Query 021220
Match_columns 316
No_of_seqs 227 out of 1478
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 08:33:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021220.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021220hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03091 hypothetical protein; 100.0 9.3E-38 2E-42 306.2 11.2 133 1-133 1-133 (459)
2 PLN03212 Transcription repress 100.0 4.4E-37 9.5E-42 283.4 10.4 131 3-133 14-144 (249)
3 KOG0048 Transcription factor, 100.0 4.6E-34 1E-38 264.2 10.6 118 11-128 6-123 (238)
4 KOG0049 Transcription factor, 99.8 3E-19 6.6E-24 181.5 6.6 126 7-132 246-426 (939)
5 KOG0049 Transcription factor, 99.7 2.4E-18 5.2E-23 175.0 4.8 111 1-112 347-458 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 3.5E-16 7.5E-21 115.0 2.4 60 17-78 1-60 (60)
7 PLN03212 Transcription repress 99.6 2.4E-16 5.2E-21 146.2 -2.0 110 63-172 21-132 (249)
8 COG5147 REB1 Myb superfamily p 99.5 3.5E-15 7.5E-20 151.1 5.7 108 9-117 15-122 (512)
9 KOG0050 mRNA splicing protein 99.5 1.7E-15 3.7E-20 151.3 3.4 105 12-118 5-109 (617)
10 KOG0048 Transcription factor, 99.5 4.8E-16 1E-20 144.1 -2.9 107 63-169 5-113 (238)
11 PF13921 Myb_DNA-bind_6: Myb-l 99.5 1.4E-14 2.9E-19 106.5 2.9 59 70-128 1-59 (60)
12 PLN03091 hypothetical protein; 99.5 3.4E-15 7.5E-20 147.7 -2.7 104 63-166 10-115 (459)
13 KOG0051 RNA polymerase I termi 99.4 1.4E-13 2.9E-18 141.0 4.7 103 13-118 383-513 (607)
14 PF00249 Myb_DNA-binding: Myb- 99.4 4E-13 8.6E-18 95.1 4.9 46 67-112 1-48 (48)
15 PF00249 Myb_DNA-binding: Myb- 99.3 5.8E-13 1.3E-17 94.2 -0.4 48 14-61 1-48 (48)
16 smart00717 SANT SANT SWI3, AD 99.2 2.1E-11 4.6E-16 83.6 5.8 47 67-113 1-48 (49)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1.7E-10 3.6E-15 78.0 5.6 44 69-112 1-45 (45)
18 KOG0051 RNA polymerase I termi 99.1 5.6E-11 1.2E-15 122.1 3.3 120 12-133 306-451 (607)
19 smart00717 SANT SANT SWI3, AD 98.9 4E-10 8.6E-15 77.2 1.1 48 14-62 1-48 (49)
20 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 2.2E-09 4.7E-14 72.5 0.8 45 16-61 1-45 (45)
21 COG5147 REB1 Myb superfamily p 98.3 6E-08 1.3E-12 98.9 -2.6 98 12-112 289-396 (512)
22 KOG0050 mRNA splicing protein 98.2 3E-07 6.5E-12 93.0 0.7 80 65-144 5-85 (617)
23 KOG0457 Histone acetyltransfer 97.7 5.3E-05 1.1E-09 75.7 6.2 50 64-113 69-119 (438)
24 TIGR01557 myb_SHAQKYF myb-like 97.7 0.00013 2.7E-09 54.1 5.8 48 66-113 2-55 (57)
25 TIGR01557 myb_SHAQKYF myb-like 97.6 2E-05 4.3E-10 58.4 1.2 48 14-61 3-54 (57)
26 KOG0457 Histone acetyltransfer 97.4 3.4E-05 7.3E-10 77.1 0.2 49 12-61 70-118 (438)
27 PF08914 Myb_DNA-bind_2: Rap1 97.0 0.0009 2E-08 50.9 4.2 50 67-116 2-61 (65)
28 PF13325 MCRS_N: N-terminal re 96.9 0.0013 2.9E-08 60.1 5.3 100 16-117 1-131 (199)
29 PF13837 Myb_DNA-bind_4: Myb/S 96.9 0.00088 1.9E-08 52.2 3.4 49 67-115 1-67 (90)
30 TIGR02894 DNA_bind_RsfA transc 96.9 0.001 2.2E-08 58.8 4.1 52 66-118 3-61 (161)
31 KOG1279 Chromatin remodeling f 96.9 0.0013 2.8E-08 67.7 5.4 47 65-111 251-297 (506)
32 COG5259 RSC8 RSC chromatin rem 96.9 0.0011 2.3E-08 67.1 4.5 44 68-111 280-323 (531)
33 PRK13923 putative spore coat p 96.2 0.0051 1.1E-07 55.0 3.7 51 66-117 4-61 (170)
34 PF13873 Myb_DNA-bind_5: Myb/S 96.0 0.012 2.7E-07 45.0 4.8 48 67-114 2-71 (78)
35 KOG1279 Chromatin remodeling f 95.9 0.0026 5.7E-08 65.5 1.0 49 10-60 249-297 (506)
36 COG5259 RSC8 RSC chromatin rem 95.9 0.0021 4.6E-08 65.1 0.0 46 13-60 278-323 (531)
37 COG5114 Histone acetyltransfer 95.6 0.018 3.9E-07 56.2 5.2 49 65-113 61-110 (432)
38 PF08914 Myb_DNA-bind_2: Rap1 95.1 0.0063 1.4E-07 46.2 0.2 51 14-64 2-60 (65)
39 TIGR02894 DNA_bind_RsfA transc 95.1 0.0058 1.3E-07 54.2 -0.1 50 12-63 2-57 (161)
40 PF13837 Myb_DNA-bind_4: Myb/S 94.9 0.0043 9.2E-08 48.3 -1.2 46 15-60 2-63 (90)
41 COG5114 Histone acetyltransfer 94.2 0.0096 2.1E-07 58.1 -0.8 48 14-62 63-110 (432)
42 PF13873 Myb_DNA-bind_5: Myb/S 93.5 0.014 3E-07 44.7 -1.0 49 13-61 1-69 (78)
43 PLN03142 Probable chromatin-re 93.5 0.17 3.6E-06 56.7 6.8 100 15-115 825-987 (1033)
44 PRK13923 putative spore coat p 92.7 0.02 4.3E-07 51.3 -1.4 50 11-62 2-57 (170)
45 COG5118 BDP1 Transcription ini 91.9 0.24 5.3E-06 49.5 5.0 46 68-113 366-411 (507)
46 KOG2656 DNA methyltransferase 91.6 0.33 7.1E-06 48.7 5.5 84 36-120 75-189 (445)
47 PF12776 Myb_DNA-bind_3: Myb/S 91.3 0.47 1E-05 37.2 5.1 45 69-113 1-63 (96)
48 KOG1194 Predicted DNA-binding 91.2 0.4 8.6E-06 49.0 5.7 48 67-114 187-234 (534)
49 PF09111 SLIDE: SLIDE; InterP 89.4 0.47 1E-05 40.1 3.9 52 64-115 46-113 (118)
50 KOG4282 Transcription factor G 89.4 0.46 1E-05 46.3 4.4 49 67-115 54-116 (345)
51 PF08281 Sigma70_r4_2: Sigma-7 87.1 1.5 3.3E-05 30.8 4.8 41 72-113 12-52 (54)
52 COG5118 BDP1 Transcription ini 81.6 0.58 1.3E-05 46.9 0.7 64 14-79 365-436 (507)
53 PF09111 SLIDE: SLIDE; InterP 80.7 1.3 2.9E-05 37.4 2.5 34 11-44 46-82 (118)
54 KOG4167 Predicted DNA-binding 80.1 2.9 6.3E-05 45.2 5.3 47 67-113 619-665 (907)
55 smart00595 MADF subfamily of S 78.8 2.3 5E-05 32.8 3.2 24 89-113 30-53 (89)
56 PF04545 Sigma70_r4: Sigma-70, 73.2 7.7 0.00017 26.9 4.3 41 73-114 7-47 (50)
57 KOG4468 Polycomb-group transcr 73.1 5.2 0.00011 42.5 4.7 50 66-115 87-146 (782)
58 KOG4282 Transcription factor G 72.4 1.3 2.8E-05 43.2 0.3 47 14-60 54-112 (345)
59 PF11626 Rap1_C: TRF2-interact 71.2 3.9 8.5E-05 32.3 2.7 29 11-42 44-80 (87)
60 PRK11179 DNA-binding transcrip 70.0 7.1 0.00015 33.6 4.3 46 72-118 8-54 (153)
61 PF07750 GcrA: GcrA cell cycle 68.6 5.9 0.00013 35.1 3.6 41 69-110 2-42 (162)
62 PF13404 HTH_AsnC-type: AsnC-t 67.2 13 0.00027 25.7 4.2 38 73-111 3-41 (42)
63 PF11626 Rap1_C: TRF2-interact 66.9 5.5 0.00012 31.5 2.7 16 63-78 43-58 (87)
64 PRK11169 leucine-responsive tr 63.8 9.6 0.00021 33.2 3.9 46 72-118 13-59 (164)
65 PF10545 MADF_DNA_bdg: Alcohol 62.5 7.6 0.00016 29.0 2.7 25 89-113 29-54 (85)
66 TIGR02985 Sig70_bacteroi1 RNA 61.0 16 0.00035 30.1 4.7 35 78-113 121-155 (161)
67 KOG4329 DNA-binding protein [G 60.4 1.5E+02 0.0033 30.1 11.8 46 68-113 278-324 (445)
68 KOG2009 Transcription initiati 59.8 10 0.00022 40.1 3.9 45 66-110 408-452 (584)
69 PF13325 MCRS_N: N-terminal re 59.5 18 0.00039 33.4 5.0 45 69-114 1-48 (199)
70 KOG4167 Predicted DNA-binding 57.7 3.8 8.2E-05 44.4 0.3 44 14-59 619-662 (907)
71 cd08319 Death_RAIDD Death doma 56.9 15 0.00031 29.2 3.5 29 75-104 2-30 (83)
72 PF01388 ARID: ARID/BRIGHT DNA 55.8 25 0.00053 27.4 4.7 38 77-114 40-90 (92)
73 PF11035 SnAPC_2_like: Small n 52.1 44 0.00095 33.1 6.5 46 67-112 21-70 (344)
74 KOG3554 Histone deacetylase co 52.0 32 0.00068 35.9 5.7 41 69-109 287-328 (693)
75 cd08803 Death_ank3 Death domai 51.7 22 0.00047 28.2 3.7 31 75-106 4-34 (84)
76 PF02954 HTH_8: Bacterial regu 51.0 31 0.00067 23.4 3.9 35 74-109 6-40 (42)
77 smart00501 BRIGHT BRIGHT, ARID 50.1 31 0.00068 27.1 4.5 38 77-114 36-86 (93)
78 KOG2656 DNA methyltransferase 47.9 6.7 0.00014 39.7 0.3 51 9-60 125-180 (445)
79 TIGR02937 sigma70-ECF RNA poly 47.7 32 0.0007 27.4 4.3 36 78-114 118-153 (158)
80 PF04504 DUF573: Protein of un 47.6 28 0.0006 28.3 3.8 47 68-114 5-64 (98)
81 smart00344 HTH_ASNC helix_turn 47.1 37 0.0008 26.9 4.5 45 73-118 3-48 (108)
82 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 45.8 34 0.00074 24.7 3.6 37 72-109 6-42 (50)
83 cd08317 Death_ank Death domain 44.5 24 0.00053 27.4 3.0 30 75-105 4-33 (84)
84 cd06171 Sigma70_r4 Sigma70, re 44.1 54 0.0012 21.4 4.3 40 70-111 11-50 (55)
85 PF11035 SnAPC_2_like: Small n 43.6 39 0.00084 33.5 4.7 87 13-113 20-127 (344)
86 PRK09652 RNA polymerase sigma 43.4 41 0.00088 28.4 4.4 29 84-113 142-170 (182)
87 PF09420 Nop16: Ribosome bioge 42.3 55 0.0012 28.7 5.2 47 66-112 113-163 (164)
88 cd08804 Death_ank2 Death domai 40.8 35 0.00075 26.9 3.3 31 75-106 4-34 (84)
89 cd08318 Death_NMPP84 Death dom 40.8 36 0.00078 26.8 3.4 27 78-105 10-36 (86)
90 KOG0384 Chromodomain-helicase 40.0 29 0.00063 39.9 3.7 73 14-95 1133-1208(1373)
91 smart00005 DEATH DEATH domain, 39.9 37 0.00079 25.9 3.3 30 74-104 4-34 (88)
92 PRK11924 RNA polymerase sigma 38.7 51 0.0011 27.7 4.3 28 85-113 140-167 (179)
93 PRK04217 hypothetical protein; 37.6 63 0.0014 27.0 4.5 44 69-114 42-85 (110)
94 PF07638 Sigma70_ECF: ECF sigm 36.7 59 0.0013 28.6 4.5 38 74-112 139-176 (185)
95 cd08311 Death_p75NR Death doma 36.1 39 0.00085 26.3 2.9 33 72-106 2-34 (77)
96 PRK09643 RNA polymerase sigma 35.2 65 0.0014 28.3 4.6 27 85-112 149-175 (192)
97 cd08805 Death_ank1 Death domai 35.0 45 0.00098 26.5 3.2 27 75-102 4-30 (84)
98 cd08777 Death_RIP1 Death Domai 34.6 45 0.00099 26.4 3.1 30 76-106 3-32 (86)
99 KOG4468 Polycomb-group transcr 34.3 13 0.00028 39.7 -0.1 46 14-61 88-143 (782)
100 PF13936 HTH_38: Helix-turn-he 34.2 44 0.00096 22.9 2.6 37 69-107 4-40 (44)
101 PRK09645 RNA polymerase sigma 33.9 89 0.0019 26.5 5.1 27 86-113 134-160 (173)
102 cd08779 Death_PIDD Death Domai 33.3 50 0.0011 26.1 3.1 27 76-103 3-29 (86)
103 PRK09641 RNA polymerase sigma 32.9 72 0.0016 27.3 4.4 28 85-113 151-178 (187)
104 TIGR02954 Sig70_famx3 RNA poly 31.5 80 0.0017 26.8 4.4 29 85-114 134-162 (169)
105 PRK12523 RNA polymerase sigma 31.4 1E+02 0.0022 26.3 5.1 31 84-115 133-163 (172)
106 TIGR02939 RpoE_Sigma70 RNA pol 31.0 64 0.0014 27.7 3.8 28 86-114 154-181 (190)
107 PRK09637 RNA polymerase sigma 30.5 85 0.0018 27.4 4.5 28 85-113 121-148 (181)
108 COG2197 CitB Response regulato 30.5 72 0.0016 28.9 4.1 45 68-115 147-191 (211)
109 PRK11179 DNA-binding transcrip 30.0 14 0.0003 31.8 -0.6 46 19-66 8-53 (153)
110 PRK01905 DNA-binding protein F 29.8 1.1E+02 0.0024 23.4 4.5 37 72-109 36-72 (77)
111 PRK09047 RNA polymerase factor 29.7 1E+02 0.0022 25.6 4.7 29 85-114 121-149 (161)
112 PF10440 WIYLD: Ubiquitin-bind 29.1 38 0.00082 25.9 1.7 19 76-94 30-48 (65)
113 COG1522 Lrp Transcriptional re 28.8 98 0.0021 25.8 4.5 46 72-118 7-53 (154)
114 PRK09648 RNA polymerase sigma 28.6 1E+02 0.0022 26.7 4.6 29 85-114 154-182 (189)
115 KOG1194 Predicted DNA-binding 27.9 84 0.0018 32.7 4.4 42 68-110 471-512 (534)
116 PRK12512 RNA polymerase sigma 27.7 1.1E+02 0.0023 26.4 4.6 29 85-114 146-174 (184)
117 TIGR02943 Sig70_famx1 RNA poly 27.6 1.1E+02 0.0024 26.8 4.7 29 85-114 146-174 (188)
118 PRK12531 RNA polymerase sigma 26.8 1.1E+02 0.0025 26.7 4.7 28 86-114 157-184 (194)
119 TIGR02948 SigW_bacill RNA poly 26.6 98 0.0021 26.4 4.2 27 86-113 152-178 (187)
120 PLN03142 Probable chromatin-re 26.6 1.1E+02 0.0023 35.0 5.3 41 69-109 826-867 (1033)
121 PRK00430 fis global DNA-bindin 26.5 1.3E+02 0.0029 24.2 4.6 36 73-109 55-90 (95)
122 PRK12515 RNA polymerase sigma 26.5 1.2E+02 0.0025 26.4 4.7 28 85-113 146-173 (189)
123 PRK09642 RNA polymerase sigma 26.5 1.2E+02 0.0026 25.3 4.6 28 85-113 121-148 (160)
124 PRK12532 RNA polymerase sigma 26.5 1.3E+02 0.0027 26.3 4.9 27 85-112 151-177 (195)
125 PRK12529 RNA polymerase sigma 26.2 1.4E+02 0.003 25.8 5.0 32 85-117 142-173 (178)
126 PF07750 GcrA: GcrA cell cycle 25.9 36 0.00078 30.2 1.3 33 16-50 2-35 (162)
127 PRK12524 RNA polymerase sigma 25.7 1.2E+02 0.0026 26.6 4.6 28 85-113 151-178 (196)
128 PRK11923 algU RNA polymerase s 25.4 1.1E+02 0.0024 26.5 4.3 27 86-113 154-180 (193)
129 PRK11169 leucine-responsive tr 25.1 15 0.00032 32.1 -1.4 45 19-65 13-57 (164)
130 PRK12530 RNA polymerase sigma 25.1 1.2E+02 0.0027 26.4 4.6 28 85-113 149-176 (189)
131 PRK06759 RNA polymerase factor 24.4 1.4E+02 0.0031 24.6 4.6 27 86-113 122-148 (154)
132 cd01670 Death Death Domain: a 23.8 83 0.0018 23.3 2.8 26 78-104 2-27 (79)
133 PRK12527 RNA polymerase sigma 23.4 1.6E+02 0.0034 24.7 4.7 28 86-114 121-148 (159)
134 TIGR02952 Sig70_famx2 RNA poly 23.0 1.5E+02 0.0032 24.8 4.5 27 86-113 138-164 (170)
135 PF00196 GerE: Bacterial regul 22.7 93 0.002 22.0 2.7 42 70-114 4-45 (58)
136 cd08306 Death_FADD Fas-associa 22.5 1.2E+02 0.0025 23.9 3.5 28 78-106 5-32 (86)
137 KOG2009 Transcription initiati 22.4 50 0.0011 35.2 1.7 49 9-59 404-452 (584)
138 TIGR02999 Sig-70_X6 RNA polyme 22.2 1.6E+02 0.0035 25.1 4.7 27 86-113 150-176 (183)
139 PRK12528 RNA polymerase sigma 21.7 1.7E+02 0.0038 24.4 4.7 29 85-114 128-156 (161)
140 PRK00118 putative DNA-binding 21.6 1.8E+02 0.0039 24.0 4.5 41 72-113 19-59 (104)
141 PF01527 HTH_Tnp_1: Transposas 21.6 1.7E+02 0.0036 21.5 4.0 46 66-113 3-48 (76)
142 PRK12514 RNA polymerase sigma 21.3 1.6E+02 0.0035 25.1 4.5 27 86-113 145-171 (179)
143 PRK12536 RNA polymerase sigma 21.2 1.7E+02 0.0037 25.2 4.6 29 85-114 144-172 (181)
144 PRK09651 RNA polymerase sigma 21.1 1.4E+02 0.003 25.5 4.0 28 86-114 135-162 (172)
145 PRK09649 RNA polymerase sigma 21.0 1.6E+02 0.0034 25.7 4.4 29 86-115 146-174 (185)
146 TIGR02950 SigM_subfam RNA poly 20.9 61 0.0013 26.8 1.7 28 86-114 121-148 (154)
147 PRK12547 RNA polymerase sigma 20.2 1.9E+02 0.0042 24.4 4.7 29 85-114 127-155 (164)
148 PRK13919 putative RNA polymera 20.2 1.8E+02 0.004 24.9 4.6 28 86-114 151-178 (186)
149 COG2963 Transposase and inacti 20.0 2.7E+02 0.0059 22.4 5.3 44 67-112 5-49 (116)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=9.3e-38 Score=306.25 Aligned_cols=133 Identities=64% Similarity=1.235 Sum_probs=128.6
Q ss_pred CCCCCcccCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCCCCCCCCHHHHHHHHH
Q 021220 1 MGRSPCCEKEHTNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDLKRGNFTEEEDELIIN 80 (316)
Q Consensus 1 mgr~~~~~K~~~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EEDe~Lle 80 (316)
|||++||+|+.++||+||+|||++|+++|.+||..+|..||+.++.+|+++|||+||.+||+|.+++++||+|||++|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998756999999999999999999999999999999999
Q ss_pred HHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhhhhhhcCCCCCCCCCCCCCCC
Q 021220 81 FHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIKRKLYSRGIDPQTHRPLNSAP 133 (316)
Q Consensus 81 lv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~k~~~~~~s~~e~~~l~~~~ 133 (316)
++.+||++|++||+.|+|||+++||+||+.+++++++..++.+.+++++..+.
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~E 133 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEVE 133 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCccccc
Confidence 99999999999999999999999999999999999999999999999987653
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=4.4e-37 Score=283.38 Aligned_cols=131 Identities=66% Similarity=1.287 Sum_probs=125.4
Q ss_pred CCCcccCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCCCCCCCCHHHHHHHHHHH
Q 021220 3 RSPCCEKEHTNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDLKRGNFTEEEDELIINFH 82 (316)
Q Consensus 3 r~~~~~K~~~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EEDe~Llelv 82 (316)
|+|||.|.++++++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.+||+|.+++++||+|||++|++++
T Consensus 14 ~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~ 93 (249)
T PLN03212 14 TTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLH 93 (249)
T ss_pred CCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999865599999999999999999999999999999999999
Q ss_pred HhhCCchhHHhhcCCCCCHHHHHHHHHHhhhhhhhcCCCCCCCCCCCCCCC
Q 021220 83 SLLGNKWSLIAARLPGRTDNEIKNYWNTHIKRKLYSRGIDPQTHRPLNSAP 133 (316)
Q Consensus 83 ~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~k~~~~~~s~~e~~~l~~~~ 133 (316)
.+||++|+.||+.|+|||+++|||||+.++++++...+..+++..++....
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~~~~~ 144 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPLDANN 144 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCCCccc
Confidence 999999999999999999999999999999999999999999988876543
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=4.6e-34 Score=264.18 Aligned_cols=118 Identities=68% Similarity=1.178 Sum_probs=110.1
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCCCCCCCCHHHHHHHHHHHHhhCCchh
Q 021220 11 HTNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDLKRGNFTEEEDELIINFHSLLGNKWS 90 (316)
Q Consensus 11 ~~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EEDe~Llelv~~~GnkWs 90 (316)
.+.||+||+|||++|+.+|.+||.++|..|++.+|.+|++|+||.||.|||+|++++|.||+|||++|++|+..|||+|+
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 34579999999999999999999999999999999669999999999999999999999999999999999999999999
Q ss_pred HHhhcCCCCCHHHHHHHHHHhhhhhhhcCCCCCCCCCC
Q 021220 91 LIAARLPGRTDNEIKNYWNTHIKRKLYSRGIDPQTHRP 128 (316)
Q Consensus 91 ~IA~~lpgRT~~qcknRW~~~lk~k~~~~~~s~~e~~~ 128 (316)
.||++|||||+++|||+|+.+|++++...+.++....+
T Consensus 86 ~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~~~~~~ 123 (238)
T KOG0048|consen 86 LIAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDPSTHRP 123 (238)
T ss_pred HHHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCCCcccc
Confidence 99999999999999999999999999988755554443
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.77 E-value=3e-19 Score=181.50 Aligned_cols=126 Identities=23% Similarity=0.377 Sum_probs=115.5
Q ss_pred ccCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccccccc--------------------------------
Q 021220 7 CEKEHTNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCR-------------------------------- 54 (316)
Q Consensus 7 ~~K~~~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr-------------------------------- 54 (316)
.+.|.++|..|+.|||++|+.+...++..+|.+||..++++|+..||.
T Consensus 246 ~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~ 325 (939)
T KOG0049|consen 246 ELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSI 325 (939)
T ss_pred hcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhc
Confidence 356888999999999999999998888888888888888878888886
Q ss_pred ----------------------ceeeeccCCCCCCCCCCHHHHHHHHHHHHhhCC-chhHHhhcCCCCCHHHHHHHHHHh
Q 021220 55 ----------------------LRWINYLRPDLKRGNFTEEEDELIINFHSLLGN-KWSLIAARLPGRTDNEIKNYWNTH 111 (316)
Q Consensus 55 ----------------------~Rw~n~L~p~lkrg~WT~EEDe~Llelv~~~Gn-kWs~IA~~lpgRT~~qcknRW~~~ 111 (316)
.||...|+|.+++|+||.+||.+|+.+|.+||. .|.+|-..+|||++.|||+||.+.
T Consensus 326 nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nv 405 (939)
T KOG0049|consen 326 NSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNV 405 (939)
T ss_pred cCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHH
Confidence 789999999999999999999999999999995 599999999999999999999999
Q ss_pred hhhhhhcCCCCCCCCCCCCCC
Q 021220 112 IKRKLYSRGIDPQTHRPLNSA 132 (316)
Q Consensus 112 lk~k~~~~~~s~~e~~~l~~~ 132 (316)
|.+.++.+.|+-.++..|...
T Consensus 406 L~~s~K~~rW~l~edeqL~~~ 426 (939)
T KOG0049|consen 406 LNRSAKVERWTLVEDEQLLYA 426 (939)
T ss_pred HHHhhccCceeecchHHHHHH
Confidence 999999999999999888754
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.72 E-value=2.4e-18 Score=175.01 Aligned_cols=111 Identities=25% Similarity=0.401 Sum_probs=102.6
Q ss_pred CCCCCcccCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCCCCCCCCHHHHHHHHH
Q 021220 1 MGRSPCCEKEHTNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDLKRGNFTEEEDELIIN 80 (316)
Q Consensus 1 mgr~~~~~K~~~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EEDe~Lle 80 (316)
+||......|.+++|+||.+||.+|+.+|.+||.++|-+|-..+++ |+..|||+||.|.|+...|.+.||-.||+.||.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPn-RSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPN-RSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCC-ccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 5788899999999999999999999999999999999999999997 999999999999999999999999999999999
Q ss_pred HHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhh
Q 021220 81 FHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHI 112 (316)
Q Consensus 81 lv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~l 112 (316)
+|.+|| ++|.+||.+||+||..|.+.|=...+
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~ 458 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLI 458 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHHHHH
Confidence 999999 79999999999999966544443333
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.59 E-value=3.5e-16 Score=115.00 Aligned_cols=60 Identities=47% Similarity=0.882 Sum_probs=54.8
Q ss_pred CCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCCCCCCCCHHHHHHH
Q 021220 17 WTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDLKRGNFTEEEDELI 78 (316)
Q Consensus 17 WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EEDe~L 78 (316)
||+|||++|+.+|..|| .+|..||+.|+. |++.+|+.||.++|++.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g-~~W~~Ia~~l~~-Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYG-NDWKKIAEHLGN-RTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHT-S-HHHHHHHSTT-S-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHC-cCHHHHHHHHCc-CCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 99999999999999999 579999999975 9999999999999999999999999999987
No 7
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.55 E-value=2.4e-16 Score=146.16 Aligned_cols=110 Identities=18% Similarity=0.210 Sum_probs=96.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcC-CCCCHHHHHHHHHHhhhhhhhcCCCCCCCCCCCCCCCCCCCCCC
Q 021220 63 PDLKRGNFTEEEDELIINFHSLLG-NKWSLIAARL-PGRTDNEIKNYWNTHIKRKLYSRGIDPQTHRPLNSAPVPAPSPG 140 (316)
Q Consensus 63 p~lkrg~WT~EEDe~Llelv~~~G-nkWs~IA~~l-pgRT~~qcknRW~~~lk~k~~~~~~s~~e~~~l~~~~~~~p~~~ 140 (316)
+.+++++||+|||++|+++|++|| ++|..||+.+ ++|++.|||.||.++|++.++++.|+.+|+..|......-...|
T Consensus 21 ~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnKW 100 (249)
T PLN03212 21 MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRW 100 (249)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhccccH
Confidence 468899999999999999999999 6899999998 69999999999999999999999999999999988877777888
Q ss_pred CCCCCCCCCCCCCCCCCCCCCccchhhccccC
Q 021220 141 NNNNNNSNKRNNNTSTNTKTDCSNKFEMNVQS 172 (316)
Q Consensus 141 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 172 (316)
+.++...++|++++.+|-++....+......+
T Consensus 101 s~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i 132 (249)
T PLN03212 101 SLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGI 132 (249)
T ss_pred HHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCC
Confidence 88888889999988888777666555444333
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=99.55 E-value=3.5e-15 Score=151.06 Aligned_cols=108 Identities=31% Similarity=0.520 Sum_probs=102.5
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCCCCCCCCHHHHHHHHHHHHhhCCc
Q 021220 9 KEHTNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDLKRGNFTEEEDELIINFHSLLGNK 88 (316)
Q Consensus 9 K~~~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EEDe~Llelv~~~Gnk 88 (316)
..+.+.|.|+..||+.|+.+|.+||..+|..||..+.. |+++||+.||.++++|.+++..|+.|||+.|+.+..++|..
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~-~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ 93 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLIS-STGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcc-cccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch
Confidence 45678899999999999999999999999999999997 99999999999999999999999999999999999999999
Q ss_pred hhHHhhcCCCCCHHHHHHHHHHhhhhhhh
Q 021220 89 WSLIAARLPGRTDNEIKNYWNTHIKRKLY 117 (316)
Q Consensus 89 Ws~IA~~lpgRT~~qcknRW~~~lk~k~~ 117 (316)
|+.||..+++|+..+|.+||...+.....
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999998876555
No 9
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.55 E-value=1.7e-15 Score=151.35 Aligned_cols=105 Identities=25% Similarity=0.539 Sum_probs=99.7
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCCCCCCCCHHHHHHHHHHHHhhCCchhH
Q 021220 12 TNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDLKRGNFTEEEDELIINFHSLLGNKWSL 91 (316)
Q Consensus 12 ~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EEDe~Llelv~~~GnkWs~ 91 (316)
++.|.|+.-||+.|...|.+||...|++|++.+.. ++++||+.||..+|+|.+++..|+.|||++|+.++..+...|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~-kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNR-KTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhh-cchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 46789999999999999999999999999999986 99999999999999999999999999999999999999999999
Q ss_pred HhhcCCCCCHHHHHHHHHHhhhhhhhc
Q 021220 92 IAARLPGRTDNEIKNYWNTHIKRKLYS 118 (316)
Q Consensus 92 IA~~lpgRT~~qcknRW~~~lk~k~~~ 118 (316)
|+..| ||+.+||..||++++......
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~ 109 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSY 109 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhh
Confidence 99999 999999999999998766543
No 10
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.52 E-value=4.8e-16 Score=144.14 Aligned_cols=107 Identities=15% Similarity=0.146 Sum_probs=97.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcCC-CCCHHHHHHHHHHhhhhhhhcCCCCCCCCCCCCCCCCCCCCCC
Q 021220 63 PDLKRGNFTEEEDELIINFHSLLG-NKWSLIAARLP-GRTDNEIKNYWNTHIKRKLYSRGIDPQTHRPLNSAPVPAPSPG 140 (316)
Q Consensus 63 p~lkrg~WT~EEDe~Llelv~~~G-nkWs~IA~~lp-gRT~~qcknRW~~~lk~k~~~~~~s~~e~~~l~~~~~~~p~~~ 140 (316)
+.+.+|+||.|||++|+++|++|| ++|..|++.++ +|++++||-||.++|++.++++.|+++|++.|..+...-...+
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 345589999999999999999999 67999999998 9999999999999999999999999999999999988888899
Q ss_pred CCCCCCCCCCCCCCCCCCCCCccchhhcc
Q 021220 141 NNNNNNSNKRNNNTSTNTKTDCSNKFEMN 169 (316)
Q Consensus 141 s~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 169 (316)
+.++...++|+++..+|.++....+....
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~ 113 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLK 113 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999987665444443
No 11
>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=99.49 E-value=1.4e-14 Score=106.50 Aligned_cols=59 Identities=31% Similarity=0.588 Sum_probs=52.5
Q ss_pred CCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhhhhhhcCCCCCCCCCC
Q 021220 70 FTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIKRKLYSRGIDPQTHRP 128 (316)
Q Consensus 70 WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~k~~~~~~s~~e~~~ 128 (316)
||+|||++|+++|.+||++|..||..|+.||..+|++||+.+|++.+.+..|+++|+..
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~ 59 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQR 59 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhc
Confidence 99999999999999999999999999966999999999999999999999999888653
No 12
>PLN03091 hypothetical protein; Provisional
Probab=99.46 E-value=3.4e-15 Score=147.66 Aligned_cols=104 Identities=17% Similarity=0.243 Sum_probs=93.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcC-CCCCHHHHHHHHHHhhhhhhhcCCCCCCCCCCCCCCCCCCCCCC
Q 021220 63 PDLKRGNFTEEEDELIINFHSLLG-NKWSLIAARL-PGRTDNEIKNYWNTHIKRKLYSRGIDPQTHRPLNSAPVPAPSPG 140 (316)
Q Consensus 63 p~lkrg~WT~EEDe~Llelv~~~G-nkWs~IA~~l-pgRT~~qcknRW~~~lk~k~~~~~~s~~e~~~l~~~~~~~p~~~ 140 (316)
..++++.||+|||++|+++|.+|| ++|..||+.+ +||+++|||.||.++|++.++++.|+++|+..|......-+..+
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnKW 89 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNRW 89 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcch
Confidence 578899999999999999999999 5799999998 59999999999999999999999999999999988777777788
Q ss_pred CCCCCCCCCCCCCCCCCCCCCccchh
Q 021220 141 NNNNNNSNKRNNNTSTNTKTDCSNKF 166 (316)
Q Consensus 141 s~~~~~~~~~~~~~~~~~~~~~~~~~ 166 (316)
..++....+|+++..+|-++.+..+.
T Consensus 90 skIAk~LPGRTDnqIKNRWnslLKKk 115 (459)
T PLN03091 90 SQIAAQLPGRTDNEIKNLWNSCLKKK 115 (459)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHH
Confidence 88888888999888888777766554
No 13
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.41 E-value=1.4e-13 Score=141.05 Aligned_cols=103 Identities=29% Similarity=0.610 Sum_probs=92.8
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCC--CCCCCCHHHHHHHHHHHH-------
Q 021220 13 NKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDL--KRGNFTEEEDELIINFHS------- 83 (316)
Q Consensus 13 kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~l--krg~WT~EEDe~Llelv~------- 83 (316)
.+|+||+||++.|..++..+| ++|..|++.|+ |.+..|++||.+|....- +++.||.||+++|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g-~~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHG-NDWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhc-ccHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 799999999999999999999 67999999998 999999999999998874 899999999999999995
Q ss_pred hh-------C------------CchhHHhhcCCCCCHHHHHHHHHHhhhhhhhc
Q 021220 84 LL-------G------------NKWSLIAARLPGRTDNEIKNYWNTHIKRKLYS 118 (316)
Q Consensus 84 ~~-------G------------nkWs~IA~~lpgRT~~qcknRW~~~lk~k~~~ 118 (316)
++ | -.|+.|++.+..|+..|||.+|+.++......
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n 513 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFN 513 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhh
Confidence 33 0 14999999999999999999999988766554
No 14
>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=99.39 E-value=4e-13 Score=95.09 Aligned_cols=46 Identities=37% Similarity=0.709 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHhhCCc-hhHHhhcCC-CCCHHHHHHHHHHhh
Q 021220 67 RGNFTEEEDELIINFHSLLGNK-WSLIAARLP-GRTDNEIKNYWNTHI 112 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~~Gnk-Ws~IA~~lp-gRT~~qcknRW~~~l 112 (316)
+++||+|||++|+++|.+||.+ |..||..|+ +||..||++||++++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999987 999999999 999999999999874
No 15
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.26 E-value=5.8e-13 Score=94.25 Aligned_cols=48 Identities=40% Similarity=0.751 Sum_probs=42.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeecc
Q 021220 14 KGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYL 61 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L 61 (316)
|++||+|||++|+++|.+||.++|..||..|+++|++.||+.||.+++
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 689999999999999999998779999999994499999999999875
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.22 E-value=2.1e-11 Score=83.56 Aligned_cols=47 Identities=47% Similarity=0.893 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 67 RGNFTEEEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
+++||++||++|+.++.+|| .+|..||..|++||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998764
No 17
>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=99.10 E-value=1.7e-10 Score=78.02 Aligned_cols=44 Identities=41% Similarity=0.774 Sum_probs=41.8
Q ss_pred CCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhh
Q 021220 69 NFTEEEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHI 112 (316)
Q Consensus 69 ~WT~EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~l 112 (316)
+||.|||++|+.++.+|| .+|..||..|++||..+|++||++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999998753
No 18
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.07 E-value=5.6e-11 Score=122.06 Aligned_cols=120 Identities=25% Similarity=0.292 Sum_probs=100.9
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCC-----------------------CCccccccccCcccccccccceeeeccCCCC-CC
Q 021220 12 TNKGAWTKEEDERLINYIKVHGE-----------------------GCWRSLPKAAGLLRCGKSCRLRWINYLRPDL-KR 67 (316)
Q Consensus 12 ~kKg~WT~EEDe~L~~lV~kyG~-----------------------~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~l-kr 67 (316)
++-+.|+++||+.|...|..|-. +-|..|...|+. |+.+.++.+-++...+.- ++
T Consensus 306 ~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~-R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 306 INLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPY-RDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCc-ccchhHHHHHHhcCCcccccc
Confidence 34588999999999999988721 016788899998 999999874434333333 89
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhhhh--hhcCCCCCCCCCCCCCCC
Q 021220 68 GNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIKRK--LYSRGIDPQTHRPLNSAP 133 (316)
Q Consensus 68 g~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~k--~~~~~~s~~e~~~l~~~~ 133 (316)
|.||+||++.|..+|.++|+.|..|++.| ||.+.+|++||+++++.. ..++.|+.+|...|....
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V 451 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTV 451 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHH
Confidence 99999999999999999999999999999 999999999999999876 588889999998887654
No 19
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.90 E-value=4e-10 Score=77.19 Aligned_cols=48 Identities=44% Similarity=0.823 Sum_probs=44.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccC
Q 021220 14 KGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLR 62 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~ 62 (316)
++.||++||++|+.++..||..+|..|+..|++ |++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~-rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPG-RTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCC-CCHHHHHHHHHHHcC
Confidence 468999999999999999997789999999996 999999999998764
No 20
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.75 E-value=2.2e-09 Score=72.48 Aligned_cols=45 Identities=42% Similarity=0.765 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeecc
Q 021220 16 AWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYL 61 (316)
Q Consensus 16 ~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L 61 (316)
.||++||++|+.++..||..+|..|++.+++ |++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~-rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPG-RTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCC-CCHHHHHHHHHHhC
Confidence 5999999999999999997789999999997 99999999997653
No 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.29 E-value=6e-08 Score=98.91 Aligned_cols=98 Identities=33% Similarity=0.664 Sum_probs=84.9
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCC--CCCCCCCCHHHHHHHHHHHHhhC---
Q 021220 12 TNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRP--DLKRGNFTEEEDELIINFHSLLG--- 86 (316)
Q Consensus 12 ~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p--~lkrg~WT~EEDe~Llelv~~~G--- 86 (316)
..+|.||++|++.|...+..+| +.|..|.+.++ |-+..||+||.+|... .+++++|+.||+++|...|...-
T Consensus 289 ~~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~ 365 (512)
T COG5147 289 EQRGKWTKEEEQELAKLVVEHG-GSWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEA 365 (512)
T ss_pred hhhccCcccccccccccccccc-chhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHH
Confidence 3578999999999999999999 56999999887 8999999999999988 68899999999999999987422
Q ss_pred -----CchhHHhhcCCCCCHHHHHHHHHHhh
Q 021220 87 -----NKWSLIAARLPGRTDNEIKNYWNTHI 112 (316)
Q Consensus 87 -----nkWs~IA~~lpgRT~~qcknRW~~~l 112 (316)
-.|..|++.+++|...+|+.++..+.
T Consensus 366 ~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 366 QQSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred hhhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 24999999999888888887775543
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.22 E-value=3e-07 Score=93.00 Aligned_cols=80 Identities=21% Similarity=0.310 Sum_probs=74.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhhhhhhhcCCCCCCCCCCCCCCCCCCCCCCCCC
Q 021220 65 LKRGNFTEEEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHIKRKLYSRGIDPQTHRPLNSAPVPAPSPGNNN 143 (316)
Q Consensus 65 lkrg~WT~EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~lk~k~~~~~~s~~e~~~l~~~~~~~p~~~s~~ 143 (316)
++.|-|+.-||+.|..+|.+|| ++|+.|+..++-.|..||++||..+|.+.+++-.|+.+++..+..+..--|.++..+
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 5678999999999999999999 789999999999999999999999999999999999999999999888888887765
Q ss_pred C
Q 021220 144 N 144 (316)
Q Consensus 144 ~ 144 (316)
.
T Consensus 85 a 85 (617)
T KOG0050|consen 85 A 85 (617)
T ss_pred H
Confidence 3
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.73 E-value=5.3e-05 Score=75.72 Aligned_cols=50 Identities=22% Similarity=0.403 Sum_probs=45.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 64 DLKRGNFTEEEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 64 ~lkrg~WT~EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
.+-...||.+|+.+|++++..|| ++|..||.++..|+..+|+.||.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 45567999999999999999999 999999999999999999999987653
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=97.65 E-value=0.00013 Score=54.13 Aligned_cols=48 Identities=17% Similarity=0.228 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHHHHhhCC-ch---hHHhhcCC-CC-CHHHHHHHHHHhhh
Q 021220 66 KRGNFTEEEDELIINFHSLLGN-KW---SLIAARLP-GR-TDNEIKNYWNTHIK 113 (316)
Q Consensus 66 krg~WT~EEDe~Llelv~~~Gn-kW---s~IA~~lp-gR-T~~qcknRW~~~lk 113 (316)
.+-.||+||.+++++++..+|. +| ..|+..|. .| |..||+.|+..+..
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 3568999999999999999995 99 99999984 35 99999999987653
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=97.63 E-value=2e-05 Score=58.40 Aligned_cols=48 Identities=13% Similarity=0.288 Sum_probs=42.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCc---cccccccCccc-ccccccceeeecc
Q 021220 14 KGAWTKEEDERLINYIKVHGEGCW---RSLPKAAGLLR-CGKSCRLRWINYL 61 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~kyG~~nW---~~IAk~l~~~R-t~kQCr~Rw~n~L 61 (316)
+-.||+||.++++.+|..+|.++| ..|+..|...| +..||+.+++.|.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 457999999999999999998899 99999887557 9999999888764
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.43 E-value=3.4e-05 Score=77.08 Aligned_cols=49 Identities=18% Similarity=0.501 Sum_probs=45.1
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeecc
Q 021220 12 TNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYL 61 (316)
Q Consensus 12 ~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L 61 (316)
+-...||.+|+-+|++++..||.|||..||+.+|. |+..+|+++|.+++
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGt-Ktkeeck~hy~k~f 118 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGT-KTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcc-cchHHHHHHHHHHH
Confidence 33577999999999999999999999999999996 99999999998864
No 27
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.03 E-value=0.0009 Score=50.86 Aligned_cols=50 Identities=24% Similarity=0.474 Sum_probs=33.1
Q ss_pred CCCCCHHHHHHHHHHHHhhC--------Cc-hhHHhhcCC-CCCHHHHHHHHHHhhhhhh
Q 021220 67 RGNFTEEEDELIINFHSLLG--------NK-WSLIAARLP-GRTDNEIKNYWNTHIKRKL 116 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~~G--------nk-Ws~IA~~lp-gRT~~qcknRW~~~lk~k~ 116 (316)
+.+||.|||+.|++.|.++. |+ |.+++...+ .+|.+..|+||...|+.+.
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 46899999999999997642 22 999999987 9999999999998887654
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.95 E-value=0.0013 Score=60.15 Aligned_cols=100 Identities=21% Similarity=0.316 Sum_probs=71.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCcc--cccccccceeeecc-CCC--------------------CCCCCCCH
Q 021220 16 AWTKEEDERLINYIKVHGEGCWRSLPKAAGLL--RCGKSCRLRWINYL-RPD--------------------LKRGNFTE 72 (316)
Q Consensus 16 ~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~--Rt~kQCr~Rw~n~L-~p~--------------------lkrg~WT~ 72 (316)
+|++++|-+|+.+|..-. +-+.|+..+... -|-..+.+||...| +|. ..+.+||.
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 699999999999998643 566666554331 35566678888764 222 22358999
Q ss_pred HHHHHHHHHHHhhCC---chhHHhh-----cCCCCCHHHHHHHHHHhhhhhhh
Q 021220 73 EEDELIINFHSLLGN---KWSLIAA-----RLPGRTDNEIKNYWNTHIKRKLY 117 (316)
Q Consensus 73 EEDe~Llelv~~~Gn---kWs~IA~-----~lpgRT~~qcknRW~~~lk~k~~ 117 (316)
+||++|......... .+.+|=. +-++||+.++.++|..+.+..+.
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchh
Confidence 999999998766543 4666632 24789999999999966555544
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.91 E-value=0.00088 Score=52.16 Aligned_cols=49 Identities=33% Similarity=0.565 Sum_probs=34.6
Q ss_pred CCCCCHHHHHHHHHHHHh------hC--C------chhHHhhcC----CCCCHHHHHHHHHHhhhhh
Q 021220 67 RGNFTEEEDELIINFHSL------LG--N------KWSLIAARL----PGRTDNEIKNYWNTHIKRK 115 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~------~G--n------kWs~IA~~l----pgRT~~qcknRW~~~lk~k 115 (316)
|..||.+|...||+++.. ++ + -|..||..| ..||..||+++|.++.+.-
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 357999999999999877 21 1 399999886 3699999999999965543
No 30
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.90 E-value=0.001 Score=58.83 Aligned_cols=52 Identities=21% Similarity=0.350 Sum_probs=45.3
Q ss_pred CCCCCCHHHHHHHHHHHHhh---CC----chhHHhhcCCCCCHHHHHHHHHHhhhhhhhc
Q 021220 66 KRGNFTEEEDELIINFHSLL---GN----KWSLIAARLPGRTDNEIKNYWNTHIKRKLYS 118 (316)
Q Consensus 66 krg~WT~EEDe~Llelv~~~---Gn----kWs~IA~~lpgRT~~qcknRW~~~lk~k~~~ 118 (316)
....||.|||.+|.+.|..| |+ -+..++..| +||..+|.=||+.++++.+..
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 45689999999999999988 32 288999999 999999999999999987654
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.89 E-value=0.0013 Score=67.67 Aligned_cols=47 Identities=19% Similarity=0.361 Sum_probs=43.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHh
Q 021220 65 LKRGNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTH 111 (316)
Q Consensus 65 lkrg~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~ 111 (316)
..++.||.+|.-+|++++..||.+|.+||.++.+||..||-.||..+
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 45679999999999999999999999999999999999999999663
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.88 E-value=0.0011 Score=67.13 Aligned_cols=44 Identities=16% Similarity=0.289 Sum_probs=41.8
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHh
Q 021220 68 GNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTH 111 (316)
Q Consensus 68 g~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~ 111 (316)
..||.+|..+|++.++.||.+|.+||.++..||..||--||.++
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 48999999999999999999999999999999999999999763
No 33
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.15 E-value=0.0051 Score=55.03 Aligned_cols=51 Identities=18% Similarity=0.311 Sum_probs=42.9
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCc-------hhHHhhcCCCCCHHHHHHHHHHhhhhhhh
Q 021220 66 KRGNFTEEEDELIINFHSLLGNK-------WSLIAARLPGRTDNEIKNYWNTHIKRKLY 117 (316)
Q Consensus 66 krg~WT~EEDe~Llelv~~~Gnk-------Ws~IA~~lpgRT~~qcknRW~~~lk~k~~ 117 (316)
+...||.|||.+|.+.|..|+.. ...++..| +||..+|..||+.++++++.
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Ye 61 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQ 61 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHH
Confidence 46789999999999999988732 66677778 99999999999999986543
No 34
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.02 E-value=0.012 Score=44.98 Aligned_cols=48 Identities=29% Similarity=0.547 Sum_probs=39.6
Q ss_pred CCCCCHHHHHHHHHHHHhhC----C-------------chhHHhhcC-----CCCCHHHHHHHHHHhhhh
Q 021220 67 RGNFTEEEDELIINFHSLLG----N-------------KWSLIAARL-----PGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~~G----n-------------kWs~IA~~l-----pgRT~~qcknRW~~~lk~ 114 (316)
...||.+|.+.|+++|.+|. + -|..|+..| +.||..+++.+|.++...
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 45899999999999998873 1 199999875 359999999999986643
No 35
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=95.95 E-value=0.0026 Score=65.48 Aligned_cols=49 Identities=20% Similarity=0.551 Sum_probs=43.6
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeec
Q 021220 10 EHTNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINY 60 (316)
Q Consensus 10 ~~~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~ 60 (316)
...-++-||.+|+.+|++.|+.|| .+|.+|+.+++. |+..||..++.+.
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~-ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGT-KSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCC-CCHHHHHHHHHhc
Confidence 344578899999999999999999 569999999996 9999999998775
No 36
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=95.90 E-value=0.0021 Score=65.08 Aligned_cols=46 Identities=20% Similarity=0.527 Sum_probs=42.1
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeec
Q 021220 13 NKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINY 60 (316)
Q Consensus 13 kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~ 60 (316)
....||.+|..+|++.|+.|| .+|.+||+++|+ |+.-||..||.++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~yg-DdW~kVA~HVgt-Kt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYG-DDWDKVARHVGT-KTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhh-hhHHHHHHHhCC-CCHHHHHHHHHcC
Confidence 455899999999999999999 569999999996 9999999998875
No 37
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.64 E-value=0.018 Score=56.23 Aligned_cols=49 Identities=24% Similarity=0.427 Sum_probs=44.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 65 LKRGNFTEEEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 65 lkrg~WT~EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
+-...|+.+|+-+|++....+| ++|..||.++..|+..+||.||..+..
T Consensus 61 I~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 3446899999999999999999 899999999988999999999987654
No 38
>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=95.11 E-value=0.0063 Score=46.25 Aligned_cols=51 Identities=27% Similarity=0.513 Sum_probs=32.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCC------CC--ccccccccCcccccccccceeeeccCCC
Q 021220 14 KGAWTKEEDERLINYIKVHGE------GC--WRSLPKAAGLLRCGKSCRLRWINYLRPD 64 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~kyG~------~n--W~~IAk~l~~~Rt~kQCr~Rw~n~L~p~ 64 (316)
+-+||.|||+.|+.+|..+.. ++ |..++..-++.++..+-|+||...|.+.
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 347999999999999976531 22 9999988775589999999999888654
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=95.07 E-value=0.0058 Score=54.16 Aligned_cols=50 Identities=34% Similarity=0.649 Sum_probs=42.1
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCC-C-----CccccccccCcccccccccceeeeccCC
Q 021220 12 TNKGAWTKEEDERLINYIKVHGE-G-----CWRSLPKAAGLLRCGKSCRLRWINYLRP 63 (316)
Q Consensus 12 ~kKg~WT~EEDe~L~~lV~kyG~-~-----nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p 63 (316)
.++-.||.|||.+|-+.|.+|-. | .+.++++.++ ||+-.|.-||+.++..
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 46778999999999999998832 1 3788889886 9999999999998763
No 40
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=94.94 E-value=0.0043 Score=48.28 Aligned_cols=46 Identities=30% Similarity=0.631 Sum_probs=32.4
Q ss_pred CCCCHHHHHHHHHHHHH--h----C--CC-----Ccccccccc---Ccccccccccceeeec
Q 021220 15 GAWTKEEDERLINYIKV--H----G--EG-----CWRSLPKAA---GLLRCGKSCRLRWINY 60 (316)
Q Consensus 15 g~WT~EEDe~L~~lV~k--y----G--~~-----nW~~IAk~l---~~~Rt~kQCr~Rw~n~ 60 (316)
..||.+|...|+.++.. + + .. -|..||..| |..|++.||+.||.++
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 299999876 4569999999999885
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.24 E-value=0.0096 Score=58.06 Aligned_cols=48 Identities=19% Similarity=0.480 Sum_probs=44.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccC
Q 021220 14 KGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLR 62 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~ 62 (316)
---|+..|+.+|++.....|.+||..||..+|. |....|+++|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGs-r~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGS-RAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhh-hhhHHHHHHHHHHHh
Confidence 346999999999999999999999999999996 999999999988765
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=93.50 E-value=0.014 Score=44.70 Aligned_cols=49 Identities=22% Similarity=0.436 Sum_probs=38.6
Q ss_pred CcCCCCHHHHHHHHHHHHHhCC----------------CCcccccccc----Ccccccccccceeeecc
Q 021220 13 NKGAWTKEEDERLINYIKVHGE----------------GCWRSLPKAA----GLLRCGKSCRLRWINYL 61 (316)
Q Consensus 13 kKg~WT~EEDe~L~~lV~kyG~----------------~nW~~IAk~l----~~~Rt~kQCr~Rw~n~L 61 (316)
++..||.+|.+.|+.+|.+|.. .-|..|+..| +..|+..|++.+|.++.
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 4578999999999999998821 1299998766 22499999999998754
No 43
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=93.47 E-value=0.17 Score=56.65 Aligned_cols=100 Identities=18% Similarity=0.301 Sum_probs=75.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccCccccccccc-------ceeee----------------------------
Q 021220 15 GAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCR-------LRWIN---------------------------- 59 (316)
Q Consensus 15 g~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr-------~Rw~n---------------------------- 59 (316)
.-|+.-+=..++.+..+||-.+-..||..|.+ ++...++ .||..
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~-k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~ 903 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEG-KTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAI 903 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcC-CCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34888888888888999998888888888865 7766665 11111
Q ss_pred -------------c-c-CCCCCCCCCCHHHHHHHHHHHHhhC-CchhHHhhc------------CCCCCHHHHHHHHHHh
Q 021220 60 -------------Y-L-RPDLKRGNFTEEEDELIINFHSLLG-NKWSLIAAR------------LPGRTDNEIKNYWNTH 111 (316)
Q Consensus 60 -------------~-L-~p~lkrg~WT~EEDe~Llelv~~~G-nkWs~IA~~------------lpgRT~~qcknRW~~~ 111 (316)
. + -+..++..||.|||..|+-++.+|| ++|..|-.. |..||+..+..|-.++
T Consensus 904 ~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 904 GKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred HHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 0 0 0223345699999999999999999 789998322 3579999999999998
Q ss_pred hhhh
Q 021220 112 IKRK 115 (316)
Q Consensus 112 lk~k 115 (316)
|+-.
T Consensus 984 ~~~~ 987 (1033)
T PLN03142 984 IRLI 987 (1033)
T ss_pred HHHH
Confidence 8754
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=92.68 E-value=0.02 Score=51.32 Aligned_cols=50 Identities=28% Similarity=0.519 Sum_probs=39.6
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCC------ccccccccCcccccccccceeeeccC
Q 021220 11 HTNKGAWTKEEDERLINYIKVHGEGC------WRSLPKAAGLLRCGKSCRLRWINYLR 62 (316)
Q Consensus 11 ~~kKg~WT~EEDe~L~~lV~kyG~~n------W~~IAk~l~~~Rt~kQCr~Rw~n~L~ 62 (316)
..++..||.|||.+|-+.|..|+... ...++..|. |++..|..||+.+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 35678999999999999999886533 455566665 999999999976655
No 45
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.93 E-value=0.24 Score=49.49 Aligned_cols=46 Identities=26% Similarity=0.369 Sum_probs=42.7
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 68 GNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 68 g~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
.+|+.+|-++..++....|..++.|+..||.|...|||.+|.+--+
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek 411 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEK 411 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhh
Confidence 4899999999999999999999999999999999999999976444
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=91.61 E-value=0.33 Score=48.70 Aligned_cols=84 Identities=18% Similarity=0.369 Sum_probs=63.0
Q ss_pred CccccccccCcccccccccceeeeccCCC-------------------------CCCCCCCHHHHHHHHHHHHhhCCchh
Q 021220 36 CWRSLPKAAGLLRCGKSCRLRWINYLRPD-------------------------LKRGNFTEEEDELIINFHSLLGNKWS 90 (316)
Q Consensus 36 nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~-------------------------lkrg~WT~EEDe~Llelv~~~GnkWs 90 (316)
.|.-++=..+- |...--..||....++. +....||.||-+-|++|.+.|.-+|.
T Consensus 75 ~W~w~pFtn~a-RkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~ 153 (445)
T KOG2656|consen 75 PWKWVPFTNSA-RKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCCcc-ccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 37666544443 66666677887763221 22246999999999999999999999
Q ss_pred HHhhc-----CCC-CCHHHHHHHHHHhhhhhhhcCC
Q 021220 91 LIAAR-----LPG-RTDNEIKNYWNTHIKRKLYSRG 120 (316)
Q Consensus 91 ~IA~~-----lpg-RT~~qcknRW~~~lk~k~~~~~ 120 (316)
.||.. ++. ||-.++|+||+...+.-++.+.
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 99987 555 9999999999998877666543
No 47
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=91.27 E-value=0.47 Score=37.19 Aligned_cols=45 Identities=31% Similarity=0.572 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhh---CC----------chhHHhhcC---CC--CCHHHHHHHHHHhhh
Q 021220 69 NFTEEEDELIINFHSLL---GN----------KWSLIAARL---PG--RTDNEIKNYWNTHIK 113 (316)
Q Consensus 69 ~WT~EEDe~Llelv~~~---Gn----------kWs~IA~~l---pg--RT~~qcknRW~~~lk 113 (316)
.||+++++.|++++.+. |+ .|..|+..| .| .+..||++||..+.+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 59999999999998653 21 299998886 23 578999999977554
No 48
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=91.23 E-value=0.4 Score=48.97 Aligned_cols=48 Identities=21% Similarity=0.346 Sum_probs=43.8
Q ss_pred CCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 67 RGNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
...||.||--++-+++..||.++.+|-+.||.|+-..+..+|+..-+.
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~ 234 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKT 234 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHH
Confidence 468999999999999999999999999999999999999999876553
No 49
>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=89.43 E-value=0.47 Score=40.09 Aligned_cols=52 Identities=29% Similarity=0.447 Sum_probs=40.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhCC----chhHHhhc------------CCCCCHHHHHHHHHHhhhhh
Q 021220 64 DLKRGNFTEEEDELIINFHSLLGN----KWSLIAAR------------LPGRTDNEIKNYWNTHIKRK 115 (316)
Q Consensus 64 ~lkrg~WT~EEDe~Llelv~~~Gn----kWs~IA~~------------lpgRT~~qcknRW~~~lk~k 115 (316)
..++..||+|||..|+-++.+||- .|..|-.. |..||+..+..|-..+|+-.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 446779999999999999999995 79888543 35699999999999988643
No 50
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=89.42 E-value=0.46 Score=46.30 Aligned_cols=49 Identities=20% Similarity=0.332 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHHhh----------CCchhHHhhcC----CCCCHHHHHHHHHHhhhhh
Q 021220 67 RGNFTEEEDELIINFHSLL----------GNKWSLIAARL----PGRTDNEIKNYWNTHIKRK 115 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~~----------GnkWs~IA~~l----pgRT~~qcknRW~~~lk~k 115 (316)
...|+.+|-..||++..+. +.-|..||..+ .-||+.+|+++|.++.++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Y 116 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKY 116 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 3689999999999998653 23499999965 3499999999999977653
No 51
>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=87.13 E-value=1.5 Score=30.82 Aligned_cols=41 Identities=22% Similarity=0.273 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 72 EEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 72 ~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
++++..++.++...|-.|.+||..+ |.|...|+.+...-++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 4678889999999999999999999 9999999998876554
No 52
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=81.56 E-value=0.58 Score=46.88 Aligned_cols=64 Identities=19% Similarity=0.333 Sum_probs=50.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeec--cCCC-----C-CCCCCCHHHHHHHH
Q 021220 14 KGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINY--LRPD-----L-KRGNFTEEEDELII 79 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~--L~p~-----l-krg~WT~EEDe~Ll 79 (316)
--+||.+|.+++.+++..+|+ ++..|+..+|+ |..+|++.+|.+- .+|. + .+-++..+|...|.
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP~-R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~ 436 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGT-DFSLISSLFPN-RERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLR 436 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcc-hHHHHHHhcCc-hhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHH
Confidence 457999999999999999995 59999999997 9999999998764 2221 1 24578888775543
No 53
>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=80.74 E-value=1.3 Score=37.39 Aligned_cols=34 Identities=24% Similarity=0.476 Sum_probs=28.6
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCC---CCcccccccc
Q 021220 11 HTNKGAWTKEEDERLINYIKVHGE---GCWRSLPKAA 44 (316)
Q Consensus 11 ~~kKg~WT~EEDe~L~~lV~kyG~---~nW~~IAk~l 44 (316)
..++..||.+||.-|+-++.+||. +.|..|-..+
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 667889999999999999999999 7899997665
No 54
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=80.13 E-value=2.9 Score=45.18 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 67 RGNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
...||..|-.+..+++..|..++..|++.++++|-.+|-.+|+...|
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWKK 665 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWKK 665 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHHH
Confidence 35899999999999999999999999999999999999998876543
No 55
>smart00595 MADF subfamily of SANT domain.
Probab=78.79 E-value=2.3 Score=32.85 Aligned_cols=24 Identities=33% Similarity=0.594 Sum_probs=21.0
Q ss_pred hhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 89 WSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 89 Ws~IA~~lpgRT~~qcknRW~~~lk 113 (316)
|..||..| |-+..+|+.+|+++..
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~ 53 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 99999999 5599999999988654
No 56
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=73.25 E-value=7.7 Score=26.92 Aligned_cols=41 Identities=20% Similarity=0.346 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 73 EEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 73 EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
+++..++.++-..|-.+..||..| |-|...|+.+....+++
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 566777777776677899999999 99999999988876654
No 57
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=73.12 E-value=5.2 Score=42.48 Aligned_cols=50 Identities=14% Similarity=0.428 Sum_probs=41.0
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCchhHHhhc----------CCCCCHHHHHHHHHHhhhhh
Q 021220 66 KRGNFTEEEDELIINFHSLLGNKWSLIAAR----------LPGRTDNEIKNYWNTHIKRK 115 (316)
Q Consensus 66 krg~WT~EEDe~Llelv~~~GnkWs~IA~~----------lpgRT~~qcknRW~~~lk~k 115 (316)
++..||.+|.+-...++.++|.++..|-+. ..-+|..|++.+|+..+++.
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m 146 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRM 146 (782)
T ss_pred cccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHH
Confidence 366899999999999999999999888322 33468889999999887664
No 58
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=72.44 E-value=1.3 Score=43.15 Aligned_cols=47 Identities=23% Similarity=0.443 Sum_probs=36.8
Q ss_pred cCCCCHHHHHHHHHHHHHh----CC-----CCcccccccc---Ccccccccccceeeec
Q 021220 14 KGAWTKEEDERLINYIKVH----GE-----GCWRSLPKAA---GLLRCGKSCRLRWINY 60 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~ky----G~-----~nW~~IAk~l---~~~Rt~kQCr~Rw~n~ 60 (316)
-..|+.+|-..|+.+..+. .. ..|..||+.+ +..|++.||+.+|.+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl 112 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENL 112 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 3789999999999988643 11 2499999843 4559999999999884
No 59
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=71.18 E-value=3.9 Score=32.31 Aligned_cols=29 Identities=38% Similarity=0.616 Sum_probs=16.8
Q ss_pred CCCcCCCCHHHHHHH--------HHHHHHhCCCCcccccc
Q 021220 11 HTNKGAWTKEEDERL--------INYIKVHGEGCWRSLPK 42 (316)
Q Consensus 11 ~~kKg~WT~EEDe~L--------~~lV~kyG~~nW~~IAk 42 (316)
..-.|.||+|+|+.| .+++++|| +..|..
T Consensus 44 ~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~ 80 (87)
T PF11626_consen 44 DNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIER 80 (87)
T ss_dssp TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHH
T ss_pred CCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHH
Confidence 345789999999999 45667787 445553
No 60
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=69.97 E-value=7.1 Score=33.63 Aligned_cols=46 Identities=11% Similarity=0.101 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhhhhhhhc
Q 021220 72 EEEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHIKRKLYS 118 (316)
Q Consensus 72 ~EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~lk~k~~~ 118 (316)
.+-|.+|+++.++-| -.|+.||+.+ |-|...|+.|++.+....+..
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 467899999998888 5799999999 999999999998877665554
No 61
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=68.63 E-value=5.9 Score=35.13 Aligned_cols=41 Identities=24% Similarity=0.242 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHH
Q 021220 69 NFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNT 110 (316)
Q Consensus 69 ~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~ 110 (316)
.||+|+.++|.+|..+ |-.=++||..|.|.|.++|.-+-+.
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhhc
Confidence 6999999999999965 8788999999977999999876654
No 62
>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=67.24 E-value=13 Score=25.65 Aligned_cols=38 Identities=18% Similarity=0.295 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHh
Q 021220 73 EEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTH 111 (316)
Q Consensus 73 EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~ 111 (316)
+=|.+|+.+.+.-| -.|..||+.+ |=|...|..|+..+
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 45888999998888 4699999999 99999999999753
No 63
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=66.86 E-value=5.5 Score=31.49 Aligned_cols=16 Identities=44% Similarity=0.762 Sum_probs=9.8
Q ss_pred CCCCCCCCCHHHHHHH
Q 021220 63 PDLKRGNFTEEEDELI 78 (316)
Q Consensus 63 p~lkrg~WT~EEDe~L 78 (316)
|.-..|-||+|+|+.|
T Consensus 43 P~n~~GiWT~eDD~~L 58 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEML 58 (87)
T ss_dssp -TT-TT---HHHHHHH
T ss_pred CCCCCCCcCHHHHHHH
Confidence 5567899999999999
No 64
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=63.77 E-value=9.6 Score=33.23 Aligned_cols=46 Identities=13% Similarity=0.050 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhhhhhhhc
Q 021220 72 EEEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHIKRKLYS 118 (316)
Q Consensus 72 ~EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~lk~k~~~ 118 (316)
.+-|.+|+.+.++-| -.|+.||+.+ |-+...|+.|++.+.+..+..
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeE
Confidence 566999999888888 4799999999 999999999998887766543
No 65
>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=62.49 E-value=7.6 Score=29.04 Aligned_cols=25 Identities=24% Similarity=0.430 Sum_probs=20.8
Q ss_pred hhHHhhcCCC-CCHHHHHHHHHHhhh
Q 021220 89 WSLIAARLPG-RTDNEIKNYWNTHIK 113 (316)
Q Consensus 89 Ws~IA~~lpg-RT~~qcknRW~~~lk 113 (316)
|..||..|.. -+..+|+.+|.++..
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHH
Confidence 9999999953 578899999988664
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=60.97 E-value=16 Score=30.12 Aligned_cols=35 Identities=20% Similarity=0.300 Sum_probs=26.6
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 78 IINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 78 Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
++.+.-..|-.+.+||..+ |.+...|+.++...++
T Consensus 121 il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 121 IFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALK 155 (161)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3333333467799999999 9999999999987543
No 67
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=60.44 E-value=1.5e+02 Score=30.13 Aligned_cols=46 Identities=24% Similarity=0.341 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHh-hcCCCCCHHHHHHHHHHhhh
Q 021220 68 GNFTEEEDELIINFHSLLGNKWSLIA-ARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 68 g~WT~EEDe~Llelv~~~GnkWs~IA-~~lpgRT~~qcknRW~~~lk 113 (316)
..|+++|=...-+.++.||.++..|. ..++.|+--.|-.+|+...+
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKk 324 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKK 324 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhc
Confidence 47999999999999999999999995 45899999999888866543
No 68
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=59.84 E-value=10 Score=40.15 Aligned_cols=45 Identities=27% Similarity=0.392 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHH
Q 021220 66 KRGNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNT 110 (316)
Q Consensus 66 krg~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~ 110 (316)
..+.|+.+|-++...+....|.+.+.|+..+|+|...|||.+|..
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 346899999999999999999999999999999999999999865
No 69
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=59.49 E-value=18 Score=33.37 Aligned_cols=45 Identities=22% Similarity=0.260 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhc--C-CCCCHHHHHHHHHHhhhh
Q 021220 69 NFTEEEDELIINFHSLLGNKWSLIAAR--L-PGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 69 ~WT~EEDe~Llelv~~~GnkWs~IA~~--l-pgRT~~qcknRW~~~lk~ 114 (316)
.|++++|-+|+.+|.. |+.-..|+.- | -.-|-..|..||+.+|--
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd 48 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYD 48 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcC
Confidence 4999999999999976 5666666554 3 335889999999998853
No 70
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=57.71 E-value=3.8 Score=44.37 Aligned_cols=44 Identities=11% Similarity=0.113 Sum_probs=38.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeee
Q 021220 14 KGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWIN 59 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n 59 (316)
.-+||+.|..++.+++-.|. +++..|++++++ ++.+||-+-|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~-KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVKS-KTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhcc-ccHHHHHHHHHH
Confidence 45799999999999999998 789999999997 999999776654
No 71
>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=56.92 E-value=15 Score=29.19 Aligned_cols=29 Identities=24% Similarity=0.510 Sum_probs=24.6
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHHHH
Q 021220 75 DELIINFHSLLGNKWSLIAARLPGRTDNEI 104 (316)
Q Consensus 75 De~Llelv~~~GnkWs~IA~~lpgRT~~qc 104 (316)
|+.|..+....|.+|..+|.+| |=|..+|
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 5678999999999999999998 7666655
No 72
>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=55.82 E-value=25 Score=27.40 Aligned_cols=38 Identities=16% Similarity=0.242 Sum_probs=27.8
Q ss_pred HHHHHHHhhCC--------chhHHhhcCCCC---C--HHHHHHHHHHhhhh
Q 021220 77 LIINFHSLLGN--------KWSLIAARLPGR---T--DNEIKNYWNTHIKR 114 (316)
Q Consensus 77 ~Llelv~~~Gn--------kWs~IA~~lpgR---T--~~qcknRW~~~lk~ 114 (316)
.|..+|.+.|+ +|..||..|.-- + ..+++..|..+|.+
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 37777888874 599999998221 1 36899999888754
No 73
>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=52.07 E-value=44 Score=33.12 Aligned_cols=46 Identities=20% Similarity=0.426 Sum_probs=36.2
Q ss_pred CCCCCHHHHHHHHHHHHhh-CC---chhHHhhcCCCCCHHHHHHHHHHhh
Q 021220 67 RGNFTEEEDELIINFHSLL-GN---KWSLIAARLPGRTDNEIKNYWNTHI 112 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~~-Gn---kWs~IA~~lpgRT~~qcknRW~~~l 112 (316)
-..||.-|...|+.+.+-. |. +-..|++.++||+..+|++.-..+.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK 70 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLK 70 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHH
Confidence 4589999999888888765 43 3568899999999999998655433
No 74
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=51.97 E-value=32 Score=35.87 Aligned_cols=41 Identities=20% Similarity=0.335 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhc-CCCCCHHHHHHHHH
Q 021220 69 NFTEEEDELIINFHSLLGNKWSLIAAR-LPGRTDNEIKNYWN 109 (316)
Q Consensus 69 ~WT~EEDe~Llelv~~~GnkWs~IA~~-lpgRT~~qcknRW~ 109 (316)
.|+..|-.+.-++..+||.++..|-.. ||-++-..|-.+|+
T Consensus 287 EWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 287 EWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 799999999999999999999999655 69999998887764
No 75
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=51.75 E-value=22 Score=28.21 Aligned_cols=31 Identities=26% Similarity=0.359 Sum_probs=25.7
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 021220 75 DELIINFHSLLGNKWSLIAARLPGRTDNEIKN 106 (316)
Q Consensus 75 De~Llelv~~~GnkWs~IA~~lpgRT~~qckn 106 (316)
|..|..+....|.+|..+|..| |=+..+|..
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 6778889999999999999999 767665543
No 76
>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=50.98 E-value=31 Score=23.36 Aligned_cols=35 Identities=23% Similarity=0.165 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHH
Q 021220 74 EDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWN 109 (316)
Q Consensus 74 EDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~ 109 (316)
|-+.|.++...++++....|+.| |=+...+..+..
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~klk 40 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 67889999999999999999999 877777766654
No 77
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=50.14 E-value=31 Score=27.11 Aligned_cols=38 Identities=16% Similarity=0.249 Sum_probs=28.7
Q ss_pred HHHHHHHhhCC--------chhHHhhcCCCC-----CHHHHHHHHHHhhhh
Q 021220 77 LIINFHSLLGN--------KWSLIAARLPGR-----TDNEIKNYWNTHIKR 114 (316)
Q Consensus 77 ~Llelv~~~Gn--------kWs~IA~~lpgR-----T~~qcknRW~~~lk~ 114 (316)
+|..+|.+.|+ +|..||..|.-. ...+++..|..+|.+
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 37777877774 599999998332 357889999888865
No 78
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=47.90 E-value=6.7 Score=39.66 Aligned_cols=51 Identities=20% Similarity=0.294 Sum_probs=43.1
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccc-----cCcccccccccceeeec
Q 021220 9 KEHTNKGAWTKEEDERLINYIKVHGEGCWRSLPKA-----AGLLRCGKSCRLRWINY 60 (316)
Q Consensus 9 K~~~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~-----l~~~Rt~kQCr~Rw~n~ 60 (316)
..+++...||++|.+.|..+.+.|.- .|--|+.. ++..|+--..++||...
T Consensus 125 e~~l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 125 EAHLNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred HHhhccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 45677889999999999999999985 49999987 56558888999998765
No 79
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=47.69 E-value=32 Score=27.40 Aligned_cols=36 Identities=22% Similarity=0.272 Sum_probs=26.9
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 78 IINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 78 Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
++.++...|-.+..||+.+ |-+...|+++....+++
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 3334434577899999999 78999999998875543
No 80
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=47.58 E-value=28 Score=28.30 Aligned_cols=47 Identities=15% Similarity=0.148 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHHHHHHhh----C----CchhHHhhc----CC-CCCHHHHHHHHHHhhhh
Q 021220 68 GNFTEEEDELIINFHSLL----G----NKWSLIAAR----LP-GRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 68 g~WT~EEDe~Llelv~~~----G----nkWs~IA~~----lp-gRT~~qcknRW~~~lk~ 114 (316)
..||+|+|-.|++.+..| | .+|..+-.. |. .=+..|+.++.+.+-++
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~K 64 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKK 64 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHH
Confidence 469999999999999776 5 246544433 32 23778998888775544
No 81
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=47.10 E-value=37 Score=26.87 Aligned_cols=45 Identities=13% Similarity=0.087 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhhhhhhhc
Q 021220 73 EEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHIKRKLYS 118 (316)
Q Consensus 73 EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~lk~k~~~ 118 (316)
+.|.+|+.+....| -.+..||+.+ |-+...|+.+...+.+..+..
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 56888999988887 4799999999 999999999998888766554
No 82
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=45.78 E-value=34 Score=24.74 Aligned_cols=37 Identities=24% Similarity=0.441 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHH
Q 021220 72 EEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWN 109 (316)
Q Consensus 72 ~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~ 109 (316)
.++|+..+.++.+.|-+-.+||+.+ ||+.+.|+++-+
T Consensus 6 t~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 6 TDAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYLK 42 (50)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHHH
T ss_pred CHHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHhc
Confidence 3566777888888899999999999 999998887643
No 83
>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=44.51 E-value=24 Score=27.41 Aligned_cols=30 Identities=30% Similarity=0.669 Sum_probs=24.2
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHHHHH
Q 021220 75 DELIINFHSLLGNKWSLIAARLPGRTDNEIK 105 (316)
Q Consensus 75 De~Llelv~~~GnkWs~IA~~lpgRT~~qck 105 (316)
|..|..+....|.+|.++|..| |=+..+|.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~ 33 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDID 33 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHH
Confidence 5568888899999999999999 66665543
No 84
>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=44.13 E-value=54 Score=21.36 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHh
Q 021220 70 FTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTH 111 (316)
Q Consensus 70 WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~ 111 (316)
++++ +..++.++...|-.+..||..+ |-+...|+.+....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 4444 4555566656677899999998 88888887766554
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=43.64 E-value=39 Score=33.47 Aligned_cols=87 Identities=15% Similarity=0.263 Sum_probs=62.7
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCC---ccccccccCcccccccccceeeeccCCCCCCCCCCHHHHHHHHHHHHh-h---
Q 021220 13 NKGAWTKEEDERLINYIKVHGEGC---WRSLPKAAGLLRCGKSCRLRWINYLRPDLKRGNFTEEEDELIINFHSL-L--- 85 (316)
Q Consensus 13 kKg~WT~EEDe~L~~lV~kyG~~n---W~~IAk~l~~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EEDe~Llelv~~-~--- 85 (316)
.-..||.-|...|+.++.....+. -.+|++.+++ |+..++++- .+.|+ +..+.+++++ |
T Consensus 20 gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~-Rs~aEI~~f-l~~LK------------~rvareaiqkv~~~g 85 (344)
T PF11035_consen 20 GPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPG-RSEAEIRDF-LQQLK------------GRVAREAIQKVHPGG 85 (344)
T ss_pred CcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccC-cCHHHHHHH-HHHHH------------HHHHHHHHHHhcccc
Confidence 356799999999999998764333 4467788886 888887763 22232 3445566655 2
Q ss_pred --CCc------------hhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 86 --GNK------------WSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 86 --Gnk------------Ws~IA~~lpgRT~~qcknRW~~~lk 113 (316)
|.+ |..+|..+.|.-...+-.-|-+.|-
T Consensus 86 ~~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 86 LKGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred cccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 211 9999999999999999999987663
No 86
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.35 E-value=41 Score=28.36 Aligned_cols=29 Identities=14% Similarity=0.126 Sum_probs=23.5
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 84 LLGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 84 ~~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
..|-.+..||..| |.+...|+.+....++
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~ 170 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRARE 170 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3466799999999 9999999988776443
No 87
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=42.26 E-value=55 Score=28.74 Aligned_cols=47 Identities=17% Similarity=0.168 Sum_probs=38.8
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCchhHHhhcCC----CCCHHHHHHHHHHhh
Q 021220 66 KRGNFTEEEDELIINFHSLLGNKWSLIAARLP----GRTDNEIKNYWNTHI 112 (316)
Q Consensus 66 krg~WT~EEDe~Llelv~~~GnkWs~IA~~lp----gRT~~qcknRW~~~l 112 (316)
....-|..|.+-|..|+.+||.++..++.... -.|..||+.+...+.
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 34578899999999999999999999997753 379999998876653
No 88
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=40.85 E-value=35 Score=26.86 Aligned_cols=31 Identities=26% Similarity=0.455 Sum_probs=25.9
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 021220 75 DELIINFHSLLGNKWSLIAARLPGRTDNEIKN 106 (316)
Q Consensus 75 De~Llelv~~~GnkWs~IA~~lpgRT~~qckn 106 (316)
|..|..+....|.+|..+|+.| |=+..+|..
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 5678888899999999999999 777777655
No 89
>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=40.76 E-value=36 Score=26.77 Aligned_cols=27 Identities=37% Similarity=0.676 Sum_probs=21.5
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHHH
Q 021220 78 IINFHSLLGNKWSLIAARLPGRTDNEIK 105 (316)
Q Consensus 78 Llelv~~~GnkWs~IA~~lpgRT~~qck 105 (316)
|..+....|.+|..+|..| |-+..+|.
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 4446688899999999999 87777663
No 90
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=39.95 E-value=29 Score=39.93 Aligned_cols=73 Identities=18% Similarity=0.313 Sum_probs=48.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccc--cCcccccccccceeeeccCCCCCCCCCCHHHHHHHHHHHHhh-CCchh
Q 021220 14 KGAWTKEEDERLINYIKVHGEGCWRSLPKA--AGLLRCGKSCRLRWINYLRPDLKRGNFTEEEDELIINFHSLL-GNKWS 90 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~kyG~~nW~~IAk~--l~~~Rt~kQCr~Rw~n~L~p~lkrg~WT~EEDe~Llelv~~~-GnkWs 90 (316)
---|..+||..|+-.|-+||.++|..|-.- |+. +. ...+...+-.+.|=...-..|+.+...+ +.+|.
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l--~d-------Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~ 1203 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGL--TD-------KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTP 1203 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccccHHHhccCccccc--hh-------hhcccccCCchHHHHHHHHHHHHHHhhcccCCCc
Confidence 446999999999999999999999988521 221 11 1122222455667777777777777776 55566
Q ss_pred HHhhc
Q 021220 91 LIAAR 95 (316)
Q Consensus 91 ~IA~~ 95 (316)
...+.
T Consensus 1204 ~~~~~ 1208 (1373)
T KOG0384|consen 1204 KKLKR 1208 (1373)
T ss_pred hhhhc
Confidence 54443
No 91
>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=39.87 E-value=37 Score=25.90 Aligned_cols=30 Identities=27% Similarity=0.536 Sum_probs=22.8
Q ss_pred HHHHHHHHHHh-hCCchhHHhhcCCCCCHHHH
Q 021220 74 EDELIINFHSL-LGNKWSLIAARLPGRTDNEI 104 (316)
Q Consensus 74 EDe~Llelv~~-~GnkWs~IA~~lpgRT~~qc 104 (316)
-++.|..++.. .|.+|..+|+.| |-+..+|
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 45667777777 899999999999 5555554
No 92
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=38.72 E-value=51 Score=27.65 Aligned_cols=28 Identities=21% Similarity=0.183 Sum_probs=23.1
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
.|-.+..||..| |-+...|++++...++
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 167 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRARQ 167 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 456799999999 9999999998876444
No 93
>PRK04217 hypothetical protein; Provisional
Probab=37.56 E-value=63 Score=27.00 Aligned_cols=44 Identities=16% Similarity=0.092 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 69 NFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 69 ~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.-|.+| ..++.+....|-...+||+.+ |.+...|+.+++...+.
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 455555 577777777788999999999 99999999999875443
No 94
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=36.66 E-value=59 Score=28.64 Aligned_cols=38 Identities=16% Similarity=0.250 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhh
Q 021220 74 EDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHI 112 (316)
Q Consensus 74 EDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~l 112 (316)
+...++++....|-.+.+||..| |-|...|+.+|....
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 33444444445577899999999 999999999997754
No 95
>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=36.10 E-value=39 Score=26.34 Aligned_cols=33 Identities=30% Similarity=0.506 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 021220 72 EEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKN 106 (316)
Q Consensus 72 ~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qckn 106 (316)
+||-++|+..- ..|.+|..+|..| |=++..|.+
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 57777877422 5688999999999 877877765
No 96
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=35.24 E-value=65 Score=28.30 Aligned_cols=27 Identities=19% Similarity=0.123 Sum_probs=22.6
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHI 112 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~l 112 (316)
.|-...+||..| |-+...|+.|+..-+
T Consensus 149 ~g~s~~EIA~~l-g~s~~tV~~rl~rar 175 (192)
T PRK09643 149 QGYSVADAARML-GVAEGTVKSRCARGR 175 (192)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 466799999999 999999999995543
No 97
>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=35.01 E-value=45 Score=26.46 Aligned_cols=27 Identities=19% Similarity=0.279 Sum_probs=22.1
Q ss_pred HHHHHHHHHhhCCchhHHhhcCCCCCHH
Q 021220 75 DELIINFHSLLGNKWSLIAARLPGRTDN 102 (316)
Q Consensus 75 De~Llelv~~~GnkWs~IA~~lpgRT~~ 102 (316)
|.+|..+...+|.+|.++|..| |=+..
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~ 30 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVE 30 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHH
Confidence 5678888899999999999998 54443
No 98
>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=34.64 E-value=45 Score=26.38 Aligned_cols=30 Identities=33% Similarity=0.539 Sum_probs=24.2
Q ss_pred HHHHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 021220 76 ELIINFHSLLGNKWSLIAARLPGRTDNEIKN 106 (316)
Q Consensus 76 e~Llelv~~~GnkWs~IA~~lpgRT~~qckn 106 (316)
+.|-.+....|.+|..+|+.| |=++.+|..
T Consensus 3 ~~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 3 KHLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 446666788899999999999 888887765
No 99
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=34.33 E-value=13 Score=39.67 Aligned_cols=46 Identities=20% Similarity=0.377 Sum_probs=35.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcccccccc----------Ccccccccccceeeecc
Q 021220 14 KGAWTKEEDERLINYIKVHGEGCWRSLPKAA----------GLLRCGKSCRLRWINYL 61 (316)
Q Consensus 14 Kg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l----------~~~Rt~kQCr~Rw~n~L 61 (316)
|..||..|.+-+..+++.+| +++..|-+++ .. ++-.|+|.+|++.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~-Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQS-KTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhh-hhhHHHHHHHHHHH
Confidence 67899999999999999999 6798883222 22 56677888777654
No 100
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=34.20 E-value=44 Score=22.89 Aligned_cols=37 Identities=30% Similarity=0.331 Sum_probs=18.9
Q ss_pred CCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHH
Q 021220 69 NFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNY 107 (316)
Q Consensus 69 ~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknR 107 (316)
.+|.+|=..|..++ .-|-.=..||+.| ||+...|...
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHHH
Confidence 57777777776664 5677789999999 9999988753
No 101
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=33.89 E-value=89 Score=26.51 Aligned_cols=27 Identities=26% Similarity=0.342 Sum_probs=21.7
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
|-.-.+||..| |.+...|+.+.+.-++
T Consensus 134 g~s~~EIA~~l-gis~~tV~~~l~ra~~ 160 (173)
T PRK09645 134 GWSTAQIAADL-GIPEGTVKSRLHYALR 160 (173)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 55578999999 9999999998876443
No 102
>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=33.30 E-value=50 Score=26.06 Aligned_cols=27 Identities=26% Similarity=0.474 Sum_probs=21.9
Q ss_pred HHHHHHHHhhCCchhHHhhcCCCCCHHH
Q 021220 76 ELIINFHSLLGNKWSLIAARLPGRTDNE 103 (316)
Q Consensus 76 e~Llelv~~~GnkWs~IA~~lpgRT~~q 103 (316)
+.|..+..+.|.+|..+|..| |=+..+
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~~ 29 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYRE 29 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHHH
Confidence 468889999999999999998 544443
No 103
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=32.86 E-value=72 Score=27.28 Aligned_cols=28 Identities=11% Similarity=-0.060 Sum_probs=22.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
.|..+.+||..| |-|...|+++.....+
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 356689999999 9999999998876444
No 104
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=31.48 E-value=80 Score=26.77 Aligned_cols=29 Identities=17% Similarity=0.312 Sum_probs=22.8
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.|-....||..| |-|...|+.++...++.
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355688999999 88999999998775543
No 105
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=31.41 E-value=1e+02 Score=26.30 Aligned_cols=31 Identities=26% Similarity=0.394 Sum_probs=25.1
Q ss_pred hhCCchhHHhhcCCCCCHHHHHHHHHHhhhhh
Q 021220 84 LLGNKWSLIAARLPGRTDNEIKNYWNTHIKRK 115 (316)
Q Consensus 84 ~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~k 115 (316)
..|-...+||..| |.+...|+.+...-+++-
T Consensus 133 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 133 LDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3456789999999 999999999987766553
No 106
>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=31.05 E-value=64 Score=27.69 Aligned_cols=28 Identities=11% Similarity=0.036 Sum_probs=22.7
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
|-....||..| |-+...|+++....+++
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 45689999999 89999999998765543
No 107
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=30.55 E-value=85 Score=27.37 Aligned_cols=28 Identities=21% Similarity=0.056 Sum_probs=23.1
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
.|-....||..| |-+...|+.+....++
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar~ 148 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGRV 148 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 456799999999 9999999999876544
No 108
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=30.45 E-value=72 Score=28.90 Aligned_cols=45 Identities=18% Similarity=0.172 Sum_probs=36.2
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhhhh
Q 021220 68 GNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIKRK 115 (316)
Q Consensus 68 g~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~k 115 (316)
...|+.|-+.|.-+.+ |-.=.+||..| +.|...||+|..+++++-
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 4688888877766654 44458999999 999999999999988763
No 109
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=30.02 E-value=14 Score=31.85 Aligned_cols=46 Identities=11% Similarity=0.135 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCCC
Q 021220 19 KEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDLK 66 (316)
Q Consensus 19 ~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~lk 66 (316)
.+-|.+|+.++.+.|...|.+||+.++ -+...|+.|+.+.....+-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 357889999999998889999999998 5999999998887655433
No 110
>PRK01905 DNA-binding protein Fis; Provisional
Probab=29.80 E-value=1.1e+02 Score=23.41 Aligned_cols=37 Identities=24% Similarity=0.220 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHH
Q 021220 72 EEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWN 109 (316)
Q Consensus 72 ~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~ 109 (316)
.-|.+.|.+++..+|+++.+.|+.+ |-+...++.+.+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rklk 72 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKKLQ 72 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 4477789999999999999999998 767766665543
No 111
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=29.74 E-value=1e+02 Score=25.63 Aligned_cols=29 Identities=14% Similarity=0.115 Sum_probs=23.2
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.|-.-.+||..| |-+...|+.+....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355689999999 99999999998765543
No 112
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=29.15 E-value=38 Score=25.94 Aligned_cols=19 Identities=26% Similarity=0.592 Sum_probs=15.6
Q ss_pred HHHHHHHHhhCCchhHHhh
Q 021220 76 ELIINFHSLLGNKWSLIAA 94 (316)
Q Consensus 76 e~Llelv~~~GnkWs~IA~ 94 (316)
..|.+|.+.||++|..|-.
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 4588888999999999864
No 113
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=28.84 E-value=98 Score=25.83 Aligned_cols=46 Identities=11% Similarity=0.088 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHHHhhhhhhhc
Q 021220 72 EEEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWNTHIKRKLYS 118 (316)
Q Consensus 72 ~EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~~~lk~k~~~ 118 (316)
.+-|.+|+++.+.-+ -.+..||+.+ |-|...|++|-+.+.+.-+.+
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCcee
Confidence 456888888888877 4699999999 999999999998877765444
No 114
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.59 E-value=1e+02 Score=26.69 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=23.3
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.|-...+||..| |-+...|+.+....+++
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999999 99999999988765543
No 115
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=27.95 E-value=84 Score=32.68 Aligned_cols=42 Identities=21% Similarity=0.387 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHH
Q 021220 68 GNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNT 110 (316)
Q Consensus 68 g~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~ 110 (316)
-.||++|-. +++-...|+.....||..+...|+.|++.+|..
T Consensus 471 ~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 471 YGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred CCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcC
Confidence 379999987 788888899999999999999999999999954
No 116
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=27.75 E-value=1.1e+02 Score=26.36 Aligned_cols=29 Identities=14% Similarity=0.179 Sum_probs=23.2
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.|-...+||..| |-+...|+.+....+++
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 356689999999 99999999998765543
No 117
>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=27.58 E-value=1.1e+02 Score=26.78 Aligned_cols=29 Identities=14% Similarity=0.019 Sum_probs=23.6
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.|-....||..| |-+...|+.|....+++
T Consensus 146 ~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 146 LGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 456789999999 99999999998775543
No 118
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=26.76 E-value=1.1e+02 Score=26.66 Aligned_cols=28 Identities=7% Similarity=0.041 Sum_probs=22.5
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
|-...+||..| |-+...|+.|....++.
T Consensus 157 g~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 157 ELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred CCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 55688999999 99999999998765543
No 119
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=26.59 E-value=98 Score=26.43 Aligned_cols=27 Identities=11% Similarity=-0.028 Sum_probs=21.6
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
|-...+||..| |.+...|+++....++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45688999999 8899999998876443
No 120
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=26.56 E-value=1.1e+02 Score=35.05 Aligned_cols=41 Identities=22% Similarity=0.408 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHhhC-CchhHHhhcCCCCCHHHHHHHHH
Q 021220 69 NFTEEEDELIINFHSLLG-NKWSLIAARLPGRTDNEIKNYWN 109 (316)
Q Consensus 69 ~WT~EEDe~Llelv~~~G-nkWs~IA~~lpgRT~~qcknRW~ 109 (316)
.|+.-|=...+.+..+|| .+-..||..|.|+|..+|+.+..
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~ 867 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAK 867 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHH
Confidence 688888888888888999 67999999999999999986543
No 121
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=26.54 E-value=1.3e+02 Score=24.16 Aligned_cols=36 Identities=14% Similarity=0.075 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHH
Q 021220 73 EEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWN 109 (316)
Q Consensus 73 EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~ 109 (316)
-|...|.+++..+++++.+.|+.| |-+...++.+-+
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rKLk 90 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKKLK 90 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHH
Confidence 477788999999999999999998 767766655443
No 122
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.53 E-value=1.2e+02 Score=26.37 Aligned_cols=28 Identities=11% Similarity=0.036 Sum_probs=22.8
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
.|-....||..| |-|...|+.++...++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~ 173 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARK 173 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 356689999999 8899999999876443
No 123
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=26.52 E-value=1.2e+02 Score=25.32 Aligned_cols=28 Identities=11% Similarity=-0.061 Sum_probs=22.2
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
.|-.-.+||..| |-+...|++|....++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355678999999 9999999998866443
No 124
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=26.46 E-value=1.3e+02 Score=26.32 Aligned_cols=27 Identities=15% Similarity=0.081 Sum_probs=21.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHI 112 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~l 112 (316)
.|-.-..||..| |-+...|+.+....+
T Consensus 151 ~g~s~~EIA~~l-gis~~tVk~~l~Rar 177 (195)
T PRK12532 151 LGFSSDEIQQMC-GISTSNYHTIMHRAR 177 (195)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 355679999999 999999999887633
No 125
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=26.17 E-value=1.4e+02 Score=25.81 Aligned_cols=32 Identities=25% Similarity=0.107 Sum_probs=26.2
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhhhhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIKRKLY 117 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk~k~~ 117 (316)
.|-...+||..| |-+...|+.|...-+..-+.
T Consensus 142 ~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 142 DGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 456799999999 99999999999877665443
No 126
>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=25.86 E-value=36 Score=30.18 Aligned_cols=33 Identities=27% Similarity=0.393 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccC-ccccc
Q 021220 16 AWTKEEDERLINYIKVHGEGCWRSLPKAAG-LLRCG 50 (316)
Q Consensus 16 ~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~-~~Rt~ 50 (316)
.||.|+.++|.++..+ | ..=.+||..|| ..|++
T Consensus 2 ~Wtde~~~~L~~lw~~-G-~SasqIA~~lg~vsRnA 35 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-G-LSASQIARQLGGVSRNA 35 (162)
T ss_pred CCCHHHHHHHHHHHHc-C-CCHHHHHHHhCCcchhh
Confidence 4999999999999864 3 23579999999 33444
No 127
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=25.69 E-value=1.2e+02 Score=26.59 Aligned_cols=28 Identities=11% Similarity=-0.042 Sum_probs=22.7
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
.|-.+.+||..| |-+...|+.+...-++
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~ 178 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKR 178 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 456799999999 9999999988876444
No 128
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=25.44 E-value=1.1e+02 Score=26.51 Aligned_cols=27 Identities=11% Similarity=0.057 Sum_probs=21.6
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
|-....||..| |-+...|+.++...++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~ 180 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRARE 180 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 44588999999 8899999999876443
No 129
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=25.10 E-value=15 Score=32.09 Aligned_cols=45 Identities=20% Similarity=0.234 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccCcccccccccceeeeccCCCC
Q 021220 19 KEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWINYLRPDL 65 (316)
Q Consensus 19 ~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n~L~p~l 65 (316)
.+-|.+|+.++.+.|--.|.+||+.++ =+...|+.|+.+.....+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 456888999999998888999999998 488999999888765544
No 130
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=25.09 E-value=1.2e+02 Score=26.41 Aligned_cols=28 Identities=7% Similarity=-0.076 Sum_probs=22.8
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
.|-...+||..| |.+...|+.|...-++
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 355689999999 9999999999766443
No 131
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.44 E-value=1.4e+02 Score=24.60 Aligned_cols=27 Identities=15% Similarity=0.187 Sum_probs=21.2
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
|-...+||..| |.+...|+.+-...++
T Consensus 122 ~~s~~EIA~~l-~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 122 GKTMGEIALET-EMTYYQVRWIYRQALE 148 (154)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 44578899998 9999999988766544
No 132
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=23.83 E-value=83 Score=23.29 Aligned_cols=26 Identities=35% Similarity=0.680 Sum_probs=19.2
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHH
Q 021220 78 IINFHSLLGNKWSLIAARLPGRTDNEI 104 (316)
Q Consensus 78 Llelv~~~GnkWs~IA~~lpgRT~~qc 104 (316)
+..+....|.+|..+|..| |=+..+|
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I 27 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEI 27 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHH
Confidence 4566778899999999998 4444444
No 133
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.39 E-value=1.6e+02 Score=24.66 Aligned_cols=28 Identities=21% Similarity=0.251 Sum_probs=22.0
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
|-.-..||..| |-+...|+.|....++.
T Consensus 121 ~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 121 GLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 44568999999 99999999998765543
No 134
>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=23.01 E-value=1.5e+02 Score=24.79 Aligned_cols=27 Identities=26% Similarity=0.231 Sum_probs=21.5
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
|-...+||..| |.+...|+.+-...++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIK 164 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45678999999 9999999988866543
No 135
>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=22.75 E-value=93 Score=22.04 Aligned_cols=42 Identities=26% Similarity=0.320 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 70 FTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 70 WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.|+.|-+.|.-+.. |..=.+||..+ |.+...|+.+...++++
T Consensus 4 LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 4 LTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp S-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 45566554444433 55668999999 99999999999887765
No 136
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=22.50 E-value=1.2e+02 Score=23.91 Aligned_cols=28 Identities=21% Similarity=0.485 Sum_probs=20.9
Q ss_pred HHHHHHhhCCchhHHhhcCCCCCHHHHHH
Q 021220 78 IINFHSLLGNKWSLIAARLPGRTDNEIKN 106 (316)
Q Consensus 78 Llelv~~~GnkWs~IA~~lpgRT~~qckn 106 (316)
+--+....|.+|..+|+.| |=|+.+|..
T Consensus 5 f~~i~~~lG~~Wk~laR~L-Glse~~Id~ 32 (86)
T cd08306 5 FDVICENVGRDWRKLARKL-GLSETKIES 32 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 3445566799999999999 777776643
No 137
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=22.44 E-value=50 Score=35.18 Aligned_cols=49 Identities=14% Similarity=0.266 Sum_probs=42.0
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCcccccccccceeee
Q 021220 9 KEHTNKGAWTKEEDERLINYIKVHGEGCWRSLPKAAGLLRCGKSCRLRWIN 59 (316)
Q Consensus 9 K~~~kKg~WT~EEDe~L~~lV~kyG~~nW~~IAk~l~~~Rt~kQCr~Rw~n 59 (316)
.+..-.++|+.+|-++....+...|. +...|+..+++ |..+|++.+|..
T Consensus 404 sk~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p~-R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 404 SKKLETDKWDASETELFYKALSERGS-DFSLISNLFPL-RDRKQIKAKFKK 452 (584)
T ss_pred cCccccCcccchhhHHhhhHHhhhcc-ccccccccccc-ccHHHHHHHHhh
Confidence 34556789999999999999999995 59999999997 999998887654
No 138
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=22.21 E-value=1.6e+02 Score=25.09 Aligned_cols=27 Identities=22% Similarity=0.256 Sum_probs=22.2
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
|-...+||..| |-+...|+.|...-++
T Consensus 150 g~s~~EIA~~l-gis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 150 GLTVEEIAELL-GVSVRTVERDWRFARA 176 (183)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 45689999999 9999999999876543
No 139
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=21.69 E-value=1.7e+02 Score=24.44 Aligned_cols=29 Identities=31% Similarity=0.371 Sum_probs=23.2
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.|-...+||..| |-+...|+.|...-+++
T Consensus 128 ~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 128 DGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 99999999988765543
No 140
>PRK00118 putative DNA-binding protein; Validated
Probab=21.59 E-value=1.8e+02 Score=24.05 Aligned_cols=41 Identities=12% Similarity=0.077 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 72 EEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 72 ~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
++.+..++.+....|-....||+.+ |-|...|+.+.....+
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RArk 59 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTEK 59 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 4556677777777888999999999 9999999888765443
No 141
>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=21.58 E-value=1.7e+02 Score=21.45 Aligned_cols=46 Identities=20% Similarity=0.265 Sum_probs=32.1
Q ss_pred CCCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 66 KRGNFTEEEDELIINFHSLLGNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 66 krg~WT~EEDe~Llelv~~~GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
++..||+|+-..++..+..-|.....||..+ |=+..++.+ |....+
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~-gi~~~~l~~-W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREY-GISPSTLYN-WRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHH-TS-HHHHHH-HHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeeccc-ccccccccH-HHHHHh
Confidence 4568999999999999988888999999998 556665554 765554
No 142
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.29 E-value=1.6e+02 Score=25.07 Aligned_cols=27 Identities=15% Similarity=0.257 Sum_probs=21.9
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIK 113 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk 113 (316)
|-.-..||..| |.+...|+.+....++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~ 171 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLL 171 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHH
Confidence 45578999999 9999999998876544
No 143
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.17 E-value=1.7e+02 Score=25.20 Aligned_cols=29 Identities=17% Similarity=0.088 Sum_probs=23.5
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.|-...+||+.| |.+...|+++-...+++
T Consensus 144 ~g~s~~EIA~~l-~is~~tV~~~l~rar~~ 172 (181)
T PRK12536 144 EGLSVAETAQLT-GLSESAVKVGIHRGLKA 172 (181)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355689999999 99999999998765543
No 144
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=21.11 E-value=1.4e+02 Score=25.54 Aligned_cols=28 Identities=29% Similarity=0.433 Sum_probs=23.2
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
|-...+||..| |-+...|+.+...-++.
T Consensus 135 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 135 GLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 45689999999 99999999998776554
No 145
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=21.02 E-value=1.6e+02 Score=25.66 Aligned_cols=29 Identities=17% Similarity=0.055 Sum_probs=23.5
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIKRK 115 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk~k 115 (316)
|-...+||..| |-+...|+.+...-++.-
T Consensus 146 g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 146 GLSYADAAAVC-GCPVGTIRSRVARARDAL 174 (185)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45589999999 999999999987755443
No 146
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=20.90 E-value=61 Score=26.79 Aligned_cols=28 Identities=18% Similarity=0.057 Sum_probs=22.7
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
|-.+.+||..| |-+...|++++....++
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 34589999999 99999999998775443
No 147
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=20.24 E-value=1.9e+02 Score=24.41 Aligned_cols=29 Identities=24% Similarity=0.129 Sum_probs=22.9
Q ss_pred hCCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 85 LGNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 85 ~GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
.|-...+||..| |-+...|+++-...+++
T Consensus 127 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 155 (164)
T PRK12547 127 SGFSYEDAAAIC-GCAVGTIKSRVSRARNR 155 (164)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355689999999 89999999988765543
No 148
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=20.19 E-value=1.8e+02 Score=24.89 Aligned_cols=28 Identities=21% Similarity=0.163 Sum_probs=22.1
Q ss_pred CCchhHHhhcCCCCCHHHHHHHHHHhhhh
Q 021220 86 GNKWSLIAARLPGRTDNEIKNYWNTHIKR 114 (316)
Q Consensus 86 GnkWs~IA~~lpgRT~~qcknRW~~~lk~ 114 (316)
|-.-.+||..| |-+...|+.+.+..+++
T Consensus 151 ~~s~~eIA~~l-gis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 151 GYTHREAAQLL-GLPLGTLKTRARRALSR 178 (186)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 44568999999 99999999988775543
No 149
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=20.01 E-value=2.7e+02 Score=22.35 Aligned_cols=44 Identities=16% Similarity=0.269 Sum_probs=34.8
Q ss_pred CCCCCHHHHHHHHHHHHhhCCchhHHhhcCCCC-CHHHHHHHHHHhh
Q 021220 67 RGNFTEEEDELIINFHSLLGNKWSLIAARLPGR-TDNEIKNYWNTHI 112 (316)
Q Consensus 67 rg~WT~EEDe~Llelv~~~GnkWs~IA~~lpgR-T~~qcknRW~~~l 112 (316)
+..||.|+-..+++++..-|..=+.||+.+ |- ..++++ +|...+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~-~W~~~~ 49 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLY-KWRIQL 49 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHH-HHHHHH
Confidence 568999999999999999888789999999 75 555555 454433
Done!