Query 012494
Match_columns 462
No_of_seqs 278 out of 1502
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 03:14:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012494.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012494hhsearch_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 1E-32 2.3E-37 266.8 11.1 108 47-154 7-115 (238)
2 PLN03212 Transcription repress 100.0 3.9E-31 8.5E-36 256.9 15.3 113 44-156 20-133 (249)
3 PLN03091 hypothetical protein; 100.0 2.1E-29 4.6E-34 260.3 14.0 113 44-156 9-122 (459)
4 KOG0050 mRNA splicing protein 99.8 6E-19 1.3E-23 185.0 6.2 155 47-218 5-162 (617)
5 KOG0049 Transcription factor, 99.7 4.1E-17 8.9E-22 174.6 8.3 98 44-141 355-453 (939)
6 KOG0049 Transcription factor, 99.6 1E-15 2.2E-20 164.1 8.9 105 47-151 303-411 (939)
7 PF13921 Myb_DNA-bind_6: Myb-l 99.6 9.4E-16 2E-20 118.3 5.2 60 52-112 1-60 (60)
8 COG5147 REB1 Myb superfamily p 99.6 3.1E-15 6.7E-20 159.1 7.3 107 45-151 16-122 (512)
9 KOG0051 RNA polymerase I termi 99.3 1.2E-12 2.6E-17 141.1 7.7 107 48-156 383-517 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.3 2.8E-13 6.1E-18 101.0 2.0 47 49-95 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.3 4.9E-12 1.1E-16 94.3 5.4 46 101-146 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.1 5.4E-11 1.2E-15 91.8 4.6 45 104-148 1-45 (60)
13 smart00717 SANT SANT SWI3, AD 99.1 1.3E-10 2.9E-15 83.2 5.7 47 101-147 1-48 (49)
14 smart00717 SANT SANT SWI3, AD 99.0 1.5E-10 3.3E-15 82.9 3.8 48 49-96 1-48 (49)
15 PLN03212 Transcription repress 99.0 6.7E-11 1.5E-15 116.2 2.1 93 79-197 10-104 (249)
16 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 8.2E-10 1.8E-14 78.2 5.7 44 103-146 1-45 (45)
17 PLN03091 hypothetical protein; 98.9 4.1E-10 8.9E-15 118.0 2.3 55 97-151 10-66 (459)
18 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 1.2E-09 2.7E-14 77.2 3.4 45 51-95 1-45 (45)
19 KOG0051 RNA polymerase I termi 98.9 3.7E-09 8E-14 114.5 7.3 103 46-149 305-431 (607)
20 KOG0048 Transcription factor, 98.8 4.1E-10 8.9E-15 109.6 -1.2 89 98-186 6-96 (238)
21 KOG0050 mRNA splicing protein 98.2 2.1E-07 4.5E-12 99.3 -0.6 95 99-217 5-100 (617)
22 COG5147 REB1 Myb superfamily p 98.1 3.6E-07 7.8E-12 98.2 -1.5 99 46-146 288-396 (512)
23 KOG0457 Histone acetyltransfer 97.5 5.6E-05 1.2E-09 79.8 3.2 53 44-96 67-119 (438)
24 TIGR01557 myb_SHAQKYF myb-like 97.4 0.00012 2.7E-09 57.6 3.4 48 48-95 2-54 (57)
25 TIGR01557 myb_SHAQKYF myb-like 97.4 0.00037 8.1E-09 54.9 5.9 47 100-146 2-54 (57)
26 KOG0457 Histone acetyltransfer 97.4 0.00028 6E-09 74.6 6.4 48 99-146 70-118 (438)
27 TIGR02894 DNA_bind_RsfA transc 97.3 0.00031 6.8E-09 65.8 4.8 53 100-153 3-62 (161)
28 PF13325 MCRS_N: N-terminal re 97.3 0.0011 2.3E-08 64.3 8.6 100 51-152 1-132 (199)
29 PF13837 Myb_DNA-bind_4: Myb/S 96.9 0.00085 1.9E-08 54.9 3.7 52 101-153 1-70 (90)
30 COG5259 RSC8 RSC chromatin rem 96.6 0.0019 4.2E-08 69.0 4.4 44 101-144 279-322 (531)
31 COG5259 RSC8 RSC chromatin rem 96.6 0.0014 3E-08 70.1 2.8 45 48-93 278-322 (531)
32 KOG1279 Chromatin remodeling f 96.5 0.0032 7E-08 68.3 5.2 45 100-144 252-296 (506)
33 PF08914 Myb_DNA-bind_2: Rap1 96.5 0.0046 1E-07 50.0 4.6 50 101-150 2-61 (65)
34 PRK13923 putative spore coat p 96.4 0.0033 7.1E-08 59.6 4.3 53 99-152 3-62 (170)
35 KOG1279 Chromatin remodeling f 96.4 0.0021 4.5E-08 69.8 3.2 47 46-93 250-296 (506)
36 PF08914 Myb_DNA-bind_2: Rap1 95.7 0.0071 1.5E-07 48.9 2.4 50 49-98 2-60 (65)
37 PF13837 Myb_DNA-bind_4: Myb/S 95.5 0.0052 1.1E-07 50.3 1.0 45 50-94 2-63 (90)
38 PLN03142 Probable chromatin-re 95.5 0.079 1.7E-06 62.3 10.6 102 51-152 826-990 (1033)
39 TIGR02894 DNA_bind_RsfA transc 95.3 0.012 2.5E-07 55.5 2.5 48 48-96 3-56 (161)
40 PF13873 Myb_DNA-bind_5: Myb/S 95.1 0.053 1.1E-06 43.8 5.7 48 101-148 2-71 (78)
41 PF13873 Myb_DNA-bind_5: Myb/S 94.8 0.026 5.6E-07 45.6 3.0 47 49-95 2-69 (78)
42 COG5114 Histone acetyltransfer 94.7 0.035 7.6E-07 57.5 4.4 46 101-146 63-109 (432)
43 COG5114 Histone acetyltransfer 94.5 0.016 3.4E-07 59.9 1.3 47 50-96 64-110 (432)
44 PRK13923 putative spore coat p 93.3 0.034 7.5E-07 52.9 1.0 49 47-96 3-57 (170)
45 KOG2656 DNA methyltransferase 92.4 0.13 2.8E-06 54.5 3.9 84 71-154 75-189 (445)
46 PF09111 SLIDE: SLIDE; InterP 91.7 0.34 7.3E-06 43.5 5.2 51 98-148 46-112 (118)
47 COG5118 BDP1 Transcription ini 91.5 0.29 6.2E-06 51.9 5.2 48 102-149 366-413 (507)
48 KOG4282 Transcription factor G 91.5 0.41 8.8E-06 49.1 6.2 51 101-152 54-118 (345)
49 PF12776 Myb_DNA-bind_3: Myb/S 90.9 0.6 1.3E-05 38.6 5.7 50 103-153 1-68 (96)
50 KOG4282 Transcription factor G 89.5 0.89 1.9E-05 46.7 6.7 47 49-95 54-113 (345)
51 KOG1194 Predicted DNA-binding 89.5 1.1 2.3E-05 48.7 7.4 51 100-150 186-236 (534)
52 COG5118 BDP1 Transcription ini 89.0 0.38 8.3E-06 51.0 3.6 65 47-112 363-435 (507)
53 PF08281 Sigma70_r4_2: Sigma-7 85.1 2.5 5.4E-05 31.6 5.3 42 106-148 12-53 (54)
54 PF09111 SLIDE: SLIDE; InterP 84.4 1.1 2.4E-05 40.2 3.6 34 46-79 46-82 (118)
55 PF11626 Rap1_C: TRF2-interact 82.1 1.5 3.3E-05 36.9 3.3 30 45-77 43-80 (87)
56 smart00595 MADF subfamily of S 75.6 3.3 7.1E-05 33.9 3.4 23 123-146 30-52 (89)
57 KOG1194 Predicted DNA-binding 75.1 19 0.00041 39.5 9.6 50 103-152 371-420 (534)
58 KOG4167 Predicted DNA-binding 73.2 5.8 0.00013 45.5 5.5 45 102-146 620-664 (907)
59 KOG4167 Predicted DNA-binding 73.0 2.3 5E-05 48.6 2.3 43 50-93 620-662 (907)
60 PF12776 Myb_DNA-bind_3: Myb/S 72.2 3.4 7.3E-05 34.1 2.7 43 51-93 1-60 (96)
61 PF04545 Sigma70_r4: Sigma-70, 68.7 13 0.00029 27.4 5.0 41 107-148 7-47 (50)
62 KOG4468 Polycomb-group transcr 65.4 11 0.00023 42.6 5.4 46 49-95 88-143 (782)
63 PRK11179 DNA-binding transcrip 64.6 13 0.00029 33.8 5.2 45 106-151 8-53 (153)
64 KOG4468 Polycomb-group transcr 64.4 10 0.00023 42.7 5.1 52 100-151 87-148 (782)
65 PF13404 HTH_AsnC-type: AsnC-t 64.2 18 0.00038 26.7 4.8 38 107-145 3-41 (42)
66 TIGR02985 Sig70_bacteroi1 RNA 59.2 23 0.00049 30.8 5.5 38 110-148 119-156 (161)
67 PRK11169 leucine-responsive tr 59.1 17 0.00036 33.6 4.8 45 106-151 13-58 (164)
68 PF07750 GcrA: GcrA cell cycle 57.2 12 0.00026 35.3 3.6 40 103-143 2-41 (162)
69 PF11035 SnAPC_2_like: Small n 52.1 48 0.001 35.0 7.2 51 101-152 21-75 (344)
70 TIGR02937 sigma70-ECF RNA poly 50.3 36 0.00077 28.6 5.1 36 112-148 118-153 (158)
71 PF13325 MCRS_N: N-terminal re 49.5 31 0.00068 33.9 5.1 46 103-149 1-49 (199)
72 KOG2009 Transcription initiati 48.2 18 0.00038 40.7 3.6 49 101-149 409-457 (584)
73 PF01388 ARID: ARID/BRIGHT DNA 47.8 37 0.0008 28.1 4.7 37 111-147 40-89 (92)
74 PF13404 HTH_AsnC-type: AsnC-t 45.0 14 0.00031 27.2 1.6 38 55-93 3-40 (42)
75 PF10545 MADF_DNA_bdg: Alcohol 43.3 25 0.00054 27.7 2.9 26 122-147 28-54 (85)
76 cd06171 Sigma70_r4 Sigma70, re 43.0 75 0.0016 22.0 5.1 41 104-146 11-51 (55)
77 smart00344 HTH_ASNC helix_turn 41.9 54 0.0012 27.5 4.9 45 107-152 3-48 (108)
78 PRK11179 DNA-binding transcrip 41.6 18 0.00039 33.0 2.1 44 54-98 8-51 (153)
79 cd08319 Death_RAIDD Death doma 41.4 36 0.00079 28.8 3.7 29 109-138 2-30 (83)
80 PF11626 Rap1_C: TRF2-interact 41.3 14 0.00031 31.0 1.2 17 97-113 43-59 (87)
81 PRK09652 RNA polymerase sigma 41.0 59 0.0013 28.9 5.3 32 115-147 139-170 (182)
82 PLN03142 Probable chromatin-re 40.8 27 0.00059 41.8 3.8 32 48-79 925-956 (1033)
83 PF04504 DUF573: Protein of un 40.0 50 0.0011 28.6 4.4 52 101-153 4-68 (98)
84 KOG0384 Chromodomain-helicase 39.5 39 0.00084 41.2 4.7 76 48-129 1132-1208(1373)
85 PF11035 SnAPC_2_like: Small n 39.2 79 0.0017 33.4 6.4 85 50-147 22-127 (344)
86 smart00501 BRIGHT BRIGHT, ARID 38.8 63 0.0014 27.1 4.8 38 110-147 35-85 (93)
87 PF02954 HTH_8: Bacterial regu 38.1 58 0.0013 23.6 3.9 35 107-142 5-39 (42)
88 PRK11924 RNA polymerase sigma 37.9 68 0.0015 28.4 5.1 29 118-147 139-167 (179)
89 KOG2009 Transcription initiati 37.1 18 0.0004 40.6 1.6 49 44-93 404-452 (584)
90 PRK04217 hypothetical protein; 36.2 84 0.0018 28.1 5.3 45 102-148 41-85 (110)
91 PRK09643 RNA polymerase sigma 36.0 93 0.002 28.9 5.9 29 117-146 147-175 (192)
92 cd08803 Death_ank3 Death domai 35.1 58 0.0012 27.6 4.0 30 109-139 4-33 (84)
93 PRK11169 leucine-responsive tr 35.0 20 0.00043 33.1 1.3 45 54-99 13-57 (164)
94 PF15349 DCA16: DDB1- and CUL4 34.8 14 0.0003 35.2 0.2 13 331-343 168-180 (216)
95 PF07638 Sigma70_ECF: ECF sigm 34.3 84 0.0018 29.4 5.3 37 109-146 140-176 (185)
96 KOG4329 DNA-binding protein [G 33.7 69 0.0015 34.5 5.1 46 102-147 278-324 (445)
97 cd08317 Death_ank Death domain 32.4 51 0.0011 27.3 3.2 29 109-138 4-32 (84)
98 COG2197 CitB Response regulato 32.3 70 0.0015 30.8 4.6 44 102-148 147-190 (211)
99 KOG1878 Nuclear receptor coreg 31.7 21 0.00045 44.0 1.0 44 48-92 224-267 (1672)
100 COG2963 Transposase and inacti 31.3 1.3E+02 0.0028 25.8 5.7 46 101-148 5-51 (116)
101 PRK09641 RNA polymerase sigma 30.7 1E+02 0.0022 27.9 5.1 28 119-147 151-178 (187)
102 TIGR02939 RpoE_Sigma70 RNA pol 30.3 84 0.0018 28.5 4.6 29 119-148 153-181 (190)
103 TIGR02954 Sig70_famx3 RNA poly 29.9 1.1E+02 0.0024 27.5 5.2 30 118-148 133-162 (169)
104 KOG4329 DNA-binding protein [G 29.9 38 0.00083 36.4 2.5 41 51-92 279-320 (445)
105 PF13936 HTH_38: Helix-turn-he 29.8 59 0.0013 23.9 2.8 38 102-141 3-40 (44)
106 PRK09047 RNA polymerase factor 29.1 1.3E+02 0.0028 26.5 5.4 30 118-148 120-149 (161)
107 PRK12515 RNA polymerase sigma 28.2 1.3E+02 0.0028 27.6 5.5 30 118-148 145-174 (189)
108 smart00005 DEATH DEATH domain, 28.1 77 0.0017 25.6 3.5 30 108-138 4-34 (88)
109 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 28.0 1.2E+02 0.0027 23.6 4.4 35 107-142 7-41 (50)
110 cd08318 Death_NMPP84 Death dom 27.7 80 0.0017 26.5 3.6 25 113-138 11-35 (86)
111 PRK11923 algU RNA polymerase s 27.6 1.2E+02 0.0026 27.9 5.1 28 119-147 153-180 (193)
112 PF09905 DUF2132: Uncharacteri 27.5 73 0.0016 26.2 3.1 44 57-112 12-62 (64)
113 PF01527 HTH_Tnp_1: Transposas 27.5 1.2E+02 0.0025 23.8 4.4 46 100-147 3-48 (76)
114 PRK09637 RNA polymerase sigma 27.4 1.3E+02 0.0028 27.8 5.3 30 118-148 120-149 (181)
115 PF00196 GerE: Bacterial regul 27.2 78 0.0017 24.0 3.2 43 103-148 3-45 (58)
116 PRK12523 RNA polymerase sigma 27.2 1.4E+02 0.0031 26.9 5.5 38 112-150 127-164 (172)
117 PF09420 Nop16: Ribosome bioge 26.8 1.2E+02 0.0026 28.3 5.0 47 100-146 113-163 (164)
118 PRK05602 RNA polymerase sigma 26.4 1.6E+02 0.0034 27.0 5.6 30 118-148 142-171 (186)
119 cd08804 Death_ank2 Death domai 26.4 85 0.0018 26.4 3.5 31 109-140 4-34 (84)
120 PF00341 PDGF: PDGF/VEGF domai 26.2 18 0.00039 30.1 -0.5 12 332-344 28-39 (82)
121 PRK09648 RNA polymerase sigma 26.2 1.5E+02 0.0032 27.2 5.4 30 118-148 153-182 (189)
122 PF14967 FAM70: FAM70 protein 26.0 3.2E+02 0.0069 28.9 8.1 90 266-368 234-326 (327)
123 PRK12512 RNA polymerase sigma 26.0 1.5E+02 0.0032 27.0 5.4 30 118-148 145-174 (184)
124 TIGR02948 SigW_bacill RNA poly 25.9 1.3E+02 0.0028 27.2 4.9 28 120-148 152-179 (187)
125 PRK09645 RNA polymerase sigma 25.1 1.6E+02 0.0035 26.4 5.4 30 118-148 132-161 (173)
126 TIGR02943 Sig70_famx1 RNA poly 25.0 1.6E+02 0.0034 27.3 5.5 31 117-148 144-174 (188)
127 PRK12529 RNA polymerase sigma 24.9 1.8E+02 0.0039 26.6 5.8 34 116-150 139-172 (178)
128 KOG2923 Uncharacterized conser 24.8 33 0.00072 28.3 0.8 15 219-233 16-30 (67)
129 PRK09642 RNA polymerase sigma 24.7 1.7E+02 0.0036 25.9 5.4 30 118-148 120-149 (160)
130 PRK12524 RNA polymerase sigma 24.6 1.6E+02 0.0034 27.4 5.4 30 118-148 150-179 (196)
131 PRK12531 RNA polymerase sigma 24.4 1.7E+02 0.0036 27.2 5.5 30 118-148 155-184 (194)
132 smart00141 PDGF Platelet-deriv 24.3 36 0.00078 28.9 0.9 11 333-344 31-41 (83)
133 COG1522 Lrp Transcriptional re 24.2 1.6E+02 0.0035 26.0 5.2 44 106-150 7-51 (154)
134 PF09197 Rap1-DNA-bind: Rap1, 23.9 61 0.0013 28.9 2.3 17 51-67 1-17 (105)
135 PF04504 DUF573: Protein of un 23.6 1.2E+02 0.0027 26.2 4.1 69 49-118 4-94 (98)
136 PRK12530 RNA polymerase sigma 23.4 1.7E+02 0.0037 27.1 5.4 28 119-147 149-176 (189)
137 cd08779 Death_PIDD Death Domai 22.8 88 0.0019 26.3 3.0 32 110-142 3-37 (86)
138 KOG2656 DNA methyltransferase 22.6 24 0.00052 38.1 -0.5 45 49-94 130-180 (445)
139 PRK01905 DNA-binding protein F 22.6 2E+02 0.0043 23.6 5.0 36 106-142 36-71 (77)
140 PHA02661 vascular endothelial 22.4 41 0.00089 31.6 1.0 11 333-344 76-86 (146)
141 PRK06759 RNA polymerase factor 22.3 2.1E+02 0.0045 25.0 5.4 28 119-147 121-148 (154)
142 cd08311 Death_p75NR Death doma 22.3 96 0.0021 25.9 3.1 33 106-140 2-34 (77)
143 cd08777 Death_RIP1 Death Domai 21.9 1E+02 0.0023 26.0 3.3 29 111-140 4-32 (86)
144 TIGR02950 SigM_subfam RNA poly 21.4 76 0.0016 27.7 2.4 28 120-148 121-148 (154)
145 TIGR02952 Sig70_famx2 RNA poly 21.1 2.2E+02 0.0047 25.2 5.3 28 119-147 137-164 (170)
146 PRK09651 RNA polymerase sigma 20.8 1.8E+02 0.0038 26.5 4.8 29 119-148 134-162 (172)
147 PRK09649 RNA polymerase sigma 20.4 2E+02 0.0044 26.5 5.2 29 119-148 145-173 (185)
148 cd08805 Death_ank1 Death domai 20.4 1.2E+02 0.0027 25.7 3.4 26 109-135 4-29 (84)
149 PRK12536 RNA polymerase sigma 20.2 2.3E+02 0.0049 25.9 5.4 30 118-148 143-172 (181)
150 PRK12547 RNA polymerase sigma 20.1 2.4E+02 0.0052 25.3 5.5 30 118-148 126-155 (164)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.98 E-value=1e-32 Score=266.80 Aligned_cols=108 Identities=50% Similarity=0.919 Sum_probs=105.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCC-CCCccccccccccccCCCCCCCCCChHHHHHHHHHHHHcCCchHH
Q 012494 47 RVKGPWSPEEDAVLSRLVSQFGARNWGMIARGIP-GRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAVHGNKWAV 125 (462)
Q Consensus 47 ~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~Lp-gRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk~GnkWsk 125 (462)
..||+||+|||++|+++|.+||.++|..|++.++ +|++|+||+||.|||+|.++++.||+|||++|++||..+||+|+.
T Consensus 7 ~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrWs~ 86 (238)
T KOG0048|consen 7 LVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRWSL 86 (238)
T ss_pred ccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHHHH
Confidence 4579999999999999999999999999999998 999999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHHHHhhhhhcC
Q 012494 126 IARLLPGRTDNAIKNHWNSTLRRRYTDLG 154 (462)
Q Consensus 126 IAk~LPGRT~~QcKnRWnslLkkkl~~~~ 154 (462)
||++|||||++.|||+|++.||+|+...+
T Consensus 87 IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 87 IAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred HHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999998877
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.97 E-value=3.9e-31 Score=256.94 Aligned_cols=113 Identities=41% Similarity=0.795 Sum_probs=107.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhC-CCCCccccccccccccCCCCCCCCCChHHHHHHHHHHHHcCCc
Q 012494 44 SSSRVKGPWSPEEDAVLSRLVSQFGARNWGMIARGI-PGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAVHGNK 122 (462)
Q Consensus 44 ~~~~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~L-pgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk~Gnk 122 (462)
....+|++||+|||++|+++|++||..+|..||+.+ ++|+++|||+||.++|+|.+++++||+|||++|++++..||++
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnK 99 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNR 99 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhcccc
Confidence 677999999999999999999999998999999988 6999999999999999999999999999999999999999999
Q ss_pred hHHHhhhCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q 012494 123 WAVIARLLPGRTDNAIKNHWNSTLRRRYTDLGRF 156 (462)
Q Consensus 123 WskIAk~LPGRT~~QcKnRWnslLkkkl~~~~~~ 156 (462)
|+.||+.|||||+++|||||+.++++++...+..
T Consensus 100 Ws~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~ 133 (249)
T PLN03212 100 WSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGID 133 (249)
T ss_pred HHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCC
Confidence 9999999999999999999999999998876543
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.96 E-value=2.1e-29 Score=260.26 Aligned_cols=113 Identities=48% Similarity=0.852 Sum_probs=107.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhC-CCCCccccccccccccCCCCCCCCCChHHHHHHHHHHHHcCCc
Q 012494 44 SSSRVKGPWSPEEDAVLSRLVSQFGARNWGMIARGI-PGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAVHGNK 122 (462)
Q Consensus 44 ~~~~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~L-pgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk~Gnk 122 (462)
..+.+||+||+|||++|+++|.+||.++|..||+.+ ++|+++|||+||.++|+|.+++++||+|||++|++++++||++
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnK 88 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNR 88 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcc
Confidence 467899999999999999999999999999999988 5999999999999999999999999999999999999999999
Q ss_pred hHHHhhhCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q 012494 123 WAVIARLLPGRTDNAIKNHWNSTLRRRYTDLGRF 156 (462)
Q Consensus 123 WskIAk~LPGRT~~QcKnRWnslLkkkl~~~~~~ 156 (462)
|++||++|+|||+++|||||+.+|++++...+..
T Consensus 89 WskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~ 122 (459)
T PLN03091 89 WSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGID 122 (459)
T ss_pred hHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence 9999999999999999999999999998876543
No 4
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.75 E-value=6e-19 Score=184.96 Aligned_cols=155 Identities=24% Similarity=0.473 Sum_probs=132.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCCCCCCCCCChHHHHHHHHHHHHcCCchHHH
Q 012494 47 RVKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAVHGNKWAVI 126 (462)
Q Consensus 47 ~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk~GnkWskI 126 (462)
++.|.|+.-||++|..+|.+||.+.|++|++.++.++.+||+.||..+|||.+++..|+.|||.+||.+++.+..+|..|
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrtI 84 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRTI 84 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccchH
Confidence 45688999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhCCCCCHHHHHHHHHHHHHhhhhhcCCCCCCCCCCccCCCCCCCCCCCCccccCCCCCC---CCCCCCCCCCCCCCcc
Q 012494 127 ARLLPGRTDNAIKNHWNSTLRRRYTDLGRFKPALGDMTEDGSLDRTKGSSEETLSVGDVNP---LKPLEGRDVTMDDRPN 203 (462)
Q Consensus 127 Ak~LPGRT~~QcKnRWnslLkkkl~~~~~~k~~~~~~~ed~sldktk~SSee~ls~gdl~p---~~p~~~~ei~mDd~~~ 203 (462)
|..| |||.+||..||+.+|-......... ++..+ ..|..|+++| .++.+++.++||++++
T Consensus 85 a~i~-gr~~~qc~eRy~~ll~~~~s~~~~~---------~~~~D-------~rLk~gE~ePn~e~~~aRpd~~dmdEde~ 147 (617)
T KOG0050|consen 85 ADIM-GRTSQQCLERYNNLLDVYVSYHYHS---------EPYID-------AKLKEGEIEPNQETNPARPDGFDMDEDEG 147 (617)
T ss_pred HHHh-hhhHHHHHHHHHHHHHHHHhhhccc---------ccccc-------cccCCCcCCCccccccccCCcccchHHHH
Confidence 9999 9999999999999996654432211 11111 1267777775 5889999999999999
Q ss_pred hhhhhhhccCCcccc
Q 012494 204 RLEDMAQTNGGEFTA 218 (462)
Q Consensus 204 sm~~~~~~~~~~~~~ 218 (462)
+|..++-.+-.+++.
T Consensus 148 eMl~eaRarlaNt~g 162 (617)
T KOG0050|consen 148 EMLSEARARLANTQG 162 (617)
T ss_pred HHHHHHHHHHhcccc
Confidence 999888766555443
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.68 E-value=4.1e-17 Score=174.62 Aligned_cols=98 Identities=34% Similarity=0.634 Sum_probs=92.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCCCCCCCCCChHHHHHHHHHHHHcC-Cc
Q 012494 44 SSSRVKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAVHG-NK 122 (462)
Q Consensus 44 ~~~~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk~G-nk 122 (462)
.|++++|+||.+||.+|+.+|.+||.++|.+|-..+|||+..|||+||.|.|+...+.+.||-.||+.|+.++++|| ++
T Consensus 355 dPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g~ 434 (939)
T KOG0049|consen 355 DPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVYGKGN 434 (939)
T ss_pred CccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHHccch
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999 79
Q ss_pred hHHHhhhCCCCCHHHHHHH
Q 012494 123 WAVIARLLPGRTDNAIKNH 141 (462)
Q Consensus 123 WskIAk~LPGRT~~QcKnR 141 (462)
|.+||.+||+||..|...|
T Consensus 435 WakcA~~Lp~~t~~q~~rr 453 (939)
T KOG0049|consen 435 WAKCAMLLPKKTSRQLRRR 453 (939)
T ss_pred HHHHHHHccccchhHHHHH
Confidence 9999999999999665433
No 6
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.61 E-value=1e-15 Score=164.13 Aligned_cols=105 Identities=30% Similarity=0.562 Sum_probs=97.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC---CCHHHHhhhCCCCCccccccccccccCCCCCCCCCChHHHHHHHHHHHHcCCc-
Q 012494 47 RVKGPWSPEEDAVLSRLVSQFGA---RNWGMIARGIPGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAVHGNK- 122 (462)
Q Consensus 47 ~kKG~WT~EEDelLl~lV~kyG~---~nWskIAk~LpgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk~Gnk- 122 (462)
.....||+|||.+|+.+|..... .+|.+|-.+|+||+..|..-||...|+|.+++++||.+||.+|+.+|.+||.+
T Consensus 303 L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kd 382 (939)
T KOG0049|consen 303 LSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKD 382 (939)
T ss_pred HHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccc
Confidence 44578999999999999998853 37999999999999999999999999999999999999999999999999965
Q ss_pred hHHHhhhCCCCCHHHHHHHHHHHHHhhhh
Q 012494 123 WAVIARLLPGRTDNAIKNHWNSTLRRRYT 151 (462)
Q Consensus 123 WskIAk~LPGRT~~QcKnRWnslLkkkl~ 151 (462)
|.+|-..+|||++.||+.||.+.|.++.+
T Consensus 383 w~k~R~~vPnRSdsQcR~RY~nvL~~s~K 411 (939)
T KOG0049|consen 383 WAKVRQAVPNRSDSQCRERYTNVLNRSAK 411 (939)
T ss_pred hhhHHHhcCCccHHHHHHHHHHHHHHhhc
Confidence 99999999999999999999999977653
No 7
>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=99.60 E-value=9.4e-16 Score=118.30 Aligned_cols=60 Identities=45% Similarity=0.889 Sum_probs=54.9
Q ss_pred CCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCCCCCCCCCChHHHHHH
Q 012494 52 WSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQII 112 (462)
Q Consensus 52 WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelL 112 (462)
||+|||++|+.+|.+|| .+|..||+.|+.|+..||+.||.+.|++.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 5899999999779999999999999999999999999999987
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=99.57 E-value=3.1e-15 Score=159.14 Aligned_cols=107 Identities=32% Similarity=0.574 Sum_probs=101.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCCCCCCCCCChHHHHHHHHHHHHcCCchH
Q 012494 45 SSRVKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAVHGNKWA 124 (462)
Q Consensus 45 ~~~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk~GnkWs 124 (462)
-.++.|.|+..||+.|..+|++||+++|..||..|..|+++||+.||.++++|.+++..|+.+||..|+.+..++|.+|+
T Consensus 16 ~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ws 95 (512)
T COG5147 16 TKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWS 95 (512)
T ss_pred ceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchhh
Confidence 35678899999999999999999999999999999889999999999999999999999999999999999999999999
Q ss_pred HHhhhCCCCCHHHHHHHHHHHHHhhhh
Q 012494 125 VIARLLPGRTDNAIKNHWNSTLRRRYT 151 (462)
Q Consensus 125 kIAk~LPGRT~~QcKnRWnslLkkkl~ 151 (462)
.||..+++||..+|.+||..++..-..
T Consensus 96 tia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 96 TIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhccccCccchHHHHHHHHHHhhhhhc
Confidence 999999999999999999998866544
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.35 E-value=1.2e-12 Score=141.14 Aligned_cols=107 Identities=22% Similarity=0.499 Sum_probs=95.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCCCC--CCCCCChHHHHHHHHHHH-------H
Q 012494 48 VKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDPCL--KRKPFTDEEDQIIISAHA-------V 118 (462)
Q Consensus 48 kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P~l--krgpWTeEEDelLLeLvk-------k 118 (462)
.+|.||+||++.|..+|.++| +.|..|++.| +|.+..|++||+++...+- +++.||.||+++|+++|. +
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q 460 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQ 460 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhc
Confidence 899999999999999999999 5899999988 8999999999999999874 899999999999999995 3
Q ss_pred c-------------------CCchHHHhhhCCCCCHHHHHHHHHHHHHhhhhhcCCC
Q 012494 119 H-------------------GNKWAVIARLLPGRTDNAIKNHWNSTLRRRYTDLGRF 156 (462)
Q Consensus 119 ~-------------------GnkWskIAk~LPGRT~~QcKnRWnslLkkkl~~~~~~ 156 (462)
+ +-+|..|+..+..|+..||+.+|+.++.+........
T Consensus 461 ~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~~~ 517 (607)
T KOG0051|consen 461 PQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKRQE 517 (607)
T ss_pred ccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhcccc
Confidence 3 1159999999999999999999999998876655544
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=99.35 E-value=2.8e-13 Score=101.01 Aligned_cols=47 Identities=47% Similarity=0.967 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCC-CCCcccccccccccc
Q 012494 49 KGPWSPEEDAVLSRLVSQFGARNWGMIARGIP-GRSGKSCRLRWCNQL 95 (462)
Q Consensus 49 KG~WT~EEDelLl~lV~kyG~~nWskIAk~Lp-gRS~kQCR~RW~n~L 95 (462)
|++||+|||++|+++|.+||.++|..||..|+ +||..||+.||.++|
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 68999999999999999999877999999999 999999999999875
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=99.28 E-value=4.9e-12 Score=94.35 Aligned_cols=46 Identities=35% Similarity=0.698 Sum_probs=41.9
Q ss_pred CCCCChHHHHHHHHHHHHcCCc-hHHHhhhCC-CCCHHHHHHHHHHHH
Q 012494 101 RKPFTDEEDQIIISAHAVHGNK-WAVIARLLP-GRTDNAIKNHWNSTL 146 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~Gnk-WskIAk~LP-GRT~~QcKnRWnslL 146 (462)
+++||.|||++|++++.+||.+ |..||..|+ +||..||++||+.++
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 5799999999999999999988 999999999 999999999999875
No 12
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.13 E-value=5.4e-11 Score=91.76 Aligned_cols=45 Identities=36% Similarity=0.652 Sum_probs=39.1
Q ss_pred CChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 104 FTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 104 WTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
||+|||++|++++..||++|..||+.|+.||+.+|++||+..|+.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~ 45 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRP 45 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTST
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcc
Confidence 999999999999999999999999999669999999999996643
No 13
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.11 E-value=1.3e-10 Score=83.23 Aligned_cols=47 Identities=38% Similarity=0.773 Sum_probs=44.2
Q ss_pred CCCCChHHHHHHHHHHHHcC-CchHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 101 RKPFTDEEDQIIISAHAVHG-NKWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~G-nkWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
+++||++||.+|+.++..|| .+|..||..|++||+.+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999998764
No 14
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.05 E-value=1.5e-10 Score=82.90 Aligned_cols=48 Identities=48% Similarity=1.026 Sum_probs=44.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccC
Q 012494 49 KGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLD 96 (462)
Q Consensus 49 KG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~ 96 (462)
++.||++||++|+.++.+||..+|..||..|++|+..+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 468999999999999999996789999999999999999999988764
No 15
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.04 E-value=6.7e-11 Score=116.19 Aligned_cols=93 Identities=23% Similarity=0.340 Sum_probs=69.9
Q ss_pred CCCCCccccccccccccCCCCCCCCCChHHHHHHHHHHHHcC-CchHHHhhhC-CCCCHHHHHHHHHHHHHhhhhhcCCC
Q 012494 79 IPGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAVHG-NKWAVIARLL-PGRTDNAIKNHWNSTLRRRYTDLGRF 156 (462)
Q Consensus 79 LpgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk~G-nkWskIAk~L-PGRT~~QcKnRWnslLkkkl~~~~~~ 156 (462)
++.|+..-|. ++.+++++||+|||++|++++++|| ++|..||+.+ ++||..||+.||.++|+.
T Consensus 10 ~~~~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P-------- 74 (249)
T PLN03212 10 VSKKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRP-------- 74 (249)
T ss_pred CCCCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhch--------
Confidence 5666666553 3568899999999999999999999 5799999988 699999999999999954
Q ss_pred CCCCCCCccCCCCCCCCCCCCccccCCCCCCCCCCCCCCCC
Q 012494 157 KPALGDMTEDGSLDRTKGSSEETLSVGDVNPLKPLEGRDVT 197 (462)
Q Consensus 157 k~~~~~~~ed~sldktk~SSee~ls~gdl~p~~p~~~~ei~ 197 (462)
.+.+..|+.+|...+..+.......|..|.
T Consensus 75 -----------~I~kgpWT~EED~lLlel~~~~GnKWs~IA 104 (249)
T PLN03212 75 -----------SVKRGGITSDEEDLILRLHRLLGNRWSLIA 104 (249)
T ss_pred -----------hcccCCCChHHHHHHHHHHHhccccHHHHH
Confidence 344556666665544444444445565553
No 16
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.00 E-value=8.2e-10 Score=78.16 Aligned_cols=44 Identities=41% Similarity=0.842 Sum_probs=41.8
Q ss_pred CCChHHHHHHHHHHHHcC-CchHHHhhhCCCCCHHHHHHHHHHHH
Q 012494 103 PFTDEEDQIIISAHAVHG-NKWAVIARLLPGRTDNAIKNHWNSTL 146 (462)
Q Consensus 103 pWTeEEDelLLeLvkk~G-nkWskIAk~LPGRT~~QcKnRWnslL 146 (462)
+||.+|+.+|+.++..|| .+|..||+.|++||..+|++||+.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999998763
No 17
>PLN03091 hypothetical protein; Provisional
Probab=98.91 E-value=4.1e-10 Score=118.01 Aligned_cols=55 Identities=18% Similarity=0.369 Sum_probs=49.5
Q ss_pred CCCCCCCCChHHHHHHHHHHHHcC-CchHHHhhhCC-CCCHHHHHHHHHHHHHhhhh
Q 012494 97 PCLKRKPFTDEEDQIIISAHAVHG-NKWAVIARLLP-GRTDNAIKNHWNSTLRRRYT 151 (462)
Q Consensus 97 P~lkrgpWTeEEDelLLeLvkk~G-nkWskIAk~LP-GRT~~QcKnRWnslLkkkl~ 151 (462)
..+++++||+|||++|+++|.+|| ++|..||+.++ +|+.+|||.||+++|+..+.
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~Ik 66 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLK 66 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCccc
Confidence 568899999999999999999999 57999999884 89999999999999966553
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=98.89 E-value=1.2e-09 Score=77.22 Aligned_cols=45 Identities=49% Similarity=1.033 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCcccccccccccc
Q 012494 51 PWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQL 95 (462)
Q Consensus 51 ~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L 95 (462)
+||++||++|+.++.+||..+|..||+.|++|+..+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999778999999999999999999997653
No 19
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.86 E-value=3.7e-09 Score=114.54 Aligned_cols=103 Identities=26% Similarity=0.405 Sum_probs=87.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCC---------------C--------HHHHhhhCCCCCccccccccccccCCCC-CC
Q 012494 46 SRVKGPWSPEEDAVLSRLVSQFGAR---------------N--------WGMIARGIPGRSGKSCRLRWCNQLDPCL-KR 101 (462)
Q Consensus 46 ~~kKG~WT~EEDelLl~lV~kyG~~---------------n--------WskIAk~LpgRS~kQCR~RW~n~L~P~l-kr 101 (462)
..+-+.|+.+||+.|.+.|..|-.. . |+.|...||.|+.+.++.+-++..+|-- ++
T Consensus 305 e~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 305 EINLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPYRDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCcccchhHHHHHHhcCCcccccc
Confidence 4566889999999999999988210 1 7889999999999999884434444433 99
Q ss_pred CCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHhh
Q 012494 102 KPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRRR 149 (462)
Q Consensus 102 gpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkkk 149 (462)
|.||+||++.|..+|.++|+.|..|++.| ||.+.+|+.||+.+.+..
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 99999999999999999999999999999 999999999999988654
No 20
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.83 E-value=4.1e-10 Score=109.64 Aligned_cols=89 Identities=18% Similarity=0.156 Sum_probs=67.0
Q ss_pred CCCCCCCChHHHHHHHHHHHHcC-CchHHHhhhCC-CCCHHHHHHHHHHHHHhhhhhcCCCCCCCCCCccCCCCCCCCCC
Q 012494 98 CLKRKPFTDEEDQIIISAHAVHG-NKWAVIARLLP-GRTDNAIKNHWNSTLRRRYTDLGRFKPALGDMTEDGSLDRTKGS 175 (462)
Q Consensus 98 ~lkrgpWTeEEDelLLeLvkk~G-nkWskIAk~LP-GRT~~QcKnRWnslLkkkl~~~~~~k~~~~~~~ed~sldktk~S 175 (462)
.+.+|+||.|||++|+++|++|| ++|..|++.++ +|+.++||-||.++|+..++...-...+...+.+...+-..+|+
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 34579999999999999999999 56999999999 99999999999999988776433322233333344444455677
Q ss_pred CCccccCCCCC
Q 012494 176 SEETLSVGDVN 186 (462)
Q Consensus 176 See~ls~gdl~ 186 (462)
......+|.++
T Consensus 86 ~IA~~LPGRTD 96 (238)
T KOG0048|consen 86 LIAGRLPGRTD 96 (238)
T ss_pred HHHhhCCCcCH
Confidence 66666666655
No 21
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.22 E-value=2.1e-07 Score=99.26 Aligned_cols=95 Identities=25% Similarity=0.405 Sum_probs=85.5
Q ss_pred CCCCCCChHHHHHHHHHHHHcC-CchHHHhhhCCCCCHHHHHHHHHHHHHhhhhhcCCCCCCCCCCccCCCCCCCCCCCC
Q 012494 99 LKRKPFTDEEDQIIISAHAVHG-NKWAVIARLLPGRTDNAIKNHWNSTLRRRYTDLGRFKPALGDMTEDGSLDRTKGSSE 177 (462)
Q Consensus 99 lkrgpWTeEEDelLLeLvkk~G-nkWskIAk~LPGRT~~QcKnRWnslLkkkl~~~~~~k~~~~~~~ed~sldktk~SSe 177 (462)
++.+.|+.-||+.|..++.+|| ++|+.|++.|+-+|+.||++||+.++ ++.+.++.|+.+
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~l-------------------dp~i~~tews~e 65 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWL-------------------DPAIKKTEWSRE 65 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHh-------------------CHHHhhhhhhhh
Confidence 5678999999999999999999 67999999999999999999999887 566778899999
Q ss_pred ccccCCCCCCCCCCCCCCCCCCCCcchhhhhhhccCCccc
Q 012494 178 ETLSVGDVNPLKPLEGRDVTMDDRPNRLEDMAQTNGGEFT 217 (462)
Q Consensus 178 e~ls~gdl~p~~p~~~~ei~mDd~~~sm~~~~~~~~~~~~ 217 (462)
+...+.++.-+.|.+|++|- ..|..++.||.++|.
T Consensus 66 ederlLhlakl~p~qwrtIa-----~i~gr~~~qc~eRy~ 100 (617)
T KOG0050|consen 66 EDERLLHLAKLEPTQWRTIA-----DIMGRTSQQCLERYN 100 (617)
T ss_pred HHHHHHHHHHhcCCccchHH-----HHhhhhHHHHHHHHH
Confidence 99999999999999999985 378889999988854
No 22
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.11 E-value=3.6e-07 Score=98.24 Aligned_cols=99 Identities=25% Similarity=0.530 Sum_probs=86.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCC--CCCCCCCChHHHHHHHHHHHHcC---
Q 012494 46 SRVKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDP--CLKRKPFTDEEDQIIISAHAVHG--- 120 (462)
Q Consensus 46 ~~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P--~lkrgpWTeEEDelLLeLvkk~G--- 120 (462)
-..+|.||++|+..|...+..+|. .|+.|.+.+ +|-...||+||+++... .+++++|+.||+.+|...+...-
T Consensus 288 f~~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~~-~rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~ 365 (512)
T COG5147 288 FEQRGKWTKEEEQELAKLVVEHGG-SWTEIGKLL-GRMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEA 365 (512)
T ss_pred HhhhccCccccccccccccccccc-hhhHhhhhh-ccCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHH
Confidence 346789999999999999999994 799999977 89999999999999998 67888999999999998887332
Q ss_pred -----CchHHHhhhCCCCCHHHHHHHHHHHH
Q 012494 121 -----NKWAVIARLLPGRTDNAIKNHWNSTL 146 (462)
Q Consensus 121 -----nkWskIAk~LPGRT~~QcKnRWnslL 146 (462)
-.|..|+..+++|...+|+.++..+.
T Consensus 366 ~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 366 QQSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred hhhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 25999999999999999988876654
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.52 E-value=5.6e-05 Score=79.75 Aligned_cols=53 Identities=21% Similarity=0.470 Sum_probs=47.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccC
Q 012494 44 SSSRVKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLD 96 (462)
Q Consensus 44 ~~~~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~ 96 (462)
+-.+-..-||.+|+-+|+++++.||.+||..||.+|..|+..+|+++|.+++.
T Consensus 67 s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 67 SFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 33456677999999999999999999999999999999999999999998654
No 24
>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=97.43 E-value=0.00012 Score=57.55 Aligned_cols=48 Identities=10% Similarity=0.194 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCH---HHHhhhCC-CC-Ccccccccccccc
Q 012494 48 VKGPWSPEEDAVLSRLVSQFGARNW---GMIARGIP-GR-SGKSCRLRWCNQL 95 (462)
Q Consensus 48 kKG~WT~EEDelLl~lV~kyG~~nW---skIAk~Lp-gR-S~kQCR~RW~n~L 95 (462)
.+-.||+||..+++++|..+|.++| +.|++.|. .| |..||+.++..|.
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 4567999999999999999998899 99999873 45 9999999887664
No 25
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.42 E-value=0.00037 Score=54.89 Aligned_cols=47 Identities=19% Similarity=0.322 Sum_probs=41.3
Q ss_pred CCCCCChHHHHHHHHHHHHcCC-ch---HHHhhhCC-CC-CHHHHHHHHHHHH
Q 012494 100 KRKPFTDEEDQIIISAHAVHGN-KW---AVIARLLP-GR-TDNAIKNHWNSTL 146 (462)
Q Consensus 100 krgpWTeEEDelLLeLvkk~Gn-kW---skIAk~LP-GR-T~~QcKnRWnslL 146 (462)
.+-.||+||..++++++..+|. +| ..|+..|. .| |..||+.|++.+.
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 3568999999999999999996 99 99999884 35 9999999998765
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.39 E-value=0.00028 Score=74.63 Aligned_cols=48 Identities=21% Similarity=0.437 Sum_probs=44.3
Q ss_pred CCCCCCChHHHHHHHHHHHHcC-CchHHHhhhCCCCCHHHHHHHHHHHH
Q 012494 99 LKRKPFTDEEDQIIISAHAVHG-NKWAVIARLLPGRTDNAIKNHWNSTL 146 (462)
Q Consensus 99 lkrgpWTeEEDelLLeLvkk~G-nkWskIAk~LPGRT~~QcKnRWnslL 146 (462)
+-...||.+|+.+||+++..|| ++|..||.++..||..+|+.+|.+++
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 3456899999999999999999 99999999998899999999998876
No 27
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.28 E-value=0.00031 Score=65.83 Aligned_cols=53 Identities=26% Similarity=0.497 Sum_probs=46.8
Q ss_pred CCCCCChHHHHHHHHHHHHcC---C----chHHHhhhCCCCCHHHHHHHHHHHHHhhhhhc
Q 012494 100 KRKPFTDEEDQIIISAHAVHG---N----KWAVIARLLPGRTDNAIKNHWNSTLRRRYTDL 153 (462)
Q Consensus 100 krgpWTeEEDelLLeLvkk~G---n----kWskIAk~LPGRT~~QcKnRWnslLkkkl~~~ 153 (462)
+...||.|||.+|.+.|..|- + -+..+++.| +||+..|.-|||+++|++|...
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 467899999999999998873 2 289999999 9999999999999999998763
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.28 E-value=0.0011 Score=64.26 Aligned_cols=100 Identities=22% Similarity=0.452 Sum_probs=74.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHhhhCC---CCCcccccccccccc-CCCC--------------------CCCCCCh
Q 012494 51 PWSPEEDAVLSRLVSQFGARNWGMIARGIP---GRSGKSCRLRWCNQL-DPCL--------------------KRKPFTD 106 (462)
Q Consensus 51 ~WT~EEDelLl~lV~kyG~~nWskIAk~Lp---gRS~kQCR~RW~n~L-~P~l--------------------krgpWTe 106 (462)
+|++++|-+|+.+|..-. +-..|+..+. .-|...+..||+..| +|.+ .+-+||.
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 699999999999999766 6788887652 455667788998755 2222 3568999
Q ss_pred HHHHHHHHHHHHcCC---chHHHhh-----hCCCCCHHHHHHHHHHHHHhhhhh
Q 012494 107 EEDQIIISAHAVHGN---KWAVIAR-----LLPGRTDNAIKNHWNSTLRRRYTD 152 (462)
Q Consensus 107 EEDelLLeLvkk~Gn---kWskIAk-----~LPGRT~~QcKnRWnslLkkkl~~ 152 (462)
+|+++|......... .|.+|-. +-++||+.++.++|..+.+..+..
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL~ 132 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLLP 132 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchhh
Confidence 999999997765543 4776644 346899999999999766555543
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.94 E-value=0.00085 Score=54.93 Aligned_cols=52 Identities=29% Similarity=0.606 Sum_probs=36.0
Q ss_pred CCCCChHHHHHHHHHHHH------cC--C------chHHHhhhC----CCCCHHHHHHHHHHHHHhhhhhc
Q 012494 101 RKPFTDEEDQIIISAHAV------HG--N------KWAVIARLL----PGRTDNAIKNHWNSTLRRRYTDL 153 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk------~G--n------kWskIAk~L----PGRT~~QcKnRWnslLkkkl~~~ 153 (462)
+..||.+|...||+++.. ++ + -|..||..| ..||+.||++||+++ ++++...
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L-~~~Yk~~ 70 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL-KKKYKKI 70 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH-HHHHHCS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH-HHHHHHH
Confidence 357999999999999877 21 1 399999987 369999999999884 5556544
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.63 E-value=0.0019 Score=69.04 Aligned_cols=44 Identities=18% Similarity=0.370 Sum_probs=41.5
Q ss_pred CCCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHH
Q 012494 101 RKPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNS 144 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWns 144 (462)
..+||.+|..+|++.+..||..|.+||+++..||..||--||-+
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHc
Confidence 35899999999999999999999999999999999999999955
No 31
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.56 E-value=0.0014 Score=70.07 Aligned_cols=45 Identities=22% Similarity=0.525 Sum_probs=42.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCcccccccccc
Q 012494 48 VKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCN 93 (462)
Q Consensus 48 kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n 93 (462)
....||.+|..+|++.|+.|| .+|.+||+++.+|+..||..||.+
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCCCCHHHHHHHHHc
Confidence 566899999999999999999 489999999999999999999976
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.50 E-value=0.0032 Score=68.35 Aligned_cols=45 Identities=16% Similarity=0.357 Sum_probs=42.0
Q ss_pred CCCCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHH
Q 012494 100 KRKPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNS 144 (462)
Q Consensus 100 krgpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWns 144 (462)
-+..||++|..+|++++..||.+|.+||.++.+||..||--||..
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~ 296 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLR 296 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHh
Confidence 457899999999999999999999999999999999999999844
No 33
>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=96.45 E-value=0.0046 Score=50.00 Aligned_cols=50 Identities=28% Similarity=0.487 Sum_probs=32.8
Q ss_pred CCCCChHHHHHHHHHHHHcC--------Cc-hHHHhhhCC-CCCHHHHHHHHHHHHHhhh
Q 012494 101 RKPFTDEEDQIIISAHAVHG--------NK-WAVIARLLP-GRTDNAIKNHWNSTLRRRY 150 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~G--------nk-WskIAk~LP-GRT~~QcKnRWnslLkkkl 150 (462)
+.+||.+||++|++.++.+. |+ |.+++..-+ .+|..+.|+||...|+.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 46899999999999997542 22 999999877 8999999999988886654
No 34
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.44 E-value=0.0033 Score=59.63 Aligned_cols=53 Identities=25% Similarity=0.465 Sum_probs=45.5
Q ss_pred CCCCCCChHHHHHHHHHHHHcCCc-------hHHHhhhCCCCCHHHHHHHHHHHHHhhhhh
Q 012494 99 LKRKPFTDEEDQIIISAHAVHGNK-------WAVIARLLPGRTDNAIKNHWNSTLRRRYTD 152 (462)
Q Consensus 99 lkrgpWTeEEDelLLeLvkk~Gnk-------WskIAk~LPGRT~~QcKnRWnslLkkkl~~ 152 (462)
.+...||.|+|.+|.+.+..|+.. ...++..| +||..+|..|||.+++++|..
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 356789999999998888887632 77788899 999999999999999988865
No 35
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.43 E-value=0.0021 Score=69.78 Aligned_cols=47 Identities=19% Similarity=0.563 Sum_probs=42.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCcccccccccc
Q 012494 46 SRVKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCN 93 (462)
Q Consensus 46 ~~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n 93 (462)
.-.++.||.+|..+|+++|+.|| .+|.+||.++.+||..||..++.+
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~ks~eqCI~kFL~ 296 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGTKSQEQCILKFLR 296 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCCCCHHHHHHHHHh
Confidence 34567799999999999999999 489999999999999999999865
No 36
>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=95.70 E-value=0.0071 Score=48.91 Aligned_cols=50 Identities=26% Similarity=0.417 Sum_probs=33.1
Q ss_pred CCCCCHHHHHHHHHHHHHhC------CCC--HHHHhhhCC-CCCccccccccccccCCC
Q 012494 49 KGPWSPEEDAVLSRLVSQFG------ARN--WGMIARGIP-GRSGKSCRLRWCNQLDPC 98 (462)
Q Consensus 49 KG~WT~EEDelLl~lV~kyG------~~n--WskIAk~Lp-gRS~kQCR~RW~n~L~P~ 98 (462)
+-+||.+||++|++.|..+. .+| |..+++.-+ .+|-.+-|+||...|.+.
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 45799999999999997663 123 999998876 899999999999988764
No 37
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.54 E-value=0.0052 Score=50.29 Aligned_cols=45 Identities=29% Similarity=0.615 Sum_probs=32.2
Q ss_pred CCCCHHHHHHHHHHHHH--h----C--CC-----CHHHHhhhC----CCCCccccccccccc
Q 012494 50 GPWSPEEDAVLSRLVSQ--F----G--AR-----NWGMIARGI----PGRSGKSCRLRWCNQ 94 (462)
Q Consensus 50 G~WT~EEDelLl~lV~k--y----G--~~-----nWskIAk~L----pgRS~kQCR~RW~n~ 94 (462)
-.||.+|...|++++.. + + .. -|..||..| -.||+.||+.||.+.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 47999999999999987 2 1 11 299999987 369999999999874
No 38
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=95.47 E-value=0.079 Score=62.25 Aligned_cols=102 Identities=17% Similarity=0.333 Sum_probs=78.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCcccccc-------ccccc------c----------------------
Q 012494 51 PWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRL-------RWCNQ------L---------------------- 95 (462)
Q Consensus 51 ~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~-------RW~n~------L---------------------- 95 (462)
.|+.-+=..++.+..+||..+-..||..|.+++...++. ||... +
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~~ 905 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIGK 905 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 488888889999999999888999999998888777652 21110 0
Q ss_pred ---------------CCCCCCCCCChHHHHHHHHHHHHcC-CchHHHhh------------hCCCCCHHHHHHHHHHHHH
Q 012494 96 ---------------DPCLKRKPFTDEEDQIIISAHAVHG-NKWAVIAR------------LLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 96 ---------------~P~lkrgpWTeEEDelLLeLvkk~G-nkWskIAk------------~LPGRT~~QcKnRWnslLk 147 (462)
-+..++..||+|||..|+-++.+|| ++|..|-. +|..||+..|..|.+++++
T Consensus 906 k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~ 985 (1033)
T PLN03142 906 KLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIR 985 (1033)
T ss_pred HHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHH
Confidence 0223456799999999999999999 78999944 2358999999999999986
Q ss_pred hhhhh
Q 012494 148 RRYTD 152 (462)
Q Consensus 148 kkl~~ 152 (462)
-.-+.
T Consensus 986 ~~~~e 990 (1033)
T PLN03142 986 LIEKE 990 (1033)
T ss_pred HHHHH
Confidence 65433
No 39
>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=95.28 E-value=0.012 Score=55.50 Aligned_cols=48 Identities=23% Similarity=0.551 Sum_probs=40.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhC---C---CCHHHHhhhCCCCCccccccccccccC
Q 012494 48 VKGPWSPEEDAVLSRLVSQFG---A---RNWGMIARGIPGRSGKSCRLRWCNQLD 96 (462)
Q Consensus 48 kKG~WT~EEDelLl~lV~kyG---~---~nWskIAk~LpgRS~kQCR~RW~n~L~ 96 (462)
+.-.||.|||.+|.+.|.+|- . .-...+++.| +||+..|.-||..++.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVR 56 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHH
Confidence 566899999999999999993 1 1278888888 8999999999998775
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.14 E-value=0.053 Score=43.81 Aligned_cols=48 Identities=27% Similarity=0.535 Sum_probs=39.8
Q ss_pred CCCCChHHHHHHHHHHHHcC----C-------------chHHHhhhC-----CCCCHHHHHHHHHHHHHh
Q 012494 101 RKPFTDEEDQIIISAHAVHG----N-------------KWAVIARLL-----PGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~G----n-------------kWskIAk~L-----PGRT~~QcKnRWnslLkk 148 (462)
...||.+|...|++++.+|. + -|..|+..| +.||..+++.+|..+...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 45799999999999998763 1 299999976 259999999999987754
No 41
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.81 E-value=0.026 Score=45.61 Aligned_cols=47 Identities=32% Similarity=0.436 Sum_probs=38.5
Q ss_pred CCCCCHHHHHHHHHHHHHhC-----CC-----------CHHHHhhhC-----CCCCcccccccccccc
Q 012494 49 KGPWSPEEDAVLSRLVSQFG-----AR-----------NWGMIARGI-----PGRSGKSCRLRWCNQL 95 (462)
Q Consensus 49 KG~WT~EEDelLl~lV~kyG-----~~-----------nWskIAk~L-----pgRS~kQCR~RW~n~L 95 (462)
+..||.+|.+.|+++|.+|. .. -|..|+..| +.|+..|++.+|.++.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 56799999999999999982 11 199999876 3699999999998754
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.72 E-value=0.035 Score=57.47 Aligned_cols=46 Identities=22% Similarity=0.465 Sum_probs=42.3
Q ss_pred CCCCChHHHHHHHHHHHHcC-CchHHHhhhCCCCCHHHHHHHHHHHH
Q 012494 101 RKPFTDEEDQIIISAHAVHG-NKWAVIARLLPGRTDNAIKNHWNSTL 146 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~G-nkWskIAk~LPGRT~~QcKnRWnslL 146 (462)
-..|+..|+.+|++...-.| ++|..||.++..|+...||.+|..+.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 35799999999999999999 89999999998899999999997765
No 43
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.49 E-value=0.016 Score=59.95 Aligned_cols=47 Identities=23% Similarity=0.457 Sum_probs=43.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccC
Q 012494 50 GPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLD 96 (462)
Q Consensus 50 G~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~ 96 (462)
-.|+..|+.+|+++....|.+||..||.++..|+...|+.+|..++.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 35999999999999999999999999999999999999999988665
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=93.26 E-value=0.034 Score=52.85 Aligned_cols=49 Identities=18% Similarity=0.519 Sum_probs=38.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCC------HHHHhhhCCCCCccccccccccccC
Q 012494 47 RVKGPWSPEEDAVLSRLVSQFGARN------WGMIARGIPGRSGKSCRLRWCNQLD 96 (462)
Q Consensus 47 ~kKG~WT~EEDelLl~lV~kyG~~n------WskIAk~LpgRS~kQCR~RW~n~L~ 96 (462)
.++..||.|||.+|.+.|.+|+... ...++..| +|+..+|..||..++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHH
Confidence 3567899999999999999996332 55566666 8999999999965554
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.37 E-value=0.13 Score=54.47 Aligned_cols=84 Identities=18% Similarity=0.260 Sum_probs=63.6
Q ss_pred CHHHHhhhCCCCCccccccccccccCCC-------------------------CCCCCCChHHHHHHHHHHHHcCCchHH
Q 012494 71 NWGMIARGIPGRSGKSCRLRWCNQLDPC-------------------------LKRKPFTDEEDQIIISAHAVHGNKWAV 125 (462)
Q Consensus 71 nWskIAk~LpgRS~kQCR~RW~n~L~P~-------------------------lkrgpWTeEEDelLLeLvkk~GnkWsk 125 (462)
.|..+.=..+-|...-...||....++. ++...||.+|.+-|++|++.|.-+|-.
T Consensus 75 ~W~w~pFtn~aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~V 154 (445)
T KOG2656|consen 75 PWKWVPFTNSARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFFV 154 (445)
T ss_pred CceeeccCCccccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEEE
Confidence 4766655455666666667776653321 123569999999999999999999999
Q ss_pred Hhhh-----CCC-CCHHHHHHHHHHHHHhhhhhcC
Q 012494 126 IARL-----LPG-RTDNAIKNHWNSTLRRRYTDLG 154 (462)
Q Consensus 126 IAk~-----LPG-RT~~QcKnRWnslLkkkl~~~~ 154 (462)
||.. ++. ||-.++|.||+.++++-+....
T Consensus 155 IaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 155 IADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred EeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 9987 555 9999999999999987765443
No 46
>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=91.71 E-value=0.34 Score=43.53 Aligned_cols=51 Identities=22% Similarity=0.428 Sum_probs=40.8
Q ss_pred CCCCCCCChHHHHHHHHHHHHcCC----chHHHhhhC------------CCCCHHHHHHHHHHHHHh
Q 012494 98 CLKRKPFTDEEDQIIISAHAVHGN----KWAVIARLL------------PGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 98 ~lkrgpWTeEEDelLLeLvkk~Gn----kWskIAk~L------------PGRT~~QcKnRWnslLkk 148 (462)
..++..||++||.-|+-++.+||- .|..|-..+ ..||+..|..|.+++++-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 456789999999999999999995 799886632 479999999999998864
No 47
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.49 E-value=0.29 Score=51.94 Aligned_cols=48 Identities=19% Similarity=0.362 Sum_probs=44.3
Q ss_pred CCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHhh
Q 012494 102 KPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRRR 149 (462)
Q Consensus 102 gpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkkk 149 (462)
.+||.+|-+++.++...+|..++.|+..+|.|...|||.+|.+--|++
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~n 413 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKVN 413 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhhC
Confidence 489999999999999999999999999999999999999997766554
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.45 E-value=0.41 Score=49.12 Aligned_cols=51 Identities=20% Similarity=0.395 Sum_probs=39.8
Q ss_pred CCCCChHHHHHHHHHHHHc----------CCchHHHhhhCC----CCCHHHHHHHHHHHHHhhhhh
Q 012494 101 RKPFTDEEDQIIISAHAVH----------GNKWAVIARLLP----GRTDNAIKNHWNSTLRRRYTD 152 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~----------GnkWskIAk~LP----GRT~~QcKnRWnslLkkkl~~ 152 (462)
...|+.+|-..||++.... +..|..||+.+. -||+.||+++|.++.++ |+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~-Yk~ 118 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKK-YKK 118 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH-HHH
Confidence 4689999999999997643 234999999552 49999999999886654 443
No 49
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=90.95 E-value=0.6 Score=38.61 Aligned_cols=50 Identities=26% Similarity=0.526 Sum_probs=37.4
Q ss_pred CCChHHHHHHHHHHHHc---CC----------chHHHhhhCC-----CCCHHHHHHHHHHHHHhhhhhc
Q 012494 103 PFTDEEDQIIISAHAVH---GN----------KWAVIARLLP-----GRTDNAIKNHWNSTLRRRYTDL 153 (462)
Q Consensus 103 pWTeEEDelLLeLvkk~---Gn----------kWskIAk~LP-----GRT~~QcKnRWnslLkkkl~~~ 153 (462)
.||.++++.|++++.+. |+ .|..|+..|. ..|..||++||.. ||+.+...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~-lk~~y~~~ 68 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT-LKKDYRIW 68 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH-HHHHHHHH
Confidence 49999999999998543 21 2999998772 3588999999865 56666543
No 50
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=89.51 E-value=0.89 Score=46.66 Aligned_cols=47 Identities=28% Similarity=0.435 Sum_probs=37.6
Q ss_pred CCCCCHHHHHHHHHHHHHh---------CCCCHHHHhhhC----CCCCcccccccccccc
Q 012494 49 KGPWSPEEDAVLSRLVSQF---------GARNWGMIARGI----PGRSGKSCRLRWCNQL 95 (462)
Q Consensus 49 KG~WT~EEDelLl~lV~ky---------G~~nWskIAk~L----pgRS~kQCR~RW~n~L 95 (462)
-..|+.+|-..|+.+..+. ....|..||+.+ -.|++.||+.+|.|..
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 5789999999999998744 122499999955 3599999999998743
No 51
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=89.51 E-value=1.1 Score=48.72 Aligned_cols=51 Identities=20% Similarity=0.232 Sum_probs=45.9
Q ss_pred CCCCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHhhh
Q 012494 100 KRKPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRRRY 150 (462)
Q Consensus 100 krgpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkkkl 150 (462)
....||.||-.++-+++..||.++.+|-+.||.|+-..+..+|+...|.+-
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~~~ 236 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKTRE 236 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHHhh
Confidence 456899999999999999999999999999999999999999988776553
No 52
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=89.00 E-value=0.38 Score=51.03 Aligned_cols=65 Identities=23% Similarity=0.453 Sum_probs=51.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCcccccccccccc--CCC-----C-CCCCCChHHHHHH
Q 012494 47 RVKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQL--DPC-----L-KRKPFTDEEDQII 112 (462)
Q Consensus 47 ~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L--~P~-----l-krgpWTeEEDelL 112 (462)
..--+||.+|-+++.+++..+|+ +++.|+..+|+|+.+|++.+|.+-- +|. + .+.|+..+|-..|
T Consensus 363 ~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~ 435 (507)
T COG5118 363 KGALRWSKKEIEKFYKALSIWGT-DFSLISSLFPNRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKL 435 (507)
T ss_pred CCCCcccHHHHHHHHHHHHHhcc-hHHHHHHhcCchhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhH
Confidence 34457999999999999999996 8999999999999999999998632 221 1 2457777775443
No 53
>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=85.07 E-value=2.5 Score=31.57 Aligned_cols=42 Identities=21% Similarity=0.377 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 106 DEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 106 eEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
++++..++.++...|-.|.+||..+ |.|...|+.+....+++
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 4677888888888899999999999 99999999988776543
No 54
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=84.43 E-value=1.1 Score=40.22 Aligned_cols=34 Identities=32% Similarity=0.525 Sum_probs=28.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCHHHHhhhC
Q 012494 46 SRVKGPWSPEEDAVLSRLVSQFGA---RNWGMIARGI 79 (462)
Q Consensus 46 ~~kKG~WT~EEDelLl~lV~kyG~---~nWskIAk~L 79 (462)
...+..||.+||.-|+-++.+||. +.|..|-..+
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 456778999999999999999998 8899998765
No 55
>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=82.15 E-value=1.5 Score=36.88 Aligned_cols=30 Identities=37% Similarity=0.757 Sum_probs=18.4
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCCCCHHHHhh
Q 012494 45 SSRVKGPWSPEEDAVL--------SRLVSQFGARNWGMIAR 77 (462)
Q Consensus 45 ~~~kKG~WT~EEDelL--------l~lV~kyG~~nWskIAk 77 (462)
|....|-||+|+|+.| .+++++|| |..|+.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~ 80 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIER 80 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHH
Confidence 5577899999999999 55667787 566665
No 56
>smart00595 MADF subfamily of SANT domain.
Probab=75.60 E-value=3.3 Score=33.87 Aligned_cols=23 Identities=30% Similarity=0.582 Sum_probs=20.7
Q ss_pred hHHHhhhCCCCCHHHHHHHHHHHH
Q 012494 123 WAVIARLLPGRTDNAIKNHWNSTL 146 (462)
Q Consensus 123 WskIAk~LPGRT~~QcKnRWnslL 146 (462)
|..||..| |-|..+|+.+|+++-
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR 52 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHH
Confidence 99999999 669999999998854
No 57
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=75.13 E-value=19 Score=39.53 Aligned_cols=50 Identities=10% Similarity=0.024 Sum_probs=44.6
Q ss_pred CCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHhhhhh
Q 012494 103 PFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRRRYTD 152 (462)
Q Consensus 103 pWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkkkl~~ 152 (462)
-||.++-.++++.+++||....-|+-.+...+=-+.++.++..-|++...
T Consensus 371 ~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~mfe 420 (534)
T KOG1194|consen 371 CFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQMFE 420 (534)
T ss_pred ccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHHHHH
Confidence 59999999999999999988888888888888889999999988887655
No 58
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=73.20 E-value=5.8 Score=45.50 Aligned_cols=45 Identities=9% Similarity=0.116 Sum_probs=41.9
Q ss_pred CCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 012494 102 KPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTL 146 (462)
Q Consensus 102 gpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslL 146 (462)
..||..|-.++-+++..|..++-.|++.++++|-.||-.+|+.+.
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWK 664 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWK 664 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHH
Confidence 579999999999999999999999999999999999999887654
No 59
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=72.97 E-value=2.3 Score=48.58 Aligned_cols=43 Identities=9% Similarity=0.426 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCcccccccccc
Q 012494 50 GPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCN 93 (462)
Q Consensus 50 G~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n 93 (462)
-.||+.|-.++.+++..|. +++-+|++.|+++|.+||-+-|+.
T Consensus 620 d~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYS-KDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred ccccHHHHHHHHHHHHHhc-ccHHHHHHHhccccHHHHHHHHHH
Confidence 3699999999999999998 689999999999999999876653
No 60
>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=72.22 E-value=3.4 Score=34.13 Aligned_cols=43 Identities=28% Similarity=0.570 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------CHHHHhhhCCC-----CCcccccccccc
Q 012494 51 PWSPEEDAVLSRLVSQF---GAR---------NWGMIARGIPG-----RSGKSCRLRWCN 93 (462)
Q Consensus 51 ~WT~EEDelLl~lV~ky---G~~---------nWskIAk~Lpg-----RS~kQCR~RW~n 93 (462)
.||+++++.|++++... |.. .|..|+..|.. .+..||+.||..
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 59999999999998655 211 29999987732 345677777643
No 61
>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=68.67 E-value=13 Score=27.39 Aligned_cols=41 Identities=17% Similarity=0.297 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 107 EEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 107 EEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
+++..++.++-..+-.+.+||..| |-|...|+.+....+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 456666666666667899999999 99999999988877754
No 62
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=65.42 E-value=11 Score=42.59 Aligned_cols=46 Identities=13% Similarity=0.357 Sum_probs=34.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHhhhC----------CCCCcccccccccccc
Q 012494 49 KGPWSPEEDAVLSRLVSQFGARNWGMIARGI----------PGRSGKSCRLRWCNQL 95 (462)
Q Consensus 49 KG~WT~EEDelLl~lV~kyG~~nWskIAk~L----------pgRS~kQCR~RW~n~L 95 (462)
|..||..|.+.+..+++.+| +++..|-+.+ .-++-.|+|.+|++.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 66899999999999999999 5898883322 2345567777776644
No 63
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=64.58 E-value=13 Score=33.80 Aligned_cols=45 Identities=18% Similarity=0.206 Sum_probs=37.7
Q ss_pred hHHHHHHHHHHHHcC-CchHHHhhhCCCCCHHHHHHHHHHHHHhhhh
Q 012494 106 DEEDQIIISAHAVHG-NKWAVIARLLPGRTDNAIKNHWNSTLRRRYT 151 (462)
Q Consensus 106 eEEDelLLeLvkk~G-nkWskIAk~LPGRT~~QcKnRWnslLkkkl~ 151 (462)
.+-|.+|+++..+.| -.|++||+.+ |-|...|+.|++.+....+.
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 357888888888877 4699999999 99999999999988866543
No 64
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=64.44 E-value=10 Score=42.69 Aligned_cols=52 Identities=13% Similarity=0.323 Sum_probs=41.8
Q ss_pred CCCCCChHHHHHHHHHHHHcCCchHHHhh----------hCCCCCHHHHHHHHHHHHHhhhh
Q 012494 100 KRKPFTDEEDQIIISAHAVHGNKWAVIAR----------LLPGRTDNAIKNHWNSTLRRRYT 151 (462)
Q Consensus 100 krgpWTeEEDelLLeLvkk~GnkWskIAk----------~LPGRT~~QcKnRWnslLkkkl~ 151 (462)
++..||-+|+.-+..+++++|.++.+|-+ ...-+|..|++.+|+.++++..+
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred cccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHh
Confidence 36689999999999999999999998822 23346788999999888866543
No 65
>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=64.21 E-value=18 Score=26.74 Aligned_cols=38 Identities=21% Similarity=0.343 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHcCC-chHHHhhhCCCCCHHHHHHHHHHH
Q 012494 107 EEDQIIISAHAVHGN-KWAVIARLLPGRTDNAIKNHWNST 145 (462)
Q Consensus 107 EEDelLLeLvkk~Gn-kWskIAk~LPGRT~~QcKnRWnsl 145 (462)
+=|.+|+.+...-+. .|.+||+.+ |=|...|..|++.+
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 457888888888774 599999999 99999999999764
No 66
>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=59.25 E-value=23 Score=30.80 Aligned_cols=38 Identities=21% Similarity=0.338 Sum_probs=28.3
Q ss_pred HHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 110 QIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 110 elLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..++.+.-..|-.+.+||+.+ |.+...+++++...+++
T Consensus 119 r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 119 RKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 334444334567899999999 99999999999875543
No 67
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=59.14 E-value=17 Score=33.64 Aligned_cols=45 Identities=13% Similarity=0.167 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHHcC-CchHHHhhhCCCCCHHHHHHHHHHHHHhhhh
Q 012494 106 DEEDQIIISAHAVHG-NKWAVIARLLPGRTDNAIKNHWNSTLRRRYT 151 (462)
Q Consensus 106 eEEDelLLeLvkk~G-nkWskIAk~LPGRT~~QcKnRWnslLkkkl~ 151 (462)
.+-|.+|+.+..+.| -.|++||+.+ |-+...|..|++.+.+....
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 566888888887776 4699999999 99999999999998866553
No 68
>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=57.22 E-value=12 Score=35.29 Aligned_cols=40 Identities=30% Similarity=0.302 Sum_probs=34.0
Q ss_pred CCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHH
Q 012494 103 PFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWN 143 (462)
Q Consensus 103 pWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWn 143 (462)
.||+|..++|.+|.. -|-.=++||+.|.+.|.|.|.-+-+
T Consensus 2 ~Wtde~~~~L~~lw~-~G~SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTDERVERLRKLWA-EGLSASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCHHHHHHHHHHHH-cCCCHHHHHHHhCCcchhhhhhhhh
Confidence 599999999999984 4777899999997799998877654
No 69
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=52.09 E-value=48 Score=34.96 Aligned_cols=51 Identities=22% Similarity=0.432 Sum_probs=39.0
Q ss_pred CCCCChHHHHHHHHHHHHc-CC---chHHHhhhCCCCCHHHHHHHHHHHHHhhhhh
Q 012494 101 RKPFTDEEDQIIISAHAVH-GN---KWAVIARLLPGRTDNAIKNHWNSTLRRRYTD 152 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~-Gn---kWskIAk~LPGRT~~QcKnRWnslLkkkl~~ 152 (462)
-..||.-|...|+++.... |. .-..|++.++||+..+|++.-+. ||.+...
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~-LK~rvar 75 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQ-LKGRVAR 75 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHH-HHHHHHH
Confidence 4589999999999887655 33 35789999999999999996544 5555433
No 70
>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=50.27 E-value=36 Score=28.59 Aligned_cols=36 Identities=17% Similarity=0.354 Sum_probs=27.5
Q ss_pred HHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 112 IISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 112 LLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
++.++...|..+.+||+.+ |-+...++++.+..+++
T Consensus 118 ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 118 VLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3344445677899999999 88999999988876544
No 71
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=49.54 E-value=31 Score=33.91 Aligned_cols=46 Identities=20% Similarity=0.258 Sum_probs=36.9
Q ss_pred CCChHHHHHHHHHHHHcCCchHHHhhhCC---CCCHHHHHHHHHHHHHhh
Q 012494 103 PFTDEEDQIIISAHAVHGNKWAVIARLLP---GRTDNAIKNHWNSTLRRR 149 (462)
Q Consensus 103 pWTeEEDelLLeLvkk~GnkWskIAk~LP---GRT~~QcKnRWnslLkkk 149 (462)
.|+..+|-+|+.+| ..++.-..|++-++ .-|-..+..||+.+|-..
T Consensus 1 rW~~~DDl~Li~av-~~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~ 49 (199)
T PF13325_consen 1 RWKPEDDLLLINAV-EQTNDLESVHLGVKFSCKFTLQEIEERWYALLYDP 49 (199)
T ss_pred CCCchhhHHHHHHH-HHhcCHHHHHccCCcCCcCcHHHHHHHHHHHHcCh
Confidence 49999999999998 55777788877542 358899999999999443
No 72
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=48.16 E-value=18 Score=40.72 Aligned_cols=49 Identities=20% Similarity=0.429 Sum_probs=44.2
Q ss_pred CCCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHhh
Q 012494 101 RKPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRRR 149 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkkk 149 (462)
...||.+|-++........|.+.+.|+..+|+|+..|||.+|..--+++
T Consensus 409 ~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r~ 457 (584)
T KOG2009|consen 409 TDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKRN 457 (584)
T ss_pred cCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhcc
Confidence 4689999999999999999999999999999999999999997655444
No 73
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=47.82 E-value=37 Score=28.08 Aligned_cols=37 Identities=27% Similarity=0.412 Sum_probs=27.1
Q ss_pred HHHHHHHHcCC--------chHHHhhhCCC---CC--HHHHHHHHHHHHH
Q 012494 111 IIISAHAVHGN--------KWAVIARLLPG---RT--DNAIKNHWNSTLR 147 (462)
Q Consensus 111 lLLeLvkk~Gn--------kWskIAk~LPG---RT--~~QcKnRWnslLk 147 (462)
.|..+|...|+ +|..||+.|.- -+ ..+++..|..+|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 47777777775 59999998832 12 3678999988774
No 74
>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=44.99 E-value=14 Score=27.21 Aligned_cols=38 Identities=29% Similarity=0.392 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHhCCCCHHHHhhhCCCCCcccccccccc
Q 012494 55 EEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCN 93 (462)
Q Consensus 55 EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n 93 (462)
+=|.+|++++...+...|..||+.+ |=+...|+.|+..
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHH
Confidence 4588999999999988999999988 7888888888753
No 75
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=43.33 E-value=25 Score=27.71 Aligned_cols=26 Identities=27% Similarity=0.440 Sum_probs=20.9
Q ss_pred chHHHhhhCCC-CCHHHHHHHHHHHHH
Q 012494 122 KWAVIARLLPG-RTDNAIKNHWNSTLR 147 (462)
Q Consensus 122 kWskIAk~LPG-RT~~QcKnRWnslLk 147 (462)
-|..||..|.. -+..+|+.+|+++..
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHH
Confidence 39999999953 578899999988553
No 76
>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=42.99 E-value=75 Score=21.97 Aligned_cols=41 Identities=17% Similarity=0.361 Sum_probs=28.7
Q ss_pred CChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 012494 104 FTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTL 146 (462)
Q Consensus 104 WTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslL 146 (462)
++.+ +..++.++...|-.+..||..+ |-+...|+.+.....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRAL 51 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 4444 4455555556677899999999 888888877665543
No 77
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=41.93 E-value=54 Score=27.53 Aligned_cols=45 Identities=16% Similarity=0.158 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHcC-CchHHHhhhCCCCCHHHHHHHHHHHHHhhhhh
Q 012494 107 EEDQIIISAHAVHG-NKWAVIARLLPGRTDNAIKNHWNSTLRRRYTD 152 (462)
Q Consensus 107 EEDelLLeLvkk~G-nkWskIAk~LPGRT~~QcKnRWnslLkkkl~~ 152 (462)
+.|..|+.+....+ -.|+.||+.+ |-+...|..+.+.+.+..+..
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 56788888888776 4699999999 999999999999988776543
No 78
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=41.65 E-value=18 Score=32.97 Aligned_cols=44 Identities=11% Similarity=0.073 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCCC
Q 012494 54 PEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDPC 98 (462)
Q Consensus 54 ~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P~ 98 (462)
.+-|.+|+++..+.|...|..||+.+ |-+...|+.|+.+..+.+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~G 51 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAG 51 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCC
Confidence 35799999999999988999999998 899999999998765544
No 79
>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=41.39 E-value=36 Score=28.81 Aligned_cols=29 Identities=21% Similarity=0.322 Sum_probs=23.9
Q ss_pred HHHHHHHHHHcCCchHHHhhhCCCCCHHHH
Q 012494 109 DQIIISAHAVHGNKWAVIARLLPGRTDNAI 138 (462)
Q Consensus 109 DelLLeLvkk~GnkWskIAk~LPGRT~~Qc 138 (462)
|+.|..+....|..|..+|.+| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 5678889999999999999999 6665544
No 80
>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=41.28 E-value=14 Score=31.02 Aligned_cols=17 Identities=24% Similarity=0.323 Sum_probs=10.2
Q ss_pred CCCCCCCCChHHHHHHH
Q 012494 97 PCLKRKPFTDEEDQIII 113 (462)
Q Consensus 97 P~lkrgpWTeEEDelLL 113 (462)
|....|-||+++|+.|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 55668899999999984
No 81
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=40.95 E-value=59 Score=28.89 Aligned_cols=32 Identities=13% Similarity=0.251 Sum_probs=24.7
Q ss_pred HHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 115 AHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 115 Lvkk~GnkWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
+....|-.+..||..| |.+...++++....++
T Consensus 139 l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~ 170 (182)
T PRK09652 139 LREIEGLSYEEIAEIM-GCPIGTVRSRIFRARE 170 (182)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3334567899999999 9999999988765443
No 82
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=40.83 E-value=27 Score=41.82 Aligned_cols=32 Identities=19% Similarity=0.354 Sum_probs=28.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhC
Q 012494 48 VKGPWSPEEDAVLSRLVSQFGARNWGMIARGI 79 (462)
Q Consensus 48 kKG~WT~EEDelLl~lV~kyG~~nWskIAk~L 79 (462)
++..||.|||..|+-++.+||.++|.+|-..+
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 44569999999999999999999999998766
No 83
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=39.95 E-value=50 Score=28.62 Aligned_cols=52 Identities=12% Similarity=0.351 Sum_probs=35.4
Q ss_pred CCCCChHHHHHHHHHHHHc----C----CchHHHhhhCC-----CCCHHHHHHHHHHHHHhhhhhc
Q 012494 101 RKPFTDEEDQIIISAHAVH----G----NKWAVIARLLP-----GRTDNAIKNHWNSTLRRRYTDL 153 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~----G----nkWskIAk~LP-----GRT~~QcKnRWnslLkkkl~~~ 153 (462)
...||+++|..||+.+..| | ..|..+-..+. .=|.+|+.++.+. ||+||...
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Kirr-LK~Ky~~~ 68 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRR-LKKKYRNA 68 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHH-HHHHHHHH
Confidence 4579999999999998766 5 24555444332 2378899998877 45555543
No 84
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=39.47 E-value=39 Score=41.25 Aligned_cols=76 Identities=14% Similarity=0.132 Sum_probs=50.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCCCCCCCCCChHHHHHHHHHHHHc-CCchHHH
Q 012494 48 VKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAVH-GNKWAVI 126 (462)
Q Consensus 48 kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk~-GnkWskI 126 (462)
.---|..++|..|+-.|-+||.++|..|-- .......=+..++-.+....|-...-..|+.+...+ +.+|...
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~------Dp~L~l~dKi~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~ 1205 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRL------DPDLGLTDKIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKK 1205 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhcc------CccccchhhhcccccCCchHHHHHHHHHHHHHHhhcccCCCchh
Confidence 344699999999999999999999998843 111111111222222556677777788888888777 5566665
Q ss_pred hhh
Q 012494 127 ARL 129 (462)
Q Consensus 127 Ak~ 129 (462)
.+.
T Consensus 1206 ~~~ 1208 (1373)
T KOG0384|consen 1206 LKR 1208 (1373)
T ss_pred hhc
Confidence 543
No 85
>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=39.20 E-value=79 Score=33.42 Aligned_cols=85 Identities=26% Similarity=0.446 Sum_probs=61.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCC---CHHHHhhhCCCCCccccccccccccCCCCCCCCCChHHHHHHHHHHHH-c-----C
Q 012494 50 GPWSPEEDAVLSRLVSQFGAR---NWGMIARGIPGRSGKSCRLRWCNQLDPCLKRKPFTDEEDQIIISAHAV-H-----G 120 (462)
Q Consensus 50 G~WT~EEDelLl~lV~kyG~~---nWskIAk~LpgRS~kQCR~RW~n~L~P~lkrgpWTeEEDelLLeLvkk-~-----G 120 (462)
-.||.-|...|+++....... +-.+|++.+++|+..++++ |.+.|+ +..+.+++++ | |
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~~~ 88 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGLKG 88 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHH-HHHHHH------------HHHHHHHHHHhccccccc
Confidence 369999999999999866322 4678899999999988876 334443 1223333333 2 1
Q ss_pred C------------chHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 121 N------------KWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 121 n------------kWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
. -|..+|..+.|.-...+-.-|-++|-
T Consensus 89 ~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 89 PRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 1 29999999999999999888888773
No 86
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=38.80 E-value=63 Score=27.06 Aligned_cols=38 Identities=24% Similarity=0.350 Sum_probs=27.5
Q ss_pred HHHHHHHHHcCC--------chHHHhhhCCCC-----CHHHHHHHHHHHHH
Q 012494 110 QIIISAHAVHGN--------KWAVIARLLPGR-----TDNAIKNHWNSTLR 147 (462)
Q Consensus 110 elLLeLvkk~Gn--------kWskIAk~LPGR-----T~~QcKnRWnslLk 147 (462)
-.|..+|.+.|+ +|..||..|.-. ...+++..|..+|.
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~ 85 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLL 85 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhH
Confidence 347777777775 699999988322 35678888888774
No 87
>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=38.06 E-value=58 Score=23.61 Aligned_cols=35 Identities=29% Similarity=0.295 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHH
Q 012494 107 EEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHW 142 (462)
Q Consensus 107 EEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRW 142 (462)
-|.+.|.++...++++....|+.| |=+...+..+.
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 367788999999999999999999 87777666554
No 88
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=37.93 E-value=68 Score=28.43 Aligned_cols=29 Identities=24% Similarity=0.376 Sum_probs=23.6
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
..|-.+..||..| |-|...|++++....+
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 167 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQ 167 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 4466799999999 9999999998866443
No 89
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=37.14 E-value=18 Score=40.63 Aligned_cols=49 Identities=18% Similarity=0.388 Sum_probs=44.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCcccccccccc
Q 012494 44 SSSRVKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCN 93 (462)
Q Consensus 44 ~~~~kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n 93 (462)
++....++|+.+|-++...+...+|. +.+.|+..+++|+.+|++.+|..
T Consensus 404 sk~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 404 SKKLETDKWDASETELFYKALSERGS-DFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred cCccccCcccchhhHHhhhHHhhhcc-cccccccccccccHHHHHHHHhh
Confidence 56677889999999999999999996 79999999999999999998754
No 90
>PRK04217 hypothetical protein; Provisional
Probab=36.21 E-value=84 Score=28.07 Aligned_cols=45 Identities=13% Similarity=0.067 Sum_probs=35.6
Q ss_pred CCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 102 KPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 102 gpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..-|.+| ..++.+....|-...+||+.+ |-+...|+.+|+...++
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3456666 577777777788899999999 99999999999875544
No 91
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=36.01 E-value=93 Score=28.92 Aligned_cols=29 Identities=24% Similarity=0.343 Sum_probs=23.6
Q ss_pred HHcCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 012494 117 AVHGNKWAVIARLLPGRTDNAIKNHWNSTL 146 (462)
Q Consensus 117 kk~GnkWskIAk~LPGRT~~QcKnRWnslL 146 (462)
...|-...+||..| |-+...+++|+...+
T Consensus 147 ~~~g~s~~EIA~~l-g~s~~tV~~rl~rar 175 (192)
T PRK09643 147 DMQGYSVADAARML-GVAEGTVKSRCARGR 175 (192)
T ss_pred HHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 34566799999999 999999999995543
No 92
>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=35.11 E-value=58 Score=27.59 Aligned_cols=30 Identities=23% Similarity=0.289 Sum_probs=24.6
Q ss_pred HHHHHHHHHHcCCchHHHhhhCCCCCHHHHH
Q 012494 109 DQIIISAHAVHGNKWAVIARLLPGRTDNAIK 139 (462)
Q Consensus 109 DelLLeLvkk~GnkWskIAk~LPGRT~~QcK 139 (462)
|..|..+....|..|..+|+.| |=+..+|.
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~ 33 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEIN 33 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHH
Confidence 6678888999999999999999 76665543
No 93
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=35.02 E-value=20 Score=33.12 Aligned_cols=45 Identities=13% Similarity=0.059 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCCCC
Q 012494 54 PEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDPCL 99 (462)
Q Consensus 54 ~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P~l 99 (462)
.+-|.+|+.+..+.|.-.|..||+.+ |=+...|+.|+.+..+.++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 56789999999999988999999998 7889999999987665443
No 94
>PF15349 DCA16: DDB1- and CUL4-associated factor 16
Probab=34.79 E-value=14 Score=35.21 Aligned_cols=13 Identities=46% Similarity=1.219 Sum_probs=11.9
Q ss_pred CCCCCCCCCccCC
Q 012494 331 IIPSQCGYGCCAS 343 (462)
Q Consensus 331 ~vp~~cg~gcc~~ 343 (462)
.||+.|-.|||++
T Consensus 168 ~ipnscvsgcccg 180 (216)
T PF15349_consen 168 QIPNSCVSGCCCG 180 (216)
T ss_pred hCcchhhcccchh
Confidence 5899999999996
No 95
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=34.30 E-value=84 Score=29.35 Aligned_cols=37 Identities=14% Similarity=0.232 Sum_probs=29.1
Q ss_pred HHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHH
Q 012494 109 DQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTL 146 (462)
Q Consensus 109 DelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslL 146 (462)
...++.+....|-.|.+||..| |-+...++.+|...-
T Consensus 140 ~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 140 QRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3444555555677899999999 999999999997754
No 96
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=33.68 E-value=69 Score=34.55 Aligned_cols=46 Identities=11% Similarity=0.146 Sum_probs=40.6
Q ss_pred CCCChHHHHHHHHHHHHcCCchHHHhh-hCCCCCHHHHHHHHHHHHH
Q 012494 102 KPFTDEEDQIIISAHAVHGNKWAVIAR-LLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 102 gpWTeEEDelLLeLvkk~GnkWskIAk-~LPGRT~~QcKnRWnslLk 147 (462)
..|+++|=..+-+.++.||.++..|.. .++.|+--.|-..|+...|
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKk 324 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKK 324 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhc
Confidence 479999999999999999999999976 7899999999998866543
No 97
>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=32.38 E-value=51 Score=27.32 Aligned_cols=29 Identities=28% Similarity=0.536 Sum_probs=23.4
Q ss_pred HHHHHHHHHHcCCchHHHhhhCCCCCHHHH
Q 012494 109 DQIIISAHAVHGNKWAVIARLLPGRTDNAI 138 (462)
Q Consensus 109 DelLLeLvkk~GnkWskIAk~LPGRT~~Qc 138 (462)
|..|..+....|..|.++|+.| |=+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4567888899999999999999 6665544
No 98
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=32.32 E-value=70 Score=30.75 Aligned_cols=44 Identities=23% Similarity=0.268 Sum_probs=35.6
Q ss_pred CCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 102 KPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 102 gpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
...|+.|-+.|.-+.+=+.| ++||..| +.+...+|+|..++++|
T Consensus 147 ~~LT~RE~eVL~lla~G~sn--keIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAEGLSN--KEIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHCCCCH--HHHHHHH-CCCHhHHHHHHHHHHHH
Confidence 36888888877666544444 7999999 99999999999998866
No 99
>KOG1878 consensus Nuclear receptor coregulator SMRT/SMRTER, contains Myb-like domains [Transcription]
Probab=31.74 E-value=21 Score=43.97 Aligned_cols=44 Identities=30% Similarity=0.503 Sum_probs=35.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccc
Q 012494 48 VKGPWSPEEDAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWC 92 (462)
Q Consensus 48 kKG~WT~EEDelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~ 92 (462)
+...|+++|-+....-...|- +|...|+.+|-.++..+|..-|+
T Consensus 224 ~~n~Ws~~Ek~~fk~rf~~H~-knf~~~as~~erkSv~d~vlfyy 267 (1672)
T KOG1878|consen 224 RMNEWSPEEKELFKSRFAQHV-KNFGLIASFFERKSVSDCVLFYY 267 (1672)
T ss_pred HhhhccccccccccchhhhcC-cchhhhhhhhcccchhhceeeee
Confidence 556799999887777777776 57888999998888888887664
No 100
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=31.31 E-value=1.3e+02 Score=25.81 Aligned_cols=46 Identities=20% Similarity=0.314 Sum_probs=36.6
Q ss_pred CCCCChHHHHHHHHHHHHcCCchHHHhhhCCCC-CHHHHHHHHHHHHHh
Q 012494 101 RKPFTDEEDQIIISAHAVHGNKWAVIARLLPGR-TDNAIKNHWNSTLRR 148 (462)
Q Consensus 101 rgpWTeEEDelLLeLvkk~GnkWskIAk~LPGR-T~~QcKnRWnslLkk 148 (462)
+..||.|.-..+++++..-|..=+.||+.+ |- ..++ ..+|...+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~-l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQ-LYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHH-HHHHHHHHHH
Confidence 678999999999999999888889999999 76 5544 4557665544
No 101
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=30.72 E-value=1e+02 Score=27.89 Aligned_cols=28 Identities=11% Similarity=0.082 Sum_probs=22.9
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 119 HGNKWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 119 ~GnkWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
.|..+.+||..| |-|...++++.....+
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 456799999999 9999999998766543
No 102
>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=30.29 E-value=84 Score=28.48 Aligned_cols=29 Identities=14% Similarity=0.214 Sum_probs=23.3
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 119 HGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 119 ~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
.|-...+||..| |-|...|+++....+++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355799999999 99999999998665543
No 103
>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=29.95 E-value=1.1e+02 Score=27.47 Aligned_cols=30 Identities=17% Similarity=0.348 Sum_probs=24.0
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-...+||..| |-|...|++++...+++
T Consensus 133 ~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 133 YHDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3455789999999 89999999998776544
No 104
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=29.91 E-value=38 Score=36.40 Aligned_cols=41 Identities=20% Similarity=0.300 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCCHHHHhh-hCCCCCccccccccc
Q 012494 51 PWSPEEDAVLSRLVSQFGARNWGMIAR-GIPGRSGKSCRLRWC 92 (462)
Q Consensus 51 ~WT~EEDelLl~lV~kyG~~nWskIAk-~LpgRS~kQCR~RW~ 92 (462)
.|+.+|-..+.+.++.|| +++..|.. .++.|+...|-+-|+
T Consensus 279 ~wsEeEcr~FEegl~~yG-KDF~lIr~nkvrtRsvgElVeyYY 320 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYG-KDFHLIRANKVRTRSVGELVEYYY 320 (445)
T ss_pred cCCHHHHHHHHHHHHHhc-ccHHHHHhcccccchHHHHHHHHH
Confidence 499999999999999999 58999964 578899888877664
No 105
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=29.75 E-value=59 Score=23.93 Aligned_cols=38 Identities=29% Similarity=0.345 Sum_probs=19.0
Q ss_pred CCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHH
Q 012494 102 KPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNH 141 (462)
Q Consensus 102 gpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnR 141 (462)
..||.+|-..|..++ .-|-.-.+||+.| ||+...|.+.
T Consensus 3 ~~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHH-CS---HHHHHHHT-T--HHHHHHH
T ss_pred cchhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHHH
Confidence 357778877777775 5677789999999 9999887653
No 106
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=29.08 E-value=1.3e+02 Score=26.47 Aligned_cols=30 Identities=17% Similarity=0.211 Sum_probs=24.0
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-...+||..| |-+...|+++....+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 120 WEDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred HhcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3455789999999 99999999988765544
No 107
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=28.24 E-value=1.3e+02 Score=27.64 Aligned_cols=30 Identities=10% Similarity=0.255 Sum_probs=24.1
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-...+||..| |-|...+++++...+++
T Consensus 145 ~~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 145 YHEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466799999999 99999999998765533
No 108
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=28.07 E-value=77 Score=25.64 Aligned_cols=30 Identities=23% Similarity=0.375 Sum_probs=21.9
Q ss_pred HHHHHHHHHHH-cCCchHHHhhhCCCCCHHHH
Q 012494 108 EDQIIISAHAV-HGNKWAVIARLLPGRTDNAI 138 (462)
Q Consensus 108 EDelLLeLvkk-~GnkWskIAk~LPGRT~~Qc 138 (462)
-.+.|..++.. .|.+|..+|+.| |=+..+|
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 34566677777 899999999999 5555443
No 109
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=28.03 E-value=1.2e+02 Score=23.58 Aligned_cols=35 Identities=23% Similarity=0.323 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHH
Q 012494 107 EEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHW 142 (462)
Q Consensus 107 EEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRW 142 (462)
+.|+..+.+....|-.-.+||+.+ ||+.+-|++.-
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 445566677778899999999999 99998777653
No 110
>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=27.75 E-value=80 Score=26.51 Aligned_cols=25 Identities=24% Similarity=0.357 Sum_probs=19.8
Q ss_pred HHHHHHcCCchHHHhhhCCCCCHHHH
Q 012494 113 ISAHAVHGNKWAVIARLLPGRTDNAI 138 (462)
Q Consensus 113 LeLvkk~GnkWskIAk~LPGRT~~Qc 138 (462)
..+....|..|..+|+.| |-+..+|
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 335578899999999999 7777665
No 111
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=27.64 E-value=1.2e+02 Score=27.88 Aligned_cols=28 Identities=11% Similarity=0.146 Sum_probs=22.4
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 119 HGNKWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 119 ~GnkWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
.|-...+||..| |-|...|++++...++
T Consensus 153 ~g~s~~eIA~~l-gis~~tv~~~l~Rar~ 180 (193)
T PRK11923 153 DGLSYEDIASVM-QCPVGTVRSRIFRARE 180 (193)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355689999999 9999999998866543
No 112
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=27.52 E-value=73 Score=26.23 Aligned_cols=44 Identities=20% Similarity=0.550 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhCCCCHHHHhhhCCCCCccccccccccccCCCC-------CCCCCChHHHHHH
Q 012494 57 DAVLSRLVSQFGARNWGMIARGIPGRSGKSCRLRWCNQLDPCL-------KRKPFTDEEDQII 112 (462)
Q Consensus 57 DelLl~lV~kyG~~nWskIAk~LpgRS~kQCR~RW~n~L~P~l-------krgpWTeEEDelL 112 (462)
+.+|.++|..|| |..+++.+.-|+- .-+|++ ++.+|-.+.-+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~i~CF---------~~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERININCF---------KNNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTTSSST---------TSS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcccccC---------CCCCchHHHHHHHhcCHhHHHHHHHh
Confidence 578999999999 9999998855432 224443 3567776665544
No 113
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=27.51 E-value=1.2e+02 Score=23.76 Aligned_cols=46 Identities=20% Similarity=0.351 Sum_probs=32.8
Q ss_pred CCCCCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 100 KRKPFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 100 krgpWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
++..||.|+-..++..+..-|.....||+.+ |=+..++. +|...++
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~-gi~~~~l~-~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREY-GISPSTLY-NWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHH-TS-HHHHH-HHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeeccc-cccccccc-HHHHHHh
Confidence 4578999999999999988889999999988 66665554 4866554
No 114
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.36 E-value=1.3e+02 Score=27.84 Aligned_cols=30 Identities=20% Similarity=0.137 Sum_probs=24.0
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-.+.+||..| |-+...|+++....+++
T Consensus 120 ~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 120 LEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3466799999999 99999999998665533
No 115
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=27.21 E-value=78 Score=24.02 Aligned_cols=43 Identities=21% Similarity=0.355 Sum_probs=30.7
Q ss_pred CCChHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 103 PFTDEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 103 pWTeEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|+.|-+.|.-+. -|..=.+||..+ +.+...++.+...+.++
T Consensus 3 ~LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 35666666555443 355568999999 99999999998887755
No 116
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=27.20 E-value=1.4e+02 Score=26.92 Aligned_cols=38 Identities=24% Similarity=0.282 Sum_probs=28.6
Q ss_pred HHHHHHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHhhh
Q 012494 112 IISAHAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRRRY 150 (462)
Q Consensus 112 LLeLvkk~GnkWskIAk~LPGRT~~QcKnRWnslLkkkl 150 (462)
++.+....|-...+||..| |.+...|+.+...-+++-.
T Consensus 127 v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 127 AFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3334444566799999999 9999999999877665543
No 117
>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=26.82 E-value=1.2e+02 Score=28.31 Aligned_cols=47 Identities=17% Similarity=0.217 Sum_probs=38.5
Q ss_pred CCCCCChHHHHHHHHHHHHcCCchHHHhhhCC----CCCHHHHHHHHHHHH
Q 012494 100 KRKPFTDEEDQIIISAHAVHGNKWAVIARLLP----GRTDNAIKNHWNSTL 146 (462)
Q Consensus 100 krgpWTeEEDelLLeLvkk~GnkWskIAk~LP----GRT~~QcKnRWnslL 146 (462)
....-|..|..-|..|+.+||.++...|.-.. -.|..||+.+.+.+.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 34567899999999999999999999997432 489999999887653
No 118
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.45 E-value=1.6e+02 Score=26.96 Aligned_cols=30 Identities=13% Similarity=0.076 Sum_probs=23.3
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-...+||..| |-+...|+++....+++
T Consensus 142 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 142 YQGLSNIEAAAVM-DISVDALESLLARGRRA 171 (186)
T ss_pred hcCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 3456789999999 99999999887665544
No 119
>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=26.38 E-value=85 Score=26.37 Aligned_cols=31 Identities=23% Similarity=0.355 Sum_probs=25.2
Q ss_pred HHHHHHHHHHcCCchHHHhhhCCCCCHHHHHH
Q 012494 109 DQIIISAHAVHGNKWAVIARLLPGRTDNAIKN 140 (462)
Q Consensus 109 DelLLeLvkk~GnkWskIAk~LPGRT~~QcKn 140 (462)
|..|-.+....|.+|..+|+.| |=+...|.+
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 4567788889999999999999 777776644
No 120
>PF00341 PDGF: PDGF/VEGF domain; InterPro: IPR000072 Platelet-derived growth factor (PDGF) [, ] is a potent mitogen for cells of mesenchymal origin, including smooth muscle cells and glial cells. In both mouse and human, the PDGF signalling network consists of four ligands, PDGFA-D, and two receptors, PDGFRalpha and PDGFRbeta. All PDGFs function as secreted, disulphide-linked homodimers, but only PDGFA and B can form functional heterodimers. PDGFRs also function as homo- and heterodimers. All known PDGFs have characteristic `PDGF domains', which include eight conserved cysteines that are involved in inter- and intramolecular bonds. Alternate splicing of the A chain transcript can give rise to two different forms that differ only in their C-terminal extremity. The transforming protein of Woolly monkey sarcoma virus (WMSV) (Simian sarcoma virus), encoded by the v-sis oncogene, is derived from the B chain of PDGF. PDGFs are mitogenic during early developmental stages, driving the proliferation of undifferentiated mesenchyme and some progenitor populations. During later maturation stages, PDGF signalling has been implicated in tissue remodelling and cellular differentiation, and in inductive events involved in patterning and morphogenesis. In addition to driving mesenchymal proliferation, PDGFs have been shown to direct the migration, differentiation and function of a variety of specialised mesenchymal and migratory cell types, both during development and in the adult animal []. Other growth factors in this family include vascular endothelial growth factors B and C (VEGF-B, VEGF-C) [, ] which are active in angiogenesis and endothelial cell growth, and placenta growth factor (PlGF) which is also active in angiogenesis []. PDGF is structurally related to a number of other growth factors which also form disulphide-linked homo- or heterodimers.; GO: 0008083 growth factor activity, 0016020 membrane; PDB: 1WQ9_B 1RV6_W 1FZV_B 3MJK_Y 2XAC_B 2C7W_B 2VWE_A 2FJG_V 2QR0_U 1MJV_A ....
Probab=26.17 E-value=18 Score=30.08 Aligned_cols=12 Identities=42% Similarity=1.387 Sum_probs=9.3
Q ss_pred CCCCCCCCccCCC
Q 012494 332 IPSQCGYGCCASP 344 (462)
Q Consensus 332 vp~~cg~gcc~~~ 344 (462)
+=++|| |||...
T Consensus 28 ~v~RC~-GCC~~~ 39 (82)
T PF00341_consen 28 VVHRCG-GCCNDE 39 (82)
T ss_dssp EEEEEE-SBCSST
T ss_pred EEcccc-CCCCCC
Confidence 346899 999864
No 121
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.16 E-value=1.5e+02 Score=27.19 Aligned_cols=30 Identities=27% Similarity=0.259 Sum_probs=24.1
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-.+.+||..| |-+...|+.+....+++
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4466799999999 99999999988665543
No 122
>PF14967 FAM70: FAM70 protein
Probab=26.04 E-value=3.2e+02 Score=28.93 Aligned_cols=90 Identities=23% Similarity=0.401 Sum_probs=54.5
Q ss_pred cCCCCCCCCCCccccccccc-cccCCCCCCCCCCCCCCCCCCCCccccCCcchhhhhhhhhccCCCCCCCCCC-CCccCC
Q 012494 266 AGPKPHPTLPRPVARVSAFS-LYNSPSGLTPCSGIPRAVPTQGPLVQAPRLDLGICKFLEDVCSEPIIPSQCG-YGCCAS 343 (462)
Q Consensus 266 ~~~~~~~~l~rpva~~~af~-~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vp~~cg-~gcc~~ 343 (462)
.+...+..||-|..-+=||. .|..+....+.+++ ++|.|.+..-...+-.++ ....++.-|++++ ||....
T Consensus 234 ~~~~pp~ilynpaqqilay~gf~p~~~~lP~~ssY--PlplQ~~~~fP~s~ss~l-----s~sed~q~ps~s~s~~lp~~ 306 (327)
T PF14967_consen 234 GPSPPPQILYNPAQQILAYAGFCPSPPTLPTYSSY--PLPLQPSSSFPASPSSDL-----SLSEDPQPPSQSSSYGLPPN 306 (327)
T ss_pred CCCCCCCcCCCCCCccccccCccCCCCCCCCCCCc--CccCCccCCCCCCCCccC-----CcccCCCCCCCCcccCCCCC
Confidence 45677889999999999998 45556666666776 445554433222222221 1233566677754 344221
Q ss_pred CCCCCCCCCCCCcc-ccccCCCCCCC
Q 012494 344 PAGHHSHSSLLGPE-FVDYEEPPAFS 368 (462)
Q Consensus 344 ~~~~~~~~sllgpe-f~~~~~~~~~~ 368 (462)
.-.+-+|- |--+|.|||+.
T Consensus 307 ------aPp~y~P~yf~PgEKPPPYa 326 (327)
T PF14967_consen 307 ------APPRYAPPYFPPGEKPPPYA 326 (327)
T ss_pred ------CCCCCCCCCCCCCCCCcCCC
Confidence 22455666 78999999974
No 123
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=25.97 E-value=1.5e+02 Score=26.97 Aligned_cols=30 Identities=20% Similarity=0.221 Sum_probs=24.2
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-...+||..| |-+...|+.++...+++
T Consensus 145 ~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 145 VEGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3456789999999 99999999998766544
No 124
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.95 E-value=1.3e+02 Score=27.22 Aligned_cols=28 Identities=11% Similarity=0.070 Sum_probs=22.6
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 120 GNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 120 GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
|-...+||..| |.+...++++....+++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55689999999 99999999988665543
No 125
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=25.15 E-value=1.6e+02 Score=26.41 Aligned_cols=30 Identities=30% Similarity=0.323 Sum_probs=23.8
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-.-.+||..| |.+...|+.+....+++
T Consensus 132 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 132 YRGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3456689999999 99999999998765543
No 126
>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=25.02 E-value=1.6e+02 Score=27.34 Aligned_cols=31 Identities=13% Similarity=-0.041 Sum_probs=24.4
Q ss_pred HHcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 117 AVHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 117 kk~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
...|-...+||..| |-|...|+.|....+++
T Consensus 144 ~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 144 EVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 34456799999999 99999999988665433
No 127
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.92 E-value=1.8e+02 Score=26.58 Aligned_cols=34 Identities=18% Similarity=0.090 Sum_probs=27.5
Q ss_pred HHHcCCchHHHhhhCCCCCHHHHHHHHHHHHHhhh
Q 012494 116 HAVHGNKWAVIARLLPGRTDNAIKNHWNSTLRRRY 150 (462)
Q Consensus 116 vkk~GnkWskIAk~LPGRT~~QcKnRWnslLkkkl 150 (462)
....|-...+||..| |-+...++.|...-+++-+
T Consensus 139 ~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 139 ATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 334466799999999 9999999999987776644
No 128
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.80 E-value=33 Score=28.31 Aligned_cols=15 Identities=40% Similarity=0.837 Sum_probs=13.0
Q ss_pred cCCCCCCCCCCCCCC
Q 012494 219 VPKQHSTFPCPVGDI 233 (462)
Q Consensus 219 e~~q~~~~~~~~~~~ 233 (462)
++.|.++||||+||-
T Consensus 16 ~e~~~y~yPCpCGDr 30 (67)
T KOG2923|consen 16 EENQTYYYPCPCGDR 30 (67)
T ss_pred cCCCeEEcCCCCCCe
Confidence 567889999999995
No 129
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=24.75 E-value=1.7e+02 Score=25.93 Aligned_cols=30 Identities=7% Similarity=-0.009 Sum_probs=23.6
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-.-.+||..| |-+...|+++....+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3455789999999 99999999988665543
No 130
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=24.62 E-value=1.6e+02 Score=27.35 Aligned_cols=30 Identities=17% Similarity=0.110 Sum_probs=23.7
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-.+.+||..| |-+...|+++....+++
T Consensus 150 ~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 150 IEGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3456799999999 99999998887665543
No 131
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=24.44 E-value=1.7e+02 Score=27.18 Aligned_cols=30 Identities=7% Similarity=0.131 Sum_probs=23.7
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-...+||..| |-+...|+.|....+++
T Consensus 155 ~eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 155 LEELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred HcCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 3455789999999 99999999998665543
No 132
>smart00141 PDGF Platelet-derived and vascular endothelial growth factors (PDGF, VEGF) family. Platelet-derived growth factor is a potent activator for cells of mesenchymal origin. PDGF-A and PDGF-B form AA and BB homodimers and an AB heterodimer. Members of the VEGF family are homologues of PDGF.
Probab=24.26 E-value=36 Score=28.93 Aligned_cols=11 Identities=45% Similarity=1.431 Sum_probs=8.7
Q ss_pred CCCCCCCccCCC
Q 012494 333 PSQCGYGCCASP 344 (462)
Q Consensus 333 p~~cg~gcc~~~ 344 (462)
=.+|| |||+..
T Consensus 31 v~RCg-GCCn~e 41 (83)
T smart00141 31 VQRCG-GCCNDE 41 (83)
T ss_pred eceec-CCCCCC
Confidence 36898 999764
No 133
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=24.16 E-value=1.6e+02 Score=25.97 Aligned_cols=44 Identities=14% Similarity=0.095 Sum_probs=35.9
Q ss_pred hHHHHHHHHHHHHcC-CchHHHhhhCCCCCHHHHHHHHHHHHHhhh
Q 012494 106 DEEDQIIISAHAVHG-NKWAVIARLLPGRTDNAIKNHWNSTLRRRY 150 (462)
Q Consensus 106 eEEDelLLeLvkk~G-nkWskIAk~LPGRT~~QcKnRWnslLkkkl 150 (462)
.+-|.+|+++.+..+ -.++.||+.+ |-+...|.+|-+.+.+..+
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCc
Confidence 356778888887766 4599999999 9999999999988776654
No 134
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=23.91 E-value=61 Score=28.95 Aligned_cols=17 Identities=12% Similarity=0.403 Sum_probs=13.0
Q ss_pred CCCHHHHHHHHHHHHHh
Q 012494 51 PWSPEEDAVLSRLVSQF 67 (462)
Q Consensus 51 ~WT~EEDelLl~lV~ky 67 (462)
++|++||-.|-..|.+|
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 58999999999999877
No 135
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=23.64 E-value=1.2e+02 Score=26.18 Aligned_cols=69 Identities=17% Similarity=0.317 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHHh----CC---CCHHHHhhhCCCC-----Cccc-------cccccccccCCCCCC---CCCCh
Q 012494 49 KGPWSPEEDAVLSRLVSQF----GA---RNWGMIARGIPGR-----SGKS-------CRLRWCNQLDPCLKR---KPFTD 106 (462)
Q Consensus 49 KG~WT~EEDelLl~lV~ky----G~---~nWskIAk~LpgR-----S~kQ-------CR~RW~n~L~P~lkr---gpWTe 106 (462)
...||++++-.|++.+..| |. .+|..+...+.+. +..| .+.||.+.+.. .+. ..++.
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k-~~~g~~~~~~~ 82 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKK-SKNGKDPSFSK 82 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhh-cccCcCCCCCC
Confidence 3469999999999999888 42 2565554444211 2223 33455555443 122 26777
Q ss_pred HHHHHHHHHHHH
Q 012494 107 EEDQIIISAHAV 118 (462)
Q Consensus 107 EEDelLLeLvkk 118 (462)
.-|..+.+|.++
T Consensus 83 ~hd~~~f~Lsk~ 94 (98)
T PF04504_consen 83 PHDRRLFELSKK 94 (98)
T ss_pred HhHHHHHHHHHH
Confidence 888888877654
No 136
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=23.43 E-value=1.7e+02 Score=27.07 Aligned_cols=28 Identities=4% Similarity=-0.184 Sum_probs=23.0
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 119 HGNKWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 119 ~GnkWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
.|-...+||..| |-+...|+.|....++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 356799999999 9999999998765543
No 137
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=22.76 E-value=88 Score=26.35 Aligned_cols=32 Identities=25% Similarity=0.310 Sum_probs=24.3
Q ss_pred HHHHHHHHHcCCchHHHhhhCCCCCHHH---HHHHH
Q 012494 110 QIIISAHAVHGNKWAVIARLLPGRTDNA---IKNHW 142 (462)
Q Consensus 110 elLLeLvkk~GnkWskIAk~LPGRT~~Q---cKnRW 142 (462)
..|..+....|.+|..+|+.| |=+..+ |+.+|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~~Id~Ie~~~ 37 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYRELQRIKYNN 37 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHHHHHHHHHHC
Confidence 458888999999999999999 544443 45555
No 138
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=22.65 E-value=24 Score=38.08 Aligned_cols=45 Identities=24% Similarity=0.364 Sum_probs=37.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCHHHHhhh-----CCC-CCccccccccccc
Q 012494 49 KGPWSPEEDAVLSRLVSQFGARNWGMIARG-----IPG-RSGKSCRLRWCNQ 94 (462)
Q Consensus 49 KG~WT~EEDelLl~lV~kyG~~nWskIAk~-----Lpg-RS~kQCR~RW~n~ 94 (462)
-..||.+|-+-|.++.++|.. .|-.||.. ++. ||....++||+..
T Consensus 130 dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred cccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 356999999999999999986 58888875 544 9999999999753
No 139
>PRK01905 DNA-binding protein Fis; Provisional
Probab=22.63 E-value=2e+02 Score=23.59 Aligned_cols=36 Identities=17% Similarity=0.244 Sum_probs=28.2
Q ss_pred hHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHHHH
Q 012494 106 DEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKNHW 142 (462)
Q Consensus 106 eEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKnRW 142 (462)
.-|...|.+++..+++++++.|+.+ |=+...++.+.
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rkl 71 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKKL 71 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 4477788899999999999999999 76666554443
No 140
>PHA02661 vascular endothelial growth factor like protein; Provisional
Probab=22.44 E-value=41 Score=31.62 Aligned_cols=11 Identities=45% Similarity=1.419 Sum_probs=8.8
Q ss_pred CCCCCCCccCCC
Q 012494 333 PSQCGYGCCASP 344 (462)
Q Consensus 333 p~~cg~gcc~~~ 344 (462)
=.+|| |||+..
T Consensus 76 V~RCg-GCCnde 86 (146)
T PHA02661 76 VRRCG-GCCNDE 86 (146)
T ss_pred ecccc-CCCCCC
Confidence 36899 999865
No 141
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=22.27 E-value=2.1e+02 Score=25.04 Aligned_cols=28 Identities=18% Similarity=0.102 Sum_probs=22.3
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 119 HGNKWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 119 ~GnkWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
.|-...+||..| |.+...|+++-...++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALE 148 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355689999999 9999999998766554
No 142
>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=22.26 E-value=96 Score=25.87 Aligned_cols=33 Identities=30% Similarity=0.509 Sum_probs=25.0
Q ss_pred hHHHHHHHHHHHHcCCchHHHhhhCCCCCHHHHHH
Q 012494 106 DEEDQIIISAHAVHGNKWAVIARLLPGRTDNAIKN 140 (462)
Q Consensus 106 eEEDelLLeLvkk~GnkWskIAk~LPGRT~~QcKn 140 (462)
.||-++|+..- ..|.+|..+|..| |=+...|.+
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 57888887432 4678899999999 777777655
No 143
>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=21.92 E-value=1e+02 Score=26.02 Aligned_cols=29 Identities=31% Similarity=0.414 Sum_probs=22.9
Q ss_pred HHHHHHHHcCCchHHHhhhCCCCCHHHHHH
Q 012494 111 IIISAHAVHGNKWAVIARLLPGRTDNAIKN 140 (462)
Q Consensus 111 lLLeLvkk~GnkWskIAk~LPGRT~~QcKn 140 (462)
.|-.+....|.+|..+|+.| |=+..+|..
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 34555677899999999999 888877755
No 144
>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=21.38 E-value=76 Score=27.75 Aligned_cols=28 Identities=18% Similarity=0.165 Sum_probs=23.0
Q ss_pred CCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 120 GNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 120 GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
|-.+.+||..| |-+...|++++....++
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKE 148 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44699999999 99999999998765533
No 145
>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=21.06 E-value=2.2e+02 Score=25.23 Aligned_cols=28 Identities=29% Similarity=0.391 Sum_probs=22.2
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHHH
Q 012494 119 HGNKWAVIARLLPGRTDNAIKNHWNSTLR 147 (462)
Q Consensus 119 ~GnkWskIAk~LPGRT~~QcKnRWnslLk 147 (462)
.|-...+||+.| |-+...++++-...++
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAIK 164 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355689999999 9999999988766543
No 146
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.81 E-value=1.8e+02 Score=26.47 Aligned_cols=29 Identities=21% Similarity=0.276 Sum_probs=24.0
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 119 HGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 119 ~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
.|-...+||..| |-+...|+++....++.
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 345689999999 99999999998776644
No 147
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.37 E-value=2e+02 Score=26.48 Aligned_cols=29 Identities=17% Similarity=0.139 Sum_probs=24.0
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 119 HGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 119 ~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
.|-...+||..| |-+...|+.+....+++
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 173 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDA 173 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355689999999 99999999998776654
No 148
>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=20.37 E-value=1.2e+02 Score=25.70 Aligned_cols=26 Identities=23% Similarity=0.259 Sum_probs=21.1
Q ss_pred HHHHHHHHHHcCCchHHHhhhCCCCCH
Q 012494 109 DQIIISAHAVHGNKWAVIARLLPGRTD 135 (462)
Q Consensus 109 DelLLeLvkk~GnkWskIAk~LPGRT~ 135 (462)
|..|..+....|..|.++|+.| |=+.
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~ 29 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSV 29 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCH
Confidence 4567788899999999999988 5444
No 149
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=20.25 E-value=2.3e+02 Score=25.91 Aligned_cols=30 Identities=27% Similarity=0.319 Sum_probs=24.3
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-...+||..| |.+...|+++-...+++
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~ 172 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKA 172 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4456799999999 99999999998665543
No 150
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.14 E-value=2.4e+02 Score=25.29 Aligned_cols=30 Identities=20% Similarity=0.227 Sum_probs=23.9
Q ss_pred HcCCchHHHhhhCCCCCHHHHHHHHHHHHHh
Q 012494 118 VHGNKWAVIARLLPGRTDNAIKNHWNSTLRR 148 (462)
Q Consensus 118 k~GnkWskIAk~LPGRT~~QcKnRWnslLkk 148 (462)
..|-...+||..| |-+...|+++-...+++
T Consensus 126 ~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 126 ASGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3456789999999 99999999988765543
Done!