Query 021498
Match_columns 311
No_of_seqs 282 out of 1361
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 03:26:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/021498.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/021498hhsearch_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 6.3E-39 1.4E-43 312.3 13.4 134 1-134 1-134 (459)
2 PLN03212 Transcription repress 100.0 8.8E-39 1.9E-43 292.5 12.5 134 3-136 14-147 (249)
3 KOG0048 Transcription factor, 100.0 1.4E-33 3.1E-38 260.1 11.5 119 10-128 5-123 (238)
4 KOG0049 Transcription factor, 99.8 2.5E-20 5.3E-25 187.9 6.0 113 1-114 347-460 (939)
5 KOG0049 Transcription factor, 99.7 4.2E-18 9.1E-23 172.0 7.4 114 11-125 302-419 (939)
6 KOG0050 mRNA splicing protein 99.6 1.3E-16 2.9E-21 158.0 5.8 141 10-153 3-144 (617)
7 PF13921 Myb_DNA-bind_6: Myb-l 99.6 1.2E-16 2.5E-21 117.0 3.6 60 17-78 1-60 (60)
8 COG5147 REB1 Myb superfamily p 99.6 1.3E-15 2.7E-20 153.3 6.9 109 8-117 14-122 (512)
9 KOG0051 RNA polymerase I termi 99.5 2.8E-14 6E-19 145.1 6.0 103 13-118 383-513 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.4 1.6E-13 3.5E-18 96.5 5.1 46 67-112 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.4 6.3E-14 1.4E-18 98.6 1.1 48 14-61 1-48 (48)
12 PLN03212 Transcription repress 99.4 6.5E-13 1.4E-17 122.5 5.7 73 48-127 13-87 (249)
13 PF13921 Myb_DNA-bind_6: Myb-l 99.4 7.6E-13 1.7E-17 96.7 4.7 53 70-122 1-53 (60)
14 KOG0048 Transcription factor, 99.3 2.6E-12 5.6E-17 118.8 4.3 64 63-126 5-70 (238)
15 PLN03091 hypothetical protein; 99.2 6.7E-12 1.5E-16 123.7 4.9 65 62-126 9-75 (459)
16 smart00717 SANT SANT SWI3, AD 99.2 2.1E-11 4.6E-16 83.4 5.5 47 67-113 1-48 (49)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1.6E-10 3.5E-15 77.8 5.5 43 69-111 1-44 (45)
18 smart00717 SANT SANT SWI3, AD 99.0 1.7E-10 3.7E-15 78.9 2.1 48 14-62 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 8.4E-10 1.8E-14 74.3 1.7 44 16-60 1-44 (45)
20 KOG0051 RNA polymerase I termi 98.8 2.7E-09 5.8E-14 109.1 4.8 106 13-122 307-440 (607)
21 COG5147 REB1 Myb superfamily p 98.3 6.8E-08 1.5E-12 98.0 -2.2 98 13-113 290-397 (512)
22 TIGR01557 myb_SHAQKYF myb-like 97.9 7.1E-06 1.5E-10 60.2 2.3 49 13-61 2-54 (57)
23 KOG0050 mRNA splicing protein 97.8 1.2E-05 2.6E-10 81.0 3.5 61 65-125 5-66 (617)
24 TIGR02894 DNA_bind_RsfA transc 97.6 6.1E-05 1.3E-09 65.9 4.4 52 66-118 3-61 (161)
25 KOG0457 Histone acetyltransfer 97.6 2.3E-05 5E-10 77.6 1.9 89 12-101 70-180 (438)
26 TIGR01557 myb_SHAQKYF myb-like 97.6 0.00019 4.1E-09 52.7 5.8 46 67-112 3-54 (57)
27 KOG0457 Histone acetyltransfer 97.6 0.00012 2.7E-09 72.6 6.0 49 64-112 69-118 (438)
28 PF08914 Myb_DNA-bind_2: Rap1 97.3 0.0004 8.6E-09 52.3 4.2 51 67-117 2-62 (65)
29 COG5259 RSC8 RSC chromatin rem 97.2 0.00039 8.5E-09 69.6 4.5 55 66-120 278-334 (531)
30 KOG1279 Chromatin remodeling f 97.2 0.00051 1.1E-08 70.2 5.2 47 66-112 252-298 (506)
31 PF13837 Myb_DNA-bind_4: Myb/S 97.2 0.00037 8.1E-09 54.1 3.4 50 68-117 2-69 (90)
32 PF13325 MCRS_N: N-terminal re 96.9 0.0019 4.1E-08 58.7 5.9 99 16-116 1-130 (199)
33 COG5259 RSC8 RSC chromatin rem 96.9 0.00037 8E-09 69.8 1.4 46 13-60 278-323 (531)
34 KOG1279 Chromatin remodeling f 96.8 0.00047 1E-08 70.4 1.6 47 12-60 251-297 (506)
35 PRK13923 putative spore coat p 96.7 0.0017 3.7E-08 57.6 4.2 51 65-116 3-60 (170)
36 PF13873 Myb_DNA-bind_5: Myb/S 95.9 0.017 3.7E-07 43.9 5.1 52 67-118 2-75 (78)
37 PF08914 Myb_DNA-bind_2: Rap1 95.9 0.0023 5E-08 48.2 0.2 52 14-65 2-61 (65)
38 PF13837 Myb_DNA-bind_4: Myb/S 95.7 0.0035 7.7E-08 48.5 0.6 47 14-60 1-63 (90)
39 COG5114 Histone acetyltransfer 95.7 0.03 6.6E-07 54.1 6.8 47 67-113 63-110 (432)
40 TIGR02894 DNA_bind_RsfA transc 95.5 0.0048 1E-07 54.2 0.7 50 12-63 2-57 (161)
41 COG5114 Histone acetyltransfer 95.2 0.0066 1.4E-07 58.6 0.7 47 15-62 64-110 (432)
42 PLN03142 Probable chromatin-re 94.9 0.057 1.2E-06 59.9 6.9 101 16-117 826-989 (1033)
43 PRK13923 putative spore coat p 94.4 0.012 2.7E-07 52.2 0.2 49 12-62 3-57 (170)
44 KOG4282 Transcription factor G 93.5 0.14 3E-06 49.7 5.8 52 67-118 54-119 (345)
45 PF13873 Myb_DNA-bind_5: Myb/S 93.5 0.022 4.8E-07 43.3 0.1 49 13-61 1-69 (78)
46 KOG2656 DNA methyltransferase 92.9 0.13 2.7E-06 51.1 4.4 57 67-123 130-192 (445)
47 PF09111 SLIDE: SLIDE; InterP 92.8 0.2 4.2E-06 42.1 4.8 53 64-116 46-114 (118)
48 PF12776 Myb_DNA-bind_3: Myb/S 92.4 0.34 7.3E-06 37.8 5.4 46 69-114 1-64 (96)
49 COG5118 BDP1 Transcription ini 88.5 0.69 1.5E-05 46.0 4.8 46 69-114 367-412 (507)
50 PF08281 Sigma70_r4_2: Sigma-7 87.0 1.6 3.4E-05 30.5 4.8 42 72-114 12-53 (54)
51 PF09111 SLIDE: SLIDE; InterP 82.8 1.1 2.4E-05 37.5 2.8 34 11-44 46-82 (118)
52 KOG1194 Predicted DNA-binding 81.1 3.3 7.1E-05 42.2 5.8 47 67-113 187-233 (534)
53 PF13404 HTH_AsnC-type: AsnC-t 80.3 3.6 7.8E-05 28.1 4.1 38 73-111 3-41 (42)
54 PF11626 Rap1_C: TRF2-interact 75.5 2.5 5.3E-05 33.2 2.5 29 11-42 44-80 (87)
55 KOG4282 Transcription factor G 75.4 1.3 2.9E-05 42.9 1.2 47 14-60 54-112 (345)
56 COG5118 BDP1 Transcription ini 75.4 6.6 0.00014 39.3 5.9 111 14-126 365-489 (507)
57 KOG4468 Polycomb-group transcr 75.3 5 0.00011 42.2 5.2 52 67-118 88-149 (782)
58 KOG4167 Predicted DNA-binding 74.9 5.5 0.00012 42.8 5.5 45 68-112 620-664 (907)
59 PF04545 Sigma70_r4: Sigma-70, 74.0 8.2 0.00018 26.5 4.6 41 73-114 7-47 (50)
60 PRK11179 DNA-binding transcrip 70.5 8.6 0.00019 32.9 4.9 44 73-117 9-53 (153)
61 smart00595 MADF subfamily of S 70.4 5.1 0.00011 30.7 3.2 26 89-115 30-55 (89)
62 PF13404 HTH_AsnC-type: AsnC-t 67.4 2.3 5E-05 29.0 0.6 38 20-59 3-40 (42)
63 PF13325 MCRS_N: N-terminal re 63.5 14 0.00031 33.7 5.1 44 69-113 1-47 (199)
64 PRK11169 leucine-responsive tr 63.0 12 0.00026 32.4 4.4 44 72-116 13-57 (164)
65 cd08319 Death_RAIDD Death doma 62.1 10 0.00022 29.8 3.4 29 75-104 2-30 (83)
66 PRK11179 DNA-binding transcrip 61.7 3.5 7.6E-05 35.3 0.8 45 20-66 9-53 (153)
67 PF11035 SnAPC_2_like: Small n 61.0 31 0.00067 33.8 7.1 48 67-114 21-72 (344)
68 PF01388 ARID: ARID/BRIGHT DNA 60.6 19 0.00041 27.9 4.7 38 77-114 40-90 (92)
69 TIGR02985 Sig70_bacteroi1 RNA 60.5 21 0.00045 29.4 5.3 36 79-115 122-157 (161)
70 PRK11169 leucine-responsive tr 58.7 3.4 7.4E-05 35.9 0.2 46 19-66 13-58 (164)
71 PF12776 Myb_DNA-bind_3: Myb/S 58.4 7.7 0.00017 30.0 2.1 44 16-59 1-60 (96)
72 KOG2009 Transcription initiati 57.5 10 0.00022 39.9 3.3 50 65-114 407-456 (584)
73 smart00501 BRIGHT BRIGHT, ARID 57.1 22 0.00048 27.8 4.6 40 77-116 36-88 (93)
74 PF11626 Rap1_C: TRF2-interact 55.1 12 0.00026 29.3 2.8 17 63-79 43-59 (87)
75 PF07750 GcrA: GcrA cell cycle 52.9 15 0.00033 32.3 3.3 41 69-110 2-42 (162)
76 PF10545 MADF_DNA_bdg: Alcohol 51.2 16 0.00035 27.0 2.9 28 89-116 29-57 (85)
77 cd08803 Death_ank3 Death domai 50.3 23 0.0005 27.8 3.6 29 75-104 4-32 (84)
78 KOG4468 Polycomb-group transcr 49.9 11 0.00023 39.9 2.1 47 14-61 88-143 (782)
79 PF01388 ARID: ARID/BRIGHT DNA 49.7 3.7 8.1E-05 31.9 -1.0 40 23-62 39-89 (92)
80 KOG4167 Predicted DNA-binding 49.5 8.4 0.00018 41.5 1.3 43 14-58 619-661 (907)
81 PRK12523 RNA polymerase sigma 49.3 45 0.00097 28.4 5.7 40 82-122 131-170 (172)
82 PF04504 DUF573: Protein of un 48.7 33 0.00071 27.6 4.4 51 68-118 5-68 (98)
83 cd08317 Death_ank Death domain 48.1 18 0.0004 27.9 2.8 29 75-104 4-32 (84)
84 TIGR02937 sigma70-ECF RNA poly 48.0 46 0.00099 26.5 5.3 33 81-114 121-153 (158)
85 PRK09645 RNA polymerase sigma 45.5 49 0.0011 28.1 5.3 29 85-114 133-161 (173)
86 smart00344 HTH_ASNC helix_turn 45.5 39 0.00085 26.6 4.4 43 73-116 3-46 (108)
87 PHA03308 transcriptional regul 44.4 12 0.00026 40.5 1.5 12 200-211 1206-1217(1463)
88 PRK09652 RNA polymerase sigma 43.5 57 0.0012 27.3 5.4 32 84-116 142-173 (182)
89 cd08318 Death_NMPP84 Death dom 43.0 30 0.00064 27.0 3.2 26 78-104 10-35 (86)
90 PF11035 SnAPC_2_like: Small n 42.9 57 0.0012 32.0 5.7 86 14-113 21-127 (344)
91 PF07638 Sigma70_ECF: ECF sigm 41.9 61 0.0013 28.4 5.5 38 77-115 142-179 (185)
92 smart00501 BRIGHT BRIGHT, ARID 41.6 8 0.00017 30.3 -0.2 40 23-62 35-85 (93)
93 PRK12512 RNA polymerase sigma 41.6 62 0.0013 27.8 5.4 35 85-120 146-180 (184)
94 PRK12532 RNA polymerase sigma 40.7 65 0.0014 28.0 5.5 36 84-120 150-188 (195)
95 KOG0384 Chromodomain-helicase 40.4 28 0.00061 39.8 3.6 74 14-94 1133-1207(1373)
96 cd08804 Death_ank2 Death domai 40.4 33 0.00072 26.7 3.2 31 75-106 4-34 (84)
97 PF09420 Nop16: Ribosome bioge 40.2 73 0.0016 27.8 5.6 46 66-111 113-162 (164)
98 PRK12529 RNA polymerase sigma 40.1 67 0.0015 27.6 5.4 34 84-118 141-174 (178)
99 KOG4329 DNA-binding protein [G 39.3 54 0.0012 32.9 5.0 46 68-113 278-324 (445)
100 cd08311 Death_p75NR Death doma 37.8 33 0.00073 26.5 2.7 33 72-106 2-34 (77)
101 PF02954 HTH_8: Bacterial regu 37.3 64 0.0014 21.5 3.8 36 73-109 5-40 (42)
102 PRK04217 hypothetical protein; 37.3 1.1E+02 0.0024 25.3 5.9 46 68-115 41-86 (110)
103 PRK11924 RNA polymerase sigma 36.9 69 0.0015 26.8 4.9 29 85-114 140-168 (179)
104 PRK09641 RNA polymerase sigma 36.9 64 0.0014 27.5 4.7 30 85-115 151-180 (187)
105 PRK09643 RNA polymerase sigma 36.6 73 0.0016 27.8 5.1 30 84-114 148-177 (192)
106 cd06171 Sigma70_r4 Sigma70, re 36.0 1.1E+02 0.0023 19.8 4.8 40 70-111 11-50 (55)
107 PRK09413 IS2 repressor TnpA; R 35.9 82 0.0018 25.9 5.0 44 14-61 10-53 (121)
108 cd08777 Death_RIP1 Death Domai 35.6 39 0.00085 26.5 2.9 30 76-106 3-32 (86)
109 smart00005 DEATH DEATH domain, 35.5 43 0.00092 25.4 3.0 29 75-104 5-34 (88)
110 PLN03162 golden-2 like transcr 34.7 2.7E+02 0.0059 28.1 9.0 44 68-111 238-286 (526)
111 COG1522 Lrp Transcriptional re 34.5 54 0.0012 27.3 3.8 43 73-116 8-51 (154)
112 TIGR02939 RpoE_Sigma70 RNA pol 34.4 59 0.0013 27.8 4.1 32 85-117 153-184 (190)
113 KOG1194 Predicted DNA-binding 34.4 28 0.00062 35.7 2.3 41 68-109 471-511 (534)
114 PRK09648 RNA polymerase sigma 33.4 92 0.002 26.9 5.2 31 85-116 154-184 (189)
115 PRK09047 RNA polymerase factor 33.0 86 0.0019 26.0 4.8 29 85-114 121-149 (161)
116 PRK12531 RNA polymerase sigma 32.9 88 0.0019 27.3 5.0 32 85-117 156-187 (194)
117 cd08779 Death_PIDD Death Domai 32.5 48 0.001 25.9 2.9 21 76-96 3-23 (86)
118 PRK09642 RNA polymerase sigma 32.2 98 0.0021 25.8 5.0 30 84-114 120-149 (160)
119 PRK09649 RNA polymerase sigma 31.9 1.1E+02 0.0024 26.4 5.5 32 85-117 145-176 (185)
120 cd08805 Death_ank1 Death domai 31.3 63 0.0014 25.4 3.4 26 75-101 4-29 (84)
121 TIGR02954 Sig70_famx3 RNA poly 31.2 99 0.0021 26.1 4.9 31 85-116 134-164 (169)
122 TIGR02948 SigW_bacill RNA poly 30.3 91 0.002 26.6 4.6 30 86-116 152-181 (187)
123 PRK09637 RNA polymerase sigma 30.3 1E+02 0.0022 26.7 5.0 29 85-114 121-149 (181)
124 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 29.8 81 0.0018 22.5 3.4 34 73-107 7-40 (50)
125 TIGR02943 Sig70_famx1 RNA poly 29.3 1.2E+02 0.0025 26.5 5.2 31 84-115 145-175 (188)
126 PRK12515 RNA polymerase sigma 29.2 1.2E+02 0.0026 26.2 5.2 29 85-114 146-174 (189)
127 COG1522 Lrp Transcriptional re 28.4 23 0.00049 29.6 0.5 44 20-65 8-51 (154)
128 PRK11923 algU RNA polymerase s 28.3 1.1E+02 0.0024 26.4 4.8 28 86-114 154-181 (193)
129 TIGR02952 Sig70_famx2 RNA poly 28.0 1.3E+02 0.0028 25.0 5.1 28 86-114 138-165 (170)
130 PRK12530 RNA polymerase sigma 27.7 1.3E+02 0.0028 26.2 5.1 29 85-114 149-177 (189)
131 PRK05602 RNA polymerase sigma 27.0 1.2E+02 0.0026 26.1 4.8 30 85-115 143-172 (186)
132 PLN03142 Probable chromatin-re 26.9 56 0.0012 37.0 3.2 33 12-44 924-956 (1033)
133 PRK12527 RNA polymerase sigma 26.8 1.3E+02 0.0027 25.1 4.8 30 85-115 120-149 (159)
134 PRK12524 RNA polymerase sigma 26.8 1.3E+02 0.0028 26.2 5.1 29 85-114 151-179 (196)
135 TIGR02999 Sig-70_X6 RNA polyme 26.5 1.5E+02 0.0032 25.2 5.3 30 85-115 149-178 (183)
136 smart00344 HTH_ASNC helix_turn 26.5 32 0.00069 27.1 1.0 43 20-64 3-45 (108)
137 PHA03308 transcriptional regul 26.1 37 0.00081 36.9 1.6 7 48-54 983-989 (1463)
138 PRK01905 DNA-binding protein F 25.9 1.5E+02 0.0031 22.6 4.5 37 71-108 35-71 (77)
139 PRK00118 putative DNA-binding 25.7 1.6E+02 0.0035 24.1 5.0 41 72-113 19-59 (104)
140 PRK12547 RNA polymerase sigma 25.6 1.6E+02 0.0035 24.8 5.3 32 85-117 127-158 (164)
141 PRK12528 RNA polymerase sigma 25.5 1.4E+02 0.0029 25.0 4.7 30 84-114 127-156 (161)
142 PRK12536 RNA polymerase sigma 25.4 1.5E+02 0.0033 25.4 5.1 33 84-117 143-175 (181)
143 PRK13919 putative RNA polymera 25.2 1.5E+02 0.0033 25.2 5.1 31 85-116 150-180 (186)
144 PRK06759 RNA polymerase factor 25.0 1.6E+02 0.0034 24.2 5.0 29 85-114 121-149 (154)
145 PRK12514 RNA polymerase sigma 24.7 1.6E+02 0.0034 25.1 5.1 29 86-115 145-173 (179)
146 PRK12516 RNA polymerase sigma 24.7 1.4E+02 0.003 26.1 4.8 31 83-114 129-159 (187)
147 PRK12542 RNA polymerase sigma 24.3 1.6E+02 0.0034 25.3 5.0 31 84-115 136-166 (185)
148 TIGR02960 SigX5 RNA polymerase 24.2 1.4E+02 0.003 28.1 5.0 32 85-117 157-188 (324)
149 PRK09646 RNA polymerase sigma 23.9 1.8E+02 0.004 25.2 5.4 32 85-117 157-188 (194)
150 COG2197 CitB Response regulato 23.7 1.1E+02 0.0025 27.4 4.2 44 68-114 147-190 (211)
151 PRK09651 RNA polymerase sigma 23.7 1.2E+02 0.0025 25.9 4.1 29 85-114 134-162 (172)
152 PF07750 GcrA: GcrA cell cycle 23.6 61 0.0013 28.5 2.3 34 16-51 2-36 (162)
153 COG2963 Transposase and inacti 23.5 2E+02 0.0044 23.0 5.2 47 67-114 5-51 (116)
154 cd01670 Death Death Domain: a 23.2 79 0.0017 23.2 2.6 25 78-103 2-26 (79)
155 PF00196 GerE: Bacterial regul 23.2 95 0.0021 21.8 2.9 42 70-114 4-45 (58)
156 KOG2656 DNA methyltransferase 23.1 32 0.00069 34.6 0.4 48 12-60 128-180 (445)
157 cd08306 Death_FADD Fas-associa 23.0 1.1E+02 0.0023 23.9 3.3 25 80-105 7-31 (86)
158 TIGR02983 SigE-fam_strep RNA p 22.7 2.1E+02 0.0044 23.8 5.3 40 77-117 117-156 (162)
159 PRK00430 fis global DNA-bindin 22.5 1.8E+02 0.0039 23.2 4.6 35 73-108 55-89 (95)
160 PRK09638 RNA polymerase sigma 22.5 78 0.0017 26.8 2.7 32 85-117 141-172 (176)
161 PRK12537 RNA polymerase sigma 22.5 1.9E+02 0.0041 24.8 5.2 31 85-116 148-178 (182)
162 KOG2009 Transcription initiati 22.2 49 0.0011 34.9 1.6 49 9-59 404-452 (584)
163 PRK12546 RNA polymerase sigma 22.1 1.6E+02 0.0034 25.9 4.6 33 84-117 127-159 (188)
164 PRK12545 RNA polymerase sigma 21.6 1.9E+02 0.004 25.5 5.0 28 85-113 154-181 (201)
165 PRK06811 RNA polymerase factor 21.6 1.9E+02 0.0042 24.9 5.1 28 86-114 147-174 (189)
166 TIGR02984 Sig-70_plancto1 RNA 21.6 1.9E+02 0.0041 24.5 5.0 30 85-115 155-184 (189)
167 TIGR02950 SigM_subfam RNA poly 21.0 71 0.0015 26.3 2.1 29 86-115 121-149 (154)
168 TIGR01636 phage_rinA phage tra 20.9 2.8E+02 0.006 23.2 5.7 32 88-120 102-133 (134)
169 PRK12520 RNA polymerase sigma 20.8 2.1E+02 0.0045 24.7 5.1 29 85-114 146-174 (191)
170 PF09197 Rap1-DNA-bind: Rap1, 20.5 2.9E+02 0.0062 22.8 5.4 46 69-114 1-77 (105)
171 KOG3554 Histone deacetylase co 20.3 1.5E+02 0.0033 30.8 4.5 61 38-109 267-328 (693)
172 PRK11922 RNA polymerase sigma 20.1 1.1E+02 0.0024 27.7 3.3 29 86-115 165-193 (231)
173 PRK12519 RNA polymerase sigma 20.1 1.7E+02 0.0037 25.2 4.5 30 85-115 156-185 (194)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=6.3e-39 Score=312.30 Aligned_cols=134 Identities=66% Similarity=1.200 Sum_probs=129.5
Q ss_pred CCCCccccCCCCccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHH
Q 021498 1 MGRQPCCDKVGLKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVID 80 (311)
Q Consensus 1 mgR~~~~~K~~lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~ 80 (311)
|||++||.|.+++||+||+|||++|+++|++||..+|..||+.++.+|+++|||+||.+||+|.+++++||+|||++|++
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 99999999999999999999999999999999999999999998766999999999999999999999999999999999
Q ss_pred HHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCC
Q 021498 81 LHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLRKMGIDPLTHKPLSTTDD 134 (311)
Q Consensus 81 lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~~~~~~~k~~~~~~~ 134 (311)
+|++||++|.+||++|+|||+++||+||+.++++++++.++.+.+++++.....
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~E~ 134 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEVEN 134 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCcccccc
Confidence 999999999999999999999999999999999999999999999999877643
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=8.8e-39 Score=292.46 Aligned_cols=134 Identities=60% Similarity=1.167 Sum_probs=127.1
Q ss_pred CCccccCCCCccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHH
Q 021498 3 RQPCCDKVGLKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVIDLH 82 (311)
Q Consensus 3 R~~~~~K~~lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~lv 82 (311)
|+|||+|+++++++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.++|+|.+++++||+|||++|++++
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 67999999999999999999999999999999999999999875699999999999999999999999999999999999
Q ss_pred HHhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCCCCC
Q 021498 83 AQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLRKMGIDPLTHKPLSTTDDQQ 136 (311)
Q Consensus 83 ~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~~~~~~~k~~~~~~~~~ 136 (311)
.+||++|++||++|||||+++||+||+.++++.+++.++.|.+.+++.......
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~~~~~~~~ 147 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPLDANNIHK 147 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCCCccccCC
Confidence 999999999999999999999999999999999999999999988876654433
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=1.4e-33 Score=260.13 Aligned_cols=119 Identities=70% Similarity=1.140 Sum_probs=110.8
Q ss_pred CCCccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCh
Q 021498 10 VGLKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVIDLHAQLGNRW 89 (311)
Q Consensus 10 ~~lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~lv~~~G~kW 89 (311)
+.+.||+||+|||++|+++|++||.++|..||+.+|.+|++++||.||.|||+|++++|.||+|||.+|+++++.||++|
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 33458999999999999999999999999999999966999999999999999999999999999999999999999999
Q ss_pred hhhhhcCCCCCHHHHHHHHHHHHHHHHhhcCCCCCCCCC
Q 021498 90 SKIASHLPGRTDNEIKNHWNTHIKKKLRKMGIDPLTHKP 128 (311)
Q Consensus 90 ~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~~~~~~~k~ 128 (311)
++||++|||||++.||++|+..+++++.+.+..+.+..+
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~~~~~~ 123 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDPSTHRP 123 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCCCcccc
Confidence 999999999999999999999999999998855554333
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.80 E-value=2.5e-20 Score=187.94 Aligned_cols=113 Identities=25% Similarity=0.367 Sum_probs=103.7
Q ss_pred CCCCccccCCCCccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHH
Q 021498 1 MGRQPCCDKVGLKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVID 80 (311)
Q Consensus 1 mgR~~~~~K~~lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~ 80 (311)
+||......|++++|+||.+||.+|..+|.+||.++|.+|-+.+++ |+..|||+||+|+|+...+++.||-.||+.|+.
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 4788888999999999999999999999999999999999999997 999999999999999999999999999999999
Q ss_pred HHHHhC-CChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 81 LHAQLG-NRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 81 lv~~~G-~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
+|.+|| ++|.+||..||.||+.|.+.|=...+..
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~ 460 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAA 460 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHHHHHHH
Confidence 999999 6899999999999997765554444433
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.73 E-value=4.2e-18 Score=171.97 Aligned_cols=114 Identities=20% Similarity=0.439 Sum_probs=105.8
Q ss_pred CCccCCCCHHHHHHHHHHHHHcCC---CCcchhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCC
Q 021498 11 GLKKGPWTAEEDKKLINFILTNGQ---CCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVIDLHAQLGN 87 (311)
Q Consensus 11 ~lkkg~WT~EED~~L~~lV~k~G~---~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~lv~~~G~ 87 (311)
-++...||+|||.+|+.+|..... .+|++|-..|++ |+..|...||...|+|++++|+||.+||.+|+.+|.+||.
T Consensus 302 ~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympg-r~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~ 380 (939)
T KOG0049|consen 302 QLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPG-RTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGA 380 (939)
T ss_pred HHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCC-cchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCc
Confidence 456788999999999999988754 489999999997 9999999999999999999999999999999999999996
Q ss_pred C-hhhhhhcCCCCCHHHHHHHHHHHHHHHHhhcCCCCCC
Q 021498 88 R-WSKIASHLPGRTDNEIKNHWNTHIKKKLRKMGIDPLT 125 (311)
Q Consensus 88 k-W~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~~~~~~ 125 (311)
+ |.+|-..+|||++.|||.||.+.|....|+..|+-..
T Consensus 381 kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~e 419 (939)
T KOG0049|consen 381 KDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVE 419 (939)
T ss_pred cchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecc
Confidence 5 9999999999999999999999999999998887554
No 6
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.64 E-value=1.3e-16 Score=158.02 Aligned_cols=141 Identities=20% Similarity=0.447 Sum_probs=116.7
Q ss_pred CCCccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCh
Q 021498 10 VGLKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVIDLHAQLGNRW 89 (311)
Q Consensus 10 ~~lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~lv~~~G~kW 89 (311)
.-++.|.|+.-||+.|+.+|.+||.+.|.+|++.+.. .+++||+.||..+|+|.+++..|+.+||++|+.+.......|
T Consensus 3 i~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~-kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qw 81 (617)
T KOG0050|consen 3 IEIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNR-KTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQW 81 (617)
T ss_pred eEEecceecccHHHHHHHHHHHcchHHHHHHHHHHhh-cchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCcc
Confidence 3467899999999999999999999999999999886 999999999999999999999999999999999999999999
Q ss_pred hhhhhcCCCCCHHHHHHHHHHHHHHHHhhcCC-CCCCCCCCCCCCCCCCccccccccCCccccCc
Q 021498 90 SKIASHLPGRTDNEIKNHWNTHIKKKLRKMGI-DPLTHKPLSTTDDQQPQVKINQQEQEPLMIND 153 (311)
Q Consensus 90 ~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~~-~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 153 (311)
..||..| ||+++||-.||++++-.......- .+..+.. -......|+...+.....++..+.
T Consensus 82 rtIa~i~-gr~~~qc~eRy~~ll~~~~s~~~~~~~~~D~r-Lk~gE~ePn~e~~~aRpd~~dmdE 144 (617)
T KOG0050|consen 82 RTIADIM-GRTSQQCLERYNNLLDVYVSYHYHSEPYIDAK-LKEGEIEPNQETNPARPDGFDMDE 144 (617)
T ss_pred chHHHHh-hhhHHHHHHHHHHHHHHHHhhhcccccccccc-cCCCcCCCccccccccCCcccchH
Confidence 9999999 999999999999999887766443 3333322 233333444445555555555554
No 7
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.64 E-value=1.2e-16 Score=116.99 Aligned_cols=60 Identities=37% Similarity=0.752 Sum_probs=54.8
Q ss_pred CCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHH
Q 021498 17 WTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMV 78 (311)
Q Consensus 17 WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~L 78 (311)
||+|||++|+++|.+|| .+|..||+.+|. |++.||+.||.++|.+.+++++||.+||++|
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 689999999975 9999999999999999999999999999987
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=99.59 E-value=1.3e-15 Score=153.33 Aligned_cols=109 Identities=30% Similarity=0.481 Sum_probs=103.8
Q ss_pred cCCCCccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCC
Q 021498 8 DKVGLKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVIDLHAQLGN 87 (311)
Q Consensus 8 ~K~~lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~lv~~~G~ 87 (311)
....++.|.|+..||+.|+.+|+++|.++|.+||..+.. |+++||+.||.++++|.++++.|+.+||..|+.+..++|.
T Consensus 14 ~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~-~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~ 92 (512)
T COG5147 14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLIS-STGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT 92 (512)
T ss_pred ccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcc-cccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc
Confidence 445678899999999999999999999999999999986 9999999999999999999999999999999999999999
Q ss_pred ChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 88 RWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 88 kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
+|+.||..++||++.+|.+||...+.....
T Consensus 93 ~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 93 QWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 999999999999999999999999988766
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.48 E-value=2.8e-14 Score=145.13 Aligned_cols=103 Identities=26% Similarity=0.525 Sum_probs=93.5
Q ss_pred ccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCC--CCCCCCHHHHHHHHHHHH-------
Q 021498 13 KKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDL--KRGLLSEYEEKMVIDLHA------- 83 (311)
Q Consensus 13 kkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l--~kg~WT~EED~~Ll~lv~------- 83 (311)
++|+||+||++.|..+|.++| .+|..|++.+| |.+..||+||++|...+- +++.||.||.++|+++|+
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 89999999998 999999999999999884 899999999999999995
Q ss_pred Hh-------------------CCChhhhhhcCCCCCHHHHHHHHHHHHHHHHhh
Q 021498 84 QL-------------------GNRWSKIASHLPGRTDNEIKNHWNTHIKKKLRK 118 (311)
Q Consensus 84 ~~-------------------G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk 118 (311)
++ +-+|..|++.+..|+..|||.+|+.++......
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 125999999999999999999999998765443
No 10
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.43 E-value=1.6e-13 Score=96.46 Aligned_cols=46 Identities=28% Similarity=0.648 Sum_probs=42.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-hhhhhhcCC-CCCHHHHHHHHHHHH
Q 021498 67 RGLLSEYEEKMVIDLHAQLGNR-WSKIASHLP-GRTDNEIKNHWNTHI 112 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~k-W~kIA~~lp-gRT~~qcr~Rw~~~l 112 (311)
+++||++||++|+++|.+||.+ |.+||..|+ |||..||++||++++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999988 999999999 999999999999874
No 11
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.40 E-value=6.3e-14 Score=98.57 Aligned_cols=48 Identities=40% Similarity=0.741 Sum_probs=42.7
Q ss_pred cCCCCHHHHHHHHHHHHHcCCCCcchhhhhhccccccccccccccccc
Q 021498 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYL 61 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L 61 (311)
|++||+|||++|+++|.+||..+|..||..++++||+.||+.||.++|
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 689999999999999999997779999999995599999999999875
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.36 E-value=6.5e-13 Score=122.48 Aligned_cols=73 Identities=16% Similarity=0.412 Sum_probs=64.0
Q ss_pred ccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhC-CChhhhhhcC-CCCCHHHHHHHHHHHHHHHHhhcCCCCCC
Q 021498 48 RCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVIDLHAQLG-NRWSKIASHL-PGRTDNEIKNHWNTHIKKKLRKMGIDPLT 125 (311)
Q Consensus 48 Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~lv~~~G-~kW~kIA~~l-pgRT~~qcr~Rw~~~l~~~~kk~~~~~~~ 125 (311)
|++.-|. ++.+++++||+|||++|+++|++|| .+|..||+.+ +|||++|||.||.++|++.+++..|+..+
T Consensus 13 ~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EE 85 (249)
T PLN03212 13 KTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDE 85 (249)
T ss_pred CCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHH
Confidence 6655554 3678999999999999999999999 5799999998 69999999999999999999999987765
Q ss_pred CC
Q 021498 126 HK 127 (311)
Q Consensus 126 ~k 127 (311)
..
T Consensus 86 D~ 87 (249)
T PLN03212 86 ED 87 (249)
T ss_pred HH
Confidence 44
No 13
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.36 E-value=7.6e-13 Score=96.71 Aligned_cols=53 Identities=30% Similarity=0.664 Sum_probs=44.8
Q ss_pred CCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHhhcCCC
Q 021498 70 LSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLRKMGID 122 (311)
Q Consensus 70 WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~~~ 122 (311)
||++||.+|+++|.+||++|.+||++|+.||+.+|++||+..|++...+..|+
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt 53 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWT 53 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSS
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcC
Confidence 99999999999999999999999999966999999999999887766665554
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.27 E-value=2.6e-12 Score=118.84 Aligned_cols=64 Identities=14% Similarity=0.275 Sum_probs=58.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCC-ChhhhhhcCC-CCCHHHHHHHHHHHHHHHHhhcCCCCCCC
Q 021498 63 PDLKRGLLSEYEEKMVIDLHAQLGN-RWSKIASHLP-GRTDNEIKNHWNTHIKKKLRKMGIDPLTH 126 (311)
Q Consensus 63 p~l~kg~WT~EED~~Ll~lv~~~G~-kW~kIA~~lp-gRT~~qcr~Rw~~~l~~~~kk~~~~~~~~ 126 (311)
+.+.+|+||.|||.+|+++|++||. +|..||+.++ ||++++||.||.++|++.+++++|++.+.
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe 70 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEE 70 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHH
Confidence 3455899999999999999999995 5999999998 99999999999999999999999987663
No 15
>PLN03091 hypothetical protein; Provisional
Probab=99.23 E-value=6.7e-12 Score=123.65 Aligned_cols=65 Identities=17% Similarity=0.393 Sum_probs=59.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhCC-ChhhhhhcC-CCCCHHHHHHHHHHHHHHHHhhcCCCCCCC
Q 021498 62 RPDLKRGLLSEYEEKMVIDLHAQLGN-RWSKIASHL-PGRTDNEIKNHWNTHIKKKLRKMGIDPLTH 126 (311)
Q Consensus 62 ~p~l~kg~WT~EED~~Ll~lv~~~G~-kW~kIA~~l-pgRT~~qcr~Rw~~~l~~~~kk~~~~~~~~ 126 (311)
++.+++++||+|||++|+++|++||. +|.+||+.+ +||+++|||.||.++|++.+++..|++.+.
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED 75 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEE 75 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHH
Confidence 35788999999999999999999995 699999988 599999999999999999999999877654
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.22 E-value=2.1e-11 Score=83.37 Aligned_cols=47 Identities=40% Similarity=0.842 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChhhhhhcCCCCCHHHHHHHHHHHHH
Q 021498 67 RGLLSEYEEKMVIDLHAQLG-NRWSKIASHLPGRTDNEIKNHWNTHIK 113 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G-~kW~kIA~~lpgRT~~qcr~Rw~~~l~ 113 (311)
+++||++||.+|+.++.+|| .+|..||..|++||+.+|+.||+.+++
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=1.6e-10 Score=77.84 Aligned_cols=43 Identities=33% Similarity=0.725 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHHHhC-CChhhhhhcCCCCCHHHHHHHHHHH
Q 021498 69 LLSEYEEKMVIDLHAQLG-NRWSKIASHLPGRTDNEIKNHWNTH 111 (311)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G-~kW~kIA~~lpgRT~~qcr~Rw~~~ 111 (311)
+||.+|+..|+.++.+|| .+|..||+.+++||+.+|++||+.+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 8999999999999999999999875
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.99 E-value=1.7e-10 Score=78.86 Aligned_cols=48 Identities=40% Similarity=0.780 Sum_probs=44.3
Q ss_pred cCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccC
Q 021498 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLR 62 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~ 62 (311)
++.||++||++|+.++.+||..+|..||..+++ |++.+|+.||.+++.
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 478999999999999999998899999999996 999999999998764
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.86 E-value=8.4e-10 Score=74.31 Aligned_cols=44 Identities=39% Similarity=0.739 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccc
Q 021498 16 PWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNY 60 (311)
Q Consensus 16 ~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~ 60 (311)
+||++||+.|+.++.++|..+|..||+.+++ |++.||+.||.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~-rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPG-RTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCC-CCHHHHHHHHHHh
Confidence 5999999999999999998899999999987 9999999999865
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.83 E-value=2.7e-09 Score=109.15 Aligned_cols=106 Identities=25% Similarity=0.316 Sum_probs=85.9
Q ss_pred ccCCCCHHHHHHHHHHHHHcCC-----------------------CCcchhhhhhccccccccccc---ccccccCCCCC
Q 021498 13 KKGPWTAEEDKKLINFILTNGQ-----------------------CCWRAVPKLAGLLRCGKSCRL---RWTNYLRPDLK 66 (311)
Q Consensus 13 kkg~WT~EED~~L~~lV~k~G~-----------------------~nW~~IA~~~~~~Rt~~QCr~---Rw~n~L~p~l~ 66 (311)
+-+.|+.+||+.|.+.|..|-. +.|+.|...++. |+.+.+.. |=.+.+.+ .
T Consensus 307 ~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~-R~~~siy~~~rR~y~~FE~--~ 383 (607)
T KOG0051|consen 307 NLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPY-RDRKSIYHHLRRAYTPFEN--K 383 (607)
T ss_pred hhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCc-ccchhHHHHHHhcCCcccc--c
Confidence 3488999999999999987611 136677778887 88888766 33333443 8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHH--hhcCCC
Q 021498 67 RGLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKL--RKMGID 122 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~--kk~~~~ 122 (311)
+|.||++|++.|..+|.++|+.|..|++.| ||.+..||.||+.+.+..- +++.|+
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws 440 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWS 440 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcch
Confidence 999999999999999999999999999999 9999999999999987763 444443
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=6.8e-08 Score=97.95 Aligned_cols=98 Identities=29% Similarity=0.615 Sum_probs=85.3
Q ss_pred ccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCC--CCCCCCCCHHHHHHHHHHHHHhC----
Q 021498 13 KKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRP--DLKRGLLSEYEEKMVIDLHAQLG---- 86 (311)
Q Consensus 13 kkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p--~l~kg~WT~EED~~Ll~lv~~~G---- 86 (311)
.+|.||++|++.|...+..+| +.|..|.+.++ |-+..||+||++|... .+++++|+.||+.+|...|.+.-
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~-~~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~~ 366 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHG-GSWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEAQ 366 (512)
T ss_pred hhccCcccccccccccccccc-chhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHHh
Confidence 478999999999999999999 79999999887 9999999999999988 57888999999999999887432
Q ss_pred ----CChhhhhhcCCCCCHHHHHHHHHHHHH
Q 021498 87 ----NRWSKIASHLPGRTDNEIKNHWNTHIK 113 (311)
Q Consensus 87 ----~kW~kIA~~lpgRT~~qcr~Rw~~~l~ 113 (311)
..|..|+..++.|...+|+..+..+..
T Consensus 367 ~~~~~~~~li~~~~~~~~~~~~~~~~~~~~~ 397 (512)
T COG5147 367 QSSRILWLLIAQNIRNRLQHHCRDKYGVLIS 397 (512)
T ss_pred hhhhhhHHHHHHhhhccccCCCCCccccccc
Confidence 349999999998998888887765443
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.89 E-value=7.1e-06 Score=60.21 Aligned_cols=49 Identities=12% Similarity=0.248 Sum_probs=43.4
Q ss_pred ccCCCCHHHHHHHHHHHHHcCCCCc---chhhhhhcccc-ccccccccccccc
Q 021498 13 KKGPWTAEEDKKLINFILTNGQCCW---RAVPKLAGLLR-CGKSCRLRWTNYL 61 (311)
Q Consensus 13 kkg~WT~EED~~L~~lV~k~G~~nW---~~IA~~~~~~R-t~~QCr~Rw~n~L 61 (311)
++-.||+||..+++++|..+|.++| +.|++.|+..| |..||+.+.+.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 4567999999999999999998899 99999888657 9999999988764
No 23
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.82 E-value=1.2e-05 Score=81.01 Aligned_cols=61 Identities=25% Similarity=0.468 Sum_probs=55.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CChhhhhhcCCCCCHHHHHHHHHHHHHHHHhhcCCCCCC
Q 021498 65 LKRGLLSEYEEKMVIDLHAQLG-NRWSKIASHLPGRTDNEIKNHWNTHIKKKLRKMGIDPLT 125 (311)
Q Consensus 65 l~kg~WT~EED~~Ll~lv~~~G-~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~~~~~~ 125 (311)
++.|.|+.-||+.|..+|.+|| +.|++|++.++-.|+.||+.||...+.+.+++-.|....
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~ee 66 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREE 66 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhH
Confidence 4678899999999999999999 569999999999999999999999999999998876443
No 24
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.63 E-value=6.1e-05 Score=65.93 Aligned_cols=52 Identities=15% Similarity=0.367 Sum_probs=45.7
Q ss_pred CCCCCCHHHHHHHHHHHHHh---CCC----hhhhhhcCCCCCHHHHHHHHHHHHHHHHhh
Q 021498 66 KRGLLSEYEEKMVIDLHAQL---GNR----WSKIASHLPGRTDNEIKNHWNTHIKKKLRK 118 (311)
Q Consensus 66 ~kg~WT~EED~~Ll~lv~~~---G~k----W~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk 118 (311)
+...||.|||.+|.+.|.+| |.. +..+++.| +||+.+|.-||+..+|+.+..
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 45679999999999999988 532 89999999 999999999999999987654
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.62 E-value=2.3e-05 Score=77.64 Aligned_cols=89 Identities=18% Similarity=0.311 Sum_probs=63.7
Q ss_pred CccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhccccccccccccccccc-CCCCCCCCC-------CHHHHHHHHHH-H
Q 021498 12 LKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYL-RPDLKRGLL-------SEYEEKMVIDL-H 82 (311)
Q Consensus 12 lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L-~p~l~kg~W-------T~EED~~Ll~l-v 82 (311)
+-...||++|+-+|+++++.||-+||..||.++|. |+..+|+++|.+++ +..+-.-+| .+.|+.....- +
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGt-Ktkeeck~hy~k~fv~s~~~~~~~i~~~~~~~q~e~~~~~k~~~ 148 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGT-KTKEECKEHYLKHFVNSPIFPLPDISLGIGVNQDEDAAMAKNRA 148 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcc-cchHHHHHHHHHHHhcCccccccccccccCcchHHHhhhccccc
Confidence 34567999999999999999999999999999995 99999999999864 322222222 23444443333 2
Q ss_pred HHhCC-------------ChhhhhhcCCCCCH
Q 021498 83 AQLGN-------------RWSKIASHLPGRTD 101 (311)
Q Consensus 83 ~~~G~-------------kW~kIA~~lpgRT~ 101 (311)
..++. .=.+|+.+||+|.+
T Consensus 149 ~~~~~~~~~pr~p~~~~p~~~e~~gyMp~R~d 180 (438)
T KOG0457|consen 149 EPFQPTDLVPRKPGVSNPLRREISGYMPGRLD 180 (438)
T ss_pred ccCCCCCCCCCCCCCCCchHHHHhhhCccchh
Confidence 22322 14588889999853
No 26
>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=97.58 E-value=0.00019 Score=52.68 Aligned_cols=46 Identities=17% Similarity=0.315 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-Ch---hhhhhcCC-CC-CHHHHHHHHHHHH
Q 021498 67 RGLLSEYEEKMVIDLHAQLGN-RW---SKIASHLP-GR-TDNEIKNHWNTHI 112 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~-kW---~kIA~~lp-gR-T~~qcr~Rw~~~l 112 (311)
+-.||+||..+.+++++.+|. +| .+|+..|. .| |..||+.+.+.+.
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 456999999999999999996 89 99999884 35 9999999988664
No 27
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.56 E-value=0.00012 Score=72.55 Aligned_cols=49 Identities=24% Similarity=0.476 Sum_probs=44.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CChhhhhhcCCCCCHHHHHHHHHHHH
Q 021498 64 DLKRGLLSEYEEKMVIDLHAQLG-NRWSKIASHLPGRTDNEIKNHWNTHI 112 (311)
Q Consensus 64 ~l~kg~WT~EED~~Ll~lv~~~G-~kW~kIA~~lpgRT~~qcr~Rw~~~l 112 (311)
.+-...||.+|+.+|++++..|| ++|..||.++..|+..+|+.+|.++.
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 34556799999999999999999 89999999999999999999998654
No 28
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.25 E-value=0.0004 Score=52.32 Aligned_cols=51 Identities=20% Similarity=0.470 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHHh---C-----CC-hhhhhhcCC-CCCHHHHHHHHHHHHHHHHh
Q 021498 67 RGLLSEYEEKMVIDLHAQL---G-----NR-WSKIASHLP-GRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~---G-----~k-W~kIA~~lp-gRT~~qcr~Rw~~~l~~~~k 117 (311)
+.+||.+||..|++.|.++ | ++ |.+++..-+ .+|-.+.|+||...|+.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 4579999999999999765 2 22 999999877 99999999999988887654
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.18 E-value=0.00039 Score=69.63 Aligned_cols=55 Identities=20% Similarity=0.265 Sum_probs=46.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHH--HHHHhhcC
Q 021498 66 KRGLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHI--KKKLRKMG 120 (311)
Q Consensus 66 ~kg~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l--~~~~kk~~ 120 (311)
....||.+|..+|++.++.||..|.+||+++..||..||--||..+- .+.+.+++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~ 334 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGD 334 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhccc
Confidence 34489999999999999999999999999999999999999998652 34444443
No 30
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.16 E-value=0.00051 Score=70.20 Aligned_cols=47 Identities=17% Similarity=0.323 Sum_probs=43.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHH
Q 021498 66 KRGLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHI 112 (311)
Q Consensus 66 ~kg~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l 112 (311)
.++.||.+|..+|++++..||..|.+||.++.+||..||-.|+..+-
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 45679999999999999999999999999999999999999997653
No 31
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.16 E-value=0.00037 Score=54.08 Aligned_cols=50 Identities=28% Similarity=0.502 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHHHHHH------hC--C------ChhhhhhcC----CCCCHHHHHHHHHHHHHHHHh
Q 021498 68 GLLSEYEEKMVIDLHAQ------LG--N------RWSKIASHL----PGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 68 g~WT~EED~~Ll~lv~~------~G--~------kW~kIA~~l----pgRT~~qcr~Rw~~~l~~~~k 117 (311)
..||.+|...||+++.+ ++ . -|..||..| ..||+.||+.||.++.+...+
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk~ 69 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYKK 69 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHHH
Confidence 47999999999999877 21 1 299999987 469999999999997776544
No 32
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.91 E-value=0.0019 Score=58.70 Aligned_cols=99 Identities=21% Similarity=0.344 Sum_probs=69.9
Q ss_pred CCCHHHHHHHHHHHHHcCCCCcchhhhhhc--ccccccccccccccccC----------------CC-----CCCCCCCH
Q 021498 16 PWTAEEDKKLINFILTNGQCCWRAVPKLAG--LLRCGKSCRLRWTNYLR----------------PD-----LKRGLLSE 72 (311)
Q Consensus 16 ~WT~EED~~L~~lV~k~G~~nW~~IA~~~~--~~Rt~~QCr~Rw~n~L~----------------p~-----l~kg~WT~ 72 (311)
+|++++|-.|+.+|..-. +-..|+..+. ..-|-..+.+||+..|- |. ..+.+||.
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 699999999999997644 5566665332 22455667788887652 22 24568999
Q ss_pred HHHHHHHHHHHHhCC---Chhhhhh-----cCCCCCHHHHHHHHHHHHHHHH
Q 021498 73 YEEKMVIDLHAQLGN---RWSKIAS-----HLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 73 EED~~Ll~lv~~~G~---kW~kIA~-----~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
+|+++|......... .+.+|-. +-++||++++..+|+.+.+..+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999997766543 3776633 2379999999999996555443
No 33
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.90 E-value=0.00037 Score=69.83 Aligned_cols=46 Identities=22% Similarity=0.421 Sum_probs=42.4
Q ss_pred ccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccc
Q 021498 13 KKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNY 60 (311)
Q Consensus 13 kkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~ 60 (311)
....||.+|..+|+++|+.|| .+|.+||.++|+ |+.-||..||.+.
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 456899999999999999999 699999999996 9999999999864
No 34
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.84 E-value=0.00047 Score=70.43 Aligned_cols=47 Identities=23% Similarity=0.453 Sum_probs=42.8
Q ss_pred CccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccc
Q 021498 12 LKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNY 60 (311)
Q Consensus 12 lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~ 60 (311)
.-++.||.+|..+|+++|++|| .+|.+||.++|. |+..||..++.+.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~-ddW~kVa~hVg~-ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYG-DDWNKVADHVGT-KSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhc-ccHHHHHhccCC-CCHHHHHHHHHhc
Confidence 3467899999999999999999 799999999996 9999999998864
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.75 E-value=0.0017 Score=57.60 Aligned_cols=51 Identities=12% Similarity=0.300 Sum_probs=42.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC-------hhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 65 LKRGLLSEYEEKMVIDLHAQLGNR-------WSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 65 l~kg~WT~EED~~Ll~lv~~~G~k-------W~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
.++..||.|+|.+|.+.|..|+.. ...++..| +||..+|..||+..+++.+
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Y 60 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQY 60 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHH
Confidence 356789999999999999988732 77778888 9999999999998888643
No 36
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.91 E-value=0.017 Score=43.93 Aligned_cols=52 Identities=25% Similarity=0.479 Sum_probs=42.3
Q ss_pred CCCCCHHHHHHHHHHHHHh-----C--C----------ChhhhhhcC-----CCCCHHHHHHHHHHHHHHHHhh
Q 021498 67 RGLLSEYEEKMVIDLHAQL-----G--N----------RWSKIASHL-----PGRTDNEIKNHWNTHIKKKLRK 118 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~-----G--~----------kW~kIA~~l-----pgRT~~qcr~Rw~~~l~~~~kk 118 (311)
+..||.+|...|++++.+| | . -|..|+..| +.||..++|.+|.++....-++
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~ 75 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKK 75 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 4579999999999999887 3 1 299999876 3699999999999887665443
No 37
>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=95.87 E-value=0.0023 Score=48.16 Aligned_cols=52 Identities=23% Similarity=0.402 Sum_probs=32.1
Q ss_pred cCCCCHHHHHHHHHHHHHcCC--------CCcchhhhhhcccccccccccccccccCCCC
Q 021498 14 KGPWTAEEDKKLINFILTNGQ--------CCWRAVPKLAGLLRCGKSCRLRWTNYLRPDL 65 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~G~--------~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l 65 (311)
+.+||.|||+.|+..|..+.. .-|+++++.-+..+|...-|+||.+.|.+..
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 467999999999999976531 2388888876655888888999999887654
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.70 E-value=0.0035 Score=48.54 Aligned_cols=47 Identities=32% Similarity=0.650 Sum_probs=31.7
Q ss_pred cCCCCHHHHHHHHHHHHHc------C--C-----CCcchhhhhh---cccccccccccccccc
Q 021498 14 KGPWTAEEDKKLINFILTN------G--Q-----CCWRAVPKLA---GLLRCGKSCRLRWTNY 60 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~------G--~-----~nW~~IA~~~---~~~Rt~~QCr~Rw~n~ 60 (311)
+..||.+|...|+.++... + . .-|..||..| |..|++.||+.||.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 3579999999999998771 1 1 1499999865 4459999999999873
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.66 E-value=0.03 Score=54.14 Aligned_cols=47 Identities=28% Similarity=0.437 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChhhhhhcCCCCCHHHHHHHHHHHHH
Q 021498 67 RGLLSEYEEKMVIDLHAQLG-NRWSKIASHLPGRTDNEIKNHWNTHIK 113 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G-~kW~kIA~~lpgRT~~qcr~Rw~~~l~ 113 (311)
-..|+..|+.+|++.....| ++|..||.++..|+...||.+|....-
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 44699999999999999999 889999999999999999999986654
No 40
>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=95.49 E-value=0.0048 Score=54.17 Aligned_cols=50 Identities=28% Similarity=0.612 Sum_probs=41.4
Q ss_pred CccCCCCHHHHHHHHHHHHHcCC------CCcchhhhhhcccccccccccccccccCC
Q 021498 12 LKKGPWTAEEDKKLINFILTNGQ------CCWRAVPKLAGLLRCGKSCRLRWTNYLRP 63 (311)
Q Consensus 12 lkkg~WT~EED~~L~~lV~k~G~------~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p 63 (311)
.++..||.|||.+|.+.|.+|-. ....+|+..++ ||+.-|.-||+.++..
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 35678999999999999998832 24677888777 9999999999998863
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.22 E-value=0.0066 Score=58.59 Aligned_cols=47 Identities=21% Similarity=0.399 Sum_probs=43.9
Q ss_pred CCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccC
Q 021498 15 GPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLR 62 (311)
Q Consensus 15 g~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~ 62 (311)
-.|++.|+.+|+++....|-+||..||..+|. |+...|+++|..++.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGs-r~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGS-RAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhh-hhhHHHHHHHHHHHh
Confidence 35999999999999999999999999999995 999999999998765
No 42
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.91 E-value=0.057 Score=59.91 Aligned_cols=101 Identities=15% Similarity=0.289 Sum_probs=74.8
Q ss_pred CCCHHHHHHHHHHHHHcCCCCcchhhhhhccccccccccc-------cccc------c----------------------
Q 021498 16 PWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRL-------RWTN------Y---------------------- 60 (311)
Q Consensus 16 ~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~-------Rw~n------~---------------------- 60 (311)
.||.-+=..++.+..+||..+-..||..+.+ ++...++. ||.. +
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~-k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEG-KTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcC-CCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4888888888888899998888899988864 66655541 1111 0
Q ss_pred --------------cC-CCCCCCCCCHHHHHHHHHHHHHhC-CChhhhhhc------------CCCCCHHHHHHHHHHHH
Q 021498 61 --------------LR-PDLKRGLLSEYEEKMVIDLHAQLG-NRWSKIASH------------LPGRTDNEIKNHWNTHI 112 (311)
Q Consensus 61 --------------L~-p~l~kg~WT~EED~~Ll~lv~~~G-~kW~kIA~~------------lpgRT~~qcr~Rw~~~l 112 (311)
+. +..++..+|++||..|+-.+.+|| .+|.+|-.. +..||+..+..|...++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 00 223344599999999999999999 679999442 25899999999999888
Q ss_pred HHHHh
Q 021498 113 KKKLR 117 (311)
Q Consensus 113 ~~~~k 117 (311)
+-..+
T Consensus 985 ~~~~~ 989 (1033)
T PLN03142 985 RLIEK 989 (1033)
T ss_pred HHHHH
Confidence 76543
No 43
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.37 E-value=0.012 Score=52.20 Aligned_cols=49 Identities=22% Similarity=0.450 Sum_probs=38.0
Q ss_pred CccCCCCHHHHHHHHHHHHHcCCCCcchh------hhhhcccccccccccccccccC
Q 021498 12 LKKGPWTAEEDKKLINFILTNGQCCWRAV------PKLAGLLRCGKSCRLRWTNYLR 62 (311)
Q Consensus 12 lkkg~WT~EED~~L~~lV~k~G~~nW~~I------A~~~~~~Rt~~QCr~Rw~n~L~ 62 (311)
.++..||.|||.+|-+.|.+|+...=..+ +..+. |++.+|..||+.++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 46788999999999999999875443444 44454 999999999976654
No 44
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=93.52 E-value=0.14 Score=49.74 Aligned_cols=52 Identities=21% Similarity=0.334 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCChhhhhhcC----CCCCHHHHHHHHHHHHHHHHhh
Q 021498 67 RGLLSEYEEKMVIDLHAQL----------GNRWSKIASHL----PGRTDNEIKNHWNTHIKKKLRK 118 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~----------G~kW~kIA~~l----pgRT~~qcr~Rw~~~l~~~~kk 118 (311)
...|+.+|-..||++..+. |.-|..||+.+ .-||+.|||.||.++.++..+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~ 119 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKE 119 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3579999999999998653 23499999965 4599999999999998876554
No 45
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=93.49 E-value=0.022 Score=43.33 Aligned_cols=49 Identities=18% Similarity=0.365 Sum_probs=38.7
Q ss_pred ccCCCCHHHHHHHHHHHHHcCC----------------CCcchhhhhh----ccccccccccccccccc
Q 021498 13 KKGPWTAEEDKKLINFILTNGQ----------------CCWRAVPKLA----GLLRCGKSCRLRWTNYL 61 (311)
Q Consensus 13 kkg~WT~EED~~L~~lV~k~G~----------------~nW~~IA~~~----~~~Rt~~QCr~Rw~n~L 61 (311)
++..||.+|.+.|+++|.+|.. ..|..|+..+ ++.|+..|++.+|.+..
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 3567999999999999988721 2499999754 22599999999998753
No 46
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.93 E-value=0.13 Score=51.10 Aligned_cols=57 Identities=21% Similarity=0.260 Sum_probs=49.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhhhhc-----CCC-CCHHHHHHHHHHHHHHHHhhcCCCC
Q 021498 67 RGLLSEYEEKMVIDLHAQLGNRWSKIASH-----LPG-RTDNEIKNHWNTHIKKKLRKMGIDP 123 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~kW~kIA~~-----lpg-RT~~qcr~Rw~~~l~~~~kk~~~~~ 123 (311)
...||.+|-.-|.++.+.|.-+|-.||.. ++. ||-..+|+||+...++.++..+..+
T Consensus 130 dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s~ 192 (445)
T KOG2656|consen 130 DNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPSN 192 (445)
T ss_pred cccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCCc
Confidence 35699999999999999999999999987 555 9999999999999999888765443
No 47
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=92.79 E-value=0.2 Score=42.06 Aligned_cols=53 Identities=28% Similarity=0.445 Sum_probs=41.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----ChhhhhhcC------------CCCCHHHHHHHHHHHHHHHH
Q 021498 64 DLKRGLLSEYEEKMVIDLHAQLGN----RWSKIASHL------------PGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 64 ~l~kg~WT~EED~~Ll~lv~~~G~----kW~kIA~~l------------pgRT~~qcr~Rw~~~l~~~~ 116 (311)
..++..+|++||..|+-++.+||- .|.+|-..+ ..||+..+..|-..+++-..
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~ 114 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIE 114 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHH
Confidence 456678999999999999999996 699886643 47999999999999887543
No 48
>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=92.37 E-value=0.34 Score=37.83 Aligned_cols=46 Identities=28% Similarity=0.541 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------ChhhhhhcC---C--CCCHHHHHHHHHHHHHH
Q 021498 69 LLSEYEEKMVIDLHAQL---GN----------RWSKIASHL---P--GRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 69 ~WT~EED~~Ll~lv~~~---G~----------kW~kIA~~l---p--gRT~~qcr~Rw~~~l~~ 114 (311)
.||.++++.|++++.+. |+ .|..|+..| + ..+..||++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 49999999999998653 21 299999877 2 35789999999877665
No 49
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=88.48 E-value=0.69 Score=45.97 Aligned_cols=46 Identities=24% Similarity=0.253 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 69 LLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
+||.+|-++...+...+|..+..||..+|.|...|||-+|.+--+.
T Consensus 367 ~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 367 RWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred cccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 5999999999999999999999999999999999999999866554
No 50
>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=87.01 E-value=1.6 Score=30.51 Aligned_cols=42 Identities=21% Similarity=0.287 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 72 EYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 72 ~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
++++..++.++-..|-.+.+||..+ |.+...|+.+....+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 4667788888888999999999999 99999999998876653
No 51
>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=82.76 E-value=1.1 Score=37.51 Aligned_cols=34 Identities=24% Similarity=0.409 Sum_probs=28.3
Q ss_pred CCccCCCCHHHHHHHHHHHHHcCC---CCcchhhhhh
Q 021498 11 GLKKGPWTAEEDKKLINFILTNGQ---CCWRAVPKLA 44 (311)
Q Consensus 11 ~lkkg~WT~EED~~L~~lV~k~G~---~nW~~IA~~~ 44 (311)
+.++..||.+||.-|+-.+.+||- +.|..|-..+
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 566788999999999999999998 8999998754
No 52
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=81.12 E-value=3.3 Score=42.17 Aligned_cols=47 Identities=15% Similarity=0.177 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHH
Q 021498 67 RGLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIK 113 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~ 113 (311)
...||.||--++-+++..||.++.+|-+.||.|+-..+..-|+...+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK 233 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKK 233 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHH
Confidence 44699999999999999999999999999999999999988775543
No 53
>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=80.27 E-value=3.6 Score=28.07 Aligned_cols=38 Identities=13% Similarity=0.344 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhCC-ChhhhhhcCCCCCHHHHHHHHHHH
Q 021498 73 YEEKMVIDLHAQLGN-RWSKIASHLPGRTDNEIKNHWNTH 111 (311)
Q Consensus 73 EED~~Ll~lv~~~G~-kW~kIA~~lpgRT~~qcr~Rw~~~ 111 (311)
+=|.+|+.+.++-|. .+.+||+.+ |=|...|..|++.+
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 458889999999885 499999999 99999999998754
No 54
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=75.52 E-value=2.5 Score=33.23 Aligned_cols=29 Identities=28% Similarity=0.473 Sum_probs=16.7
Q ss_pred CCccCCCCHHHHHHH--------HHHHHHcCCCCcchhhh
Q 021498 11 GLKKGPWTAEEDKKL--------INFILTNGQCCWRAVPK 42 (311)
Q Consensus 11 ~lkkg~WT~EED~~L--------~~lV~k~G~~nW~~IA~ 42 (311)
.-..|-||+|+|+.| .+++++|| +..|+.
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 345788999999999 44667777 455554
No 55
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=75.45 E-value=1.3 Score=42.92 Aligned_cols=47 Identities=26% Similarity=0.426 Sum_probs=36.6
Q ss_pred cCCCCHHHHHHHHHHHHHc---------CCCCcchhhhh---hcccccccccccccccc
Q 021498 14 KGPWTAEEDKKLINFILTN---------GQCCWRAVPKL---AGLLRCGKSCRLRWTNY 60 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~---------G~~nW~~IA~~---~~~~Rt~~QCr~Rw~n~ 60 (311)
...|+.+|-..|+++..+. ...-|..||.. .|..|++.||+.+|.+.
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 3679999999999987542 12459999973 34459999999999873
No 56
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=75.42 E-value=6.6 Score=39.26 Aligned_cols=111 Identities=15% Similarity=0.185 Sum_probs=72.5
Q ss_pred cCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccc--cCCC-----C-CCCCCCHHHHHHHHHHH---
Q 021498 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNY--LRPD-----L-KRGLLSEYEEKMVIDLH--- 82 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~--L~p~-----l-~kg~WT~EED~~Ll~lv--- 82 (311)
.-+||.+|-++..+|+...| .+..-|+.+++. |..+|++.+|.+- .+|. + .+.|+..+|-.+|...+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wG-tdF~LIs~lfP~-R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~~~~~e~ 442 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWG-TDFSLISSLFPN-RERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLRSYLLEK 442 (507)
T ss_pred CCcccHHHHHHHHHHHHHhc-chHHHHHHhcCc-hhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHHHHHHHH
Confidence 34699999999999999999 689999999997 9999999998863 2331 1 24567777765443222
Q ss_pred -HHhCCChhhhhhcC--CCCCHHHHHHHHHHHHHHHHhhcCCCCCCC
Q 021498 83 -AQLGNRWSKIASHL--PGRTDNEIKNHWNTHIKKKLRKMGIDPLTH 126 (311)
Q Consensus 83 -~~~G~kW~kIA~~l--pgRT~~qcr~Rw~~~l~~~~kk~~~~~~~~ 126 (311)
.++-+--..|-+.+ ..|++..+-.--+.+....+.+.|.-+...
T Consensus 443 l~Elq~E~k~~~~~~EE~k~~A~E~~q~~Q~l~~~~L~k~~~~~~~T 489 (507)
T COG5118 443 LIELQNEHKHHMKEIEEAKNTAKEEDQTAQRLNDANLNKKGSGGIMT 489 (507)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHhhhhhhccCCCCCCC
Confidence 22222223333333 346666665555556666666665544443
No 57
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=75.26 E-value=5 Score=42.24 Aligned_cols=52 Identities=15% Similarity=0.350 Sum_probs=42.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhhh----------hcCCCCCHHHHHHHHHHHHHHHHhh
Q 021498 67 RGLLSEYEEKMVIDLHAQLGNRWSKIA----------SHLPGRTDNEIKNHWNTHIKKKLRK 118 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~kW~kIA----------~~lpgRT~~qcr~Rw~~~l~~~~kk 118 (311)
+..||..|.+-...+.+++|..+.+|- ..+.-+|-.|+|.+|+..+++..+-
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~ 149 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKL 149 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhh
Confidence 567999999999999999999999982 2334568889999999888775544
No 58
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=74.89 E-value=5.5 Score=42.81 Aligned_cols=45 Identities=9% Similarity=0.042 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHH
Q 021498 68 GLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHI 112 (311)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l 112 (311)
..||..|-.+.-+++..|...+-+|++.++|+|-.||-.-|+...
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWK 664 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWK 664 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHH
Confidence 359999999999999999999999999999999999998877553
No 59
>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=73.96 E-value=8.2 Score=26.54 Aligned_cols=41 Identities=27% Similarity=0.322 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 73 YEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 73 EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
+++..++.++-..|-.+.+||..+ |-|...|+.+....+++
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 455556666656677899999999 99999999998887765
No 60
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=70.54 E-value=8.6 Score=32.92 Aligned_cols=44 Identities=7% Similarity=0.156 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHhC-CChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 73 YEEKMVIDLHAQLG-NRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 73 EED~~Ll~lv~~~G-~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
+-|.+|+++.++-| ..|++||+.+ |-+...|+.|++.+....+-
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 57899999999988 4599999999 99999999999887766543
No 61
>smart00595 MADF subfamily of SANT domain.
Probab=70.40 E-value=5.1 Score=30.71 Aligned_cols=26 Identities=31% Similarity=0.640 Sum_probs=22.5
Q ss_pred hhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 89 WSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 89 W~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
|.+||..| |-+..+|+.||+++....
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR~~y 55 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLRDRY 55 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 99999999 559999999999886553
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=67.41 E-value=2.3 Score=29.02 Aligned_cols=38 Identities=18% Similarity=0.371 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHcCCCCcchhhhhhccccccccccccccc
Q 021498 20 EEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTN 59 (311)
Q Consensus 20 EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n 59 (311)
+=|.+|+.++++.|...+.+||+.+| =+...|+.|+.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 44889999999999999999999998 577778877653
No 63
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=63.47 E-value=14 Score=33.74 Aligned_cols=44 Identities=16% Similarity=0.188 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHHhCCChhhhhhcC---CCCCHHHHHHHHHHHHH
Q 021498 69 LLSEYEEKMVIDLHAQLGNRWSKIASHL---PGRTDNEIKNHWNTHIK 113 (311)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~kIA~~l---pgRT~~qcr~Rw~~~l~ 113 (311)
.|++.+|.+|+.+|.. |+.-..|++.+ -.-|-..+..||+.+|-
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 4999999999999865 66677777655 45688999999998873
No 64
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=62.99 E-value=12 Score=32.44 Aligned_cols=44 Identities=5% Similarity=0.103 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHhCC-ChhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 72 EYEEKMVIDLHAQLGN-RWSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 72 ~EED~~Ll~lv~~~G~-kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
.+-|.+|+.+.++-|. .|++||+.+ |-+...|+.|++.+.+..+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 4678899999888884 599999999 9999999999988877654
No 65
>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=62.15 E-value=10 Score=29.83 Aligned_cols=29 Identities=24% Similarity=0.598 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhCCChhhhhhcCCCCCHHHH
Q 021498 75 EKMVIDLHAQLGNRWSKIASHLPGRTDNEI 104 (311)
Q Consensus 75 D~~Ll~lv~~~G~kW~kIA~~lpgRT~~qc 104 (311)
|+.|..+....|..|..+|.+| |=|..+|
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 5678899999999999999999 6655544
No 66
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=61.74 E-value=3.5 Score=35.34 Aligned_cols=45 Identities=11% Similarity=0.217 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCC
Q 021498 20 EEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLK 66 (311)
Q Consensus 20 EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~ 66 (311)
+-|.+|+.++++.|...|.+||+.+| -+...|+.|+.+....++-
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 57999999999999999999999998 7888999998887665543
No 67
>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=61.02 E-value=31 Score=33.81 Aligned_cols=48 Identities=23% Similarity=0.390 Sum_probs=37.1
Q ss_pred CCCCCHHHHHHHHHHHHHh-CCC---hhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 67 RGLLSEYEEKMVIDLHAQL-GNR---WSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~-G~k---W~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
-..||.-|-..|+++.+.. |.. -.+|++.++||+..+|++--+.+..+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~r 72 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGR 72 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHH
Confidence 3459999999999988765 543 57899999999999998755544433
No 68
>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=60.60 E-value=19 Score=27.91 Aligned_cols=38 Identities=16% Similarity=0.380 Sum_probs=28.2
Q ss_pred HHHHHHHHhCC--------ChhhhhhcCCC---CC--HHHHHHHHHHHHHH
Q 021498 77 MVIDLHAQLGN--------RWSKIASHLPG---RT--DNEIKNHWNTHIKK 114 (311)
Q Consensus 77 ~Ll~lv~~~G~--------kW~kIA~~lpg---RT--~~qcr~Rw~~~l~~ 114 (311)
.|-.+|.+.|+ +|..||+.|.. -+ +.++|..|..+|.+
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 37788888873 59999999822 12 36899999988764
No 69
>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=60.49 E-value=21 Score=29.39 Aligned_cols=36 Identities=22% Similarity=0.321 Sum_probs=27.7
Q ss_pred HHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 79 IDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 79 l~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
+.+.-..|-.+.+||+.+ |.+...|+.|....+++-
T Consensus 122 l~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 122 FILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKEL 157 (161)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 333333477899999999 999999999998866543
No 70
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=58.67 E-value=3.4 Score=35.90 Aligned_cols=46 Identities=17% Similarity=0.242 Sum_probs=39.2
Q ss_pred HHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCC
Q 021498 19 AEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLK 66 (311)
Q Consensus 19 ~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~ 66 (311)
.+-|.+|+.++++.|...|.+||+.+| -+...|+.|+.+..+.++-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 567999999999999999999999998 6888899998887665543
No 71
>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=58.36 E-value=7.7 Score=30.03 Aligned_cols=44 Identities=20% Similarity=0.529 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHHHHc---CC----C-----Ccchhhhhhc----cccccccccccccc
Q 021498 16 PWTAEEDKKLINFILTN---GQ----C-----CWRAVPKLAG----LLRCGKSCRLRWTN 59 (311)
Q Consensus 16 ~WT~EED~~L~~lV~k~---G~----~-----nW~~IA~~~~----~~Rt~~QCr~Rw~n 59 (311)
+||+++++.|++++... |. + .|..|+..+. ...+..||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999987543 21 1 3777776443 33566777777654
No 72
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=57.46 E-value=10 Score=39.92 Aligned_cols=50 Identities=20% Similarity=0.325 Sum_probs=44.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 65 LKRGLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 65 l~kg~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
...++|+.+|-++-..+..+.|.+.+.|+..+|+|+..|||.+|..--++
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r 456 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKR 456 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhc
Confidence 34567999999999999999999999999999999999999999765444
No 73
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=57.06 E-value=22 Score=27.77 Aligned_cols=40 Identities=18% Similarity=0.336 Sum_probs=30.0
Q ss_pred HHHHHHHHhCC--------ChhhhhhcCCC-----CCHHHHHHHHHHHHHHHH
Q 021498 77 MVIDLHAQLGN--------RWSKIASHLPG-----RTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 77 ~Ll~lv~~~G~--------kW~kIA~~lpg-----RT~~qcr~Rw~~~l~~~~ 116 (311)
+|..+|.+.|+ +|.+||+.|.- ....++|..|...|.+.-
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~yE 88 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPFE 88 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHHH
Confidence 37777888773 59999999832 246788999998887653
No 74
>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=55.10 E-value=12 Score=29.27 Aligned_cols=17 Identities=24% Similarity=0.477 Sum_probs=10.1
Q ss_pred CCCCCCCCCHHHHHHHH
Q 021498 63 PDLKRGLLSEYEEKMVI 79 (311)
Q Consensus 63 p~l~kg~WT~EED~~Ll 79 (311)
|....|-||+++|..|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 55678889999999994
No 75
>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=52.91 E-value=15 Score=32.28 Aligned_cols=41 Identities=22% Similarity=0.215 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHH
Q 021498 69 LLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNT 110 (311)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~ 110 (311)
.||.|+.++|.++..+ |-.=++||+.|.|.|.++|.-+-+.
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 4999999999988855 8888999999977999998876554
No 76
>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=51.22 E-value=16 Score=27.03 Aligned_cols=28 Identities=21% Similarity=0.446 Sum_probs=22.4
Q ss_pred hhhhhhcCCC-CCHHHHHHHHHHHHHHHH
Q 021498 89 WSKIASHLPG-RTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 89 W~kIA~~lpg-RT~~qcr~Rw~~~l~~~~ 116 (311)
|..||..|.+ -+..+|+.||+++.....
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~~y~ 57 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRDRYR 57 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHHHHH
Confidence 9999999943 578899999998766543
No 77
>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=50.28 E-value=23 Score=27.81 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=23.9
Q ss_pred HHHHHHHHHHhCCChhhhhhcCCCCCHHHH
Q 021498 75 EKMVIDLHAQLGNRWSKIASHLPGRTDNEI 104 (311)
Q Consensus 75 D~~Ll~lv~~~G~kW~kIA~~lpgRT~~qc 104 (311)
|..|..+....|..|.++|..| |=+...|
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI 32 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEI 32 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHH
Confidence 5678888899999999999999 6665544
No 78
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=49.87 E-value=11 Score=39.87 Aligned_cols=47 Identities=15% Similarity=0.225 Sum_probs=35.6
Q ss_pred cCCCCHHHHHHHHHHHHHcCCCCcchhhhhhccc---------cccccccccccccc
Q 021498 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLL---------RCGKSCRLRWTNYL 61 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~---------Rt~~QCr~Rw~n~L 61 (311)
|..||..|.+-...++..+| .+..+|-+.+... ++..|.|.+|.+.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~G-KdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVG-KDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhc-ccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 56799999999999999999 7898884433221 56667777777644
No 79
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=49.68 E-value=3.7 Score=31.94 Aligned_cols=40 Identities=25% Similarity=0.463 Sum_probs=26.4
Q ss_pred HHHHHHHHHcCC-------CCcchhhhhhccccc----ccccccccccccC
Q 021498 23 KKLINFILTNGQ-------CCWRAVPKLAGLLRC----GKSCRLRWTNYLR 62 (311)
Q Consensus 23 ~~L~~lV~k~G~-------~nW~~IA~~~~~~Rt----~~QCr~Rw~n~L~ 62 (311)
-+|..+|.+.|. +.|..||..+|.... +.+.+..|.++|.
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 357778888774 369999999875331 2456666666653
No 80
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=49.50 E-value=8.4 Score=41.50 Aligned_cols=43 Identities=19% Similarity=0.196 Sum_probs=38.6
Q ss_pred cCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccc
Q 021498 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWT 58 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~ 58 (311)
...||+.|-.+..+++..|. ++.-.|++.+.+ ++.+||-+-|.
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~-KDF~~v~km~~~-KtVaqCVeyYY 661 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYS-KDFIFVQKMVKS-KTVAQCVEYYY 661 (907)
T ss_pred cccccHHHHHHHHHHHHHhc-ccHHHHHHHhcc-ccHHHHHHHHH
Confidence 45799999999999999998 799999999986 99999988665
No 81
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=49.34 E-value=45 Score=28.43 Aligned_cols=40 Identities=13% Similarity=0.135 Sum_probs=31.4
Q ss_pred HHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHhhcCCC
Q 021498 82 HAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLRKMGID 122 (311)
Q Consensus 82 v~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~~~ 122 (311)
....|-...+||..+ |.+...|+.|....+++-....+..
T Consensus 131 ~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~~~l~~~ 170 (172)
T PRK12523 131 NRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCYIALYGE 170 (172)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHhcCC
Confidence 334577899999999 9999999999988887765554443
No 82
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=48.73 E-value=33 Score=27.63 Aligned_cols=51 Identities=16% Similarity=0.173 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHHHh----CC----ChhhhhhcCC-----CCCHHHHHHHHHHHHHHHHhh
Q 021498 68 GLLSEYEEKMVIDLHAQL----GN----RWSKIASHLP-----GRTDNEIKNHWNTHIKKKLRK 118 (311)
Q Consensus 68 g~WT~EED~~Ll~lv~~~----G~----kW~kIA~~lp-----gRT~~qcr~Rw~~~l~~~~kk 118 (311)
..||++++..||+.+..| |. .|......+. .=+..|+.++.+.+.++....
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~ 68 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNA 68 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHH
Confidence 459999999999998776 62 3544444332 237789988888877775544
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=48.13 E-value=18 Score=27.87 Aligned_cols=29 Identities=28% Similarity=0.667 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhCCChhhhhhcCCCCCHHHH
Q 021498 75 EKMVIDLHAQLGNRWSKIASHLPGRTDNEI 104 (311)
Q Consensus 75 D~~Ll~lv~~~G~kW~kIA~~lpgRT~~qc 104 (311)
|..|..+.+..|..|.++|++| |=+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4567788899999999999999 6555443
No 84
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=48.01 E-value=46 Score=26.45 Aligned_cols=33 Identities=27% Similarity=0.291 Sum_probs=26.2
Q ss_pred HHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 81 LHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 81 lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
++-..|..+.+||+.+ |-+...++.+.+..+++
T Consensus 121 ~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 121 LRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334577899999999 78999999998886655
No 85
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=45.55 E-value=49 Score=28.06 Aligned_cols=29 Identities=21% Similarity=0.342 Sum_probs=23.9
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-.-.+||..| |.+...|+.|.+..+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 99999999998766544
No 86
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.48 E-value=39 Score=26.56 Aligned_cols=43 Identities=7% Similarity=0.159 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHhCC-ChhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 73 YEEKMVIDLHAQLGN-RWSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 73 EED~~Ll~lv~~~G~-kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
+.|.+|+.+..+.|. .+..||+.+ |-+...|+.|.+.+.+..+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 568889999988874 699999999 9999999999988877643
No 87
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=44.38 E-value=12 Score=40.48 Aligned_cols=12 Identities=8% Similarity=0.443 Sum_probs=6.9
Q ss_pred hhhcCCcccccC
Q 021498 200 EIMNNNFCTDDV 211 (311)
Q Consensus 200 ~~~~~~fc~d~v 211 (311)
.+|.-|+.|.|+
T Consensus 1206 ramdagwshsei 1217 (1463)
T PHA03308 1206 RAMDAGWSHSEI 1217 (1463)
T ss_pred HHHhcCcchhhh
Confidence 345556666664
No 88
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.50 E-value=57 Score=27.35 Aligned_cols=32 Identities=13% Similarity=0.085 Sum_probs=25.4
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
..|-.+..||+.| |.+...|+.+....+++-.
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRAREALR 173 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 3477899999999 9999999988876555433
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=43.05 E-value=30 Score=27.03 Aligned_cols=26 Identities=35% Similarity=0.691 Sum_probs=19.9
Q ss_pred HHHHHHHhCCChhhhhhcCCCCCHHHH
Q 021498 78 VIDLHAQLGNRWSKIASHLPGRTDNEI 104 (311)
Q Consensus 78 Ll~lv~~~G~kW~kIA~~lpgRT~~qc 104 (311)
|..+....|..|.++|+.| |-+..+|
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 3335688899999999999 7666655
No 90
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=42.86 E-value=57 Score=32.04 Aligned_cols=86 Identities=14% Similarity=0.283 Sum_probs=59.9
Q ss_pred cCCCCHHHHHHHHHHHHHcCCCCc---chhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHH-h----
Q 021498 14 KGPWTAEEDKKLINFILTNGQCCW---RAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVIDLHAQ-L---- 85 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~G~~nW---~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~lv~~-~---- 85 (311)
-..||.-|...|+++++....... .+|++.+.+ |+..++++ |.+.|+ +..+.+++++ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~-Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPG-RSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccC-cCHHHHHH-HHHHHH------------HHHHHHHHHHhccccc
Confidence 356999999999998876543444 466667776 88888776 444443 2334444444 2
Q ss_pred -CC------------ChhhhhhcCCCCCHHHHHHHHHHHHH
Q 021498 86 -GN------------RWSKIASHLPGRTDNEIKNHWNTHIK 113 (311)
Q Consensus 86 -G~------------kW~kIA~~lpgRT~~qcr~Rw~~~l~ 113 (311)
|. -|..+|..+.|.-...+---|-..|.
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 21 19999999999999998888876654
No 91
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=41.86 E-value=61 Score=28.38 Aligned_cols=38 Identities=18% Similarity=0.206 Sum_probs=29.2
Q ss_pred HHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 77 MVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 77 ~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
.++.+..-.|-.+.+||..| |-+...++.||.......
T Consensus 142 ~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~~l 179 (185)
T PF07638_consen 142 RVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARAWL 179 (185)
T ss_pred HHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 33444444578899999999 999999999998776443
No 92
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=41.65 E-value=8 Score=30.33 Aligned_cols=40 Identities=20% Similarity=0.439 Sum_probs=26.5
Q ss_pred HHHHHHHHHcCC-------CCcchhhhhhcccc----cccccccccccccC
Q 021498 23 KKLINFILTNGQ-------CCWRAVPKLAGLLR----CGKSCRLRWTNYLR 62 (311)
Q Consensus 23 ~~L~~lV~k~G~-------~nW~~IA~~~~~~R----t~~QCr~Rw~n~L~ 62 (311)
-+|..+|.+.|. ..|..||..+|... .+.+.+..|.++|.
T Consensus 35 ~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~ 85 (93)
T smart00501 35 YRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLL 85 (93)
T ss_pred HHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhH
Confidence 357888888775 46999999888521 23445556665554
No 93
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=41.62 E-value=62 Score=27.76 Aligned_cols=35 Identities=11% Similarity=0.166 Sum_probs=28.1
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHhhcC
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLRKMG 120 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~ 120 (311)
.|-...+||..| |-+...|+.|....+++-.++.+
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHHHhh
Confidence 467799999999 99999999999877776555443
No 94
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=40.73 E-value=65 Score=28.01 Aligned_cols=36 Identities=14% Similarity=0.114 Sum_probs=26.5
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHH---HHHHHhhcC
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTH---IKKKLRKMG 120 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~---l~~~~kk~~ 120 (311)
..|-.-.+||..| |-+...|+.|.... |++.+.+.+
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~~l~~~~ 188 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARESLRQCLQIKW 188 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3467789999999 99999999887754 444554443
No 95
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=40.45 E-value=28 Score=39.75 Aligned_cols=74 Identities=18% Similarity=0.221 Sum_probs=44.0
Q ss_pred cCCCCHHHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHh-CCChhhh
Q 021498 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVIDLHAQL-GNRWSKI 92 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~lv~~~-G~kW~kI 92 (311)
-.-|..++|..|+-.|-+||.++|.+|-.-.-.+=+.+ ..+......+.+=..+-..|+.+...+ +.+|.+.
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dK-------i~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~ 1205 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDK-------IFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKK 1205 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccccHHHhccCccccchhh-------hcccccCCchHHHHHHHHHHHHHHhhcccCCCchh
Confidence 45699999999999999999999999964211100000 011111334445555666666666655 4445544
Q ss_pred hh
Q 021498 93 AS 94 (311)
Q Consensus 93 A~ 94 (311)
++
T Consensus 1206 ~~ 1207 (1373)
T KOG0384|consen 1206 LK 1207 (1373)
T ss_pred hh
Confidence 43
No 96
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=40.41 E-value=33 Score=26.72 Aligned_cols=31 Identities=26% Similarity=0.514 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhCCChhhhhhcCCCCCHHHHHH
Q 021498 75 EKMVIDLHAQLGNRWSKIASHLPGRTDNEIKN 106 (311)
Q Consensus 75 D~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~ 106 (311)
|..|-.+....|.+|..+|+.| |=+...|..
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 4567778889999999999999 766666544
No 97
>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=40.17 E-value=73 Score=27.79 Aligned_cols=46 Identities=20% Similarity=0.211 Sum_probs=38.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChhhhhhcCC----CCCHHHHHHHHHHH
Q 021498 66 KRGLLSEYEEKMVIDLHAQLGNRWSKIASHLP----GRTDNEIKNHWNTH 111 (311)
Q Consensus 66 ~kg~WT~EED~~Ll~lv~~~G~kW~kIA~~lp----gRT~~qcr~Rw~~~ 111 (311)
....-|..|..-|..|+++||.++..+|.-.. -.|..||+.+....
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 34568999999999999999999999987542 47999999887654
No 98
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=40.05 E-value=67 Score=27.63 Aligned_cols=34 Identities=18% Similarity=0.028 Sum_probs=29.1
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHhh
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLRK 118 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk 118 (311)
..|-...+||..| |-+...++.|....+++-..+
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHh
Confidence 3477899999999 999999999999888876655
No 99
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=39.26 E-value=54 Score=32.91 Aligned_cols=46 Identities=20% Similarity=0.122 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhhh-hhcCCCCCHHHHHHHHHHHHH
Q 021498 68 GLLSEYEEKMVIDLHAQLGNRWSKI-ASHLPGRTDNEIKNHWNTHIK 113 (311)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kW~kI-A~~lpgRT~~qcr~Rw~~~l~ 113 (311)
..|+++|=...-+..+.||+.+..| +..++.|+--.|-.-|+...+
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKk 324 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKK 324 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhc
Confidence 3599999999999999999999999 557899999999887765543
No 100
>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=37.85 E-value=33 Score=26.45 Aligned_cols=33 Identities=24% Similarity=0.501 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHH
Q 021498 72 EYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKN 106 (311)
Q Consensus 72 ~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~ 106 (311)
+||-++|+..- ..|.+|..+|..| |=+...|++
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 57888888322 5688999999999 777766643
No 101
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=37.33 E-value=64 Score=21.54 Aligned_cols=36 Identities=19% Similarity=0.313 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHH
Q 021498 73 YEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWN 109 (311)
Q Consensus 73 EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~ 109 (311)
-|-..|.++...+|++-.+.|+.| |=+...+..|-+
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~klk 40 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 366778899999999999999999 777777766543
No 102
>PRK04217 hypothetical protein; Provisional
Probab=37.30 E-value=1.1e+02 Score=25.29 Aligned_cols=46 Identities=13% Similarity=0.059 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 68 GLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
..-|.+| ..++.++...|-...+||+.+ |-+...|+.+++...++-
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 3466666 677778777888999999999 999999999988765553
No 103
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=36.92 E-value=69 Score=26.76 Aligned_cols=29 Identities=21% Similarity=0.227 Sum_probs=23.8
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-....||..| |-+...|+.+....+++
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 467799999999 99999999888765544
No 104
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=36.90 E-value=64 Score=27.49 Aligned_cols=30 Identities=10% Similarity=-0.012 Sum_probs=24.7
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
.|....+||..+ |-+...++++....+++-
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~L 180 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREAL 180 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 367799999999 999999999987666553
No 105
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=36.59 E-value=73 Score=27.84 Aligned_cols=30 Identities=17% Similarity=0.207 Sum_probs=24.6
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
..|-...+||..| |-+...|+.|....+++
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3577899999999 99999999999655444
No 106
>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=35.97 E-value=1.1e+02 Score=19.76 Aligned_cols=40 Identities=28% Similarity=0.356 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHH
Q 021498 70 LSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTH 111 (311)
Q Consensus 70 WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~ 111 (311)
.+.+ +..++.++-..|-.+..||..+ |-+...|+.+.+..
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3444 4445555555678899999998 78888887665544
No 107
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=35.88 E-value=82 Score=25.87 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=29.3
Q ss_pred cCCCCHHHHHHHHHHHHHcCCCCcchhhhhhccccccccccccccccc
Q 021498 14 KGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYL 61 (311)
Q Consensus 14 kg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L 61 (311)
+.+||.|+-...+..+...| ..=..||..+|. +.. --.+|.+.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g-~sv~evA~e~gI--s~~-tl~~W~r~y 53 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG-MTVSLVARQHGV--AAS-QLFLWRKQY 53 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC-CCHHHHHHHHCc--CHH-HHHHHHHHH
Confidence 57799999887777776666 455688887774 333 334566543
No 108
>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=35.65 E-value=39 Score=26.51 Aligned_cols=30 Identities=37% Similarity=0.636 Sum_probs=22.7
Q ss_pred HHHHHHHHHhCCChhhhhhcCCCCCHHHHHH
Q 021498 76 KMVIDLHAQLGNRWSKIASHLPGRTDNEIKN 106 (311)
Q Consensus 76 ~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~ 106 (311)
+.|-.+....|.+|..+|+.| |=+..+|..
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 345556678899999999999 777766643
No 109
>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=35.45 E-value=43 Score=25.36 Aligned_cols=29 Identities=28% Similarity=0.596 Sum_probs=21.1
Q ss_pred HHHHHHHHHH-hCCChhhhhhcCCCCCHHHH
Q 021498 75 EKMVIDLHAQ-LGNRWSKIASHLPGRTDNEI 104 (311)
Q Consensus 75 D~~Ll~lv~~-~G~kW~kIA~~lpgRT~~qc 104 (311)
.+.|..++.. .|..|.++|+.| |-+..++
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 4556667777 899999999999 4444443
No 110
>PLN03162 golden-2 like transcription factor; Provisional
Probab=34.73 E-value=2.7e+02 Score=28.14 Aligned_cols=44 Identities=18% Similarity=0.100 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCC---hhhhhhcC--CCCCHHHHHHHHHHH
Q 021498 68 GLLSEYEEKMVIDLHAQLGNR---WSKIASHL--PGRTDNEIKNHWNTH 111 (311)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~k---W~kIA~~l--pgRT~~qcr~Rw~~~ 111 (311)
-.||.|--++.+++|.++|.. =++|-+.| +|=|..+|+.+.+.+
T Consensus 238 LrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKY 286 (526)
T PLN03162 238 VDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKY 286 (526)
T ss_pred ccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 349999999999999999932 56676665 889999998876544
No 111
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=34.48 E-value=54 Score=27.29 Aligned_cols=43 Identities=7% Similarity=0.124 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHHhCC-ChhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 73 YEEKMVIDLHAQLGN-RWSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 73 EED~~Ll~lv~~~G~-kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
+-|.+|+++.++-|. .+..||+.+ |-+...|+.|-+.+.+..+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCc
Confidence 567888988888885 599999999 9999999999987777653
No 112
>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=34.38 E-value=59 Score=27.82 Aligned_cols=32 Identities=9% Similarity=0.020 Sum_probs=25.6
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
.|-...+||..+ |-|...|+.|....+++-.+
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHH
Confidence 356799999999 89999999998777665443
No 113
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=34.38 E-value=28 Score=35.66 Aligned_cols=41 Identities=20% Similarity=0.166 Sum_probs=37.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHH
Q 021498 68 GLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWN 109 (311)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~ 109 (311)
-.||++|-. +++...-||.+...||..+...|+.|++.+|.
T Consensus 471 ~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~ 511 (534)
T KOG1194|consen 471 YGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYM 511 (534)
T ss_pred CCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhc
Confidence 359999888 88888899999999999999999999999995
No 114
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=33.39 E-value=92 Score=26.85 Aligned_cols=31 Identities=13% Similarity=0.171 Sum_probs=25.5
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
.|....+||..| |-+...|+.|.+..+++-.
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRALARLR 184 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 467799999999 9999999999877666543
No 115
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=33.04 E-value=86 Score=25.97 Aligned_cols=29 Identities=14% Similarity=0.231 Sum_probs=24.0
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-.-.+||..| |-+...|+.|....+++
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 466789999999 99999999998766554
No 116
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=32.93 E-value=88 Score=27.26 Aligned_cols=32 Identities=9% Similarity=0.034 Sum_probs=25.7
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
.|-...+||..| |-+...|+.|.+..+++-.+
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHH
Confidence 467799999999 99999999998776665433
No 117
>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=32.49 E-value=48 Score=25.90 Aligned_cols=21 Identities=29% Similarity=0.646 Sum_probs=19.0
Q ss_pred HHHHHHHHHhCCChhhhhhcC
Q 021498 76 KMVIDLHAQLGNRWSKIASHL 96 (311)
Q Consensus 76 ~~Ll~lv~~~G~kW~kIA~~l 96 (311)
..|..+..+.|..|..+|.+|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L 23 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL 23 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc
Confidence 458888999999999999998
No 118
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=32.21 E-value=98 Score=25.77 Aligned_cols=30 Identities=10% Similarity=-0.056 Sum_probs=24.2
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
..|-.-.+||..| |-+...|+.|....+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467789999999 99999999987765544
No 119
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=31.90 E-value=1.1e+02 Score=26.44 Aligned_cols=32 Identities=19% Similarity=0.184 Sum_probs=26.4
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
.|-.-.+||..| |-+...|+.|....+++-.+
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDALLA 176 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 356789999999 99999999999877766544
No 120
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=31.31 E-value=63 Score=25.40 Aligned_cols=26 Identities=23% Similarity=0.399 Sum_probs=20.8
Q ss_pred HHHHHHHHHHhCCChhhhhhcCCCCCH
Q 021498 75 EKMVIDLHAQLGNRWSKIASHLPGRTD 101 (311)
Q Consensus 75 D~~Ll~lv~~~G~kW~kIA~~lpgRT~ 101 (311)
|.+|..+.+..|..|.++|.+| |=+.
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~ 29 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSV 29 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCH
Confidence 4567788899999999999998 4333
No 121
>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=31.23 E-value=99 Score=26.06 Aligned_cols=31 Identities=16% Similarity=0.187 Sum_probs=25.1
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
.|-...+||..+ |-|...|+.|....+++-.
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 466789999999 8899999999887766543
No 122
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=30.29 E-value=91 Score=26.55 Aligned_cols=30 Identities=10% Similarity=-0.005 Sum_probs=24.4
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 86 GNRWSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 86 G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
|..-.+||..| |.+...|+.|....+++-.
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREALR 181 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 56789999999 9999999999877665543
No 123
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=30.26 E-value=1e+02 Score=26.71 Aligned_cols=29 Identities=24% Similarity=0.139 Sum_probs=24.5
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-...+||..| |-+...|+.|....+++
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 467899999999 99999999998766554
No 124
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=29.76 E-value=81 Score=22.53 Aligned_cols=34 Identities=29% Similarity=0.421 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHH
Q 021498 73 YEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNH 107 (311)
Q Consensus 73 EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~R 107 (311)
..|+..+.++.+.|-.-.+||+.+ ||+...|++-
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~y 40 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRY 40 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHH
Confidence 455667778888999999999999 9999877653
No 125
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=29.30 E-value=1.2e+02 Score=26.46 Aligned_cols=31 Identities=13% Similarity=0.000 Sum_probs=25.2
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
..|....+||..| |-+...|+.|....+++-
T Consensus 145 ~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~L 175 (188)
T TIGR02943 145 VLGFESDEICQEL-EISTSNCHVLLYRARLSL 175 (188)
T ss_pred HhCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 3467799999999 999999999987665543
No 126
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=29.18 E-value=1.2e+02 Score=26.18 Aligned_cols=29 Identities=14% Similarity=0.146 Sum_probs=23.9
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-...+||..| |-+...++.|....+++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466799999999 88999999998765544
No 127
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=28.44 E-value=23 Score=29.63 Aligned_cols=44 Identities=7% Similarity=0.166 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCCC
Q 021498 20 EEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPDL 65 (311)
Q Consensus 20 EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l 65 (311)
+-|.++++++++.+...+.+||+.+| -+...|+.|-.+..+.++
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCc
Confidence 56889999999999999999999998 788888888666555443
No 128
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=28.27 E-value=1.1e+02 Score=26.38 Aligned_cols=28 Identities=14% Similarity=0.141 Sum_probs=23.1
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 86 GNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 86 G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
|-...+||..+ |-+...|+.|....+++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56789999999 89999999998766554
No 129
>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=27.99 E-value=1.3e+02 Score=25.03 Aligned_cols=28 Identities=29% Similarity=0.290 Sum_probs=23.3
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 86 GNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 86 G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
|-.-.+||+.| |-+...|+.|....+++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 66789999999 99999999988766554
No 130
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=27.69 E-value=1.3e+02 Score=26.20 Aligned_cols=29 Identities=7% Similarity=-0.041 Sum_probs=23.9
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-...+||..| |-+...|+.|....+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 177 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARLQ 177 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 367799999999 99999999997765543
No 131
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.99 E-value=1.2e+02 Score=26.05 Aligned_cols=30 Identities=7% Similarity=-0.022 Sum_probs=23.7
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
.|-...+||+.| |-+...|+.|.+..+++-
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~L 172 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRAL 172 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHH
Confidence 466789999999 999999998877655443
No 132
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=26.87 E-value=56 Score=36.96 Aligned_cols=33 Identities=15% Similarity=0.214 Sum_probs=28.5
Q ss_pred CccCCCCHHHHHHHHHHHHHcCCCCcchhhhhh
Q 021498 12 LKKGPWTAEEDKKLINFILTNGQCCWRAVPKLA 44 (311)
Q Consensus 12 lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~ 44 (311)
.++..+|.|||.-|+-.+.+||-.+|.+|-..+
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 345569999999999999999999999997655
No 133
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=26.81 E-value=1.3e+02 Score=25.11 Aligned_cols=30 Identities=27% Similarity=0.356 Sum_probs=24.2
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
.|-.-.+||..| |-+...++.|....++.-
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~~~L 149 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAMKHC 149 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 355689999999 999999999987666543
No 134
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.75 E-value=1.3e+02 Score=26.18 Aligned_cols=29 Identities=10% Similarity=-0.023 Sum_probs=23.6
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-.+.+||..| |-+...|+.|....+++
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 467799999999 98999999888765554
No 135
>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=26.54 E-value=1.5e+02 Score=25.21 Aligned_cols=30 Identities=20% Similarity=0.237 Sum_probs=24.8
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
.|-...+||..+ |-+...|+.|....+++-
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 178 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAWL 178 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 366799999999 999999999988766553
No 136
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=26.46 E-value=32 Score=27.10 Aligned_cols=43 Identities=14% Similarity=0.176 Sum_probs=34.5
Q ss_pred HHHHHHHHHHHHcCCCCcchhhhhhcccccccccccccccccCCC
Q 021498 20 EEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTNYLRPD 64 (311)
Q Consensus 20 EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n~L~p~ 64 (311)
+.|.+++.++.+.|...+..||+.++ -+...|+.|..+..+.+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 56889999999999889999999987 67777887776654443
No 137
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=26.11 E-value=37 Score=36.94 Aligned_cols=7 Identities=29% Similarity=0.615 Sum_probs=4.0
Q ss_pred ccccccc
Q 021498 48 RCGKSCR 54 (311)
Q Consensus 48 Rt~~QCr 54 (311)
|.+.||+
T Consensus 983 ~rgg~~~ 989 (1463)
T PHA03308 983 NRGGRCV 989 (1463)
T ss_pred cccccee
Confidence 4466665
No 138
>PRK01905 DNA-binding protein Fis; Provisional
Probab=25.95 E-value=1.5e+02 Score=22.55 Aligned_cols=37 Identities=24% Similarity=0.235 Sum_probs=28.4
Q ss_pred CHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHH
Q 021498 71 SEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHW 108 (311)
Q Consensus 71 T~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw 108 (311)
..-|...+.+++..+|.++.+.|+.+ |=+...++.+.
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rkl 71 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKKL 71 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHH
Confidence 34567778899999999999999998 66666655543
No 139
>PRK00118 putative DNA-binding protein; Validated
Probab=25.74 E-value=1.6e+02 Score=24.06 Aligned_cols=41 Identities=10% Similarity=0.090 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHH
Q 021498 72 EYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIK 113 (311)
Q Consensus 72 ~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~ 113 (311)
++.+..++.++...|-...+||+.+ |-|...++.+....++
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 3455667777777789999999999 9999999888765443
No 140
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=25.59 E-value=1.6e+02 Score=24.78 Aligned_cols=32 Identities=16% Similarity=0.119 Sum_probs=25.8
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
.|-.-.+||..+ |-+...|+.|-...+++-..
T Consensus 127 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 127 SGFSYEDAAAIC-GCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 466799999999 99999999998877665443
No 141
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=25.48 E-value=1.4e+02 Score=24.99 Aligned_cols=30 Identities=23% Similarity=0.265 Sum_probs=25.0
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
-.|-...+||..+ |-+...|+.|....+++
T Consensus 127 ~~g~s~~EIA~~l-~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 127 VDGLGYGEIATEL-GISLATVKRYLNKAAMR 156 (161)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3477899999999 99999999998776554
No 142
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=25.36 E-value=1.5e+02 Score=25.37 Aligned_cols=33 Identities=15% Similarity=0.095 Sum_probs=26.5
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
..|-...+||..| |.+...|++|-...+++-.+
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3467799999999 99999999998776665443
No 143
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=25.22 E-value=1.5e+02 Score=25.25 Aligned_cols=31 Identities=16% Similarity=0.137 Sum_probs=24.8
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
.|-.-.+||..+ |-+...|+.|.+..+++-.
T Consensus 150 ~~~s~~eIA~~l-gis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 150 QGYTHREAAQLL-GLPLGTLKTRARRALSRLK 180 (186)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 356689999999 9999999998877665543
No 144
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.96 E-value=1.6e+02 Score=24.20 Aligned_cols=29 Identities=17% Similarity=0.247 Sum_probs=23.6
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-...+||..+ |.+...|+.|-...+++
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356689999999 99999999987776554
No 145
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=24.75 E-value=1.6e+02 Score=25.10 Aligned_cols=29 Identities=14% Similarity=0.194 Sum_probs=24.2
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 86 GNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 86 G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
|-.-.+||..| |.+...++.|....+++-
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHHH
Confidence 66789999999 999999999987666543
No 146
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=24.67 E-value=1.4e+02 Score=26.08 Aligned_cols=31 Identities=19% Similarity=0.193 Sum_probs=24.7
Q ss_pred HHhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 83 AQLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 83 ~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
...|-...+||..| |-+...|+.|-...+++
T Consensus 129 ~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 129 GASGFAYEEAAEIC-GCAVGTIKSRVNRARQR 159 (187)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34477899999999 99999999987765544
No 147
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=24.28 E-value=1.6e+02 Score=25.33 Aligned_cols=31 Identities=16% Similarity=0.338 Sum_probs=25.2
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
..|-.-.+||..| |-+...|+.|....+++-
T Consensus 136 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 166 (185)
T PRK12542 136 FYNLTYQEISSVM-GITEANVRKQFERARKRV 166 (185)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3467789999999 999999999987666543
No 148
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 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=24.20 E-value=1.4e+02 Score=28.15 Aligned_cols=32 Identities=19% Similarity=0.178 Sum_probs=25.9
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
.|-.-.+||..| |.+...||.|....+++-.+
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~ 188 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARATLDE 188 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 466789999999 99999999998776655433
No 149
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=23.87 E-value=1.8e+02 Score=25.22 Aligned_cols=32 Identities=13% Similarity=0.142 Sum_probs=24.9
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
.|-...+||+.| |-+...||.|-...+++-.+
T Consensus 157 ~~~s~~EIA~~L-gis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 157 GGLTYREVAERL-AVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred cCCCHHHHHHHh-CCChHhHHHHHHHHHHHHHH
Confidence 356789999999 88999999987766655443
No 150
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=23.74 E-value=1.1e+02 Score=27.43 Aligned_cols=44 Identities=25% Similarity=0.319 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 68 GLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
...|+.|-+.|.-+.+ |-.=++||..| +.+..-||.+..++++|
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHH
Confidence 3688888886655443 55568999999 99999999999998887
No 151
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=23.65 E-value=1.2e+02 Score=25.89 Aligned_cols=29 Identities=24% Similarity=0.283 Sum_probs=24.4
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-...+||+.+ |-+...|+.|....++.
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 356799999999 99999999998776655
No 152
>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=23.56 E-value=61 Score=28.49 Aligned_cols=34 Identities=21% Similarity=0.350 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHHHHHcCCCCcchhhhhhc-cccccc
Q 021498 16 PWTAEEDKKLINFILTNGQCCWRAVPKLAG-LLRCGK 51 (311)
Q Consensus 16 ~WT~EED~~L~~lV~k~G~~nW~~IA~~~~-~~Rt~~ 51 (311)
.||.|+.++|+++... | ..=.+||..+| ..|++.
T Consensus 2 ~Wtde~~~~L~~lw~~-G-~SasqIA~~lg~vsRnAV 36 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-G-LSASQIARQLGGVSRNAV 36 (162)
T ss_pred CCCHHHHHHHHHHHHc-C-CCHHHHHHHhCCcchhhh
Confidence 5999999999998754 4 35689999999 345553
No 153
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.55 E-value=2e+02 Score=22.96 Aligned_cols=47 Identities=19% Similarity=0.239 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 67 RGLLSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 67 kg~WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
+..||.|.-..+++++..-|..=+.||+.+ |--..+...+|...+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHHHHHH
Confidence 457999999999999999999889999999 76333445567655544
No 154
>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=23.25 E-value=79 Score=23.25 Aligned_cols=25 Identities=40% Similarity=0.741 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChhhhhhcCCCCCHHH
Q 021498 78 VIDLHAQLGNRWSKIASHLPGRTDNE 103 (311)
Q Consensus 78 Ll~lv~~~G~kW~kIA~~lpgRT~~q 103 (311)
+..+....|..|..+|+.+ |=+..+
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~ 26 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGE 26 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHH
Confidence 3456677899999999998 433333
No 155
>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=23.22 E-value=95 Score=21.77 Aligned_cols=42 Identities=31% Similarity=0.385 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 70 LSEYEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 70 WT~EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|+.|-+.|.-+. -|..=.+||..+ |.+...|+.+...++++
T Consensus 4 LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 4 LTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp S-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 5666666444333 366678999999 99999999988877766
No 156
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=23.10 E-value=32 Score=34.65 Aligned_cols=48 Identities=15% Similarity=0.200 Sum_probs=40.2
Q ss_pred CccCCCCHHHHHHHHHHHHHcCCCCcchhhhh-----hcccccccccccccccc
Q 021498 12 LKKGPWTAEEDKKLINFILTNGQCCWRAVPKL-----AGLLRCGKSCRLRWTNY 60 (311)
Q Consensus 12 lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~-----~~~~Rt~~QCr~Rw~n~ 60 (311)
+.-..||.+|-+.|.++.++|. -.|--||.. .+..||--..++||..+
T Consensus 128 l~dn~WskeETD~LF~lck~fD-LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFD-LRFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hccccccHHHHHHHHHHHHhcC-eeEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 4457799999999999999998 678889876 56559999999999754
No 157
>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=23.01 E-value=1.1e+02 Score=23.91 Aligned_cols=25 Identities=28% Similarity=0.667 Sum_probs=18.5
Q ss_pred HHHHHhCCChhhhhhcCCCCCHHHHH
Q 021498 80 DLHAQLGNRWSKIASHLPGRTDNEIK 105 (311)
Q Consensus 80 ~lv~~~G~kW~kIA~~lpgRT~~qcr 105 (311)
-+.+..|..|..+|+.| |=|..+|.
T Consensus 7 ~i~~~lG~~Wk~laR~L-Glse~~Id 31 (86)
T cd08306 7 VICENVGRDWRKLARKL-GLSETKIE 31 (86)
T ss_pred HHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 34566799999999999 65555543
No 158
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=22.68 E-value=2.1e+02 Score=23.78 Aligned_cols=40 Identities=15% Similarity=0.137 Sum_probs=29.3
Q ss_pred HHHHHHHHhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 77 MVIDLHAQLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 77 ~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
.++.+.-..|-.-.+||..| |-+...|+.|....+++-.+
T Consensus 117 ~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 117 AVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARLRE 156 (162)
T ss_pred HHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 33334344567789999999 99999999998877765443
No 159
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=22.49 E-value=1.8e+02 Score=23.20 Aligned_cols=35 Identities=11% Similarity=0.110 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHhCCChhhhhhcCCCCCHHHHHHHH
Q 021498 73 YEEKMVIDLHAQLGNRWSKIASHLPGRTDNEIKNHW 108 (311)
Q Consensus 73 EED~~Ll~lv~~~G~kW~kIA~~lpgRT~~qcr~Rw 108 (311)
-|...|..++..+|.+..+.|+.+ |=+...++.|-
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rKL 89 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKKL 89 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHH
Confidence 477778899999999999999999 66666655443
No 160
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=22.46 E-value=78 Score=26.79 Aligned_cols=32 Identities=22% Similarity=0.341 Sum_probs=25.2
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
+|-....||..| |-+...|+.+....+++-.+
T Consensus 141 ~g~s~~eIA~~l-~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 141 YGYTYEEIAKML-NIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred cCCCHHHHHHHH-CCChhHHHHHHHHHHHHHHH
Confidence 466799999999 88999999888766655443
No 161
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.46 E-value=1.9e+02 Score=24.82 Aligned_cols=31 Identities=23% Similarity=0.226 Sum_probs=25.2
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKKL 116 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~ 116 (311)
.|-.-.+||..+ |-+...|+.|....+++-.
T Consensus 148 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 148 DGCSHAEIAQRL-GAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred cCCCHHHHHHHH-CCChhhHHHHHHHHHHHHH
Confidence 466789999999 9999999999887776543
No 162
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=22.19 E-value=49 Score=34.94 Aligned_cols=49 Identities=18% Similarity=0.327 Sum_probs=42.7
Q ss_pred CCCCccCCCCHHHHHHHHHHHHHcCCCCcchhhhhhccccccccccccccc
Q 021498 9 KVGLKKGPWTAEEDKKLINFILTNGQCCWRAVPKLAGLLRCGKSCRLRWTN 59 (311)
Q Consensus 9 K~~lkkg~WT~EED~~L~~lV~k~G~~nW~~IA~~~~~~Rt~~QCr~Rw~n 59 (311)
.+....++|+.+|-++...+....| .+...|+...++ |..+|++..|..
T Consensus 404 sk~~~~~~w~~se~e~fyka~~~~g-s~~slis~l~p~-R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 404 SKKLETDKWDASETELFYKALSERG-SDFSLISNLFPL-RDRKQIKAKFKK 452 (584)
T ss_pred cCccccCcccchhhHHhhhHHhhhc-cccccccccccc-ccHHHHHHHHhh
Confidence 3456678999999999999999999 689999999887 999999987764
No 163
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.11 E-value=1.6e+02 Score=25.85 Aligned_cols=33 Identities=15% Similarity=0.124 Sum_probs=26.5
Q ss_pred HhCCChhhhhhcCCCCCHHHHHHHHHHHHHHHHh
Q 021498 84 QLGNRWSKIASHLPGRTDNEIKNHWNTHIKKKLR 117 (311)
Q Consensus 84 ~~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~k 117 (311)
..|-...+||..| |-+...|+.|....+++-.+
T Consensus 127 ~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 127 ASGFSYEEAAEMC-GVAVGTVKSRANRARARLAE 159 (188)
T ss_pred hcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 4577799999999 99999999998877655443
No 164
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=21.64 E-value=1.9e+02 Score=25.48 Aligned_cols=28 Identities=18% Similarity=0.045 Sum_probs=22.7
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIK 113 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~ 113 (311)
.|-.-.+||..| |.+...|+.|....++
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~ 181 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRART 181 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 356789999999 9999999988765443
No 165
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=21.64 E-value=1.9e+02 Score=24.94 Aligned_cols=28 Identities=36% Similarity=0.476 Sum_probs=23.3
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 86 GNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 86 G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
|-.-.+||..| |.+...|++|-+..+++
T Consensus 147 g~s~~EIAe~l-gis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 147 GEKIEEIAKKL-GLTRSAIDNRLSRGRKK 174 (189)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 56679999999 99999999998766555
No 166
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=21.63 E-value=1.9e+02 Score=24.49 Aligned_cols=30 Identities=13% Similarity=0.418 Sum_probs=24.6
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
.|-.-.+||..+ |-|...|+.+....+++-
T Consensus 155 ~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~L 184 (189)
T TIGR02984 155 EGLSFAEVAERM-DRSEGAVSMLWVRGLARL 184 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 467789999999 999999999887766553
No 167
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=21.02 E-value=71 Score=26.28 Aligned_cols=29 Identities=17% Similarity=0.118 Sum_probs=24.1
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 86 GNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 86 G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
|-.+.+||..| |-+...|+.|....+++-
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~L 149 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKEL 149 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 45699999999 999999999988776553
No 168
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=20.90 E-value=2.8e+02 Score=23.21 Aligned_cols=32 Identities=16% Similarity=0.116 Sum_probs=23.4
Q ss_pred ChhhhhhcCCCCCHHHHHHHHHHHHHHHHhhcC
Q 021498 88 RWSKIASHLPGRTDNEIKNHWNTHIKKKLRKMG 120 (311)
Q Consensus 88 kW~kIA~~lpgRT~~qcr~Rw~~~l~~~~kk~~ 120 (311)
.|..||..+ |=+..+|..+=+..+.+.....|
T Consensus 102 t~~~Ia~~l-~iS~~t~~r~r~~~l~kla~~lG 133 (134)
T TIGR01636 102 TLVGLAQQL-FISKSTAYRLRNHIIEAVAEELG 133 (134)
T ss_pred CHHHHHHHh-CCCHHHHHHHHHHHHHHHHHHhC
Confidence 799999998 88888887665555555555444
No 169
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=20.77 E-value=2.1e+02 Score=24.71 Aligned_cols=29 Identities=14% Similarity=-0.052 Sum_probs=23.5
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.|-.-.+||..| |-+...|+.|....+++
T Consensus 146 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 174 (191)
T PRK12520 146 LELETEEICQEL-QITATNAWVLLYRARMR 174 (191)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 366789999999 99999999998765443
No 170
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=20.46 E-value=2.9e+02 Score=22.82 Aligned_cols=46 Identities=13% Similarity=0.338 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHHh------------CC-----------------C--hhhhhhcCCCCCHHHHHHHHHHHHHH
Q 021498 69 LLSEYEEKMVIDLHAQL------------GN-----------------R--WSKIASHLPGRTDNEIKNHWNTHIKK 114 (311)
Q Consensus 69 ~WT~EED~~Ll~lv~~~------------G~-----------------k--W~kIA~~lpgRT~~qcr~Rw~~~l~~ 114 (311)
.+|.+||..|...|.+| |. . ....+...|..|..+=|.||+..+..
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv~~ 77 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFVSE 77 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTHHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHHHH
Confidence 37999999999988654 11 1 45667777999999999999987765
No 171
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=20.25 E-value=1.5e+02 Score=30.78 Aligned_cols=61 Identities=20% Similarity=0.248 Sum_probs=46.9
Q ss_pred chhhhhhcccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCChhhhhh-cCCCCCHHHHHHHHH
Q 021498 38 RAVPKLAGLLRCGKSCRLRWTNYLRPDLKRGLLSEYEEKMVIDLHAQLGNRWSKIAS-HLPGRTDNEIKNHWN 109 (311)
Q Consensus 38 ~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l~kg~WT~EED~~Ll~lv~~~G~kW~kIA~-~lpgRT~~qcr~Rw~ 109 (311)
+.|+-.++. --+.-||+. -..|+..|-.+.-++..+||..+..|.+ +||-++-..|-.-|+
T Consensus 267 ~Ais~LVPl-GGPvLCRDe----------mEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 267 KAISYLVPL-GGPVLCRDE----------MEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred HHHHHhhcC-CCceeehhh----------hhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 455555554 446667764 3469999999999999999999999955 669998888877665
No 172
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=20.09 E-value=1.1e+02 Score=27.67 Aligned_cols=29 Identities=14% Similarity=0.129 Sum_probs=23.6
Q ss_pred CCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 86 GNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 86 G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
|-...+||..| |.+...|+.|.+..+++-
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~kL 193 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARRLL 193 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 56689999999 999999999987665543
No 173
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=20.08 E-value=1.7e+02 Score=25.17 Aligned_cols=30 Identities=27% Similarity=0.188 Sum_probs=23.5
Q ss_pred hCCChhhhhhcCCCCCHHHHHHHHHHHHHHH
Q 021498 85 LGNRWSKIASHLPGRTDNEIKNHWNTHIKKK 115 (311)
Q Consensus 85 ~G~kW~kIA~~lpgRT~~qcr~Rw~~~l~~~ 115 (311)
.|-.-.+||..| |-+...|+.|....+++-
T Consensus 156 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~L 185 (194)
T PRK12519 156 EGLSQSEIAKRL-GIPLGTVKARARQGLLKL 185 (194)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 466789999999 889999998877655543
Done!