0.658 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-HHHHHhhCC-CCCHHHHHHHHHHHh
Q 046419 87 KGTFSPEEERLIVELHAQLGNK-WARMAAQLP-GRTDNEIKNYWNTRV 132 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG~k-WskIAk~Lp-gRT~~qcKnRW~~ll 132 (505)
+++||+|||++|+++|.+||.+ |..||..|+ +||..||++||+.++
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 5789999999999999999988 999999999 999999999999864
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.15 E-value=2.7e-11 Score=120.05 Aligned_cols=89 Identities=15% Similarity=0.293 Sum_probs=72.0
Q ss_pred cCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhC-CCHHHHHhhC-CCCCHHHHHHHHHHHhhhhhhcCCC
Q 046419 64 TGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQLG-NKWARMAAQL-PGRTDNEIKNYWNTRVKRRHRQGLP 141 (505)
Q Consensus 64 m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~kyG-~kWskIAk~L-pgRT~~qcKnRW~~llkk~~r~~~~ 141 (505)
++ +|+.--|. +..+++++||+|||++|+++|++|| .+|.+||+.+ ++|+++|||.||..+|+..++++.|
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-KKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGI 81 (249)
T ss_pred CC-CCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCC
Confidence 45 56555443 2467899999999999999999999 5799999998 5999999999999999999999999
Q ss_pred CCCCCCCchhhhhhhhccc
Q 046419 142 LYPPEIQPQHQHQHQHQNH 160 (505)
Q Consensus 142 ~~~~e~q~~~~~~~~~qq~ 160 (505)
+.+++......+......|
T Consensus 82 T~EED~lLlel~~~~GnKW 100 (249)
T PLN03212 82 TSDEEDLILRLHRLLGNRW 100 (249)
T ss_pred ChHHHHHHHHHHHhccccH
Confidence 9988766554444333333
No 13
>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=99.14 E-value=7.5e-11 Score=92.32 Aligned_cols=53 Identities=28% Similarity=0.617 Sum_probs=43.9
Q ss_pred CCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhhhhcCCCC
Q 046419 90 FSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRRHRQGLPL 142 (505)
Q Consensus 90 WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~~r~~~~~ 142 (505)
||+|||++|+++|++||.+|.+||+.|+.||..+|++||+..++....++.+.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt 53 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWT 53 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSS
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcC
Confidence 99999999999999999999999999966999999999999776665555443
No 14
>PLN03091 hypothetical protein; Provisional
Probab=99.07 E-value=5.9e-11 Score=125.40 Aligned_cols=71 Identities=21% Similarity=0.354 Sum_probs=63.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCC-CHHHHHhhCC-CCCHHHHHHHHHHHhhhhhhcCCCCCCCCCCchhhh
Q 046419 83 PNLKKGTFSPEEERLIVELHAQLGN-KWARMAAQLP-GRTDNEIKNYWNTRVKRRHRQGLPLYPPEIQPQHQH 153 (505)
Q Consensus 83 p~lkkg~WT~EED~lLlelV~kyG~-kWskIAk~Lp-gRT~~qcKnRW~~llkk~~r~~~~~~~~e~q~~~~~ 153 (505)
..++++.||+|||++|+++|++||. +|.+||+.+. +|+++|||.||..+|+..++++.|+.+++......+
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~ 82 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELH 82 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHH
Confidence 4678999999999999999999995 6999999984 899999999999999999999999988886554443
No 15
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.05 E-value=4e-10 Score=82.23 Aligned_cols=47 Identities=40% Similarity=0.888 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHHhh
Q 046419 87 KGTFSPEEERLIVELHAQLG-NKWARMAAQLPGRTDNEIKNYWNTRVK 133 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG-~kWskIAk~LpgRT~~qcKnRW~~llk 133 (505)
++.||+|||++|++++.+|| .+|..||..|++||..+|+.||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999998765
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.00 E-value=1.6e-10 Score=114.32 Aligned_cols=71 Identities=15% Similarity=0.183 Sum_probs=62.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC-CHHHHHhhCC-CCCHHHHHHHHHHHhhhhhhcCCCCCCCCCCchhhhh
Q 046419 84 NLKKGTFSPEEERLIVELHAQLGN-KWARMAAQLP-GRTDNEIKNYWNTRVKRRHRQGLPLYPPEIQPQHQHQ 154 (505)
Q Consensus 84 ~lkkg~WT~EED~lLlelV~kyG~-kWskIAk~Lp-gRT~~qcKnRW~~llkk~~r~~~~~~~~e~q~~~~~~ 154 (505)
.+.||+||.|||++|+++|++||. +|..||+.++ +|++++||-||..+|+..++++.++.++|......|.
T Consensus 6 ~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~ 78 (238)
T KOG0048|consen 6 ELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHA 78 (238)
T ss_pred cccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHH
Confidence 345799999999999999999995 5999999999 9999999999999999999999998888755544443
No 17
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.94 E-value=3.2e-10 Score=82.71 Aligned_cols=48 Identities=42% Similarity=0.893 Sum_probs=44.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccC
Q 046419 34 KGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLR 82 (505)
Q Consensus 34 KG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~ 82 (505)
++.||++||++|+.++.+||..+|..||+.|+ +|+..+|+.||.+++.
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 47899999999999999999559999999999 9999999999998764
No 18
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.92 E-value=2.6e-09 Score=76.87 Aligned_cols=44 Identities=32% Similarity=0.772 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHHh
Q 046419 89 TFSPEEERLIVELHAQLG-NKWARMAAQLPGRTDNEIKNYWNTRV 132 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG-~kWskIAk~LpgRT~~qcKnRW~~ll 132 (505)
+||+|||++|++++.+|| .+|..||+.|++|+..+|+.||..++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999998753
No 19
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.82 E-value=2.9e-09 Score=116.58 Aligned_cols=118 Identities=24% Similarity=0.333 Sum_probs=97.4
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCC-----------------------CCcchhccccCCccccccccc---ccccccCC
Q 046419 30 VQLKKGPWTAAEDAILTEYVRKHGE-----------------------GNWNAVQRNTGLARCGKSCRL---RWANHLRP 83 (505)
Q Consensus 30 ~~lkKG~WT~EEDelL~~lV~k~G~-----------------------~nW~~IAk~m~~gRT~kQCR~---Rw~n~L~p 83 (505)
..++-+.|+.+||+.|...|..|-. +-|+.|.+.++ -|+.+..+. |-.+.+.+
T Consensus 304 ~e~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~ 382 (607)
T KOG0051|consen 304 DEINLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFEN 382 (607)
T ss_pred hhhhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCcccc
Confidence 3567789999999999999988822 13678888898 599988876 33334433
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhhh--hcCCCCCCCCCCchh
Q 046419 84 NLKKGTFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRRH--RQGLPLYPPEIQPQH 151 (505)
Q Consensus 84 ~lkkg~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~~--r~~~~~~~~e~q~~~ 151 (505)
++|.||+||++.|..+|.++|+.|..|++.| ||.+..|+.||+.+.+... +++.|..+++.....
T Consensus 383 --~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk 449 (607)
T KOG0051|consen 383 --KRGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLK 449 (607)
T ss_pred --ccCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHH
Confidence 8999999999999999999999999999999 9999999999999998885 777788777655443
No 20
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.79 E-value=2e-09 Score=77.44 Aligned_cols=44 Identities=43% Similarity=0.886 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccc
Q 046419 36 PWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANH 80 (505)
Q Consensus 36 ~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~ 80 (505)
.||+|||++|+.++.+||..+|..||+.|+ +|+..+|+.||.++
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 599999999999999999569999999998 89999999999765
No 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.07 E-value=1.2e-06 Score=95.29 Aligned_cols=131 Identities=20% Similarity=0.181 Sum_probs=107.5
Q ss_pred cccCCCcceecccCCC---CCCCCCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccc
Q 046419 2 LLGNSNGEQLESGVGG---LNVSDGSGGEGGVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWA 78 (505)
Q Consensus 2 ~~g~~~~~~~~s~~gg---~~~~~~s~~~~~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~ 78 (505)
-+|.-+|+.+++.+.- .+....+.....+.++++.|+.|||+.|+.+-.++|. .|..||..++ +|+..+|.+||.
T Consensus 37 ~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~-~wstia~~~d-~rt~~~~~ery~ 114 (512)
T COG5147 37 KLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT-QWSTIADYKD-RRTAQQCVERYV 114 (512)
T ss_pred hcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc-hhhhhccccC-ccchHHHHHHHH
Confidence 3677788888888776 2333344446788999999999999999999999999 7999999998 999999999999
Q ss_pred cccCCCCCCCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 79 NHLRPNLKKGTFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 79 n~L~p~lkkg~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
+.+..... ..|+..++...+-.+..|...|.++......+-...|.+++..+..+.
T Consensus 115 ~~~~~~~s-~~~s~~~~~~~f~k~d~f~~~~~~~~~~~~~~~~~~~~N~~~~~~~~~ 170 (512)
T COG5147 115 NTLEDLSS-THDSKLQRRNEFDKIDPFNENSARRPDIYEDELLEREVNREASYRLRV 170 (512)
T ss_pred HHhhhhhc-cccccccchhhccccCchhhhhhhhhhhhhcccchhhhhHHHHHHHHc
Confidence 99986555 889999888888888888888888887776777777788876655443
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.86 E-value=7.2e-06 Score=65.02 Aligned_cols=49 Identities=12% Similarity=0.163 Sum_probs=43.4
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCc---chhccccCCcc-ccccccccccccc
Q 046419 33 KKGPWTAAEDAILTEYVRKHGEGNW---NAVQRNTGLAR-CGKSCRLRWANHL 81 (505)
Q Consensus 33 kKG~WT~EEDelL~~lV~k~G~~nW---~~IAk~m~~gR-T~kQCR~Rw~n~L 81 (505)
+|-.||+||.++++++|+.+|.++| ++|++.|+..| |..||+.|++.|.
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 4567999999999999999999999 99999987667 9999999877654
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=97.66 E-value=0.00011 Score=58.20 Aligned_cols=48 Identities=10% Similarity=0.270 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-CH---HHHHhhCC-CC-CHHHHHHHHHHHhhh
Q 046419 87 KGTFSPEEERLIVELHAQLGN-KW---ARMAAQLP-GR-TDNEIKNYWNTRVKR 134 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG~-kW---skIAk~Lp-gR-T~~qcKnRW~~llkk 134 (505)
+-.||+||+.+++++++.||. +| ..|++.|. .| |..||+.+++.+.-+
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 457999999999999999996 89 99999985 35 999999999887643
No 24
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.56 E-value=4.3e-05 Score=82.67 Aligned_cols=76 Identities=16% Similarity=0.296 Sum_probs=65.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC-CHHHHHhhCCCCCHHHHHHHHHHHhhhhhhcCCCCCCCCCCchhhhhhhhccc
Q 046419 85 LKKGTFSPEEERLIVELHAQLGN-KWARMAAQLPGRTDNEIKNYWNTRVKRRHRQGLPLYPPEIQPQHQHQHQHQNH 160 (505)
Q Consensus 85 lkkg~WT~EED~lLlelV~kyG~-kWskIAk~LpgRT~~qcKnRW~~llkk~~r~~~~~~~~e~q~~~~~~~~~qq~ 160 (505)
++.+.|+.-||++|..+|.+||. .|++|+..+.-++..||++||...+...+++..|...++.+..+...-.+.+|
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qw 81 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQW 81 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCcc
Confidence 46788999999999999999995 59999999999999999999999999999999999888877766554443333
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.48 E-value=3.7e-05 Score=81.79 Aligned_cols=53 Identities=25% Similarity=0.581 Sum_probs=48.4
Q ss_pred CCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccC
Q 046419 29 GVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLR 82 (505)
Q Consensus 29 ~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~ 82 (505)
...+-..-||.+|+-+|+++++.||-|||.+||..|| +|+..+|+++|.+++.
T Consensus 67 s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 67 SFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHHh
Confidence 3456678899999999999999999999999999999 9999999999988764
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.40 E-value=0.00027 Score=75.42 Aligned_cols=51 Identities=20% Similarity=0.412 Sum_probs=45.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 85 LKKGTFSPEEERLIVELHAQLG-NKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 85 lkkg~WT~EED~lLlelV~kyG-~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
+-...||.+||.+||++++.|| ++|..||.++..|+..+||.+|.+.+-..
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~s 121 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVNS 121 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhcC
Confidence 4456799999999999999999 88999999999999999999998766543
No 27
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.88 E-value=0.00035 Score=75.11 Aligned_cols=47 Identities=23% Similarity=0.557 Sum_probs=43.8
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCccccccccccccccc
Q 046419 33 KKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHL 81 (505)
Q Consensus 33 kKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L 81 (505)
....||.+|..+|+++|+.||. +|.+||+++| +|+..||..||.++-
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVg-tKt~EqCIl~FL~LP 324 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVG-TKTKEQCILHFLQLP 324 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhC-CCCHHHHHHHHHcCC
Confidence 6679999999999999999999 9999999999 999999999987753
No 28
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.75 E-value=0.0019 Score=61.19 Aligned_cols=53 Identities=19% Similarity=0.343 Sum_probs=46.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-------CHHHHHhhCCCCCHHHHHHHHHHHhhhhhhcC
Q 046419 86 KKGTFSPEEERLIVELHAQLGN-------KWARMAAQLPGRTDNEIKNYWNTRVKRRHRQG 139 (505)
Q Consensus 86 kkg~WT~EED~lLlelV~kyG~-------kWskIAk~LpgRT~~qcKnRW~~llkk~~r~~ 139 (505)
+...||.|||.+|.+.|.+|-. -..++++.| +||..+|.=||+..+|+.+...
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 5678999999999999998853 289999999 9999999999999999887643
No 29
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.74 E-value=0.0019 Score=71.03 Aligned_cols=47 Identities=13% Similarity=0.302 Sum_probs=43.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHh
Q 046419 86 KKGTFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRV 132 (505)
Q Consensus 86 kkg~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~ll 132 (505)
.+..||++|..+|+++|+.||.+|.+||.++.+||..||--||.++=
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 34579999999999999999999999999999999999999997643
No 30
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.72 E-value=0.003 Score=61.86 Aligned_cols=99 Identities=19% Similarity=0.338 Sum_probs=70.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhccccCCcc--cccccccccccccCC-C--------------------CCCCCCCH
Q 046419 36 PWTAAEDAILTEYVRKHGEGNWNAVQRNTGLAR--CGKSCRLRWANHLRP-N--------------------LKKGTFSP 92 (505)
Q Consensus 36 ~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gR--T~kQCR~Rw~n~L~p-~--------------------lkkg~WT~ 92 (505)
+|++++|-+|+.+|..-. +-..|++-+.+.| |-+.+.+||+.+|-- . ..+..||.
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 699999999999998765 4566655443222 456667799888732 1 14568999
Q ss_pred HHHHHHHHHHHHhCC---CHHHHHhh-----CCCCCHHHHHHHHHHHhhhhh
Q 046419 93 EEERLIVELHAQLGN---KWARMAAQ-----LPGRTDNEIKNYWNTRVKRRH 136 (505)
Q Consensus 93 EED~lLlelV~kyG~---kWskIAk~-----LpgRT~~qcKnRW~~llkk~~ 136 (505)
+||++|......... .+.+|=.. .++||+.++.++|+.+.+...
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999997665543 36666433 267999999999996655443
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.70 E-value=0.0018 Score=69.84 Aligned_cols=45 Identities=18% Similarity=0.280 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHH
Q 046419 87 KGTFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTR 131 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~l 131 (505)
...|+.+|..+|++.|+.||..|.+||++++.|+..||--||.++
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 347999999999999999999999999999999999999999764
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.69 E-value=0.00071 Score=74.22 Aligned_cols=49 Identities=24% Similarity=0.565 Sum_probs=44.6
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCccccccccccccccc
Q 046419 31 QLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHL 81 (505)
Q Consensus 31 ~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L 81 (505)
..-++.||.+|+.+|+++|+.||. +|.+||.+++ +|+..||..|+.++-
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLRLP 298 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHhcC
Confidence 345688999999999999999999 9999999999 999999999887653
No 33
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.51 E-value=0.0024 Score=53.15 Aligned_cols=49 Identities=27% Similarity=0.567 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHHH------hC--C------CHHHHHhhC----CCCCHHHHHHHHHHHhhhhh
Q 046419 88 GTFSPEEERLIVELHAQ------LG--N------KWARMAAQL----PGRTDNEIKNYWNTRVKRRH 136 (505)
Q Consensus 88 g~WT~EED~lLlelV~k------yG--~------kWskIAk~L----pgRT~~qcKnRW~~llkk~~ 136 (505)
..||.+|...||+++.+ ++ . .|..||..| ..||..||++||+.+.++-.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 47999999999999877 21 1 399999998 35999999999998666544
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=96.13 E-value=0.0085 Score=48.84 Aligned_cols=51 Identities=14% Similarity=0.378 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-------C--HHHHHhhCC-CCCHHHHHHHHHHHhhhhhh
Q 046419 87 KGTFSPEEERLIVELHAQLGN-------K--WARMAAQLP-GRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG~-------k--WskIAk~Lp-gRT~~qcKnRW~~llkk~~r 137 (505)
+.+||.|||..|++.|+++.. + |.++++.-+ .+|-...|+||.+.++.+.+
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 357999999999999976531 1 999999987 89999999999988876543
No 35
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.10 E-value=0.0015 Score=61.74 Aligned_cols=50 Identities=30% Similarity=0.607 Sum_probs=43.1
Q ss_pred CccCCCCHHHHHHHHHHHHHhCC------CCcchhccccCCcccccccccccccccCC
Q 046419 32 LKKGPWTAAEDAILTEYVRKHGE------GNWNAVQRNTGLARCGKSCRLRWANHLRP 83 (505)
Q Consensus 32 lkKG~WT~EEDelL~~lV~k~G~------~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p 83 (505)
.++..||.|||.+|.+.|-+|-. ....+|++.+ +||+..|.-||..+++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L--~RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL--NRTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH--cccHHHhcchHHHHHHH
Confidence 46788999999999999999932 2688999998 59999999999998863
No 36
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.06 E-value=0.0013 Score=54.72 Aligned_cols=48 Identities=25% Similarity=0.583 Sum_probs=33.2
Q ss_pred cCCCCHHHHHHHHHHHHH--h----C--C-----CCcchhcccc---CCccccccccccccccc
Q 046419 34 KGPWTAAEDAILTEYVRK--H----G--E-----GNWNAVQRNT---GLARCGKSCRLRWANHL 81 (505)
Q Consensus 34 KG~WT~EEDelL~~lV~k--~----G--~-----~nW~~IAk~m---~~gRT~kQCR~Rw~n~L 81 (505)
|-.||.+|...|++++.. + + . .-|.+||..| |..|++.||+.||.++.
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 357999999999999887 2 1 1 1499999986 56899999999998754
No 37
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.00 E-value=0.013 Score=48.06 Aligned_cols=51 Identities=27% Similarity=0.539 Sum_probs=42.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-----------------CHHHHHhhC-----CCCCHHHHHHHHHHHhhhhhh
Q 046419 87 KGTFSPEEERLIVELHAQLGN-----------------KWARMAAQL-----PGRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG~-----------------kWskIAk~L-----pgRT~~qcKnRW~~llkk~~r 137 (505)
+..||.+|.+.|+++|++|.. -|.+|+..| +.|+..+|+.+|..+.....+
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk 74 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK 74 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 457999999999999998731 299999997 359999999999988776544
No 38
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.82 E-value=0.011 Score=56.76 Aligned_cols=53 Identities=17% Similarity=0.358 Sum_probs=45.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC-------HHHHHhhCCCCCHHHHHHHHHHHhhhhhhc
Q 046419 85 LKKGTFSPEEERLIVELHAQLGNK-------WARMAAQLPGRTDNEIKNYWNTRVKRRHRQ 138 (505)
Q Consensus 85 lkkg~WT~EED~lLlelV~kyG~k-------WskIAk~LpgRT~~qcKnRW~~llkk~~r~ 138 (505)
.++..||.|||.+|.+.|.+|+.. ...++..| +||..+|.-||+.++++++..
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 356789999999999999988742 77788888 999999999999999988754
No 39
>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=95.40 E-value=0.0043 Score=50.58 Aligned_cols=51 Identities=29% Similarity=0.567 Sum_probs=32.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCC------C--CcchhccccCCcccccccccccccccCCC
Q 046419 34 KGPWTAAEDAILTEYVRKHGE------G--NWNAVQRNTGLARCGKSCRLRWANHLRPN 84 (505)
Q Consensus 34 KG~WT~EEDelL~~lV~k~G~------~--nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~ 84 (505)
|-+||.|||++|++.|.++.. | =|.++++..++.+|-.+-|+||...|.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 467999999999999977632 2 39999888765777888899999988754
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.27 E-value=0.019 Score=59.63 Aligned_cols=48 Identities=25% Similarity=0.455 Sum_probs=43.5
Q ss_pred CCCCHHHHHHHHHHHHHhC-CCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 88 GTFSPEEERLIVELHAQLG-NKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 88 g~WT~EED~lLlelV~kyG-~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
..|+.+|+.+|+++...+| ++|..||.+++.|+..+||.+|.++....
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~es 112 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYDES 112 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHhhc
Confidence 4699999999999999999 78999999999999999999998766543
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.17 E-value=0.0053 Score=63.63 Aligned_cols=50 Identities=22% Similarity=0.500 Sum_probs=45.7
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccC
Q 046419 32 LKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLR 82 (505)
Q Consensus 32 lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~ 82 (505)
+----|+.+|+-+|+++..-.|.|||..||..+| .|+...|+++|..++.
T Consensus 61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 3345799999999999999999999999999999 9999999999988765
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.97 E-value=0.0059 Score=50.07 Aligned_cols=49 Identities=27% Similarity=0.468 Sum_probs=39.8
Q ss_pred ccCCCCHHHHHHHHHHHHHhCC----------------CCcchhcccc----CCccccccccccccccc
Q 046419 33 KKGPWTAAEDAILTEYVRKHGE----------------GNWNAVQRNT----GLARCGKSCRLRWANHL 81 (505)
Q Consensus 33 kKG~WT~EEDelL~~lV~k~G~----------------~nW~~IAk~m----~~gRT~kQCR~Rw~n~L 81 (505)
++..||.+|.++|+++|.+|.. ..|.+|+..+ +..|+..||+.+|.++.
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 4678999999999999999822 3599998876 22689999999998764
No 43
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.90 E-value=0.066 Score=63.75 Aligned_cols=102 Identities=15% Similarity=0.313 Sum_probs=77.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhccccCCccccccccc-------ccccc----------------------------
Q 046419 36 PWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRL-------RWANH---------------------------- 80 (505)
Q Consensus 36 ~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~-------Rw~n~---------------------------- 80 (505)
-|+.-|=..++.+..+||..+-..||..|. +++...++. ||..+
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 388888888888889999888899999997 788666552 22211
Q ss_pred -------------c--CCCCCCCCCCHHHHHHHHHHHHHhC-CCHHHHHhhC------------CCCCHHHHHHHHHHHh
Q 046419 81 -------------L--RPNLKKGTFSPEEERLIVELHAQLG-NKWARMAAQL------------PGRTDNEIKNYWNTRV 132 (505)
Q Consensus 81 -------------L--~p~lkkg~WT~EED~lLlelV~kyG-~kWskIAk~L------------pgRT~~qcKnRW~~ll 132 (505)
- ....++..||+|||..|+-++.+|| .+|.+|-..+ ..||...|..|...++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 0 0122345699999999999999999 6799995553 5799999999999988
Q ss_pred hhhhhc
Q 046419 133 KRRHRQ 138 (505)
Q Consensus 133 kk~~r~ 138 (505)
+-..+.
T Consensus 985 ~~~~~e 990 (1033)
T PLN03142 985 RLIEKE 990 (1033)
T ss_pred HHHHHH
Confidence 876553
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=93.20 E-value=0.015 Score=55.65 Aligned_cols=50 Identities=26% Similarity=0.587 Sum_probs=40.6
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCC------CcchhccccCCcccccccccccccccC
Q 046419 31 QLKKGPWTAAEDAILTEYVRKHGEG------NWNAVQRNTGLARCGKSCRLRWANHLR 82 (505)
Q Consensus 31 ~lkKG~WT~EEDelL~~lV~k~G~~------nW~~IAk~m~~gRT~kQCR~Rw~n~L~ 82 (505)
..++..||.|||.+|.+.|-+|+.. ...+++..+ +|+..+|..||.-+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHH
Confidence 3577899999999999999999652 356677777 5999999999966654
No 45
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=91.80 E-value=0.43 Score=40.12 Aligned_cols=47 Identities=30% Similarity=0.630 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------CHHHHHhhCC-----CCCHHHHHHHHHHHhhhh
Q 046419 89 TFSPEEERLIVELHAQL---GN----------KWARMAAQLP-----GRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 89 ~WT~EED~lLlelV~ky---G~----------kWskIAk~Lp-----gRT~~qcKnRW~~llkk~ 135 (505)
.||.++++.|++++.+. |+ .|..|++.|. ..+..||++||..+.+.-
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~y 65 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKDY 65 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHHH
Confidence 49999999999998553 21 2999999882 357899999998665543
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.51 E-value=0.34 Score=50.59 Aligned_cols=52 Identities=17% Similarity=0.344 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC----------CCHHHHHhhC----CCCCHHHHHHHHHHHhhhhhhc
Q 046419 87 KGTFSPEEERLIVELHAQLG----------NKWARMAAQL----PGRTDNEIKNYWNTRVKRRHRQ 138 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG----------~kWskIAk~L----pgRT~~qcKnRW~~llkk~~r~ 138 (505)
...|+.+|-..||++..+.. ..|..||+.+ --|++.+||.||.++.++..+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~ 119 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKE 119 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHH
Confidence 46899999999999886542 2499999976 2399999999999888776543
No 47
>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=91.41 E-value=0.37 Score=43.74 Aligned_cols=54 Identities=28% Similarity=0.506 Sum_probs=43.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----CHHHHHhhC------------CCCCHHHHHHHHHHHhhhhhh
Q 046419 84 NLKKGTFSPEEERLIVELHAQLGN----KWARMAAQL------------PGRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 84 ~lkkg~WT~EED~lLlelV~kyG~----kWskIAk~L------------pgRT~~qcKnRW~~llkk~~r 137 (505)
..++..||+|||.-|+-++.+||- .|.+|-..+ ..||...|..|...+++-..+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~K 115 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIEK 115 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHHC
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHHH
Confidence 456778999999999999999996 599887764 579999999999998876543
No 48
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.33 E-value=0.43 Score=50.94 Aligned_cols=46 Identities=17% Similarity=0.272 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhh
Q 046419 89 TFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKR 134 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk 134 (505)
+|+.+|-+++.+++..+|-.++.|+..||.|.+.|||.+|.+--|+
T Consensus 367 ~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 367 RWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred cccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 6999999999999999999999999999999999999999764444
No 49
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=88.30 E-value=0.39 Score=50.15 Aligned_cols=48 Identities=25% Similarity=0.450 Sum_probs=37.8
Q ss_pred cCCCCHHHHHHHHHHHHHh----CC-----CCcchhcccc---CCccccccccccccccc
Q 046419 34 KGPWTAAEDAILTEYVRKH----GE-----GNWNAVQRNT---GLARCGKSCRLRWANHL 81 (505)
Q Consensus 34 KG~WT~EEDelL~~lV~k~----G~-----~nW~~IAk~m---~~gRT~kQCR~Rw~n~L 81 (505)
-..|+.+|-..|+++..+. .. .-|.+||+.+ |..|++.||+.||.++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 3789999999999987644 11 2599999843 55799999999988743
No 50
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=88.10 E-value=0.64 Score=49.84 Aligned_cols=86 Identities=17% Similarity=0.302 Sum_probs=63.3
Q ss_pred CcchhccccCCcccccccccccccccCCC-------------------------CCCCCCCHHHHHHHHHHHHHhCCCHH
Q 046419 56 NWNAVQRNTGLARCGKSCRLRWANHLRPN-------------------------LKKGTFSPEEERLIVELHAQLGNKWA 110 (505)
Q Consensus 56 nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~-------------------------lkkg~WT~EED~lLlelV~kyG~kWs 110 (505)
.|+.+.=..+ .|...-...||.+.-++. ++...||+||-+.|.+|.+.|.-+|-
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 5666644443 566666667777763321 13346999999999999999999999
Q ss_pred HHHhh-----CCC-CCHHHHHHHHHHHhhhhhhcCCCC
Q 046419 111 RMAAQ-----LPG-RTDNEIKNYWNTRVKRRHRQGLPL 142 (505)
Q Consensus 111 kIAk~-----Lpg-RT~~qcKnRW~~llkk~~r~~~~~ 142 (505)
-||.. ++. ||-.++|.||...-++..+...+.
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 99988 455 999999999998777766554433
No 51
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=84.60 E-value=2.6 Score=46.19 Aligned_cols=52 Identities=17% Similarity=0.321 Sum_probs=46.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhhhh
Q 046419 86 KKGTFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 86 kkg~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~~r 137 (505)
-...||.||-.++-+++..||.++.+|-+.|+.|+-..+...|....|.+..
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~~~ 237 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTREY 237 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHhhH
Confidence 3557999999999999999999999999999999999999998877666543
No 52
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=83.20 E-value=2.9 Score=31.61 Aligned_cols=42 Identities=29% Similarity=0.396 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhh
Q 046419 92 PEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKR 134 (505)
Q Consensus 92 ~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk 134 (505)
++++..++.++...|-.|.+||+.+ |.+...|+.+....+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 4667778888888888999999999 99999999998776654
No 53
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=82.01 E-value=1.8 Score=46.47 Aligned_cols=65 Identities=14% Similarity=0.158 Sum_probs=51.2
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCC--------CCCCCCCHHHHHHHH
Q 046419 33 KKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPN--------LKKGTFSPEEERLIV 99 (505)
Q Consensus 33 kKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~--------lkkg~WT~EED~lLl 99 (505)
.--+|+.+|-+++.+++...|. ++.-|+.++| +|..+|++.+|.+--+.+ ..+.++..+|..++.
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP-~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~ 436 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGT-DFSLISSLFP-NRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLR 436 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcc-hHHHHHHhcC-chhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHH
Confidence 3457999999999999999999 9999999999 999999999887643221 124467777765543
No 54
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=80.17 E-value=14 Score=39.79 Aligned_cols=43 Identities=23% Similarity=0.282 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHH-HhhCCCCCHHHHHHHHHHH
Q 046419 89 TFSPEEERLIVELHAQLGNKWARM-AAQLPGRTDNEIKNYWNTR 131 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG~kWskI-Ak~LpgRT~~qcKnRW~~l 131 (505)
.|+++|-..+.+.++.||+++..| +.+++.|+--.|-..|...
T Consensus 279 ~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred cCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 699999999999999999999999 5668999999998877643
No 55
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=77.70 E-value=5.7 Score=45.89 Aligned_cols=44 Identities=14% Similarity=0.241 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHH
Q 046419 88 GTFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTR 131 (505)
Q Consensus 88 g~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~l 131 (505)
..||..|..++-+++..|.+++-.|++.++++|-.+|-..|+..
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 47999999999999999999999999999999999998876543
No 56
>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=76.84 E-value=1.8 Score=39.23 Aligned_cols=34 Identities=29% Similarity=0.505 Sum_probs=28.4
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCC---CCcchhcccc
Q 046419 31 QLKKGPWTAAEDAILTEYVRKHGE---GNWNAVQRNT 64 (505)
Q Consensus 31 ~lkKG~WT~EEDelL~~lV~k~G~---~nW~~IAk~m 64 (505)
.-++..||.+||.-|+-++.+||- +.|.+|...+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 456788999999999999999999 8999997765
No 57
>smart00595 MADF subfamily of SANT domain.
Probab=76.59 E-value=3.4 Score=34.31 Aligned_cols=26 Identities=31% Similarity=0.622 Sum_probs=22.0
Q ss_pred HHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 109 WARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 109 WskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|.+||..| |.+..+|+.+|+.+...-
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~y 55 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDRY 55 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 99999999 559999999998765543
No 58
>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=75.73 E-value=7.2 Score=29.00 Aligned_cols=38 Identities=24% Similarity=0.409 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHhCC-CHHHHHhhCCCCCHHHHHHHHHHH
Q 046419 93 EEERLIVELHAQLGN-KWARMAAQLPGRTDNEIKNYWNTR 131 (505)
Q Consensus 93 EED~lLlelV~kyG~-kWskIAk~LpgRT~~qcKnRW~~l 131 (505)
+=|.+|++++.+-|. .|.+||+.+ |=+...|..|++.+
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 458889999988885 499999999 99999999999865
No 59
>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=75.45 E-value=1.4 Score=37.06 Aligned_cols=44 Identities=20% Similarity=0.524 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHHHh---CC---------CCcchhccccC----Cccccccccccccc
Q 046419 36 PWTAAEDAILTEYVRKH---GE---------GNWNAVQRNTG----LARCGKSCRLRWAN 79 (505)
Q Consensus 36 ~WT~EEDelL~~lV~k~---G~---------~nW~~IAk~m~----~gRT~kQCR~Rw~n 79 (505)
.||+++++.|++++.+. |. ..|..|++.|. ...+.+||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999988655 21 14778877663 23456677777654
No 60
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=75.08 E-value=4.5 Score=45.77 Aligned_cols=53 Identities=17% Similarity=0.465 Sum_probs=43.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCHHHHH----------hhCCCCCHHHHHHHHHHHhhhhhhc
Q 046419 86 KKGTFSPEEERLIVELHAQLGNKWARMA----------AQLPGRTDNEIKNYWNTRVKRRHRQ 138 (505)
Q Consensus 86 kkg~WT~EED~lLlelV~kyG~kWskIA----------k~LpgRT~~qcKnRW~~llkk~~r~ 138 (505)
++..||-+|++-+..+++++|.++.+|- ..+.-+|..|++.+|++.++++.+-
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~ 149 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKL 149 (782)
T ss_pred cccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhh
Confidence 4678999999999999999999998882 2234578899999999888887654
No 61
>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=73.66 E-value=11 Score=39.86 Aligned_cols=51 Identities=29% Similarity=0.517 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHHh-CC---CHHHHHhhCCCCCHHHHHHHHHHHhhhhhh
Q 046419 87 KGTFSPEEERLIVELHAQL-GN---KWARMAAQLPGRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 87 kg~WT~EED~lLlelV~ky-G~---kWskIAk~LpgRT~~qcKnRW~~llkk~~r 137 (505)
-..|+..|...|+++.+.. |. +-++|++.++||+..+|++.-+.+..+..+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvar 75 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAR 75 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHH
Confidence 3479999999999999765 33 367899999999999999987766665544
No 62
>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=73.42 E-value=3.8 Score=39.04 Aligned_cols=41 Identities=22% Similarity=0.277 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHH
Q 046419 89 TFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNT 130 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~ 130 (505)
.||+|+.++|.+|..+ |-.=++||+.|.|.|.+.|.-+.+.
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 5999999999999865 7778999999987999999877654
No 63
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=73.37 E-value=1.5 Score=50.39 Aligned_cols=42 Identities=14% Similarity=0.278 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccc
Q 046419 35 GPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWA 78 (505)
Q Consensus 35 G~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~ 78 (505)
..||+.|..++.+++-.|.+ ++-.|++++. +++.+||-+.|+
T Consensus 620 d~WTp~E~~lF~kA~y~~~K-DF~~v~km~~-~KtVaqCVeyYY 661 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSK-DFIFVQKMVK-SKTVAQCVEYYY 661 (907)
T ss_pred ccccHHHHHHHHHHHHHhcc-cHHHHHHHhc-cccHHHHHHHHH
Confidence 57999999999999999999 9999999998 999999998765
No 64
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=73.27 E-value=6.4 Score=36.42 Aligned_cols=46 Identities=17% Similarity=0.132 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHhCC-CHHHHHhhCCCCCHHHHHHHHHHHhhhhhhc
Q 046419 92 PEEERLIVELHAQLGN-KWARMAAQLPGRTDNEIKNYWNTRVKRRHRQ 138 (505)
Q Consensus 92 ~EED~lLlelV~kyG~-kWskIAk~LpgRT~~qcKnRW~~llkk~~r~ 138 (505)
.+-|.+|++++++-|. .|++||+.+ |-+...|+.|++++.....-+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 3578889999888875 599999999 999999999999988877544
No 65
>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=69.85 E-value=12 Score=27.98 Aligned_cols=42 Identities=19% Similarity=0.313 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 93 EEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 93 EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
+++..++.++--.|..+.+||+.| |-+...|+.+....+++.
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKKL 48 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHHh
Confidence 455556666555566799999999 999999999988877764
No 66
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=69.41 E-value=58 Score=34.60 Aligned_cols=87 Identities=15% Similarity=0.298 Sum_probs=64.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCC---CcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHH-h-----
Q 046419 35 GPWTAAEDAILTEYVRKHGEG---NWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQ-L----- 105 (505)
Q Consensus 35 G~WT~EEDelL~~lV~k~G~~---nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~k-y----- 105 (505)
..||.-|...|+++++..... +-.+|++.+. +|+..++++ |.+.|+ +..+.+++++ |
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~~ 87 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGLK 87 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHH-HHHHHH------------HHHHHHHHHHhcccccc
Confidence 479999999999998876332 4568888888 999888876 344442 3445566655 2
Q ss_pred CC------------CHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GN------------KWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~------------kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|. .|..+|+.+.|.-...+-.-|-+.+.-.
T Consensus 88 ~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ia 129 (344)
T PF11035_consen 88 GPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLTIA 129 (344)
T ss_pred cccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHHHh
Confidence 11 2999999999999999999998877654
No 67
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=69.24 E-value=7.6 Score=36.39 Aligned_cols=46 Identities=11% Similarity=0.070 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHhCC-CHHHHHhhCCCCCHHHHHHHHHHHhhhhhhc
Q 046419 92 PEEERLIVELHAQLGN-KWARMAAQLPGRTDNEIKNYWNTRVKRRHRQ 138 (505)
Q Consensus 92 ~EED~lLlelV~kyG~-kWskIAk~LpgRT~~qcKnRW~~llkk~~r~ 138 (505)
.+-|.+|+.++++-|. .|++||+.+ |-+...|+.|++++.+...-+
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 5678889998888875 599999999 999999999999988877543
No 68
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=68.87 E-value=71 Score=34.77 Aligned_cols=72 Identities=14% Similarity=0.112 Sum_probs=46.7
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCHH
Q 046419 31 QLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQLGNKWA 110 (505)
Q Consensus 31 ~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~kyG~kWs 110 (505)
+..-|.|+++=|+.+.+++.-|.. .||+..-+++.- +-||+ =.
T Consensus 73 ~daegvWSpdIEqsFqEALaiypp-----------cGrrKIilsdeg-------------------------kmyGR-NE 115 (455)
T KOG3841|consen 73 RDAEGVWSPDIEQSFQEALAIYPP-----------CGRRKIILSDEG-------------------------KMYGR-NE 115 (455)
T ss_pred cccccccChhHHHHHHHHHhhcCC-----------CCceeEEEccCc-------------------------cccch-HH
Confidence 466799999999999999998876 234433222210 11221 23
Q ss_pred HHHhhC-----CCCCHHHHHHHHHHHhhhhhhcC
Q 046419 111 RMAAQL-----PGRTDNEIKNYWNTRVKRRHRQG 139 (505)
Q Consensus 111 kIAk~L-----pgRT~~qcKnRW~~llkk~~r~~ 139 (505)
.||+++ ..||++||..|-+.+.|++.|..
T Consensus 116 LIarYIKlrtgktRTrKQVSSHIQVlarrk~rei 149 (455)
T KOG3841|consen 116 LIARYIKLRTGKTRTRKQVSSHIQVLARRKLREI 149 (455)
T ss_pred HHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHH
Confidence 444443 46999999999888777776643
No 69
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=68.81 E-value=2.7 Score=47.44 Aligned_cols=49 Identities=18% Similarity=0.361 Sum_probs=37.9
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCcchhccc----------cCCcccccccccccccccCC
Q 046419 33 KKGPWTAAEDAILTEYVRKHGEGNWNAVQRN----------TGLARCGKSCRLRWANHLRP 83 (505)
Q Consensus 33 kKG~WT~EEDelL~~lV~k~G~~nW~~IAk~----------m~~gRT~kQCR~Rw~n~L~p 83 (505)
+|..||-.|.+.+..+++++|+ ++.+|-+. +- -++..|+|.+|++.+..
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~-~Ktkdqvr~~yY~~~~~ 145 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQ-SKTKDQVRHYYYRLVRR 145 (782)
T ss_pred cccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchh-hhhhHHHHHHHHHHHHH
Confidence 3668999999999999999999 99888222 22 35677888888877653
No 70
>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=66.88 E-value=4.8 Score=34.24 Aligned_cols=23 Identities=39% Similarity=0.803 Sum_probs=13.8
Q ss_pred CccCCCCHHHHHHH--------HHHHHHhCC
Q 046419 32 LKKGPWTAAEDAIL--------TEYVRKHGE 54 (505)
Q Consensus 32 lkKG~WT~EEDelL--------~~lV~k~G~ 54 (505)
-..|-||+|+|+.| .+++++||.
T Consensus 45 n~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 45 NMPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp T-TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 45789999999999 456677773
No 71
>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=64.49 E-value=8.6 Score=32.68 Aligned_cols=17 Identities=24% Similarity=0.716 Sum_probs=10.0
Q ss_pred CCCCCCCCCHHHHHHHH
Q 046419 83 PNLKKGTFSPEEERLIV 99 (505)
Q Consensus 83 p~lkkg~WT~EED~lLl 99 (505)
|.-..|-||+|+|+.|.
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 55667889999999983
No 72
>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=58.12 E-value=24 Score=31.23 Aligned_cols=37 Identities=19% Similarity=0.249 Sum_probs=28.0
Q ss_pred HHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 98 IVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 98 LlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
++.+.-..|-.+.+||+.+ |.+...|+.++...+++.
T Consensus 121 il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 121 IFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKEL 157 (161)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3333333466799999999 999999999998876654
No 73
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=57.95 E-value=17 Score=31.79 Aligned_cols=49 Identities=16% Similarity=0.209 Sum_probs=33.8
Q ss_pred CCCCCHHHHHHHHHHHHHh----C----CCHHHHHhhCCC-----CCHHHHHHHHHHHhhhh
Q 046419 87 KGTFSPEEERLIVELHAQL----G----NKWARMAAQLPG-----RTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 87 kg~WT~EED~lLlelV~ky----G----~kWskIAk~Lpg-----RT~~qcKnRW~~llkk~ 135 (505)
...||+|+|..||+.+..| | ..|......+.+ =+..|+..+.+.+.++-
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky 65 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKY 65 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 3469999999999999877 5 246555444422 26778877777665554
No 74
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=57.13 E-value=4.1e+02 Score=33.36 Aligned_cols=9 Identities=22% Similarity=0.578 Sum_probs=3.5
Q ss_pred HHHHHHHHH
Q 046419 41 EDAILTEYV 49 (505)
Q Consensus 41 EDelL~~lV 49 (505)
||..++.-+
T Consensus 1234 e~D~~l~~I 1242 (1605)
T KOG0260|consen 1234 EDDVFLKCI 1242 (1605)
T ss_pred chhHHHHHH
Confidence 444443333
No 75
>PLN03162 golden-2 like transcription factor; Provisional
Probab=55.36 E-value=81 Score=34.29 Aligned_cols=49 Identities=24% Similarity=0.256 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC---HHHHHhhC--CCCCHHHHHHHHHHHhhhh
Q 046419 87 KGTFSPEEERLIVELHAQLGNK---WARMAAQL--PGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG~k---WskIAk~L--pgRT~~qcKnRW~~llkk~ 135 (505)
+-.||.|=.++++++|.++|.. =++|-+.| .|=|..+||.+.+++...+
T Consensus 237 RLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~r 290 (526)
T PLN03162 237 KVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHR 290 (526)
T ss_pred cccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhc
Confidence 3469999999999999999932 56676665 7789999999987765544
No 76
>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=54.70 E-value=27 Score=29.27 Aligned_cols=37 Identities=14% Similarity=0.290 Sum_probs=27.9
Q ss_pred HHHHHHHhCC--------CHHHHHhhCCCCC-----HHHHHHHHHHHhhh
Q 046419 98 IVELHAQLGN--------KWARMAAQLPGRT-----DNEIKNYWNTRVKR 134 (505)
Q Consensus 98 LlelV~kyG~--------kWskIAk~LpgRT-----~~qcKnRW~~llkk 134 (505)
|..+|.+.|+ +|.+||+.|.--. ..++|..|.++|..
T Consensus 41 Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 41 LYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 7788888874 5999999993321 47899999888754
No 77
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=54.51 E-value=5.7 Score=42.88 Aligned_cols=50 Identities=12% Similarity=0.249 Sum_probs=42.8
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCcchhccc-----cCCccccccccccccccc
Q 046419 31 QLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRN-----TGLARCGKSCRLRWANHL 81 (505)
Q Consensus 31 ~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~-----m~~gRT~kQCR~Rw~n~L 81 (505)
.++-..||+||.+-|.++.++|.- .|.-||.+ .+..||....++||....
T Consensus 127 ~l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 344567999999999999999999 99999988 675599999999997654
No 78
>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=53.23 E-value=4 Score=30.35 Aligned_cols=38 Identities=13% Similarity=0.253 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhCCCCcchhccccCCccccccccccccc
Q 046419 40 AEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWAN 79 (505)
Q Consensus 40 EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n 79 (505)
+=|.+|+.++++-+...|.+||+.+| =+...|+.|+.+
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 44888999999999999999999996 777788887653
No 79
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=53.17 E-value=15 Score=44.96 Aligned_cols=72 Identities=15% Similarity=0.245 Sum_probs=44.5
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHh-CCCHHH
Q 046419 33 KKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQL-GNKWAR 111 (505)
Q Consensus 33 kKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~ky-G~kWsk 111 (505)
.---|..+||..|+-.|-+||.++|.+|-. = +.-|... ...+...+-.+.|=..+...|+.++.++ +.+|.+
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 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRL-D-----PDLGLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhcc-C-----ccccchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 345699999999999999999999999921 1 1111110 1111112344556667777777777665 333443
No 80
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=49.73 E-value=33 Score=29.25 Aligned_cols=45 Identities=18% Similarity=0.169 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHhCC-CHHHHHhhCCCCCHHHHHHHHHHHhhhhhhc
Q 046419 93 EEERLIVELHAQLGN-KWARMAAQLPGRTDNEIKNYWNTRVKRRHRQ 138 (505)
Q Consensus 93 EED~lLlelV~kyG~-kWskIAk~LpgRT~~qcKnRW~~llkk~~r~ 138 (505)
+.|.+|++++.+.+. .|.+||+.+ |-+...|+.+.+.+.++..-+
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 578889999988774 599999999 999999999999888876433
No 81
>smart00351 PAX Paired Box domain.
Probab=48.56 E-value=47 Score=29.97 Aligned_cols=80 Identities=16% Similarity=0.204 Sum_probs=51.6
Q ss_pred CCCCCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCccc-cccccccccc--ccCCCCC----CCCCCHHHHHHH
Q 046419 26 GEGGVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARC-GKSCRLRWAN--HLRPNLK----KGTFSPEEERLI 98 (505)
Q Consensus 26 ~~~~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT-~kQCR~Rw~n--~L~p~lk----kg~WT~EED~lL 98 (505)
.-++.-....+++.|+-++++.++. -|. .-.+||+.++..|. ...+..||.. .+.+... ...-+.+++..|
T Consensus 7 ~~~~~~~~~~~~s~~~R~riv~~~~-~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I 84 (125)
T smart00351 7 QLGGVFVNGRPLPDEERQRIVELAQ-NGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKI 84 (125)
T ss_pred cCCCeecCCCCCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHH
Confidence 3345556667799999999998886 454 78999999986553 4445555543 2444221 123566667777
Q ss_pred HHHHHHhCC
Q 046419 99 VELHAQLGN 107 (505)
Q Consensus 99 lelV~kyG~ 107 (505)
++++++.+.
T Consensus 85 ~~~~~~~p~ 93 (125)
T smart00351 85 ADYKQENPG 93 (125)
T ss_pred HHHHHHCCC
Confidence 777776653
No 82
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=48.20 E-value=18 Score=41.13 Aligned_cols=50 Identities=18% Similarity=0.354 Sum_probs=44.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 86 KKGTFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 86 kkg~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
....|+.+|-++..++....|.+.+.|+..+++|.+.|||.+|..--+++
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r~ 457 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKRN 457 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhcc
Confidence 34579999999999999999999999999999999999999997544443
No 83
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=47.89 E-value=35 Score=33.83 Aligned_cols=45 Identities=20% Similarity=0.307 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhC---CCCCHHHHHHHHHHHhhh
Q 046419 89 TFSPEEERLIVELHAQLGNKWARMAAQL---PGRTDNEIKNYWNTRVKR 134 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG~kWskIAk~L---pgRT~~qcKnRW~~llkk 134 (505)
.|+.++|.+|+.+|.. ++.-..|++-+ -.-|-..|..||+.++--
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd 48 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYD 48 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcC
Confidence 4999999999999976 55566666654 235889999999987653
No 84
>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=47.75 E-value=45 Score=28.59 Aligned_cols=35 Identities=20% Similarity=0.190 Sum_probs=26.7
Q ss_pred HHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 100 ELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 100 elV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.++...|..+.+||+.+ |-+...|+.+....+++.
T Consensus 120 ~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 120 VLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKKL 154 (158)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 33333467799999999 779999999988876654
No 85
>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=47.10 E-value=39 Score=31.94 Aligned_cols=46 Identities=17% Similarity=0.181 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHhhCC-C---CCHHHHHHHHHHHh
Q 046419 87 KGTFSPEEERLIVELHAQLGNKWARMAAQLP-G---RTDNEIKNYWNTRV 132 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG~kWskIAk~Lp-g---RT~~qcKnRW~~ll 132 (505)
...-+..|..-|..||++||.++..+|.-.. + .|..||+.+...+.
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 4467899999999999999999999998765 3 79999998877653
No 86
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=46.53 E-value=43 Score=28.37 Aligned_cols=38 Identities=16% Similarity=0.308 Sum_probs=29.2
Q ss_pred HHHHHHHhCC--------CHHHHHhhCCCC-----CHHHHHHHHHHHhhhh
Q 046419 98 IVELHAQLGN--------KWARMAAQLPGR-----TDNEIKNYWNTRVKRR 135 (505)
Q Consensus 98 LlelV~kyG~--------kWskIAk~LpgR-----T~~qcKnRW~~llkk~ 135 (505)
|..+|.+.|+ .|.+||+.|.-. ...++|..|.+++..-
T Consensus 37 Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 37 LYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 7777888774 599999999433 3577899998887664
No 87
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=44.37 E-value=8.6 Score=35.57 Aligned_cols=45 Identities=9% Similarity=0.124 Sum_probs=38.0
Q ss_pred HHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCC
Q 046419 39 AAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNL 85 (505)
Q Consensus 39 ~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~l 85 (505)
.+-|.+|++++++-|...|.+||+.+| -+...|+.|+.+..+..+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 357899999999999989999999996 888889998887766543
No 88
>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=43.01 E-value=66 Score=22.63 Aligned_cols=42 Identities=19% Similarity=0.323 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhh
Q 046419 90 FSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVK 133 (505)
Q Consensus 90 WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llk 133 (505)
++.++ ..++.++...|..+..||+.+ |-+...|+.+.....+
T Consensus 11 l~~~~-~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPERE-REVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHH-HHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 44444 445555555667799999999 7888888777665443
No 89
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=41.64 E-value=62 Score=29.30 Aligned_cols=31 Identities=10% Similarity=0.066 Sum_probs=24.3
Q ss_pred HhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 104 QLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 104 kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
..|-.+.+||+.| |.+...|+.+....+++.
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~L 172 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRAREAL 172 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3456799999999 899999998877655544
No 90
>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=41.48 E-value=7.9 Score=32.55 Aligned_cols=39 Identities=26% Similarity=0.419 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCC-------CCcchhccccCCccc----cccccccccccc
Q 046419 43 AILTEYVRKHGE-------GNWNAVQRNTGLARC----GKSCRLRWANHL 81 (505)
Q Consensus 43 elL~~lV~k~G~-------~nW~~IAk~m~~gRT----~kQCR~Rw~n~L 81 (505)
-.|..+|.++|. ..|.+|++.+|.... ..+++..|.++|
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L 88 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYL 88 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHT
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHh
Confidence 357778888875 479999999985442 234556666555
No 91
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=41.10 E-value=55 Score=31.05 Aligned_cols=39 Identities=21% Similarity=0.232 Sum_probs=29.5
Q ss_pred HHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 96 RLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 96 ~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.+++++..-.|-.+.+||+.| |-+...|+.+|.....+.
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARAWL 179 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 344444444566799999999 999999999998776443
No 92
>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=40.66 E-value=40 Score=28.81 Aligned_cols=28 Identities=25% Similarity=0.621 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCCCHHH
Q 046419 95 ERLIVELHAQLGNKWARMAAQLPGRTDNE 123 (505)
Q Consensus 95 D~lLlelV~kyG~kWskIAk~LpgRT~~q 123 (505)
|+.|..+....|..|..+|++| |=+..+
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~ 29 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTD 29 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHH
Confidence 5678889999999999999999 544444
No 93
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=39.94 E-value=8.3 Score=36.14 Aligned_cols=45 Identities=16% Similarity=0.156 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCC
Q 046419 39 AAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNL 85 (505)
Q Consensus 39 ~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~l 85 (505)
.+-|.+|+.++++-+...|.+||+.+| -+...|+.|+.++.+..+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 567889999999999999999999996 778889988887776554
No 94
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=39.79 E-value=61 Score=29.26 Aligned_cols=30 Identities=17% Similarity=0.149 Sum_probs=24.1
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 105 LGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 105 yG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.|..+.+||+.| |-+...|++++....++.
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~~l 169 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRARQLL 169 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 355799999999 999999999887655554
No 95
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=39.76 E-value=60 Score=23.75 Aligned_cols=35 Identities=20% Similarity=0.268 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHH
Q 046419 94 EERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWN 129 (505)
Q Consensus 94 ED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~ 129 (505)
|.+.|.+++++++++..+.|+.| |=+...+..|-+
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~klk 40 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 67789999999999999999999 777776666544
No 96
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=39.30 E-value=53 Score=29.58 Aligned_cols=46 Identities=13% Similarity=0.124 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHhCC-CHHHHHhhCCCCCHHHHHHHHHHHhhhhhhc
Q 046419 92 PEEERLIVELHAQLGN-KWARMAAQLPGRTDNEIKNYWNTRVKRRHRQ 138 (505)
Q Consensus 92 ~EED~lLlelV~kyG~-kWskIAk~LpgRT~~qcKnRW~~llkk~~r~ 138 (505)
.+-|.+|++++++-+. .+.+||+.+ |-+...|+.|-+++.+..+-+
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCcee
Confidence 4568888888888775 499999999 999999999999888877543
No 97
>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=38.26 E-value=37 Score=27.19 Aligned_cols=28 Identities=21% Similarity=0.458 Sum_probs=22.2
Q ss_pred HHHHHhhCCC-CCHHHHHHHHHHHhhhhh
Q 046419 109 WARMAAQLPG-RTDNEIKNYWNTRVKRRH 136 (505)
Q Consensus 109 WskIAk~Lpg-RT~~qcKnRW~~llkk~~ 136 (505)
|..||..|.. -+..+|+.||+.+...-.
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~ 57 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRDRYR 57 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHHHHH
Confidence 9999999953 577889999988665543
No 98
>PRK04217 hypothetical protein; Provisional
Probab=35.78 E-value=89 Score=28.16 Aligned_cols=45 Identities=13% Similarity=0.070 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 89 TFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.-+++| ..++.++...|-...+||+.+ |.+...|+.+++...++.
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 356666 567777777778899999999 999999999998655544
No 99
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=35.69 E-value=20 Score=39.60 Aligned_cols=47 Identities=13% Similarity=0.188 Sum_probs=38.7
Q ss_pred CCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCccccccccccc
Q 046419 29 GVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRW 77 (505)
Q Consensus 29 ~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw 77 (505)
+.......||.||--+|.+++..||+ ++.+|.+.|+ .|+-..++.-|
T Consensus 182 rr~~~~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~LP-~rsLaSlvqyY 228 (534)
T KOG1194|consen 182 RRTEFPDEWTAEDIVLFEQAFQFFGK-DFHKIRQALP-HRSLASLVQYY 228 (534)
T ss_pred hcCCCcccchHHHHHHHHHHHHHhcc-cHHHHHHHcc-CccHHHHHHHH
Confidence 34556678999999999999999999 9999999998 88866655433
No 100
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=35.13 E-value=22 Score=40.38 Aligned_cols=49 Identities=14% Similarity=0.345 Sum_probs=43.8
Q ss_pred CCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCccccccccccccc
Q 046419 29 GVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWAN 79 (505)
Q Consensus 29 ~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n 79 (505)
......++|+.+|-++...+....|. +...|+..++ +|..+|+|.+|..
T Consensus 404 sk~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 404 SKKLETDKWDASETELFYKALSERGS-DFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred cCccccCcccchhhHHhhhHHhhhcc-cccccccccc-cccHHHHHHHHhh
Confidence 44566789999999999999999999 9999999998 9999999987754
No 101
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=34.82 E-value=83 Score=29.73 Aligned_cols=30 Identities=23% Similarity=0.207 Sum_probs=23.9
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 105 LGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 105 yG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.|....+||..| |-+...|+.|+....++.
T Consensus 149 ~g~s~~EIA~~l-g~s~~tV~~rl~rar~~L 178 (192)
T PRK09643 149 QGYSVADAARML-GVAEGTVKSRCARGRARL 178 (192)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 355699999999 999999999986655544
No 102
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.21 E-value=1.1e+02 Score=26.55 Aligned_cols=48 Identities=19% Similarity=0.238 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCC-CHHHHHHHHHHHhhhh
Q 046419 87 KGTFSPEEERLIVELHAQLGNKWARMAAQLPGR-TDNEIKNYWNTRVKRR 135 (505)
Q Consensus 87 kg~WT~EED~lLlelV~kyG~kWskIAk~LpgR-T~~qcKnRW~~llkk~ 135 (505)
...||.|+...+++++.+-|..=+.||+.+ |- ...+++.+++.+....
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~~~~~~~ 53 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRIQLQKGG 53 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHHHHHHcc
Confidence 557999999999999999888789999999 75 7777766665555544
No 103
>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=32.85 E-value=69 Score=27.36 Aligned_cols=29 Identities=24% Similarity=0.446 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCCCHHHH
Q 046419 95 ERLIVELHAQLGNKWARMAAQLPGRTDNEI 124 (505)
Q Consensus 95 D~lLlelV~kyG~kWskIAk~LpgRT~~qc 124 (505)
|.+|..+....|..|.++|+.| |=+...|
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI 32 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEI 32 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHH
Confidence 6678888899999999999999 6555444
No 104
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=32.33 E-value=56 Score=26.94 Aligned_cols=23 Identities=22% Similarity=0.573 Sum_probs=18.9
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCC
Q 046419 95 ERLIVELHAQLGNKWARMAAQLPGR 119 (505)
Q Consensus 95 D~lLlelV~kyG~kWskIAk~LpgR 119 (505)
+.+|-+||+.|| |..+++.+.=|
T Consensus 12 e~il~~Lv~~yG--W~~L~~~i~i~ 34 (64)
T PF09905_consen 12 ETILTELVEHYG--WEELGERININ 34 (64)
T ss_dssp HHHHHHHHHHT---HHHHHHHTTSS
T ss_pred HHHHHHHHHHhC--HHHHHhhcccc
Confidence 577889999998 99999998554
No 105
>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=32.08 E-value=26 Score=25.71 Aligned_cols=30 Identities=20% Similarity=0.333 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHhCCCCcchhccccCCcccc
Q 046419 40 AEDAILTEYVRKHGEGNWNAVQRNTGLARCG 70 (505)
Q Consensus 40 EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~ 70 (505)
-|.+.|.+++++++. +..+.|+.+|..|+.
T Consensus 5 ~E~~~i~~aL~~~~g-n~~~aA~~Lgisr~t 34 (42)
T PF02954_consen 5 FEKQLIRQALERCGG-NVSKAARLLGISRRT 34 (42)
T ss_dssp HHHHHHHHHHHHTTT--HHHHHHHHTS-HHH
T ss_pred HHHHHHHHHHHHhCC-CHHHHHHHHCCCHHH
Confidence 477888999999987 999999999866653
No 106
>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=31.94 E-value=98 Score=28.25 Aligned_cols=30 Identities=13% Similarity=0.315 Sum_probs=23.9
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRRH 136 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~~ 136 (505)
|-...+||+.| |-+...|++++...+++..
T Consensus 135 g~s~~eiA~~l-gis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 135 DLTIKEIAEVM-NKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 44689999999 8899999999887666543
No 107
>cd01852 AIG1 AIG1 (avrRpt2-induced gene 1). This represents Arabidoposis protein AIG1 that appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 exhibits RPS2- and avrRpt1-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2. This subfamily also includes IAN-4 protein, which has GTP-binding activity and shares sequence homology with a novel family of putative GTP-binding proteins: the immuno-associated nucleotide (IAN) family. The evolutionary conservation of the IAN family provides a unique example of a plant pathogen response gene conserved in animals. The IAN/IMAP subfamily has been proposed to regulate apoptosis in vertebrates and angiosperm plants, particularly in relation to cancer, diabetes, and infections. The human IAN genes were renamed GIMAP (GTPase of the immunity associated proteins).
Probab=31.37 E-value=74 Score=30.01 Aligned_cols=67 Identities=10% Similarity=0.078 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCHHHHHh
Q 046419 36 PWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFSPEEERLIVELHAQLGNKWARMAA 114 (505)
Q Consensus 36 ~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT~EED~lLlelV~kyG~kWskIAk 114 (505)
.|+.+|.+.|..+.+.+|..-|..+--.+ ++..+--..+ -..|-.+.+..|.++++++|.++-.+..
T Consensus 95 ~~t~~d~~~l~~l~~~fg~~~~~~~ivv~--T~~d~l~~~~----------~~~~~~~~~~~l~~l~~~c~~r~~~f~~ 161 (196)
T cd01852 95 RFTEEEEQAVETLQELFGEKVLDHTIVLF--TRGDDLEGGT----------LEDYLENSCEALKRLLEKCGGRYVAFNN 161 (196)
T ss_pred CcCHHHHHHHHHHHHHhChHhHhcEEEEE--ECccccCCCc----------HHHHHHhccHHHHHHHHHhCCeEEEEeC
Confidence 37776666666666666765554332222 2322211111 1123334456788899998887644433
No 108
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=31.29 E-value=12 Score=31.71 Aligned_cols=39 Identities=23% Similarity=0.445 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCC-------CCcchhccccCCccc----cccccccccccc
Q 046419 43 AILTEYVRKHGE-------GNWNAVQRNTGLARC----GKSCRLRWANHL 81 (505)
Q Consensus 43 elL~~lV~k~G~-------~nW~~IAk~m~~gRT----~kQCR~Rw~n~L 81 (505)
-+|..+|.+.|. ..|.+|++.++...+ ..+.+..|.++|
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L 84 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYL 84 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHh
Confidence 357778888765 479999999984321 233445555554
No 109
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.07 E-value=1e+02 Score=28.38 Aligned_cols=29 Identities=7% Similarity=-0.029 Sum_probs=23.4
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|..+.+||..| |-+...|+++.....++.
T Consensus 152 ~~s~~eIA~~l-gis~~~v~~~l~Rar~~L 180 (187)
T PRK09641 152 DLSLKEISEIL-DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45689999999 999999999887665554
No 110
>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=30.95 E-value=81 Score=29.10 Aligned_cols=30 Identities=7% Similarity=0.032 Sum_probs=23.8
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRRH 136 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~~ 136 (505)
|....+||+.| |-+...|+++....+++..
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 44689999999 8889999999876665543
No 111
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=30.90 E-value=97 Score=24.26 Aligned_cols=34 Identities=24% Similarity=0.483 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHH
Q 046419 94 EERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYW 128 (505)
Q Consensus 94 ED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW 128 (505)
+|+-.+.++.+.|-.-.+||+.+ ||+...|++.-
T Consensus 8 ~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 8 AEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 44555667778898899999999 99999887753
No 112
>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=30.55 E-value=58 Score=27.26 Aligned_cols=29 Identities=24% Similarity=0.675 Sum_probs=22.6
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCCCHHHH
Q 046419 95 ERLIVELHAQLGNKWARMAAQLPGRTDNEI 124 (505)
Q Consensus 95 D~lLlelV~kyG~kWskIAk~LpgRT~~qc 124 (505)
|..|..+.+..|.+|.++|++| |=+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4567788888999999999999 5554443
No 113
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=29.19 E-value=15 Score=45.44 Aligned_cols=32 Identities=22% Similarity=0.486 Sum_probs=25.9
Q ss_pred HhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 104 QLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 104 kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
++|..|++|+..+...+..+|++.|.++.++.
T Consensus 371 eh~R~~aai~p~vvt~tes~c~na~a~~~~r~ 402 (1672)
T KOG1878|consen 371 EHGREWAAILPKVVTKTESQCKNAYAKYKNRH 402 (1672)
T ss_pred hhhhhHHHhcCccceecccchhhHHHhhhhhh
Confidence 44578999999999999999998776655544
No 114
>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=29.08 E-value=75 Score=26.92 Aligned_cols=25 Identities=32% Similarity=0.634 Sum_probs=18.7
Q ss_pred HHHHHHhCCCHHHHHhhCCCCCHHHH
Q 046419 99 VELHAQLGNKWARMAAQLPGRTDNEI 124 (505)
Q Consensus 99 lelV~kyG~kWskIAk~LpgRT~~qc 124 (505)
..+....|.+|.++|+.| |-+..+|
T Consensus 11 ~~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 11 TVFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 335577799999999999 6565554
No 115
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=28.96 E-value=2.5e+02 Score=21.05 Aligned_cols=48 Identities=23% Similarity=0.477 Sum_probs=37.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----CHHHHHhhCCCCCHHHHHHHHHHHhhh
Q 046419 86 KKGTFSPEEERLIVELHAQLGN----KWARMAAQLPGRTDNEIKNYWNTRVKR 134 (505)
Q Consensus 86 kkg~WT~EED~lLlelV~kyG~----kWskIAk~LpgRT~~qcKnRW~~llkk 134 (505)
++..+|.++-..|.+.+..... .-..||..+ |=+..+|+++|.....+
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~nrR~k 54 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQNRRRK 54 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHHhHHH
Confidence 4567999999999988887432 268899999 99999999998765443
No 116
>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=28.46 E-value=20 Score=32.19 Aligned_cols=17 Identities=29% Similarity=0.485 Sum_probs=13.1
Q ss_pred CCCHHHHHHHHHHHHHh
Q 046419 36 PWTAAEDAILTEYVRKH 52 (505)
Q Consensus 36 ~WT~EEDelL~~lV~k~ 52 (505)
+||++||-.|...|.+|
T Consensus 1 kfTA~dDY~Lc~~i~~~ 17 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQ 17 (105)
T ss_dssp ---HHHHHHHHHHHHHH
T ss_pred CCChHHHHHHHHHHHHH
Confidence 58999999999999887
No 117
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=28.36 E-value=1.2e+02 Score=28.42 Aligned_cols=30 Identities=17% Similarity=0.067 Sum_probs=23.7
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 105 LGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 105 yG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.|-.+.+||..| |.+...|+.+....+++.
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar~~L 150 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGRVKL 150 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 355799999999 999999999987655443
No 118
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.20 E-value=1.3e+02 Score=28.01 Aligned_cols=31 Identities=16% Similarity=0.194 Sum_probs=24.3
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHhhhhh
Q 046419 105 LGNKWARMAAQLPGRTDNEIKNYWNTRVKRRH 136 (505)
Q Consensus 105 yG~kWskIAk~LpgRT~~qcKnRW~~llkk~~ 136 (505)
.|....+||..| |-+...|+.+....+++..
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALARLR 184 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 355689999999 8889999998876665543
No 119
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=28.11 E-value=1.4e+02 Score=26.65 Aligned_cols=29 Identities=17% Similarity=0.187 Sum_probs=23.3
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|-.-.+||..| |-+...|+.|....+++.
T Consensus 122 g~s~~EIA~~l-gis~~tV~~~l~ra~~~L 150 (161)
T PRK09047 122 DMDVAETAAAM-GCSEGSVKTHCSRATHAL 150 (161)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 44689999999 899999999987655544
No 120
>KOG4786 consensus Ubinuclein, nuclear protein interacting with cellular and viral transcription factors [Transcription; Signal transduction mechanisms]
Probab=27.94 E-value=3.1e+02 Score=32.57 Aligned_cols=63 Identities=22% Similarity=0.314 Sum_probs=30.4
Q ss_pred cCCCCCccCCCCCCCCCCCCccccccCCCccccccccccccCCCCCCCCCCCccCCCCCCCCccCCccCCCCC
Q 046419 272 NNISNTFNMPRTPPLLQNPPRFKRFHSDTSINTFAANQNDINNNNNINSSSSFQGSNNFSMPFLPFFRSPSSP 344 (505)
Q Consensus 272 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~p 344 (505)
.+.+..|.+.-+--+.+.|+.-.+|-|+..-+ +...|++++.++-..-|+.-.++|+-+.+.|
T Consensus 1005 ~~~~~S~~~S~sV~~~~S~L~~~~Y~S~S~~~----------~~s~~SNS~~~~TP~P~P~H~~~~S~~~~~~ 1067 (1136)
T KOG4786|consen 1005 ANRRSSFTMSHSVQQHQSPLQQQFYQSPSHHN----------NSSSMSNSSLMQTPSPFPSHTSPMSQRFHTP 1067 (1136)
T ss_pred hccccccccchhhhhccChhhhccccCCCccc----------cccccccccccccCCCCccccccccccccCC
Confidence 34566676665555555666655453432222 2223444444554555554445554443333
No 121
>PRK01905 DNA-binding protein Fis; Provisional
Probab=27.64 E-value=1.4e+02 Score=24.71 Aligned_cols=37 Identities=22% Similarity=0.220 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHH
Q 046419 92 PEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWN 129 (505)
Q Consensus 92 ~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~ 129 (505)
.-|.+.|+++++++|.++.+.|+.+ |=+...++.+.+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rklk 72 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKKLQ 72 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 4477789999999999999999999 666666555443
No 122
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=27.51 E-value=33 Score=37.08 Aligned_cols=41 Identities=12% Similarity=0.188 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhcc-ccCCcccccccccccc
Q 046419 36 PWTAAEDAILTEYVRKHGEGNWNAVQR-NTGLARCGKSCRLRWA 78 (505)
Q Consensus 36 ~WT~EEDelL~~lV~k~G~~nW~~IAk-~m~~gRT~kQCR~Rw~ 78 (505)
.|+.+|-..+.+.++.||+ ++--|.+ ++. +|+...|..-|.
T Consensus 279 ~wsEeEcr~FEegl~~yGK-DF~lIr~nkvr-tRsvgElVeyYY 320 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYGK-DFHLIRANKVR-TRSVGELVEYYY 320 (445)
T ss_pred cCCHHHHHHHHHHHHHhcc-cHHHHHhcccc-cchHHHHHHHHH
Confidence 6999999999999999999 8888854 454 777777766553
No 123
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.12 E-value=72 Score=23.46 Aligned_cols=35 Identities=20% Similarity=0.322 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHH
Q 046419 92 PEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYW 128 (505)
Q Consensus 92 ~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW 128 (505)
.++-..++.++.+ |....+||+.+ |-+...|....
T Consensus 4 ~~~R~~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~w~ 38 (50)
T PF13384_consen 4 EERRAQIIRLLRE-GWSIREIAKRL-GVSRSTVYRWI 38 (50)
T ss_dssp ------HHHHHHH-T--HHHHHHHH-TS-HHHHHHHH
T ss_pred hhHHHHHHHHHHC-CCCHHHHHHHH-CcCHHHHHHHH
Confidence 3445567788877 88899999999 88888776643
No 124
>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=26.97 E-value=47 Score=31.70 Aligned_cols=35 Identities=17% Similarity=0.285 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCCcchhccccCCccccccc
Q 046419 36 PWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSC 73 (505)
Q Consensus 36 ~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQC 73 (505)
.||.|+.++|.++..+ |. .=.+||+.|| +.+...+
T Consensus 2 ~Wtde~~~~L~~lw~~-G~-SasqIA~~lg-~vsRnAV 36 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GL-SASQIARQLG-GVSRNAV 36 (162)
T ss_pred CCCHHHHHHHHHHHHc-CC-CHHHHHHHhC-Ccchhhh
Confidence 4999999999999854 33 6789999998 4444333
No 125
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=26.90 E-value=1.4e+02 Score=28.05 Aligned_cols=30 Identities=10% Similarity=0.025 Sum_probs=23.6
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 105 LGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 105 yG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.|....+||..| |-+...|+.|....+++.
T Consensus 146 ~g~s~~EIA~~l-gis~~tvk~rl~Rar~~L 175 (188)
T TIGR02943 146 LGFESDEICQEL-EISTSNCHVLLYRARLSL 175 (188)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 355689999999 999999999877655544
No 126
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=26.36 E-value=1.3e+02 Score=28.08 Aligned_cols=29 Identities=7% Similarity=0.054 Sum_probs=22.6
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|-...+||+.| |-+...|+.++...+++.
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~L 182 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREAI 182 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34589999999 888999999987655544
No 127
>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=26.30 E-value=79 Score=27.02 Aligned_cols=30 Identities=40% Similarity=0.688 Sum_probs=22.3
Q ss_pred HHHHHHHHHhCCCHHHHHhhCCCCCHHHHHH
Q 046419 96 RLIVELHAQLGNKWARMAAQLPGRTDNEIKN 126 (505)
Q Consensus 96 ~lLlelV~kyG~kWskIAk~LpgRT~~qcKn 126 (505)
+.|-.+....|.+|..+|+.| |=++.+|..
T Consensus 3 ~~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 3 KHLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 345555678899999999999 766666554
No 128
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.93 E-value=1.3e+02 Score=27.65 Aligned_cols=29 Identities=7% Similarity=-0.029 Sum_probs=22.9
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|....+||+.| |.+...|+++.....++.
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~L 180 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34589999999 889999999887665554
No 129
>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=25.91 E-value=91 Score=26.44 Aligned_cols=31 Identities=26% Similarity=0.526 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHH
Q 046419 95 ERLIVELHAQLGNKWARMAAQLPGRTDNEIKN 126 (505)
Q Consensus 95 D~lLlelV~kyG~kWskIAk~LpgRT~~qcKn 126 (505)
|.+|..+....|.+|.++|+.| |=+...|..
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 5567777888999999999999 666655544
No 130
>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=25.54 E-value=39 Score=31.96 Aligned_cols=30 Identities=23% Similarity=0.396 Sum_probs=25.7
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCCcchhcc
Q 046419 32 LKKGPWTAAEDAILTEYVRKHGEGNWNAVQR 62 (505)
Q Consensus 32 lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk 62 (505)
.+..+=+..|.+-|..+|++||. ++.+.+.
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMar 141 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMAR 141 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhc
Confidence 45677899999999999999998 8888765
No 131
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=25.40 E-value=1.5e+02 Score=27.93 Aligned_cols=30 Identities=7% Similarity=-0.038 Sum_probs=23.3
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 105 LGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 105 yG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.|-.+.+||+.| |-+...|+.+....+++.
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~L 180 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRAL 180 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 345699999999 888899988877655544
No 132
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=25.33 E-value=1.5e+02 Score=27.39 Aligned_cols=30 Identities=13% Similarity=0.181 Sum_probs=24.0
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRRH 136 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~~ 136 (505)
|....+||..| |-+...|+.++...+++..
T Consensus 147 g~s~~eIA~~l-~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 147 GASIKETAAKL-SMSEGAVRVALHRGLAALA 176 (184)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHHHH
Confidence 45689999999 9999999999876665543
No 133
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.28 E-value=1.6e+02 Score=27.76 Aligned_cols=30 Identities=10% Similarity=0.047 Sum_probs=23.7
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRRH 136 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~~ 136 (505)
|-...+||..| |-+...|+.|....+++..
T Consensus 157 g~s~~EIA~~l-gis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 157 ELPHQQVAEMF-DIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred CCCHHHHHHHh-CcCHHHHHHHHHHHHHHHH
Confidence 45689999999 9999999999876665543
No 134
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.09 E-value=1.6e+02 Score=26.83 Aligned_cols=29 Identities=24% Similarity=0.325 Sum_probs=23.0
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|-.-.+||+.| |.+...|+.|....+++.
T Consensus 134 g~s~~EIA~~l-gis~~tV~~~l~ra~~~L 162 (173)
T PRK09645 134 GWSTAQIAADL-GIPEGTVKSRLHYALRAL 162 (173)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 44579999999 999999999987655544
No 135
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=25.05 E-value=1.6e+02 Score=27.44 Aligned_cols=29 Identities=10% Similarity=0.092 Sum_probs=23.4
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|-...+||+.| |-+...|+.++...+++.
T Consensus 147 ~~s~~eIA~~l-gis~~tV~~~l~Rar~~L 175 (189)
T PRK12515 147 EKSVEEVGEIV-GIPESTVKTRMFYARKKL 175 (189)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 45689999999 889999999987655544
No 136
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=24.84 E-value=1.4e+02 Score=27.71 Aligned_cols=40 Identities=23% Similarity=0.472 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHhC--CCHHHHHhhCCCCCHHHHHHHHHHHhhh
Q 046419 93 EEERLIVELHAQLG--NKWARMAAQLPGRTDNEIKNYWNTRVKR 134 (505)
Q Consensus 93 EED~lLlelV~kyG--~kWskIAk~LpgRT~~qcKnRW~~llkk 134 (505)
+|++.+++|.-.-. ..|..||..+ +-+..+|+.++ .-+|.
T Consensus 84 de~k~Ii~lry~~r~~~TW~~IA~~l-~i~erta~r~~-~~fK~ 125 (130)
T PF05263_consen 84 DEEKRIIKLRYDRRSRRTWYQIAQKL-HISERTARRWR-DRFKN 125 (130)
T ss_pred HHHHHHHHHHHcccccchHHHHHHHh-CccHHHHHHHH-HHHHH
Confidence 34555665553333 4599999999 56666666443 33443
No 137
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=24.71 E-value=1.7e+02 Score=26.27 Aligned_cols=29 Identities=10% Similarity=-0.037 Sum_probs=22.7
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|-.-.+||+.| |-+...|++|....+++.
T Consensus 122 g~s~~EIA~~l-gis~~tV~~~l~Rar~~L 150 (160)
T PRK09642 122 EKSYQEIALQE-KIEVKTVEMKLYRARKWI 150 (160)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 44579999999 999999999877555443
No 138
>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=24.65 E-value=89 Score=25.60 Aligned_cols=30 Identities=27% Similarity=0.588 Sum_probs=21.0
Q ss_pred HHHHHHHHHHH-hCCCHHHHHhhCCCCCHHHH
Q 046419 94 EERLIVELHAQ-LGNKWARMAAQLPGRTDNEI 124 (505)
Q Consensus 94 ED~lLlelV~k-yG~kWskIAk~LpgRT~~qc 124 (505)
-++.|..++.. .|.+|..+|+.| |=+..+|
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 34556666666 789999999999 4444443
No 139
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.15 E-value=1.9e+02 Score=25.77 Aligned_cols=29 Identities=10% Similarity=0.212 Sum_probs=22.5
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|....+||+.+ |.+...|+.+-...+++.
T Consensus 122 ~~s~~EIA~~l-~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 122 GKTMGEIALET-EMTYYQVRWIYRQALEKM 150 (154)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34578999998 899999998877666554
No 140
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=24.08 E-value=1.1e+02 Score=34.33 Aligned_cols=42 Identities=21% Similarity=0.371 Sum_probs=35.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHHh-hCCCCCHHHHHHHHH
Q 046419 88 GTFSPEEERLIVELHAQLGNKWARMAA-QLPGRTDNEIKNYWN 129 (505)
Q Consensus 88 g~WT~EED~lLlelV~kyG~kWskIAk-~LpgRT~~qcKnRW~ 129 (505)
..|+.-|-.++.+++++||.++..|.. +|+-++-..|-..|.
T Consensus 286 EEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 286 EEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 479999999999999999999999954 568888888877653
No 141
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.07 E-value=1.7e+02 Score=27.58 Aligned_cols=28 Identities=0% Similarity=-0.066 Sum_probs=22.8
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKR 134 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk 134 (505)
|-...+||..| |.+...||.|....+++
T Consensus 150 g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 177 (189)
T PRK12530 150 ELSSEQICQEC-DISTSNLHVLLYRARLQ 177 (189)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45689999999 99999999997655444
No 142
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.06 E-value=1.7e+02 Score=27.14 Aligned_cols=32 Identities=19% Similarity=0.090 Sum_probs=25.7
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHhhhhhh
Q 046419 105 LGNKWARMAAQLPGRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 105 yG~kWskIAk~LpgRT~~qcKnRW~~llkk~~r 137 (505)
.|-...+||+.| |-+...||.|...-+++-..
T Consensus 142 ~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 142 DGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 355689999999 99999999998876665543
No 143
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.90 E-value=1.8e+02 Score=26.68 Aligned_cols=31 Identities=19% Similarity=0.332 Sum_probs=24.8
Q ss_pred HhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 104 QLGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 104 kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
-.|-...+||+.| |.+...|+.+...-+++-
T Consensus 133 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 133 LDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3455789999999 999999999987666554
No 144
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=23.19 E-value=1.8e+02 Score=25.25 Aligned_cols=36 Identities=17% Similarity=0.144 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHH
Q 046419 93 EEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWN 129 (505)
Q Consensus 93 EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~ 129 (505)
-|...|.++++.++.++.+.|+.| |=++..++.+-+
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rKLk 90 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKKLK 90 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHH
Confidence 477788999999999999999999 767666555443
No 145
>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=22.95 E-value=2.2e+02 Score=32.46 Aligned_cols=91 Identities=21% Similarity=0.325 Sum_probs=50.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCC--------CcchhccccC-Ccccccccccccccc------------cCCCCCCC----C
Q 046419 35 GPWTAAEDAILTEYVRKHGEG--------NWNAVQRNTG-LARCGKSCRLRWANH------------LRPNLKKG----T 89 (505)
Q Consensus 35 G~WT~EEDelL~~lV~k~G~~--------nW~~IAk~m~-~gRT~kQCR~Rw~n~------------L~p~lkkg----~ 89 (505)
..|+.+++..|.+++..|+.. .|- -..+. ..|+.+++..+-... -....+++ .
T Consensus 93 ~~~~~~~~~e~~~l~i~~~~~~~~~~D~vdwi--~~~L~~~~r~Rr~~~~~l~~~Gl~~~~~~~~~~k~a~~kk~~~rll 170 (566)
T PF05029_consen 93 EVWTEEEEEELRQLYIEVKDLDEEDQDLVDWI--LDNLSDATRTRRQWEKKLVEMGLADSAKDLIETKSAMFKKGRLRLL 170 (566)
T ss_pred ccccchhHHHHHHHHHHHhhhcccchhHHHHH--HHHhccchhhhHHHHHHHHHcccccccccccccccccccCCccccc
Confidence 689999998888877666542 341 11121 124433332211000 00223444 6
Q ss_pred CCHHHHHHHHHHHHHhCCC---HHHHHhhC-CCCCHHHHHHH
Q 046419 90 FSPEEERLIVELHAQLGNK---WARMAAQL-PGRTDNEIKNY 127 (505)
Q Consensus 90 WT~EED~lLlelV~kyG~k---WskIAk~L-pgRT~~qcKnR 127 (505)
||.+++..|..|+..|... =..|...+ ..|+..++..+
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 9999999999999777642 34454444 33666666544
No 146
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.93 E-value=1.6e+02 Score=28.98 Aligned_cols=46 Identities=15% Similarity=0.140 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhhhh
Q 046419 89 TFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~~r 137 (505)
..|+.|-+. ++++.+ |....+||+.| +-+...||.+...+++|..-
T Consensus 155 ~Lt~rE~~V-l~l~~~-G~s~~eIA~~L-~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 155 LLTHREKEI-LNKLRI-GASNNEIARSL-FISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHH-HHHHHc-CCCHHHHHHHh-CCCHHHHHHHHHHHHHHhCC
Confidence 467655555 455555 88899999999 89999999999988887643
No 147
>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=22.83 E-value=89 Score=26.28 Aligned_cols=33 Identities=30% Similarity=0.554 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHH
Q 046419 92 PEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKN 126 (505)
Q Consensus 92 ~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKn 126 (505)
.||.++|+..= ..|.+|..+|++| |=+...|+.
T Consensus 2 ~~~v~~ll~~~-nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLESG-RPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhCC-CCccCHHHHHHHc-CCCHHHHHH
Confidence 57778877322 4678899999999 766666654
No 148
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=22.79 E-value=1.3e+02 Score=36.68 Aligned_cols=41 Identities=20% Similarity=0.430 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHhCC-CHHHHHhhCCCCCHHHHHHHHH
Q 046419 89 TFSPEEERLIVELHAQLGN-KWARMAAQLPGRTDNEIKNYWN 129 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG~-kWskIAk~LpgRT~~qcKnRW~ 129 (505)
.|+..|=..++++..+||. .-..||..|.|+|..+|+.+.+
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~ 867 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAK 867 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHH
Confidence 4999999999999999995 5999999999999999986543
No 149
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=22.75 E-value=2.2e+02 Score=26.70 Aligned_cols=33 Identities=27% Similarity=0.354 Sum_probs=25.9
Q ss_pred CCHHHHHhhCCCCCHHHHHHHHHHHhhhhhhcCC
Q 046419 107 NKWARMAAQLPGRTDNEIKNYWNTRVKRRHRQGL 140 (505)
Q Consensus 107 ~kWskIAk~LpgRT~~qcKnRW~~llkk~~r~~~ 140 (505)
-.=.+||+.| |.+...|+++-...+++.....+
T Consensus 148 ~s~~EIAe~l-gis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 148 EKIEEIAKKL-GLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred CCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHccc
Confidence 3468899999 99999999998877777665544
No 150
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.75 E-value=94 Score=29.58 Aligned_cols=40 Identities=23% Similarity=0.310 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHH
Q 046419 89 TFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWN 129 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~ 129 (505)
.||+|..++|.+|..+ |-.=++||++|.|=+++.|.-+-+
T Consensus 2 nWtdERve~LkKLWse-GLSASQIAaQLGGVsRnAVIGKVH 41 (169)
T COG5352 2 NWTDERVETLKKLWSE-GLSASQIAAQLGGVSRNAVIGKVH 41 (169)
T ss_pred CchHHHHHHHHHHHHc-ccCHHHHHHHhcCcchhhhheeee
Confidence 5999999999988765 555789999999999988765443
No 151
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=22.71 E-value=1e+02 Score=27.43 Aligned_cols=81 Identities=22% Similarity=0.304 Sum_probs=0.0
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCCCCCCCCCC---------------------
Q 046419 33 KKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRPNLKKGTFS--------------------- 91 (505)
Q Consensus 33 kKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p~lkkg~WT--------------------- 91 (505)
++.+||.|+-..++..+...|. .-.+||+.++. ..+-..+|.+.+......+. +
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~-sv~evA~e~gI---s~~tl~~W~r~y~~~~~~~~-~~~~~~~~~~~~~~~~~ei~~L 83 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM-TVSLVARQHGV---AASQLFLWRKQYQEGSLTAV-AAGEQVVPASELAAAMKQIKEL 83 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC-CHHHHHHHHCc---CHHHHHHHHHHHhhcccccc-cccccCCchhHHHHHHHHHHHH
Q ss_pred -------HHHHHHHHHHHHHhC-CCHHHHHhhCCC
Q 046419 92 -------PEEERLIVELHAQLG-NKWARMAAQLPG 118 (505)
Q Consensus 92 -------~EED~lLlelV~kyG-~kWskIAk~Lpg 118 (505)
..|-+.|.+++.-++ .+|..++.+++|
T Consensus 84 ~~el~~L~~E~diLKKa~~~~~~~~~~~~~~~~~~ 118 (121)
T PRK09413 84 QRLLGKKTMENELLKEAVEYGRAKKWIAHAPLLPG 118 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHhchhhhhhcCCCCCC
No 152
>cd00131 PAX Paired Box domain
Probab=22.44 E-value=2.2e+02 Score=25.89 Aligned_cols=87 Identities=17% Similarity=0.187 Sum_probs=53.6
Q ss_pred CCCCCccCCCCHHHHHHHHHHHHHhCCCCcchhccccCCccc-ccccccccccc--cCCCCCCC----CCCHHHHHHHHH
Q 046419 28 GGVQLKKGPWTAAEDAILTEYVRKHGEGNWNAVQRNTGLARC-GKSCRLRWANH--LRPNLKKG----TFSPEEERLIVE 100 (505)
Q Consensus 28 ~~~~lkKG~WT~EEDelL~~lV~k~G~~nW~~IAk~m~~gRT-~kQCR~Rw~n~--L~p~lkkg----~WT~EED~lLle 100 (505)
++...--.+.+.++-++++.+++ -|. ...+||+.++..+. ..-+..||... +.|....+ .-+.+++..|++
T Consensus 9 ~~~~~m~~~lS~d~R~rIv~~~~-~G~-s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~ 86 (128)
T cd00131 9 GGVFVNGRPLPDSIRQRIVELAQ-SGI-RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEI 86 (128)
T ss_pred CccccCCCcCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHH
Confidence 34455567899999999998885 455 89999999975543 33444555432 34432211 246677777777
Q ss_pred HHHHhCCC-HHHHHhhC
Q 046419 101 LHAQLGNK-WARMAAQL 116 (505)
Q Consensus 101 lV~kyG~k-WskIAk~L 116 (505)
++.+.+.. =.+|++.|
T Consensus 87 ~v~~~p~~Tl~El~~~L 103 (128)
T cd00131 87 YKQENPGMFAWEIRDRL 103 (128)
T ss_pred HHHHCCCCCHHHHHHHH
Confidence 78776642 23334443
No 153
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=22.40 E-value=2e+02 Score=26.43 Aligned_cols=29 Identities=17% Similarity=0.226 Sum_probs=23.6
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|-...+||..| |-+...|+.|....+++.
T Consensus 150 g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 178 (183)
T TIGR02999 150 GLTVEEIAELL-GVSVRTVERDWRFARAWL 178 (183)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 44689999999 999999999987766554
No 154
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=22.31 E-value=1.9e+02 Score=26.00 Aligned_cols=29 Identities=24% Similarity=0.253 Sum_probs=22.7
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|-...+||+.| |.+...|+.+-...+++.
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~~L 166 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIKKL 166 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 44578999999 888999998877666554
No 155
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=21.83 E-value=1.2e+02 Score=22.37 Aligned_cols=37 Identities=27% Similarity=0.434 Sum_probs=18.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHH
Q 046419 89 TFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNY 127 (505)
Q Consensus 89 ~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnR 127 (505)
.+|.+|-..|..++ +-|..=.+||+.| ||+..-|...
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHHH
Confidence 57788888877775 4566689999999 9998887653
No 156
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=21.34 E-value=38 Score=28.88 Aligned_cols=42 Identities=12% Similarity=0.076 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHhCCCCcchhccccCCcccccccccccccccCC
Q 046419 40 AEDAILTEYVRKHGEGNWNAVQRNTGLARCGKSCRLRWANHLRP 83 (505)
Q Consensus 40 EEDelL~~lV~k~G~~nW~~IAk~m~~gRT~kQCR~Rw~n~L~p 83 (505)
+.|.+++.++.+.+...|.+||+.++ -+...|+.|..+..+.
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHC
Confidence 56888999999988889999999996 7777777776665543
No 157
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=21.23 E-value=1.9e+02 Score=27.05 Aligned_cols=29 Identities=7% Similarity=0.041 Sum_probs=22.3
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|-.-.+||+.| |-+...|+.|....+++.
T Consensus 152 g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 180 (195)
T PRK12532 152 GFSSDEIQQMC-GISTSNYHTIMHRARESL 180 (195)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45679999999 999999998877544443
No 158
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=20.92 E-value=80 Score=28.07 Aligned_cols=28 Identities=14% Similarity=0.113 Sum_probs=23.4
Q ss_pred CHHHHHhhCCCCCHHHHHHHHHHHhhhhh
Q 046419 108 KWARMAAQLPGRTDNEIKNYWNTRVKRRH 136 (505)
Q Consensus 108 kWskIAk~LpgRT~~qcKnRW~~llkk~~ 136 (505)
.+.+||+.| |-+...|++++....++..
T Consensus 123 s~~eIA~~l-gis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 123 SYKEIAELL-NLSLAKVKSNLFRARKELK 150 (154)
T ss_pred cHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 589999999 9999999999887666543
No 159
>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=20.83 E-value=1.2e+02 Score=25.89 Aligned_cols=22 Identities=32% Similarity=0.608 Sum_probs=19.4
Q ss_pred HHHHHHHHHHhCCCHHHHHhhC
Q 046419 95 ERLIVELHAQLGNKWARMAAQL 116 (505)
Q Consensus 95 D~lLlelV~kyG~kWskIAk~L 116 (505)
|.+|..+.+..|..|.++|++|
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L 25 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL 25 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc
Confidence 5667788889999999999999
No 160
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.64 E-value=2e+02 Score=26.93 Aligned_cols=31 Identities=19% Similarity=0.090 Sum_probs=24.8
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~~r 137 (505)
|-...+||+.| |-+...|+.|....+++...
T Consensus 146 g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 146 GLSYADAAAVC-GCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 34589999999 99999999998876665543
No 161
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=20.64 E-value=2.2e+02 Score=26.14 Aligned_cols=30 Identities=20% Similarity=0.453 Sum_probs=23.5
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 105 LGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 105 yG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.|-...+||..| |-+...|+.+....+++.
T Consensus 155 ~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~L 184 (189)
T TIGR02984 155 EGLSFAEVAERM-DRSEGAVSMLWVRGLARL 184 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 345688999998 899999999887666654
No 162
>PRK00118 putative DNA-binding protein; Validated
Probab=20.54 E-value=2.5e+02 Score=25.08 Aligned_cols=42 Identities=14% Similarity=0.115 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhh
Q 046419 92 PEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKR 134 (505)
Q Consensus 92 ~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk 134 (505)
.+.+..++.+....|-...+||+.+ |-+...|+.+.....++
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArkk 60 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEKL 60 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3455666677777788899999999 99999998876654433
No 163
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=20.33 E-value=2.2e+02 Score=26.89 Aligned_cols=30 Identities=23% Similarity=0.168 Sum_probs=23.2
Q ss_pred hCCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 105 LGNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 105 yG~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
.|-...+||+.| |-+...||.|-...+++.
T Consensus 131 ~g~s~~EIA~~L-gis~~tVk~~l~Rar~~L 160 (187)
T PRK12516 131 SGFAYEEAAEIC-GCAVGTIKSRVNRARQRL 160 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 355689999999 899999999876555443
No 164
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=20.11 E-value=2e+02 Score=28.02 Aligned_cols=47 Identities=15% Similarity=0.215 Sum_probs=38.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCCHHHHHhhCCCCCHHHHHHHHHHHhhhhhh
Q 046419 88 GTFSPEEERLIVELHAQLGNKWARMAAQLPGRTDNEIKNYWNTRVKRRHR 137 (505)
Q Consensus 88 g~WT~EED~lLlelV~kyG~kWskIAk~LpgRT~~qcKnRW~~llkk~~r 137 (505)
...|+.|-+.|.-+.+ |-.=++||..| +.+..-||.|..++++|..-
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~KL~v 193 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRKLGV 193 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHHcCC
Confidence 3688888887765554 55568999999 99999999999999998743
No 165
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=20.09 E-value=2.1e+02 Score=26.54 Aligned_cols=29 Identities=10% Similarity=0.051 Sum_probs=21.6
Q ss_pred CCCHHHHHhhCCCCCHHHHHHHHHHHhhhh
Q 046419 106 GNKWARMAAQLPGRTDNEIKNYWNTRVKRR 135 (505)
Q Consensus 106 G~kWskIAk~LpgRT~~qcKnRW~~llkk~ 135 (505)
|....+||+.| |-+...|+.+....+++.
T Consensus 144 g~s~~EIA~~l-gis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 144 GLSNIEAAAVM-DISVDALESLLARGRRAL 172 (186)
T ss_pred CCCHHHHHHHh-CcCHHHHHHHHHHHHHHH
Confidence 44678889888 888888888876555443
Done!