Query 038824
Match_columns 187
No_of_seqs 191 out of 1409
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 03:42:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038824.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038824hhsearch_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 5.4E-31 1.2E-35 233.1 9.0 102 1-102 1-132 (459)
2 PLN03212 Transcription repress 100.0 4.4E-30 9.5E-35 213.4 8.6 86 15-100 56-141 (249)
3 KOG0048 Transcription factor, 100.0 1.9E-29 4.1E-34 211.2 9.1 94 4-97 28-122 (238)
4 PLN03212 Transcription repress 99.8 1E-19 2.2E-24 151.6 5.1 90 3-115 14-105 (249)
5 KOG0048 Transcription factor, 99.8 8.6E-20 1.9E-24 152.9 3.2 84 32-115 4-89 (238)
6 PLN03091 hypothetical protein; 99.7 6.8E-18 1.5E-22 150.1 4.5 85 31-115 8-94 (459)
7 KOG0049 Transcription factor, 99.7 1.2E-16 2.6E-21 146.9 8.4 104 6-109 329-433 (939)
8 PF13921 Myb_DNA-bind_6: Myb-l 99.6 6.5E-16 1.4E-20 102.8 4.0 59 40-98 1-59 (60)
9 PF00249 Myb_DNA-binding: Myb- 99.5 9.3E-15 2E-19 93.4 5.3 46 37-82 1-48 (48)
10 smart00717 SANT SANT SWI3, AD 99.4 1.1E-12 2.3E-17 82.1 5.9 47 37-83 1-48 (49)
11 cd00167 SANT 'SWI3, ADA2, N-Co 99.3 1.2E-11 2.5E-16 76.2 5.9 44 39-82 1-45 (45)
12 KOG0049 Transcription factor, 99.2 1.1E-11 2.3E-16 114.7 5.0 106 3-109 272-381 (939)
13 COG5147 REB1 Myb superfamily p 99.1 6.1E-11 1.3E-15 108.5 5.1 80 8-87 43-122 (512)
14 KOG0050 mRNA splicing protein 99.0 2.8E-10 6E-15 103.1 5.3 82 7-89 29-110 (617)
15 PF13921 Myb_DNA-bind_6: Myb-l 98.8 4.8E-09 1E-13 69.5 4.7 41 8-48 20-60 (60)
16 COG5147 REB1 Myb superfamily p 98.6 1.4E-08 3E-13 93.1 2.6 82 34-115 17-99 (512)
17 KOG0050 mRNA splicing protein 98.6 3.6E-08 7.8E-13 89.6 3.8 81 35-115 5-86 (617)
18 KOG0051 RNA polymerase I termi 98.6 1.3E-07 2.9E-12 87.8 7.4 97 7-104 353-452 (607)
19 KOG0051 RNA polymerase I termi 98.5 1.7E-07 3.6E-12 87.2 6.9 80 14-93 411-519 (607)
20 TIGR01557 myb_SHAQKYF myb-like 97.9 4.9E-05 1.1E-09 50.4 6.2 47 37-83 3-55 (57)
21 KOG0457 Histone acetyltransfer 97.8 5.2E-05 1.1E-09 68.1 6.1 49 34-82 69-118 (438)
22 TIGR02894 DNA_bind_RsfA transc 97.7 5.8E-05 1.3E-09 59.7 4.8 53 35-88 2-61 (161)
23 PF08914 Myb_DNA-bind_2: Rap1 97.7 6.2E-05 1.3E-09 51.2 4.2 51 37-87 2-62 (65)
24 PF13837 Myb_DNA-bind_4: Myb/S 97.3 0.00022 4.9E-09 50.2 3.4 48 37-84 1-66 (90)
25 COG5259 RSC8 RSC chromatin rem 96.9 0.0013 2.9E-08 59.8 4.7 46 36-81 278-323 (531)
26 KOG1279 Chromatin remodeling f 96.8 0.0023 4.9E-08 59.3 5.3 45 37-81 253-297 (506)
27 PRK13923 putative spore coat p 96.7 0.0026 5.5E-08 51.0 4.2 52 35-87 3-61 (170)
28 COG5114 Histone acetyltransfer 96.5 0.003 6.6E-08 55.2 4.3 48 36-83 62-110 (432)
29 PF13873 Myb_DNA-bind_5: Myb/S 96.5 0.0067 1.5E-07 41.8 4.9 48 37-84 2-71 (78)
30 PF00249 Myb_DNA-binding: Myb- 96.2 0.0032 7E-08 39.6 2.0 25 7-31 23-48 (48)
31 PF09111 SLIDE: SLIDE; InterP 95.4 0.023 5.1E-07 43.0 4.1 52 34-85 46-113 (118)
32 smart00717 SANT SANT SWI3, AD 93.8 0.07 1.5E-06 32.2 2.7 28 6-33 22-49 (49)
33 PF12776 Myb_DNA-bind_3: Myb/S 93.6 0.25 5.5E-06 34.9 5.7 46 39-84 1-64 (96)
34 KOG2656 DNA methyltransferase 92.9 0.16 3.5E-06 45.6 4.7 61 26-90 123-189 (445)
35 KOG4282 Transcription factor G 92.8 0.24 5.2E-06 43.5 5.6 47 38-84 55-115 (345)
36 cd00167 SANT 'SWI3, ADA2, N-Co 91.6 0.19 4.1E-06 29.8 2.5 26 6-31 20-45 (45)
37 PF13325 MCRS_N: N-terminal re 91.4 0.72 1.6E-05 38.0 6.5 73 15-87 30-131 (199)
38 PF08281 Sigma70_r4_2: Sigma-7 90.9 0.74 1.6E-05 29.0 4.9 41 42-83 12-52 (54)
39 COG5118 BDP1 Transcription ini 90.9 0.43 9.3E-06 42.9 4.9 44 39-82 367-410 (507)
40 PLN03142 Probable chromatin-re 89.9 0.26 5.6E-06 49.6 3.0 71 15-85 902-987 (1033)
41 KOG1194 Predicted DNA-binding 83.4 2.9 6.2E-05 38.5 5.7 47 37-83 187-233 (534)
42 PF13837 Myb_DNA-bind_4: Myb/S 82.2 1.1 2.3E-05 31.1 2.1 18 13-30 46-63 (90)
43 KOG4167 Predicted DNA-binding 79.4 4.2 9E-05 39.6 5.5 57 26-82 605-664 (907)
44 PF04545 Sigma70_r4: Sigma-70, 79.1 6.3 0.00014 24.4 4.8 41 43-84 7-47 (50)
45 PF13404 HTH_AsnC-type: AsnC-t 75.8 7.7 0.00017 23.7 4.3 38 43-81 3-41 (42)
46 PRK11179 DNA-binding transcrip 72.3 7.9 0.00017 29.9 4.6 45 43-88 9-54 (153)
47 PF11035 SnAPC_2_like: Small n 71.7 17 0.00037 32.1 6.9 47 38-84 22-72 (344)
48 TIGR02985 Sig70_bacteroi1 RNA 70.4 12 0.00026 27.9 5.2 39 44-83 117-155 (161)
49 smart00595 MADF subfamily of S 70.2 4.7 0.0001 27.9 2.7 24 59-83 30-53 (89)
50 PF07750 GcrA: GcrA cell cycle 68.8 7 0.00015 31.0 3.7 40 39-79 2-41 (162)
51 PF01388 ARID: ARID/BRIGHT DNA 68.4 15 0.00034 25.5 5.1 41 44-84 37-90 (92)
52 PF11626 Rap1_C: TRF2-interact 65.7 6.9 0.00015 27.6 2.8 17 33-49 43-59 (87)
53 KOG2009 Transcription initiati 65.5 7.3 0.00016 37.0 3.6 49 33-81 405-453 (584)
54 smart00501 BRIGHT BRIGHT, ARID 64.9 18 0.00039 25.5 4.9 41 45-85 34-87 (93)
55 PRK11169 leucine-responsive tr 63.4 11 0.00024 29.5 3.8 46 42-88 13-59 (164)
56 PF13325 MCRS_N: N-terminal re 63.1 18 0.00038 29.9 5.1 45 39-84 1-48 (199)
57 cd08319 Death_RAIDD Death doma 61.4 14 0.0003 26.1 3.7 30 45-75 2-31 (83)
58 PRK09645 RNA polymerase sigma 61.0 27 0.00059 26.7 5.7 34 49-83 127-160 (173)
59 KOG4468 Polycomb-group transcr 58.4 29 0.00062 33.4 6.1 49 37-85 88-146 (782)
60 cd08803 Death_ank3 Death domai 55.3 22 0.00049 25.0 3.9 31 45-76 4-34 (84)
61 PF10545 MADF_DNA_bdg: Alcohol 55.1 14 0.0003 24.7 2.7 26 58-83 28-54 (85)
62 TIGR02937 sigma70-ECF RNA poly 53.7 32 0.00069 24.7 4.8 39 45-84 115-153 (158)
63 PF07638 Sigma70_ECF: ECF sigm 53.1 28 0.00061 27.5 4.7 40 42-82 137-176 (185)
64 PRK09652 RNA polymerase sigma 50.0 39 0.00085 25.6 4.9 34 49-83 137-170 (182)
65 PRK11924 RNA polymerase sigma 48.6 41 0.00088 25.4 4.8 32 51-83 136-167 (179)
66 cd08317 Death_ank Death domain 47.8 24 0.00052 24.4 3.1 31 45-76 4-34 (84)
67 PRK12529 RNA polymerase sigma 47.3 61 0.0013 25.1 5.7 38 50-88 137-174 (178)
68 PRK09643 RNA polymerase sigma 46.9 47 0.001 26.2 5.0 36 46-82 140-175 (192)
69 PRK09641 RNA polymerase sigma 46.9 45 0.00098 25.7 4.9 32 51-83 147-178 (187)
70 PF09905 DUF2132: Uncharacteri 46.5 27 0.00058 23.6 2.9 23 45-69 12-34 (64)
71 smart00344 HTH_ASNC helix_turn 45.6 55 0.0012 23.1 4.8 45 43-88 3-48 (108)
72 PRK04217 hypothetical protein; 45.5 98 0.0021 23.0 6.2 43 39-83 42-84 (110)
73 cd08804 Death_ank2 Death domai 44.9 34 0.00073 24.0 3.5 31 45-76 4-34 (84)
74 PRK09047 RNA polymerase factor 43.6 65 0.0014 24.1 5.2 31 52-83 118-148 (161)
75 TIGR02894 DNA_bind_RsfA transc 43.5 9.4 0.0002 30.4 0.5 20 14-33 38-57 (161)
76 PRK12532 RNA polymerase sigma 42.6 75 0.0016 24.9 5.6 30 51-81 147-176 (195)
77 PF13936 HTH_38: Helix-turn-he 41.8 31 0.00068 21.0 2.6 36 39-76 4-39 (44)
78 cd06171 Sigma70_r4 Sigma70, re 41.3 72 0.0016 18.5 4.8 39 40-80 11-49 (55)
79 PRK09648 RNA polymerase sigma 40.9 69 0.0015 24.9 5.1 33 51-84 150-182 (189)
80 PRK12523 RNA polymerase sigma 40.7 72 0.0016 24.4 5.1 37 47-84 126-162 (172)
81 TIGR02939 RpoE_Sigma70 RNA pol 40.4 50 0.0011 25.5 4.2 28 55-83 153-180 (190)
82 TIGR02954 Sig70_famx3 RNA poly 39.9 68 0.0015 24.4 4.9 32 51-83 130-161 (169)
83 PRK05602 RNA polymerase sigma 39.9 90 0.0019 24.2 5.6 31 51-82 139-169 (186)
84 PRK12512 RNA polymerase sigma 39.6 91 0.002 24.0 5.6 37 47-84 138-174 (184)
85 cd08318 Death_NMPP84 Death dom 39.0 49 0.0011 23.1 3.6 32 40-75 5-36 (86)
86 PRK09637 RNA polymerase sigma 38.6 74 0.0016 24.9 5.0 35 48-83 114-148 (181)
87 PRK11923 algU RNA polymerase s 38.4 69 0.0015 24.9 4.8 29 54-83 152-180 (193)
88 PRK12530 RNA polymerase sigma 38.3 78 0.0017 24.8 5.1 31 51-82 145-175 (189)
89 TIGR02943 Sig70_famx1 RNA poly 38.1 83 0.0018 24.7 5.2 35 48-83 139-173 (188)
90 PRK09642 RNA polymerase sigma 38.0 87 0.0019 23.5 5.1 32 51-83 117-148 (160)
91 TIGR02948 SigW_bacill RNA poly 37.6 70 0.0015 24.6 4.6 28 55-83 151-178 (187)
92 PRK12515 RNA polymerase sigma 37.6 84 0.0018 24.5 5.1 32 51-83 142-173 (189)
93 PF09420 Nop16: Ribosome bioge 37.5 88 0.0019 24.5 5.2 47 36-82 113-163 (164)
94 cd08777 Death_RIP1 Death Domai 37.4 46 0.00099 23.5 3.2 29 47-76 4-32 (86)
95 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 37.4 76 0.0016 20.3 3.9 34 43-77 7-40 (50)
96 PRK12531 RNA polymerase sigma 36.9 87 0.0019 24.6 5.1 32 51-83 152-183 (194)
97 PRK12545 RNA polymerase sigma 36.8 92 0.002 24.7 5.3 28 54-82 153-180 (201)
98 cd08805 Death_ank1 Death domai 36.4 52 0.0011 23.2 3.3 22 45-66 4-25 (84)
99 PRK12527 RNA polymerase sigma 36.0 1E+02 0.0022 23.2 5.2 32 51-83 116-147 (159)
100 smart00005 DEATH DEATH domain, 35.8 52 0.0011 22.4 3.3 30 44-74 4-34 (88)
101 PF09197 Rap1-DNA-bind: Rap1, 35.8 1.3E+02 0.0029 22.2 5.5 46 39-84 1-77 (105)
102 PRK13923 putative spore coat p 35.3 17 0.00038 29.2 0.8 18 15-32 40-57 (170)
103 PRK12514 RNA polymerase sigma 34.7 96 0.0021 23.8 5.0 28 55-83 144-171 (179)
104 PF02954 HTH_8: Bacterial regu 33.8 1.1E+02 0.0023 18.2 4.1 33 43-76 5-37 (42)
105 KOG4282 Transcription factor G 33.6 37 0.00079 29.7 2.7 18 14-31 96-113 (345)
106 PLN03142 Probable chromatin-re 33.4 90 0.002 32.0 5.6 41 39-79 826-867 (1033)
107 TIGR02999 Sig-70_X6 RNA polyme 33.2 1.1E+02 0.0024 23.4 5.1 29 54-83 148-176 (183)
108 KOG4329 DNA-binding protein [G 33.0 88 0.0019 28.4 4.9 42 39-80 279-321 (445)
109 TIGR02960 SigX5 RNA polymerase 32.6 2E+02 0.0044 24.3 7.1 31 52-83 154-184 (324)
110 PRK09651 RNA polymerase sigma 32.4 89 0.0019 24.0 4.4 30 53-83 132-161 (172)
111 PRK08241 RNA polymerase factor 32.2 1.9E+02 0.004 24.9 6.8 30 54-84 167-196 (339)
112 PRK12524 RNA polymerase sigma 32.2 1.1E+02 0.0024 24.0 5.1 34 49-83 145-178 (196)
113 cd08311 Death_p75NR Death doma 32.1 58 0.0013 22.5 2.9 33 42-76 2-34 (77)
114 TIGR02952 Sig70_famx2 RNA poly 31.7 1.2E+02 0.0026 22.8 5.0 28 55-83 137-164 (170)
115 PRK06759 RNA polymerase factor 31.3 1.3E+02 0.0028 22.3 5.1 29 54-83 120-148 (154)
116 PRK12528 RNA polymerase sigma 31.2 1.3E+02 0.0028 22.6 5.2 34 49-83 122-155 (161)
117 PRK09649 RNA polymerase sigma 31.0 1.1E+02 0.0024 23.8 4.9 30 53-83 143-172 (185)
118 PRK09636 RNA polymerase sigma 30.8 2.6E+02 0.0056 23.6 7.4 30 54-84 129-158 (293)
119 PRK12536 RNA polymerase sigma 30.2 1.3E+02 0.0028 23.2 5.1 34 49-83 138-171 (181)
120 PRK12516 RNA polymerase sigma 29.9 1.3E+02 0.0028 23.6 5.1 37 46-83 122-158 (187)
121 COG2963 Transposase and inacti 29.8 2E+02 0.0043 20.7 5.7 44 37-81 5-49 (116)
122 TIGR02950 SigM_subfam RNA poly 29.8 41 0.0009 25.0 2.1 27 56-83 121-147 (154)
123 PRK12547 RNA polymerase sigma 29.5 1.4E+02 0.0031 22.6 5.2 33 50-83 122-154 (164)
124 PF10440 WIYLD: Ubiquitin-bind 29.3 43 0.00094 22.7 1.8 19 46-64 30-48 (65)
125 PRK12542 RNA polymerase sigma 29.3 1.3E+02 0.0029 23.2 5.0 32 51-83 133-164 (185)
126 PRK13919 putative RNA polymera 29.1 1.4E+02 0.003 23.0 5.1 29 55-84 150-178 (186)
127 TIGR02983 SigE-fam_strep RNA p 29.1 1.3E+02 0.0029 22.4 4.9 40 44-84 114-153 (162)
128 TIGR02984 Sig-70_plancto1 RNA 29.0 1.4E+02 0.003 22.9 5.0 34 49-83 149-182 (189)
129 PRK15201 fimbriae regulatory p 29.0 1.7E+02 0.0037 24.1 5.5 43 39-84 133-175 (198)
130 TIGR02957 SigX4 RNA polymerase 29.0 2.8E+02 0.006 23.3 7.2 31 53-84 121-151 (281)
131 COG2197 CitB Response regulato 28.5 1.6E+02 0.0034 23.9 5.5 43 39-84 148-190 (211)
132 PRK12537 RNA polymerase sigma 28.5 1.4E+02 0.003 23.1 5.0 30 54-84 147-176 (182)
133 cd08779 Death_PIDD Death Domai 28.4 1.2E+02 0.0026 21.2 4.1 21 46-66 3-23 (86)
134 PRK12520 RNA polymerase sigma 27.7 1.5E+02 0.0033 23.0 5.1 29 54-83 145-173 (191)
135 PRK12546 RNA polymerase sigma 27.2 1.3E+02 0.0029 23.6 4.7 36 47-83 120-155 (188)
136 PRK10360 DNA-binding transcrip 27.0 1.9E+02 0.004 21.7 5.4 44 38-84 136-179 (196)
137 PF05263 DUF722: Protein of un 26.9 1.2E+02 0.0026 23.3 4.1 45 21-76 72-118 (130)
138 COG1522 Lrp Transcriptional re 26.5 1.5E+02 0.0032 22.1 4.7 45 43-88 8-53 (154)
139 PRK06811 RNA polymerase factor 24.9 1.8E+02 0.0039 22.6 5.1 29 54-83 145-173 (189)
140 PRK10100 DNA-binding transcrip 24.9 2E+02 0.0043 23.4 5.4 43 39-84 155-197 (216)
141 PRK11922 RNA polymerase sigma 24.4 87 0.0019 25.5 3.3 27 56-83 165-191 (231)
142 PRK09415 RNA polymerase factor 23.7 1.7E+02 0.0037 22.5 4.7 28 55-83 142-169 (179)
143 PRK00118 putative DNA-binding 23.4 2.3E+02 0.005 20.7 5.0 38 42-80 19-56 (104)
144 PRK09639 RNA polymerase sigma 23.4 2E+02 0.0044 21.5 4.9 33 49-83 121-153 (166)
145 PRK09646 RNA polymerase sigma 23.2 2E+02 0.0044 22.4 5.1 29 54-83 156-184 (194)
146 KOG0384 Chromodomain-helicase 23.1 57 0.0012 34.0 2.2 27 38-64 1134-1161(1373)
147 PRK12518 RNA polymerase sigma 23.0 94 0.002 23.6 3.0 27 56-83 136-162 (175)
148 PRK12526 RNA polymerase sigma 22.6 2.1E+02 0.0046 22.7 5.1 28 55-83 168-195 (206)
149 PRK01905 DNA-binding protein F 22.6 2.5E+02 0.0055 19.0 4.8 55 19-74 5-67 (77)
150 PF13384 HTH_23: Homeodomain-l 22.5 1.2E+02 0.0025 18.2 2.8 33 42-76 4-36 (50)
151 PF04504 DUF573: Protein of un 22.4 1.9E+02 0.0042 20.7 4.4 18 38-55 5-22 (98)
152 PRK12544 RNA polymerase sigma 22.4 2.2E+02 0.0047 22.8 5.2 29 54-83 162-190 (206)
153 PRK12519 RNA polymerase sigma 22.1 1.7E+02 0.0036 22.7 4.4 29 54-83 155-183 (194)
154 KOG1194 Predicted DNA-binding 22.0 47 0.001 30.9 1.2 41 39-80 472-512 (534)
155 PF09019 EcoRII-C: EcoRII C te 21.6 20 0.00043 28.7 -1.1 10 22-31 97-106 (164)
156 cd08306 Death_FADD Fas-associa 21.6 1.5E+02 0.0033 20.6 3.6 28 48-76 5-32 (86)
157 PRK09647 RNA polymerase sigma 21.4 2.3E+02 0.005 22.6 5.1 29 54-83 152-180 (203)
158 PRK06986 fliA flagellar biosyn 21.3 2E+02 0.0043 23.4 4.8 33 51-84 195-227 (236)
159 PRK15411 rcsA colanic acid cap 21.2 3.4E+02 0.0073 21.7 6.1 43 39-84 137-179 (207)
160 COG4628 Uncharacterized conser 20.8 95 0.0021 23.6 2.5 22 44-67 20-41 (136)
161 PRK09638 RNA polymerase sigma 20.7 95 0.0021 23.7 2.6 29 54-83 140-168 (176)
162 PRK12538 RNA polymerase sigma 20.5 1.9E+02 0.0041 23.8 4.5 29 54-83 185-213 (233)
163 TIGR02989 Sig-70_gvs1 RNA poly 20.3 2.7E+02 0.0058 20.5 5.1 24 56-80 127-150 (159)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=99.97 E-value=5.4e-31 Score=233.06 Aligned_cols=102 Identities=66% Similarity=1.226 Sum_probs=95.9
Q ss_pred CCCcchhhHhhhcc------------------------------CCCCChHHHHHHHHhhhCCCCCCCCCCHHHHHHHHH
Q 038824 1 MGRPPCCDKLNVKK------------------------------GLRRCGKSCRLRWTNYLRPDLKHESFTPQEEEMIIR 50 (187)
Q Consensus 1 ~~~~~~~~~~~~~~------------------------------g~~Rt~~qCr~RW~~~L~P~l~k~~wT~eED~~Ll~ 50 (187)
|||++||+|..+++ |++|+++|||+||.+||+|+|++++||+|||++|++
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 99999999999888 468999999999999999999999999999999999
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCCCCcchHHHH
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTEMGIDPVTHKPFSQI 102 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~~~~t~~~~~~~~~~ 102 (187)
+|..||++|..||++|||||+++|||||+.+|+++++..++.+.+++++.+.
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~ 132 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEV 132 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCcccc
Confidence 9999999999999999999999999999999999999888888777776543
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.96 E-value=4.4e-30 Score=213.36 Aligned_cols=86 Identities=65% Similarity=1.246 Sum_probs=82.4
Q ss_pred CCCCChHHHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCCC
Q 038824 15 GLRRCGKSCRLRWTNYLRPDLKHESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTEMGIDPV 94 (187)
Q Consensus 15 g~~Rt~~qCr~RW~~~L~P~l~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~~~~t~~ 94 (187)
|++|+++|||+||.+||+|+|++++||+|||++|++++..||++|+.||++|||||+++|||||+.++++.+.+.+.++.
T Consensus 56 g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~ 135 (249)
T PLN03212 56 GLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQ 135 (249)
T ss_pred hcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCC
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CcchHH
Q 038824 95 THKPFS 100 (187)
Q Consensus 95 ~~~~~~ 100 (187)
+.+++.
T Consensus 136 ~~kp~~ 141 (249)
T PLN03212 136 THKPLD 141 (249)
T ss_pred CCCCCC
Confidence 877753
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.96 E-value=1.9e-29 Score=211.24 Aligned_cols=94 Identities=65% Similarity=1.137 Sum_probs=84.3
Q ss_pred cchhhHhhhcc-CCCCChHHHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 4 PPCCDKLNVKK-GLRRCGKSCRLRWTNYLRPDLKHESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 4 ~~~~~~~~~~~-g~~Rt~~qCr~RW~~~L~P~l~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
++.+|..+.++ |++|++||||+||.|||+|+|+++.||+|||++|+++|+.+|++|+.||++||||||++|||+|++.+
T Consensus 28 G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~l 107 (238)
T KOG0048|consen 28 GKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHL 107 (238)
T ss_pred CCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHH
Confidence 34566666665 55999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhCCCCCCCcc
Q 038824 83 RKKLTEMGIDPVTHK 97 (187)
Q Consensus 83 ~~~~~~~~~t~~~~~ 97 (187)
++++.+....+.+..
T Consensus 108 kkkl~~~~~~~~~~~ 122 (238)
T KOG0048|consen 108 KKKLLKMGIDPSTHR 122 (238)
T ss_pred HHHHHHcCCCCCccc
Confidence 999999875555533
No 4
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.78 E-value=1e-19 Score=151.55 Aligned_cols=90 Identities=23% Similarity=0.460 Sum_probs=83.8
Q ss_pred CcchhhHhhhccCCCCChHHHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhhhC-CCCCHHHHHHHHHH
Q 038824 3 RPPCCDKLNVKKGLRRCGKSCRLRWTNYLRPDLKHESFTPQEEEMIIRLHAAIG-SRWSIIAQQL-PGRTDNDVKNYWNT 80 (187)
Q Consensus 3 ~~~~~~~~~~~~g~~Rt~~qCr~RW~~~L~P~l~k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~l-pgRt~~q~k~rw~~ 80 (187)
|.|||+|.+++++ +||+|||++|+++|+.|| .+|..||+.+ +|||++||+.||.+
T Consensus 14 ~~pcc~K~glKRg-----------------------~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N 70 (249)
T PLN03212 14 TTPCCTKMGMKRG-----------------------PWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMN 70 (249)
T ss_pred CCCCcccCCCcCC-----------------------CCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHH
Confidence 5688888777766 899999999999999999 6899999998 79999999999999
Q ss_pred HhhhhhhhCCCCCCCcchHHHHHHHhcCCCCCCCC
Q 038824 81 KLRKKLTEMGIDPVTHKPFSQILADYGNIGGLPKS 115 (187)
Q Consensus 81 ~l~~~~~~~~~t~~~~~~~~~~~~~~g~~~~~~~~ 115 (187)
+|+|.+.+++|+.+|+..++.++..+|+.|+.++.
T Consensus 71 ~L~P~I~kgpWT~EED~lLlel~~~~GnKWs~IAk 105 (249)
T PLN03212 71 YLRPSVKRGGITSDEEDLILRLHRLLGNRWSLIAG 105 (249)
T ss_pred hhchhcccCCCChHHHHHHHHHHHhccccHHHHHh
Confidence 99999999999999999999999999999987764
No 5
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.77 E-value=8.6e-20 Score=152.89 Aligned_cols=84 Identities=19% Similarity=0.241 Sum_probs=78.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhhhCC-CCCHHHHHHHHHHHhhhhhhhCCCCCCCcchHHHHHHHhcCC
Q 038824 32 RPDLKHESFTPQEEEMIIRLHAAIG-SRWSIIAQQLP-GRTDNDVKNYWNTKLRKKLTEMGIDPVTHKPFSQILADYGNI 109 (187)
Q Consensus 32 ~P~l~k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~lp-gRt~~q~k~rw~~~l~~~~~~~~~t~~~~~~~~~~~~~~g~~ 109 (187)
+|.+.|||||+|||++|+++|..|| .+|..||+.++ ||++++||.||.++|+|.++++.||++|+..+.++++.+||.
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 4566789999999999999999999 67999999998 999999999999999999999999999999999999999999
Q ss_pred CCCCCC
Q 038824 110 GGLPKS 115 (187)
Q Consensus 110 ~~~~~~ 115 (187)
|+.++.
T Consensus 84 Ws~IA~ 89 (238)
T KOG0048|consen 84 WSLIAG 89 (238)
T ss_pred HHHHHh
Confidence 986663
No 6
>PLN03091 hypothetical protein; Provisional
Probab=99.70 E-value=6.8e-18 Score=150.09 Aligned_cols=85 Identities=20% Similarity=0.320 Sum_probs=79.8
Q ss_pred hCCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhhhC-CCCCHHHHHHHHHHHhhhhhhhCCCCCCCcchHHHHHHHhcC
Q 038824 31 LRPDLKHESFTPQEEEMIIRLHAAIG-SRWSIIAQQL-PGRTDNDVKNYWNTKLRKKLTEMGIDPVTHKPFSQILADYGN 108 (187)
Q Consensus 31 L~P~l~k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~l-pgRt~~q~k~rw~~~l~~~~~~~~~t~~~~~~~~~~~~~~g~ 108 (187)
.++.+++++||+|||++|+++|.+|| .+|..||+.+ +|||++|||.||.++|+|.+++++|+++|+..|++++..+|+
T Consensus 8 ~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~Gn 87 (459)
T PLN03091 8 YKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGN 87 (459)
T ss_pred cCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCc
Confidence 35789999999999999999999999 6799999988 699999999999999999999999999999999999999999
Q ss_pred CCCCCCC
Q 038824 109 IGGLPKS 115 (187)
Q Consensus 109 ~~~~~~~ 115 (187)
.|..++.
T Consensus 88 KWskIAk 94 (459)
T PLN03091 88 RWSQIAA 94 (459)
T ss_pred chHHHHH
Confidence 9987664
No 7
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.67 E-value=1.2e-16 Score=146.91 Aligned_cols=104 Identities=19% Similarity=0.291 Sum_probs=99.1
Q ss_pred hhhHhhhccCCCCChHHHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 6 CCDKLNVKKGLRRCGKSCRLRWTNYLRPDLKHESFTPQEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 6 ~~~~~~~~~g~~Rt~~qCr~RW~~~L~P~l~k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
.-|+.++-.++||+..|..-||.+.|+|+|++|+||++||.+|+.+|.+|| ..|..|...+|||++.|||.||.+.|..
T Consensus 329 I~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~ 408 (939)
T KOG0049|consen 329 IQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNR 408 (939)
T ss_pred cchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHH
Confidence 457778888999999999999999999999999999999999999999999 5599999999999999999999999999
Q ss_pred hhhhCCCCCCCcchHHHHHHHhcCC
Q 038824 85 KLTEMGIDPVTHKPFSQILADYGNI 109 (187)
Q Consensus 85 ~~~~~~~t~~~~~~~~~~~~~~g~~ 109 (187)
.++++.|+-.++..++.++..||-.
T Consensus 409 s~K~~rW~l~edeqL~~~V~~YG~g 433 (939)
T KOG0049|consen 409 SAKVERWTLVEDEQLLYAVKVYGKG 433 (939)
T ss_pred hhccCceeecchHHHHHHHHHHccc
Confidence 9999999999999999999999955
No 8
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.60 E-value=6.5e-16 Score=102.83 Aligned_cols=59 Identities=27% Similarity=0.531 Sum_probs=52.6
Q ss_pred CCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCCCCcch
Q 038824 40 FTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTEMGIDPVTHKP 98 (187)
Q Consensus 40 wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~~~~t~~~~~~ 98 (187)
||+|||++|+++|..||++|..||..|+.||..+|++||...|++.+.+.+|+++++..
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~ 59 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQR 59 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhc
Confidence 99999999999999999999999999966999999999999999999999999888654
No 9
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.54 E-value=9.3e-15 Score=93.44 Aligned_cols=46 Identities=26% Similarity=0.580 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-hHHHhhhCC-CCCHHHHHHHHHHHh
Q 038824 37 HESFTPQEEEMIIRLHAAIGSR-WSIIAQQLP-GRTDNDVKNYWNTKL 82 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~~G~~-W~~Ia~~lp-gRt~~q~k~rw~~~l 82 (187)
|++||+|||++|+++|.+||.. |..||..|| |||..||++||+.++
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 5799999999999999999977 999999999 999999999999875
No 10
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.38 E-value=1.1e-12 Score=82.07 Aligned_cols=47 Identities=36% Similarity=0.774 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 37 HESFTPQEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+++||++||.+|+.++..|| .+|..||..|++||+.+|++||..+++
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 11
>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=99.27 E-value=1.2e-11 Score=76.16 Aligned_cols=44 Identities=32% Similarity=0.731 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 39 SFTPQEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
+||++||..|+.++..+| .+|..||..|++||+.+|++||..++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999998753
No 12
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.21 E-value=1.1e-11 Score=114.69 Aligned_cols=106 Identities=15% Similarity=0.293 Sum_probs=97.7
Q ss_pred CcchhhHhhhccCCCCChHHHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHHhC----CChHHHhhhCCCCCHHHHHHHH
Q 038824 3 RPPCCDKLNVKKGLRRCGKSCRLRWTNYLRPDLKHESFTPQEEEMIIRLHAAIG----SRWSIIAQQLPGRTDNDVKNYW 78 (187)
Q Consensus 3 ~~~~~~~~~~~~g~~Rt~~qCr~RW~~~L~P~l~k~~wT~eED~~Ll~~v~~~G----~~W~~Ia~~lpgRt~~q~k~rw 78 (187)
+.-.|.++.+..|.+|+..||..|....++- |+...||+|||.+|+++|.... -+|.+|-.+||||+.-|+-.||
T Consensus 272 ~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~-L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~ 350 (939)
T KOG0049|consen 272 KFVSWPMIALNLGTNRSSYQCMEKFKTEVSQ-LSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRF 350 (939)
T ss_pred ccccHHHHHHHhCCCcchHHHHHHHHHHHHH-HHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhh
Confidence 3456888889999999999999999999874 6668999999999999998875 3599999999999999999999
Q ss_pred HHHhhhhhhhCCCCCCCcchHHHHHHHhcCC
Q 038824 79 NTKLRKKLTEMGIDPVTHKPFSQILADYGNI 109 (187)
Q Consensus 79 ~~~l~~~~~~~~~t~~~~~~~~~~~~~~g~~ 109 (187)
...|.|.++++.|+++||..++.+++.||..
T Consensus 351 ~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~k 381 (939)
T KOG0049|consen 351 SHTLDPSVKHGRWTDQEDVLLVCAVSRYGAK 381 (939)
T ss_pred eeccCccccCCCCCCHHHHHHHHHHHHhCcc
Confidence 9999999999999999999999999999976
No 13
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.12 E-value=6.1e-11 Score=108.47 Aligned_cols=80 Identities=26% Similarity=0.431 Sum_probs=72.1
Q ss_pred hHhhhccCCCCChHHHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhhhhh
Q 038824 8 DKLNVKKGLRRCGKSCRLRWTNYLRPDLKHESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRKKLT 87 (187)
Q Consensus 8 ~~~~~~~g~~Rt~~qCr~RW~~~L~P~l~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~ 87 (187)
|-.+..+..-++++||+.||.++++|.+++..|+.|||..|+.+...+|..|..||..++|||+.+|.+||...+.....
T Consensus 43 ws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 43 WSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred HHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 33344444448999999999999999999999999999999999999999999999999999999999999999987666
No 14
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.02 E-value=2.8e-10 Score=103.12 Aligned_cols=82 Identities=22% Similarity=0.422 Sum_probs=74.1
Q ss_pred hhHhhhccCCCCChHHHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhhhh
Q 038824 7 CDKLNVKKGLRRCGKSCRLRWTNYLRPDLKHESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRKKL 86 (187)
Q Consensus 7 ~~~~~~~~g~~Rt~~qCr~RW~~~L~P~l~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~ 86 (187)
-|..+.+.....+.+||+.||-.+|+|.|++..|+.|||.+||.+...+-..|..||..| |||++||-.||+.++.-.+
T Consensus 29 qws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrtIa~i~-gr~~~qc~eRy~~ll~~~~ 107 (617)
T KOG0050|consen 29 QWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRTIADIM-GRTSQQCLERYNNLLDVYV 107 (617)
T ss_pred HHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccchHHHHh-hhhHHHHHHHHHHHHHHHH
Confidence 355566667888999999999999999999999999999999999999999999999998 9999999999999998766
Q ss_pred hhC
Q 038824 87 TEM 89 (187)
Q Consensus 87 ~~~ 89 (187)
...
T Consensus 108 s~~ 110 (617)
T KOG0050|consen 108 SYH 110 (617)
T ss_pred hhh
Confidence 553
No 15
>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=98.84 E-value=4.8e-09 Score=69.51 Aligned_cols=41 Identities=32% Similarity=0.507 Sum_probs=36.1
Q ss_pred hHhhhccCCCCChHHHHHHHHhhhCCCCCCCCCCHHHHHHH
Q 038824 8 DKLNVKKGLRRCGKSCRLRWTNYLRPDLKHESFTPQEEEMI 48 (187)
Q Consensus 8 ~~~~~~~g~~Rt~~qCr~RW~~~L~P~l~k~~wT~eED~~L 48 (187)
|+.+.+....|++.||+.||.++|+|.+++++||++||++|
T Consensus 20 W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 20 WKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred HHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 66777777459999999999999999999999999999987
No 16
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.63 E-value=1.4e-08 Score=93.14 Aligned_cols=82 Identities=21% Similarity=0.305 Sum_probs=76.8
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCCCCcchHHHHHHHhcCCCCC
Q 038824 34 DLKHESFTPQEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTEMGIDPVTHKPFSQILADYGNIGGL 112 (187)
Q Consensus 34 ~l~k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~~~~t~~~~~~~~~~~~~~g~~~~~ 112 (187)
.++.|.|+..||+.|..+|..|| ++|+.||..|.-|++++|++||+.++.+.+.+..|+.+++..+..+...+|..|+.
T Consensus 17 ~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~wst 96 (512)
T COG5147 17 KRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQWST 96 (512)
T ss_pred eecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchhhh
Confidence 46778999999999999999999 77999999998899999999999999999999999999999999999999999876
Q ss_pred CCC
Q 038824 113 PKS 115 (187)
Q Consensus 113 ~~~ 115 (187)
++.
T Consensus 97 ia~ 99 (512)
T COG5147 97 IAD 99 (512)
T ss_pred hcc
Confidence 654
No 17
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.58 E-value=3.6e-08 Score=89.62 Aligned_cols=81 Identities=16% Similarity=0.193 Sum_probs=75.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCCCCcchHHHHHHHhcCCCCCC
Q 038824 35 LKHESFTPQEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTEMGIDPVTHKPFSQILADYGNIGGLP 113 (187)
Q Consensus 35 l~k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~~~~t~~~~~~~~~~~~~~g~~~~~~ 113 (187)
++.+.|+.-||++|-..|..|| +.|+.|+..++-.|..||++||...++|.+++..|+.+++..++.+.......|..+
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrtI 84 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRTI 84 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccchH
Confidence 5678899999999999999999 779999999999999999999999999999999999999999999988888888866
Q ss_pred CC
Q 038824 114 KS 115 (187)
Q Consensus 114 ~~ 115 (187)
+.
T Consensus 85 a~ 86 (617)
T KOG0050|consen 85 AD 86 (617)
T ss_pred HH
Confidence 63
No 18
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.58 E-value=1.3e-07 Score=87.78 Aligned_cols=97 Identities=21% Similarity=0.239 Sum_probs=80.5
Q ss_pred hhHhhhccCCCCChHHHHHHHHhhhCC-CCCCCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhhh
Q 038824 7 CDKLNVKKGLRRCGKSCRLRWTNYLRP-DLKHESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRKK 85 (187)
Q Consensus 7 ~~~~~~~~g~~Rt~~qCr~RW~~~L~P-~l~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~ 85 (187)
+|....+..+-|+.++....-++.-.| +.++|.||+||++.|..+|.++|+.|..|+..| ||.+..|+.||..+....
T Consensus 353 l~n~~~~~Lp~R~~~siy~~~rR~y~~FE~~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 353 LYNNLYKLLPYRDRKSIYHHLRRAYTPFENKRGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred HHHhhhhhcCcccchhHHHHHHhcCCccccccCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 445555666668888876533344444 239999999999999999999999999999998 999999999999999876
Q ss_pred --hhhCCCCCCCcchHHHHHH
Q 038824 86 --LTEMGIDPVTHKPFSQILA 104 (187)
Q Consensus 86 --~~~~~~t~~~~~~~~~~~~ 104 (187)
..+..|+.+|...+++++.
T Consensus 432 ~~~~r~~Ws~eEe~~Llk~V~ 452 (607)
T KOG0051|consen 432 SKRNRGAWSIEEEEKLLKTVN 452 (607)
T ss_pred cccccCcchHHHHHHHHHHHH
Confidence 4778999999998888885
No 19
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.54 E-value=1.7e-07 Score=87.18 Aligned_cols=80 Identities=19% Similarity=0.407 Sum_probs=66.9
Q ss_pred cCCCCChHHHHHHHHhhhCCC--CCCCCCCHHHHHHHHHHHH-------Hh-------------------CCChHHHhhh
Q 038824 14 KGLRRCGKSCRLRWTNYLRPD--LKHESFTPQEEEMIIRLHA-------AI-------------------GSRWSIIAQQ 65 (187)
Q Consensus 14 ~g~~Rt~~qCr~RW~~~L~P~--l~k~~wT~eED~~Ll~~v~-------~~-------------------G~~W~~Ia~~ 65 (187)
+.+||.+..||+||++|..++ .+++.||.||+++|+++|. ++ +-+|..|+..
T Consensus 411 ~~lgr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~ 490 (607)
T KOG0051|consen 411 KALGRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEM 490 (607)
T ss_pred HHHccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHh
Confidence 466899999999999999998 5999999999999999995 33 1259999998
Q ss_pred CCCCCHHHHHHHHHHHhhhh-hhhCCCCC
Q 038824 66 LPGRTDNDVKNYWNTKLRKK-LTEMGIDP 93 (187)
Q Consensus 66 lpgRt~~q~k~rw~~~l~~~-~~~~~~t~ 93 (187)
+..|+.-||+..|..++... ..++.+..
T Consensus 491 ~~TR~~~qCr~Kw~kl~~~~s~n~~~~~~ 519 (607)
T KOG0051|consen 491 LGTRSRIQCRYKWYKLTTSPSFNKRQESK 519 (607)
T ss_pred hcCCCcchHHHHHHHHHhhHHhhcccccc
Confidence 89999999999999887654 44444443
No 20
>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=4.9e-05 Score=50.38 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=41.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-Ch---HHHhhhCC-CC-CHHHHHHHHHHHhh
Q 038824 37 HESFTPQEEEMIIRLHAAIGS-RW---SIIAQQLP-GR-TDNDVKNYWNTKLR 83 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~~G~-~W---~~Ia~~lp-gR-t~~q~k~rw~~~l~ 83 (187)
+-.||+||..+.++.+..+|. .| ..|+..|. .| |..||+.|.+.+.-
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 457999999999999999995 99 99999883 34 99999999987753
No 21
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.76 E-value=5.2e-05 Score=68.12 Aligned_cols=49 Identities=20% Similarity=0.424 Sum_probs=44.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 34 DLKHESFTPQEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 34 ~l~k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
.+-...||.+|+-+||+++..|| ++|..||.++.-||..+|+.+|.++.
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 34456899999999999999999 99999999999999999999997654
No 22
>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=97.70 E-value=5.8e-05 Score=59.72 Aligned_cols=53 Identities=23% Similarity=0.408 Sum_probs=44.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHh---CC----ChHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 038824 35 LKHESFTPQEEEMIIRLHAAI---GS----RWSIIAQQLPGRTDNDVKNYWNTKLRKKLTE 88 (187)
Q Consensus 35 l~k~~wT~eED~~Ll~~v~~~---G~----~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~ 88 (187)
.+.+.||.|||.+|-+.|-.| |+ -...++..| +||+.+|.=|||+++|+....
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 356789999999999999888 32 278888887 999999999999999975443
No 23
>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=97.69 E-value=6.2e-05 Score=51.21 Aligned_cols=51 Identities=14% Similarity=0.333 Sum_probs=33.0
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------CC-hHHHhhhCC-CCCHHHHHHHHHHHhhhhhh
Q 038824 37 HESFTPQEEEMIIRLHAAIG--------SR-WSIIAQQLP-GRTDNDVKNYWNTKLRKKLT 87 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~~G--------~~-W~~Ia~~lp-gRt~~q~k~rw~~~l~~~~~ 87 (187)
+.+||.|||++|+..|..+. +. |.+++..-| .+|-...|+||...|++...
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 45899999999999996552 22 999999987 99999999999988887553
No 24
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.32 E-value=0.00022 Score=50.20 Aligned_cols=48 Identities=27% Similarity=0.547 Sum_probs=34.2
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--C------ChHHHhhhC----CCCCHHHHHHHHHHHhhh
Q 038824 37 HESFTPQEEEMIIRLHAA------IG--S------RWSIIAQQL----PGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~------~G--~------~W~~Ia~~l----pgRt~~q~k~rw~~~l~~ 84 (187)
|..||.+|...||+++.. ++ . -|..||..| ..||+.||+.+|.++.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~ 66 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKK 66 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence 347999999999998877 21 1 399999987 469999999999886654
No 25
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.89 E-value=0.0013 Score=59.77 Aligned_cols=46 Identities=13% Similarity=0.265 Sum_probs=42.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHH
Q 038824 36 KHESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTK 81 (187)
Q Consensus 36 ~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~ 81 (187)
....||.+|..+|++.+..||..|.+||.++..+|..||--||.++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 3458999999999999999999999999999999999999999754
No 26
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.76 E-value=0.0023 Score=59.28 Aligned_cols=45 Identities=13% Similarity=0.287 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHH
Q 038824 37 HESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTK 81 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~ 81 (187)
++.||.+|..+|++.+..||..|.+||.+...||..||--++..+
T Consensus 253 ~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 253 RPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 458999999999999999999999999999999999999988654
No 27
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.65 E-value=0.0026 Score=51.03 Aligned_cols=52 Identities=15% Similarity=0.326 Sum_probs=41.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC-------hHHHhhhCCCCCHHHHHHHHHHHhhhhhh
Q 038824 35 LKHESFTPQEEEMIIRLHAAIGSR-------WSIIAQQLPGRTDNDVKNYWNTKLRKKLT 87 (187)
Q Consensus 35 l~k~~wT~eED~~Ll~~v~~~G~~-------W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~ 87 (187)
.+.+.||.|||.+|-+.|-.|+.. ...++..| +||..+|.-|||.++++...
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Ye 61 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQ 61 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHH
Confidence 356789999999999988888722 44444555 89999999999999997543
No 28
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.54 E-value=0.003 Score=55.20 Aligned_cols=48 Identities=21% Similarity=0.419 Sum_probs=43.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 36 KHESFTPQEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 36 ~k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
--..|+.+|+.+|++...-.| ++|..||.++..|+...||.+|..+..
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 344799999999999999999 899999999999999999999976554
No 29
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.46 E-value=0.0067 Score=41.79 Aligned_cols=48 Identities=27% Similarity=0.506 Sum_probs=39.7
Q ss_pred CCCCCHHHHHHHHHHHHHh-----C--C----------ChHHHhhhC-----CCCCHHHHHHHHHHHhhh
Q 038824 37 HESFTPQEEEMIIRLHAAI-----G--S----------RWSIIAQQL-----PGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~~-----G--~----------~W~~Ia~~l-----pgRt~~q~k~rw~~~l~~ 84 (187)
+..||.+|..+|++++..| | . -|..|+..| +.||..+++.+|..+...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 4579999999999999877 2 1 299999986 369999999999887654
No 30
>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=96.22 E-value=0.0032 Score=39.61 Aligned_cols=25 Identities=36% Similarity=0.392 Sum_probs=20.7
Q ss_pred hhHhhhccCC-CCChHHHHHHHHhhh
Q 038824 7 CDKLNVKKGL-RRCGKSCRLRWTNYL 31 (187)
Q Consensus 7 ~~~~~~~~g~-~Rt~~qCr~RW~~~L 31 (187)
-|+.+....+ +||+.||+.||.++|
T Consensus 23 ~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 23 NWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp HHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 4666777766 999999999999875
No 31
>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=95.40 E-value=0.023 Score=42.96 Aligned_cols=52 Identities=19% Similarity=0.414 Sum_probs=41.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----ChHHHhhhC------------CCCCHHHHHHHHHHHhhhh
Q 038824 34 DLKHESFTPQEEEMIIRLHAAIGS----RWSIIAQQL------------PGRTDNDVKNYWNTKLRKK 85 (187)
Q Consensus 34 ~l~k~~wT~eED~~Ll~~v~~~G~----~W~~Ia~~l------------pgRt~~q~k~rw~~~l~~~ 85 (187)
.-++..||++||.-|+-++..||- .|..|...+ ..||+..+..|-+++++-.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 556778999999999999999996 698887543 4599999999999988743
No 32
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=93.76 E-value=0.07 Score=32.17 Aligned_cols=28 Identities=32% Similarity=0.493 Sum_probs=22.9
Q ss_pred hhhHhhhccCCCCChHHHHHHHHhhhCC
Q 038824 6 CCDKLNVKKGLRRCGKSCRLRWTNYLRP 33 (187)
Q Consensus 6 ~~~~~~~~~g~~Rt~~qCr~RW~~~L~P 33 (187)
.-|..+....++|++.+|+.||.+.+++
T Consensus 22 ~~w~~Ia~~~~~rt~~~~~~~~~~~~~~ 49 (49)
T smart00717 22 NNWEKIAKELPGRTAEQCRERWNNLLKP 49 (49)
T ss_pred CCHHHHHHHcCCCCHHHHHHHHHHHcCC
Confidence 3467777778899999999999987753
No 33
>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=93.56 E-value=0.25 Score=34.86 Aligned_cols=46 Identities=30% Similarity=0.621 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------ChHHHhhhC---CC--CCHHHHHHHHHHHhhh
Q 038824 39 SFTPQEEEMIIRLHAAI---GS----------RWSIIAQQL---PG--RTDNDVKNYWNTKLRK 84 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~---G~----------~W~~Ia~~l---pg--Rt~~q~k~rw~~~l~~ 84 (187)
.||++++..|++++... |+ .|..|+..| +| .|..||++||..+.+.
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 49999999999988544 21 299999887 33 5678999999766543
No 34
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=92.95 E-value=0.16 Score=45.61 Aligned_cols=61 Identities=23% Similarity=0.359 Sum_probs=50.9
Q ss_pred HHHhhhCCCCCCCCCCHHHHHHHHHHHHHhCCChHHHhhh-----CCC-CCHHHHHHHHHHHhhhhhhhCC
Q 038824 26 RWTNYLRPDLKHESFTPQEEEMIIRLHAAIGSRWSIIAQQ-----LPG-RTDNDVKNYWNTKLRKKLTEMG 90 (187)
Q Consensus 26 RW~~~L~P~l~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~-----lpg-Rt~~q~k~rw~~~l~~~~~~~~ 90 (187)
-|..+|+ ...||.+|-+-|.++++.|.-+|-.||.. ++. ||-..+|.||....++-++...
T Consensus 123 EYe~~l~----dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 123 EYEAHLN----DNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred HHHHhhc----cccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 4555544 36899999999999999999999999987 666 9999999999998887665543
No 35
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.80 E-value=0.24 Score=43.48 Aligned_cols=47 Identities=17% Similarity=0.368 Sum_probs=38.7
Q ss_pred CCCCHHHHHHHHHHHHHh----------CCChHHHhhhC----CCCCHHHHHHHHHHHhhh
Q 038824 38 ESFTPQEEEMIIRLHAAI----------GSRWSIIAQQL----PGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 38 ~~wT~eED~~Ll~~v~~~----------G~~W~~Ia~~l----pgRt~~q~k~rw~~~l~~ 84 (187)
..|+.+|-..||++.... +..|..||+.+ .-||+.+|+++|.++.++
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~ 115 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKK 115 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 689999999999987543 23499999965 449999999999987775
No 36
>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=91.65 E-value=0.19 Score=29.76 Aligned_cols=26 Identities=35% Similarity=0.389 Sum_probs=21.1
Q ss_pred hhhHhhhccCCCCChHHHHHHHHhhh
Q 038824 6 CCDKLNVKKGLRRCGKSCRLRWTNYL 31 (187)
Q Consensus 6 ~~~~~~~~~g~~Rt~~qCr~RW~~~L 31 (187)
..|..+.....+|++.+|+.||.+++
T Consensus 20 ~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 20 NNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 34677777788899999999998753
No 37
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=91.44 E-value=0.72 Score=38.00 Aligned_cols=73 Identities=18% Similarity=0.353 Sum_probs=49.7
Q ss_pred CCCCChHHHHHHHHhhh----------------CCCC-----CCCCCCHHHHHHHHHHHHHhCC---ChHHHhh-----h
Q 038824 15 GLRRCGKSCRLRWTNYL----------------RPDL-----KHESFTPQEEEMIIRLHAAIGS---RWSIIAQ-----Q 65 (187)
Q Consensus 15 g~~Rt~~qCr~RW~~~L----------------~P~l-----~k~~wT~eED~~Ll~~v~~~G~---~W~~Ia~-----~ 65 (187)
--.-|-....+||...| .|.+ .+.+||.+|+++|......... .+.+|-. +
T Consensus 30 S~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vF 109 (199)
T PF13325_consen 30 SCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVF 109 (199)
T ss_pred CCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhh
Confidence 33445566677886554 3322 2458999999999997766543 3666643 3
Q ss_pred CCCCCHHHHHHHHHHHhhhhhh
Q 038824 66 LPGRTDNDVKNYWNTKLRKKLT 87 (187)
Q Consensus 66 lpgRt~~q~k~rw~~~l~~~~~ 87 (187)
-++||+.++..+|....+..+.
T Consensus 110 h~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 110 HPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred ccccCHHHHHHHHHHHHHhchh
Confidence 3889999999999866555443
No 38
>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=90.89 E-value=0.74 Score=29.03 Aligned_cols=41 Identities=24% Similarity=0.346 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 42 PQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 42 ~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
++++..++.++...|-.|.+||..+ |.|...|+.+....++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 5778888889899999999999999 8999999998876554
No 39
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.88 E-value=0.43 Score=42.91 Aligned_cols=44 Identities=18% Similarity=0.354 Sum_probs=41.4
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
+||.+|-++...+....|..++.||..+|.|...|||..|.+--
T Consensus 367 ~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Ee 410 (507)
T COG5118 367 RWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEE 410 (507)
T ss_pred cccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHh
Confidence 79999999999999999999999999999999999999997543
No 40
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=89.91 E-value=0.26 Score=49.64 Aligned_cols=71 Identities=11% Similarity=0.260 Sum_probs=52.9
Q ss_pred CCCCChHHHHHHHHhhh--CCCCCCCCCCHHHHHHHHHHHHHhC-CChHHHhhh------------CCCCCHHHHHHHHH
Q 038824 15 GLRRCGKSCRLRWTNYL--RPDLKHESFTPQEEEMIIRLHAAIG-SRWSIIAQQ------------LPGRTDNDVKNYWN 79 (187)
Q Consensus 15 g~~Rt~~qCr~RW~~~L--~P~l~k~~wT~eED~~Ll~~v~~~G-~~W~~Ia~~------------lpgRt~~q~k~rw~ 79 (187)
.+.+--.+|+.-|...- -+.-++..||.|||..|+-++..|| .+|..|... +..||+..+..|..
T Consensus 902 ~~~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~ 981 (1033)
T PLN03142 902 AIGKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCD 981 (1033)
T ss_pred HHHHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHH
Confidence 44444456666663311 1445566799999999999999999 789998533 24799999999999
Q ss_pred HHhhhh
Q 038824 80 TKLRKK 85 (187)
Q Consensus 80 ~~l~~~ 85 (187)
++++-.
T Consensus 982 ~l~~~~ 987 (1033)
T PLN03142 982 TLIRLI 987 (1033)
T ss_pred HHHHHH
Confidence 998764
No 41
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=83.39 E-value=2.9 Score=38.55 Aligned_cols=47 Identities=17% Similarity=0.313 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 37 HESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
...||.||--++-+....||....+|.+.||.|+-..+..+|....+
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 34799999999999999999999999999999999999988865443
No 42
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=82.16 E-value=1.1 Score=31.14 Aligned_cols=18 Identities=33% Similarity=0.864 Sum_probs=11.9
Q ss_pred ccCCCCChHHHHHHHHhh
Q 038824 13 KKGLRRCGKSCRLRWTNY 30 (187)
Q Consensus 13 ~~g~~Rt~~qCr~RW~~~ 30 (187)
..|..|++.||+.+|.+.
T Consensus 46 ~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 46 EHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp HHC----HHHHHHHHHHH
T ss_pred HcCCCCCHHHHHHHHHHH
Confidence 349999999999999884
No 43
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=79.39 E-value=4.2 Score=39.64 Aligned_cols=57 Identities=12% Similarity=0.193 Sum_probs=47.2
Q ss_pred HHHhhhCCCC---CCCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 26 RWTNYLRPDL---KHESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 26 RW~~~L~P~l---~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
||..|+--+. -...||+.|-.+.-++...|...+-.|++.++++|-.||-.+|.+..
T Consensus 605 ~~~~h~la~Y~Y~gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWK 664 (907)
T KOG4167|consen 605 RLKCHPLANYHYAGSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWK 664 (907)
T ss_pred CccccccceeeecCcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHH
Confidence 5666554432 13479999999999999999999999999999999999999887654
No 44
>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=79.14 E-value=6.3 Score=24.36 Aligned_cols=41 Identities=29% Similarity=0.387 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 43 QEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 43 eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
+++..++.+.-..|..+.+||..| |-|...|+.+....+++
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 455666666555567899999998 77999999888776654
No 45
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=75.77 E-value=7.7 Score=23.68 Aligned_cols=38 Identities=21% Similarity=0.368 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHH
Q 038824 43 QEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTK 81 (187)
Q Consensus 43 eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~ 81 (187)
+=|..|+.+...-| -.|..||..+ |=|...|..|+..+
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 44788888888888 5699999998 88999999998643
No 46
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=72.28 E-value=7.9 Score=29.89 Aligned_cols=45 Identities=9% Similarity=0.118 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 038824 43 QEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTE 88 (187)
Q Consensus 43 eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~ 88 (187)
+-|.+|+.+..+-| ..|++||+.+ |-+...|+.|+..+....+.+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 56888888888888 6799999998 999999999999887776554
No 47
>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=71.67 E-value=17 Score=32.09 Aligned_cols=47 Identities=21% Similarity=0.523 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHh-CCC---hHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 38 ESFTPQEEEMIIRLHAAI-GSR---WSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 38 ~~wT~eED~~Ll~~v~~~-G~~---W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
..||.-|...|+.+.... |.. -..|++.++||+..+|++.-+.+..+
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~r 72 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGR 72 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHH
Confidence 479999999999887665 543 57899999999999999976655444
No 48
>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=70.35 E-value=12 Score=27.89 Aligned_cols=39 Identities=23% Similarity=0.261 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 44 EEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 44 ED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
++..++.+.-..|..+.+||..+ |.+...|+.+....++
T Consensus 117 ~~r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 155 (161)
T TIGR02985 117 QCRKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALK 155 (161)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 44445555445578899999987 8899999999987554
No 49
>smart00595 MADF subfamily of SANT domain.
Probab=70.17 E-value=4.7 Score=27.87 Aligned_cols=24 Identities=25% Similarity=0.484 Sum_probs=20.8
Q ss_pred hHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 59 WSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 59 W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
|..||..|.. |..+|+.+|.++-.
T Consensus 30 W~~Ia~~l~~-~~~~~~~kw~~LR~ 53 (89)
T smart00595 30 WEEIAEELGL-SVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHHCc-CHHHHHHHHHHHHH
Confidence 9999999954 99999999987644
No 50
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=68.82 E-value=7 Score=31.03 Aligned_cols=40 Identities=35% Similarity=0.303 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHH
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWN 79 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~ 79 (187)
.||.|+.++|.+|. .-|..=++||..|.|.|.+.|--+-+
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhh
Confidence 49999999999886 66788899999998899988876554
No 51
>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=68.42 E-value=15 Score=25.54 Aligned_cols=41 Identities=15% Similarity=0.257 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhCC--------ChHHHhhhCCC---CC--HHHHHHHHHHHhhh
Q 038824 44 EEEMIIRLHAAIGS--------RWSIIAQQLPG---RT--DNDVKNYWNTKLRK 84 (187)
Q Consensus 44 ED~~Ll~~v~~~G~--------~W~~Ia~~lpg---Rt--~~q~k~rw~~~l~~ 84 (187)
+=..|-.+|...|+ .|..||..|.. -+ +.+++..|..+|.+
T Consensus 37 DL~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 37 DLYKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp SHHHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred cHHHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 34567778888873 59999999822 22 36899999988764
No 52
>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=65.72 E-value=6.9 Score=27.59 Aligned_cols=17 Identities=35% Similarity=0.653 Sum_probs=9.9
Q ss_pred CCCCCCCCCHHHHHHHH
Q 038824 33 PDLKHESFTPQEEEMII 49 (187)
Q Consensus 33 P~l~k~~wT~eED~~Ll 49 (187)
|.-..|-||+|+|..|.
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 55567889999999994
No 53
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=65.50 E-value=7.3 Score=36.99 Aligned_cols=49 Identities=20% Similarity=0.426 Sum_probs=44.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHH
Q 038824 33 PDLKHESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTK 81 (187)
Q Consensus 33 P~l~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~ 81 (187)
+....++||.+|-++-.......|...+.|+..+|+|+..|||..+..-
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~e 453 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKE 453 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhh
Confidence 3455679999999999999999999999999999999999999988643
No 54
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=64.86 E-value=18 Score=25.48 Aligned_cols=41 Identities=20% Similarity=0.270 Sum_probs=30.9
Q ss_pred HHHHHHHHHHhCC--------ChHHHhhhCCC-----CCHHHHHHHHHHHhhhh
Q 038824 45 EEMIIRLHAAIGS--------RWSIIAQQLPG-----RTDNDVKNYWNTKLRKK 85 (187)
Q Consensus 45 D~~Ll~~v~~~G~--------~W~~Ia~~lpg-----Rt~~q~k~rw~~~l~~~ 85 (187)
=..|..+|..+|+ .|..||..|.- ..+.+++..|..+|.+-
T Consensus 34 L~~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 34 LYRLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 4567778888774 59999999822 24678999999988763
No 55
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=63.40 E-value=11 Score=29.47 Aligned_cols=46 Identities=9% Similarity=0.045 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 038824 42 PQEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTE 88 (187)
Q Consensus 42 ~eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~ 88 (187)
.+-|.+|+.+...-| -.|++||+.+ |=+...|+.|+..+.+..+.+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeE
Confidence 456888888877777 6799999998 899999999999888876554
No 56
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=63.13 E-value=18 Score=29.86 Aligned_cols=45 Identities=11% Similarity=0.230 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhC---CCCCHHHHHHHHHHHhhh
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQL---PGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~l---pgRt~~q~k~rw~~~l~~ 84 (187)
.|++++|.+|+..|. .|+.-..|+.-+ -.-|-..|..||+.+|.-
T Consensus 1 rW~~~DDl~Li~av~-~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd 48 (199)
T PF13325_consen 1 RWKPEDDLLLINAVE-QTNDLESVHLGVKFSCKFTLQEIEERWYALLYD 48 (199)
T ss_pred CCCchhhHHHHHHHH-HhcCHHHHHccCCcCCcCcHHHHHHHHHHHHcC
Confidence 499999999998865 455666666643 557889999999998863
No 57
>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=61.42 E-value=14 Score=26.07 Aligned_cols=30 Identities=20% Similarity=0.511 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhCCChHHHhhhCCCCCHHHHH
Q 038824 45 EEMIIRLHAAIGSRWSIIAQQLPGRTDNDVK 75 (187)
Q Consensus 45 D~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k 75 (187)
|+.|..+....|..|..+|.+| |=|..+|.
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~ 31 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIY 31 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 5678888999999999999998 55665543
No 58
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=60.95 E-value=27 Score=26.74 Aligned_cols=34 Identities=26% Similarity=0.213 Sum_probs=24.7
Q ss_pred HHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 49 IRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 49 l~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+.+....|-.-.+||..| |.+...|+.+....++
T Consensus 127 l~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~ 160 (173)
T PRK09645 127 LVRSYYRGWSTAQIAADL-GIPEGTVKSRLHYALR 160 (173)
T ss_pred HHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 334444567789999998 8889999998875443
No 59
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=58.42 E-value=29 Score=33.38 Aligned_cols=49 Identities=20% Similarity=0.414 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhhhC----------CCCCHHHHHHHHHHHhhhh
Q 038824 37 HESFTPQEEEMIIRLHAAIGSRWSIIAQQL----------PGRTDNDVKNYWNTKLRKK 85 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~l----------pgRt~~q~k~rw~~~l~~~ 85 (187)
|..||-.|+.-.....+++|..+..|-.++ .-.|-.|++.+|...+++.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m 146 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRM 146 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHH
Confidence 668999999999999999999998884332 2245568999888877764
No 60
>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=55.31 E-value=22 Score=25.02 Aligned_cols=31 Identities=13% Similarity=0.381 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhCCChHHHhhhCCCCCHHHHHH
Q 038824 45 EEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 45 D~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
|..|..+....|..|..+|..| |=+...|.+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 6678888899999999999998 555554443
No 61
>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=55.06 E-value=14 Score=24.74 Aligned_cols=26 Identities=27% Similarity=0.484 Sum_probs=20.9
Q ss_pred ChHHHhhhCC-CCCHHHHHHHHHHHhh
Q 038824 58 RWSIIAQQLP-GRTDNDVKNYWNTKLR 83 (187)
Q Consensus 58 ~W~~Ia~~lp-gRt~~q~k~rw~~~l~ 83 (187)
-|..||..|. +-+..+|+.+|.++-.
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHH
Confidence 3999999995 3578899999987554
No 62
>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=53.69 E-value=32 Score=24.74 Aligned_cols=39 Identities=26% Similarity=0.274 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 45 EEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 45 D~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
+..++.++-..|..+.+||+.+ |-+...|+++....+++
T Consensus 115 ~~~ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 115 EREVLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHHHHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3344444445678899999998 56888899888776543
No 63
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=53.12 E-value=28 Score=27.51 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 42 PQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 42 ~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
.++...++.+....|-.+.+||..| |-+...|+.+|...-
T Consensus 137 ~~~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 137 DPRQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred CHHHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3445556666666788999999999 999999999997553
No 64
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=50.01 E-value=39 Score=25.60 Aligned_cols=34 Identities=21% Similarity=0.186 Sum_probs=25.1
Q ss_pred HHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 49 IRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 49 l~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+.+.-..|-.+.+||..| |.+...|+.+....++
T Consensus 137 l~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~ 170 (182)
T PRK09652 137 ITLREIEGLSYEEIAEIM-GCPIGTVRSRIFRARE 170 (182)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334444577899999998 7899999888765443
No 65
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=48.63 E-value=41 Score=25.44 Aligned_cols=32 Identities=25% Similarity=0.228 Sum_probs=23.9
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+....|-...+||..| |-+...|+++.....+
T Consensus 136 l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~ 167 (179)
T PRK11924 136 LRYVEGLSYREIAEIL-GVPVGTVKSRLRRARQ 167 (179)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3344567899999998 7888899988775443
No 66
>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=47.80 E-value=24 Score=24.44 Aligned_cols=31 Identities=23% Similarity=0.561 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhCCChHHHhhhCCCCCHHHHHH
Q 038824 45 EEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 45 D~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
|..|..+....|..|.++|+.| |=+..+|..
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~~ 34 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDIDL 34 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHHH
Confidence 5567788889999999999998 555554443
No 67
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=47.32 E-value=61 Score=25.15 Aligned_cols=38 Identities=24% Similarity=0.137 Sum_probs=29.0
Q ss_pred HHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 038824 50 RLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTE 88 (187)
Q Consensus 50 ~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~ 88 (187)
.++...|-...+||..| |-+...|+.|....+..-+..
T Consensus 137 ~L~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 137 LMATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHh
Confidence 34445577899999998 889999999998777665443
No 68
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=46.93 E-value=47 Score=26.19 Aligned_cols=36 Identities=17% Similarity=0.077 Sum_probs=26.5
Q ss_pred HHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 46 EMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 46 ~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
..++.+.-..|-...+||..| |-+...|++|+....
T Consensus 140 r~i~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar 175 (192)
T PRK09643 140 RAALVAVDMQGYSVADAARML-GVAEGTVKSRCARGR 175 (192)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 334444445577899999998 889999999985443
No 69
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=46.91 E-value=45 Score=25.66 Aligned_cols=32 Identities=16% Similarity=-0.004 Sum_probs=23.8
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+....|..+.+||..| |-|...|+++.....+
T Consensus 147 l~~~~~~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T PRK09641 147 LKYIEDLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred hHHhhCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3334567799999998 8889999888765443
No 70
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=46.54 E-value=27 Score=23.59 Aligned_cols=23 Identities=17% Similarity=0.459 Sum_probs=18.7
Q ss_pred HHHHHHHHHHhCCChHHHhhhCCCC
Q 038824 45 EEMIIRLHAAIGSRWSIIAQQLPGR 69 (187)
Q Consensus 45 D~~Ll~~v~~~G~~W~~Ia~~lpgR 69 (187)
+.+|-++|..|| |...+..+.-|
T Consensus 12 e~il~~Lv~~yG--W~~L~~~i~i~ 34 (64)
T PF09905_consen 12 ETILTELVEHYG--WEELGERININ 34 (64)
T ss_dssp HHHHHHHHHHT---HHHHHHHTTSS
T ss_pred HHHHHHHHHHhC--HHHHHhhcccc
Confidence 578899999998 99999988554
No 71
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=45.59 E-value=55 Score=23.11 Aligned_cols=45 Identities=11% Similarity=0.099 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 038824 43 QEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTE 88 (187)
Q Consensus 43 eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~ 88 (187)
+.|..|+.+....| -.+..||+.+ |-+...|+.+...+....+.+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 56888888888877 5799999998 889999999998887765544
No 72
>PRK04217 hypothetical protein; Provisional
Probab=45.52 E-value=98 Score=22.98 Aligned_cols=43 Identities=16% Similarity=0.090 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.-|.+| ..++.+....|-...+||+.+ |-+...|+.++....+
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArk 84 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARK 84 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 355555 577777777788999999998 8999999999876544
No 73
>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=44.91 E-value=34 Score=23.96 Aligned_cols=31 Identities=23% Similarity=0.501 Sum_probs=24.6
Q ss_pred HHHHHHHHHHhCCChHHHhhhCCCCCHHHHHH
Q 038824 45 EEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 45 D~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
|..|-.+....|..|..+|+.| |=++..|.+
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 4567778899999999999998 566666554
No 74
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=43.63 E-value=65 Score=24.06 Aligned_cols=31 Identities=13% Similarity=0.040 Sum_probs=23.8
Q ss_pred HHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 52 HAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 52 v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+...|-.-.+||..| |-+...|+.+....++
T Consensus 118 ~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~ 148 (161)
T PRK09047 118 RYWEDMDVAETAAAM-GCSEGSVKTHCSRATH 148 (161)
T ss_pred HHHhcCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334466789999998 8899999998875544
No 75
>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=43.48 E-value=9.4 Score=30.43 Aligned_cols=20 Identities=35% Similarity=0.969 Sum_probs=17.5
Q ss_pred cCCCCChHHHHHHHHhhhCC
Q 038824 14 KGLRRCGKSCRLRWTNYLRP 33 (187)
Q Consensus 14 ~g~~Rt~~qCr~RW~~~L~P 33 (187)
.-++||+.-|.-||.-+++.
T Consensus 38 ~~L~RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 38 RALNRTAAACGFRWNAYVRK 57 (161)
T ss_pred HHHcccHHHhcchHHHHHHH
Confidence 35789999999999999883
No 76
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=42.55 E-value=75 Score=24.87 Aligned_cols=30 Identities=17% Similarity=0.184 Sum_probs=23.1
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHH
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTK 81 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~ 81 (187)
+....|-.-.+||..| |-+...|+.+....
T Consensus 147 L~~~~g~s~~EIA~~l-gis~~tVk~~l~Ra 176 (195)
T PRK12532 147 LKEILGFSSDEIQQMC-GISTSNYHTIMHRA 176 (195)
T ss_pred hHHHhCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 3444567789999998 88899999888753
No 77
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=41.81 E-value=31 Score=20.95 Aligned_cols=36 Identities=33% Similarity=0.457 Sum_probs=18.1
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHH
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
.+|.+|-..|..++ .-|..=.+||+.| ||+...|.+
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHH
Confidence 57888888877664 5777889999998 888877765
No 78
>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=41.34 E-value=72 Score=18.48 Aligned_cols=39 Identities=23% Similarity=0.325 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHH
Q 038824 40 FTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNT 80 (187)
Q Consensus 40 wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~ 80 (187)
.+++ +..++.++-..|-.+..||..+ |-+...|+.+...
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~ 49 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHR 49 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 4444 4555555556678899999997 6677777665544
No 79
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=40.88 E-value=69 Score=24.90 Aligned_cols=33 Identities=21% Similarity=0.256 Sum_probs=24.7
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
++...|....+||..| |-+...|+.+....+++
T Consensus 150 l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 150 LRVVVGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4344567899999998 88889999888755543
No 80
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=40.72 E-value=72 Score=24.43 Aligned_cols=37 Identities=24% Similarity=0.315 Sum_probs=27.3
Q ss_pred HHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 47 MIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 47 ~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
.++.+....|-...+||..| |-+...|+.+-...++.
T Consensus 126 ~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 126 AAFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33444445577899999998 88999999988766554
No 81
>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=40.37 E-value=50 Score=25.47 Aligned_cols=28 Identities=14% Similarity=0.054 Sum_probs=21.9
Q ss_pred hCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 55 IGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 55 ~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.|-...+||..| |-|...|+++....++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~ 180 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRARE 180 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 456789999998 7788999998865544
No 82
>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=39.95 E-value=68 Score=24.38 Aligned_cols=32 Identities=22% Similarity=0.300 Sum_probs=23.4
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
++-..|....+||..| |-|...|+++....++
T Consensus 130 l~~~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~ 161 (169)
T TIGR02954 130 LRYYHDLTIKEIAEVM-NKPEGTVKTYLHRALK 161 (169)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3334466789999988 6788899988875544
No 83
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=39.85 E-value=90 Score=24.17 Aligned_cols=31 Identities=10% Similarity=-0.047 Sum_probs=21.7
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
+....|-...+||..| |-+...|+.+.+..+
T Consensus 139 l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar 169 (186)
T PRK05602 139 LQYYQGLSNIEAAAVM-DISVDALESLLARGR 169 (186)
T ss_pred HHHhcCCCHHHHHHHh-CcCHHHHHHHHHHHH
Confidence 3334466788899887 778888888776443
No 84
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=39.65 E-value=91 Score=24.04 Aligned_cols=37 Identities=14% Similarity=0.146 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 47 MIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 47 ~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
.++.+....|....+||..| |-+...|+.+....+++
T Consensus 138 ~v~~l~~~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 138 DVVQSISVEGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred HHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 33334444577889999998 88889999988765543
No 85
>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=39.03 E-value=49 Score=23.14 Aligned_cols=32 Identities=19% Similarity=0.506 Sum_probs=22.9
Q ss_pred CCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHH
Q 038824 40 FTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVK 75 (187)
Q Consensus 40 wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k 75 (187)
-|.++=+. +....|..|..+|..| |=++.+|.
T Consensus 5 ~t~~~l~~---ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 5 VTGEQITV---FANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred CCHHHHHH---HHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 45554444 4588899999999998 66776663
No 86
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=38.61 E-value=74 Score=24.85 Aligned_cols=35 Identities=23% Similarity=0.164 Sum_probs=25.5
Q ss_pred HHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 48 IIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 48 Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
++.+.-..|-...+||..| |-+...|+.+....++
T Consensus 114 i~~l~~~~g~~~~EIA~~l-gis~~tV~~~l~Rar~ 148 (181)
T PRK09637 114 ALRLTELEGLSQKEIAEKL-GLSLSGAKSRVQRGRV 148 (181)
T ss_pred HHHHHHhcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3334445577899999998 8888899998865443
No 87
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=38.36 E-value=69 Score=24.94 Aligned_cols=29 Identities=14% Similarity=-0.010 Sum_probs=22.0
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|-...+||..| |-+...|+.+....++
T Consensus 152 ~~g~s~~eIA~~l-gis~~tv~~~l~Rar~ 180 (193)
T PRK11923 152 FDGLSYEDIASVM-QCPVGTVRSRIFRARE 180 (193)
T ss_pred hcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3456789999998 7788999998875443
No 88
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=38.30 E-value=78 Score=24.82 Aligned_cols=31 Identities=6% Similarity=0.012 Sum_probs=23.9
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
+....|-...+||..| |-+...|+.|.....
T Consensus 145 L~~~~g~s~~EIA~~l-gis~~tVk~~l~RAr 175 (189)
T PRK12530 145 MREYLELSSEQICQEC-DISTSNLHVLLYRAR 175 (189)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3334467799999998 899999999876544
No 89
>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=38.15 E-value=83 Score=24.68 Aligned_cols=35 Identities=11% Similarity=0.126 Sum_probs=25.7
Q ss_pred HHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 48 IIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 48 Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
++.++...|....+||..| |-+...|+.|....++
T Consensus 139 v~~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~ 173 (188)
T TIGR02943 139 VFMMREVLGFESDEICQEL-EISTSNCHVLLYRARL 173 (188)
T ss_pred HHHHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3334444567789999998 8899999988775544
No 90
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=38.00 E-value=87 Score=23.50 Aligned_cols=32 Identities=16% Similarity=-0.034 Sum_probs=23.8
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+....|-.-.+||..| |-+...|+++....++
T Consensus 117 l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 117 AHYLEEKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred HHHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3344566789999998 8899999998765443
No 91
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=37.64 E-value=70 Score=24.58 Aligned_cols=28 Identities=14% Similarity=-0.024 Sum_probs=21.4
Q ss_pred hCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 55 IGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 55 ~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.|..-.+||..| |-+...|+++.+..++
T Consensus 151 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 151 EDLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 356789999988 7788899988765444
No 92
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=37.62 E-value=84 Score=24.46 Aligned_cols=32 Identities=13% Similarity=0.022 Sum_probs=24.3
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+....|-...+||..| |-+...|+++....++
T Consensus 142 l~~~~~~s~~eIA~~l-gis~~tV~~~l~Rar~ 173 (189)
T PRK12515 142 LVYYHEKSVEEVGEIV-GIPESTVKTRMFYARK 173 (189)
T ss_pred HHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3344567899999998 7799999998875443
No 93
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=37.47 E-value=88 Score=24.52 Aligned_cols=47 Identities=17% Similarity=0.174 Sum_probs=37.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChHHHhhhCC----CCCHHHHHHHHHHHh
Q 038824 36 KHESFTPQEEEMIIRLHAAIGSRWSIIAQQLP----GRTDNDVKNYWNTKL 82 (187)
Q Consensus 36 ~k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lp----gRt~~q~k~rw~~~l 82 (187)
....-|..|..-|..|+..||..+...|.-.. -.|..||+.+...+.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 34568999999999999999999998887542 478999988776543
No 94
>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=37.45 E-value=46 Score=23.46 Aligned_cols=29 Identities=24% Similarity=0.571 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCChHHHhhhCCCCCHHHHHH
Q 038824 47 MIIRLHAAIGSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 47 ~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
.|-.+....|..|..+|+.| |=++.+|..
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 34455588899999999998 667777665
No 95
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=37.43 E-value=76 Score=20.28 Aligned_cols=34 Identities=21% Similarity=0.448 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHH
Q 038824 43 QEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNY 77 (187)
Q Consensus 43 eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~r 77 (187)
++|+-.+.+..+.|-.-.+||+.+ ||+-+.|+++
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 455566677788999999999998 8998877764
No 96
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=36.90 E-value=87 Score=24.58 Aligned_cols=32 Identities=9% Similarity=-0.074 Sum_probs=23.6
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+....|-...+||..| |-+...|+.|....++
T Consensus 152 l~~~eg~s~~EIA~~l-gis~~tVk~rl~ra~~ 183 (194)
T PRK12531 152 AVYLEELPHQQVAEMF-DIPLGTVKSRLRLAVE 183 (194)
T ss_pred HHHHcCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 3334466789999988 8888999988765544
No 97
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=36.75 E-value=92 Score=24.72 Aligned_cols=28 Identities=14% Similarity=-0.005 Sum_probs=21.9
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKL 82 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l 82 (187)
..|-.-.+||..| |.+...|+.|....+
T Consensus 153 ~eg~s~~EIA~~l-gis~~tVk~~l~RAr 180 (201)
T PRK12545 153 FLDFEIDDICTEL-TLTANHCSVLLYRAR 180 (201)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3456789999998 889999999876433
No 98
>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=36.39 E-value=52 Score=23.19 Aligned_cols=22 Identities=23% Similarity=0.525 Sum_probs=19.1
Q ss_pred HHHHHHHHHHhCCChHHHhhhC
Q 038824 45 EEMIIRLHAAIGSRWSIIAQQL 66 (187)
Q Consensus 45 D~~Ll~~v~~~G~~W~~Ia~~l 66 (187)
|-.|-.+....|..|..+|..|
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L 25 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL 25 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc
Confidence 5567778899999999999998
No 99
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=36.01 E-value=1e+02 Score=23.16 Aligned_cols=32 Identities=22% Similarity=0.236 Sum_probs=22.8
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+....|-.-.+||..| |-+...|+.|....++
T Consensus 116 l~~~~~~s~~eIA~~l-gis~~tv~~~l~ra~~ 147 (159)
T PRK12527 116 LRKLEGLSHQQIAEHL-GISRSLVEKHIVNAMK 147 (159)
T ss_pred HHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3334455678999988 8888899988765443
No 100
>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=35.77 E-value=52 Score=22.36 Aligned_cols=30 Identities=23% Similarity=0.494 Sum_probs=21.4
Q ss_pred HHHHHHHHHHH-hCCChHHHhhhCCCCCHHHH
Q 038824 44 EEEMIIRLHAA-IGSRWSIIAQQLPGRTDNDV 74 (187)
Q Consensus 44 ED~~Ll~~v~~-~G~~W~~Ia~~lpgRt~~q~ 74 (187)
-++.|..++.. .|..|..+|+.|.. ++.+|
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~Lg~-~~~~i 34 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKLGL-SEADI 34 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHcCC-CHHHH
Confidence 34566667777 89999999999843 44443
No 101
>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=35.76 E-value=1.3e+02 Score=22.24 Aligned_cols=46 Identities=20% Similarity=0.370 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHHHHh------------CC-----------------C--hHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 39 SFTPQEEEMIIRLHAAI------------GS-----------------R--WSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~------------G~-----------------~--W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
.||++||..|...|..+ |. . ....+...|..|..+=|.||...+..
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 48999999999988544 11 1 45667778999999988888766654
No 102
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=35.31 E-value=17 Score=29.18 Aligned_cols=18 Identities=33% Similarity=0.940 Sum_probs=15.9
Q ss_pred CCCCChHHHHHHHHhhhC
Q 038824 15 GLRRCGKSCRLRWTNYLR 32 (187)
Q Consensus 15 g~~Rt~~qCr~RW~~~L~ 32 (187)
-++|+...|..||.-+|+
T Consensus 40 ~L~rt~aac~fRwNs~vr 57 (170)
T PRK13923 40 ALKRTAAACGFRWNSVVR 57 (170)
T ss_pred HHhhhHHHHHhHHHHHHH
Confidence 578999999999987776
No 103
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=34.72 E-value=96 Score=23.78 Aligned_cols=28 Identities=14% Similarity=0.214 Sum_probs=22.0
Q ss_pred hCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 55 IGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 55 ~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.|..-.+||..| |.+...|+.+.+..++
T Consensus 144 ~g~s~~eIA~~l-gis~~tV~~~l~Rar~ 171 (179)
T PRK12514 144 EGLSYKELAERH-DVPLNTMRTWLRRSLL 171 (179)
T ss_pred cCCCHHHHHHHH-CCChHHHHHHHHHHHH
Confidence 366789999998 8899999988775544
No 104
>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=33.78 E-value=1.1e+02 Score=18.24 Aligned_cols=33 Identities=21% Similarity=0.214 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHH
Q 038824 43 QEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 43 eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
=|.+.|.+....+|++....|+.| |=+...+..
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~ 37 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHH
Confidence 377888889999999999999987 444444433
No 105
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=33.57 E-value=37 Score=29.71 Aligned_cols=18 Identities=28% Similarity=0.477 Sum_probs=15.9
Q ss_pred cCCCCChHHHHHHHHhhh
Q 038824 14 KGLRRCGKSCRLRWTNYL 31 (187)
Q Consensus 14 ~g~~Rt~~qCr~RW~~~L 31 (187)
.|.-|++.||+.+|.+..
T Consensus 96 ~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 96 LGYPRSPKQCKAKIENLK 113 (345)
T ss_pred hCCCCCHHHHHHHHHHHH
Confidence 499999999999998853
No 106
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=33.40 E-value=90 Score=31.97 Aligned_cols=41 Identities=22% Similarity=0.445 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHH
Q 038824 39 SFTPQEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWN 79 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~ 79 (187)
.||.-+-...+.+...|| ..-..||..+.|.|..+|+.+..
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~ 867 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAK 867 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHH
Confidence 588888888888999999 67999999999999999986543
No 107
>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=33.19 E-value=1.1e+02 Score=23.44 Aligned_cols=29 Identities=24% Similarity=0.247 Sum_probs=22.1
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|-...+||..| |-+...|+.|.+..++
T Consensus 148 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 176 (183)
T TIGR02999 148 FAGLTVEEIAELL-GVSVRTVERDWRFARA 176 (183)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3456789999988 8888899988875443
No 108
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=32.99 E-value=88 Score=28.41 Aligned_cols=42 Identities=12% Similarity=0.231 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhh-CCCCCHHHHHHHHHH
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQ-LPGRTDNDVKNYWNT 80 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~-lpgRt~~q~k~rw~~ 80 (187)
.|+++|=...-+-...||.....|.+. ++-|+-..|-.+|.-
T Consensus 279 ~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred cCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH
Confidence 799999999999999999999999885 799999999988753
No 109
>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=32.55 E-value=2e+02 Score=24.34 Aligned_cols=31 Identities=19% Similarity=0.212 Sum_probs=23.9
Q ss_pred HHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 52 HAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 52 v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
....|-.-.+||..| |.+...|+.|....++
T Consensus 154 ~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 184 (324)
T TIGR02960 154 RDVLGWRAAETAELL-GTSTASVNSALQRARA 184 (324)
T ss_pred HHHhCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334567789999998 8899999998875443
No 110
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=32.38 E-value=89 Score=24.00 Aligned_cols=30 Identities=30% Similarity=0.351 Sum_probs=23.3
Q ss_pred HHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 53 AAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 53 ~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
...|-...+||..| |-+...|+++....+.
T Consensus 132 ~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~ 161 (172)
T PRK09651 132 QLDGLTYSEIAHKL-GVSVSSVKKYVAKATE 161 (172)
T ss_pred hccCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 34456789999998 8899999998876554
No 111
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=32.24 E-value=1.9e+02 Score=24.89 Aligned_cols=30 Identities=13% Similarity=0.090 Sum_probs=23.6
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
..|-.-.+||..| |.+...|+.+....+++
T Consensus 167 ~~g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 196 (339)
T PRK08241 167 VLGWSAAEVAELL-DTSVAAVNSALQRARAT 196 (339)
T ss_pred hhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 4466789999998 89999999988755543
No 112
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=32.23 E-value=1.1e+02 Score=24.01 Aligned_cols=34 Identities=18% Similarity=0.057 Sum_probs=23.7
Q ss_pred HHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 49 IRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 49 l~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+.++...|-.+.+||..| |=+...|+.+-...++
T Consensus 145 ~~L~~~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~ 178 (196)
T PRK12524 145 VVLRHIEGLSNPEIAEVM-EIGVEAVESLTARGKR 178 (196)
T ss_pred HHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 334444567899999998 7788888887764433
No 113
>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=32.05 E-value=58 Score=22.54 Aligned_cols=33 Identities=24% Similarity=0.495 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHH
Q 038824 42 PQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 42 ~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
.||-++|+.. ...|..|...|..| |=++..|.+
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5777888743 25678899999998 666766665
No 114
>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=31.67 E-value=1.2e+02 Score=22.79 Aligned_cols=28 Identities=21% Similarity=0.224 Sum_probs=20.6
Q ss_pred hCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 55 IGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 55 ~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.|-.-.+||..| |-+...|+.+-...++
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAIK 164 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 356778899888 7788888887755443
No 115
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=31.27 E-value=1.3e+02 Score=22.28 Aligned_cols=29 Identities=21% Similarity=0.187 Sum_probs=21.2
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|-...+||..| |-+...|+.+-...++
T Consensus 120 ~~~~s~~EIA~~l-~is~~tV~~~~~ra~~ 148 (154)
T PRK06759 120 FVGKTMGEIALET-EMTYYQVRWIYRQALE 148 (154)
T ss_pred hcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3456678888887 8888888887665443
No 116
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=31.19 E-value=1.3e+02 Score=22.57 Aligned_cols=34 Identities=29% Similarity=0.310 Sum_probs=24.3
Q ss_pred HHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 49 IRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 49 l~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+.+.-..|-...+||..+ |-+...|+.|....++
T Consensus 122 ~~L~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 122 FLLAQVDGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334444567789999988 7888888888765543
No 117
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=30.99 E-value=1.1e+02 Score=23.82 Aligned_cols=30 Identities=10% Similarity=0.073 Sum_probs=23.4
Q ss_pred HHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 53 AAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 53 ~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
...|-.-.+||..| |-+...|+.+....++
T Consensus 143 ~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 172 (185)
T PRK09649 143 QLLGLSYADAAAVC-GCPVGTIRSRVARARD 172 (185)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 34456789999998 8899999998875554
No 118
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=30.84 E-value=2.6e+02 Score=23.58 Aligned_cols=30 Identities=20% Similarity=0.340 Sum_probs=23.6
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
.+|-.-.+||..| |.+...|+.+.+...++
T Consensus 129 ~~g~s~~EIA~~l-g~s~~tVk~~l~RAr~~ 158 (293)
T PRK09636 129 VFGVPFDEIASTL-GRSPAACRQLASRARKH 158 (293)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4466789999998 99999999988755443
No 119
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.16 E-value=1.3e+02 Score=23.22 Aligned_cols=34 Identities=24% Similarity=0.099 Sum_probs=25.4
Q ss_pred HHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 49 IRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 49 l~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+.++...|-...+||..| |.+...|+++-...++
T Consensus 138 ~~l~~~~g~s~~EIA~~l-~is~~tV~~~l~rar~ 171 (181)
T PRK12536 138 IVHVKLEGLSVAETAQLT-GLSESAVKVGIHRGLK 171 (181)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334445577889999998 8899999998765544
No 120
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=29.90 E-value=1.3e+02 Score=23.65 Aligned_cols=37 Identities=22% Similarity=0.135 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 46 EMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 46 ~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..++.|....|-...+||..| |-+...|+.|-...++
T Consensus 122 r~i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~ 158 (187)
T PRK12516 122 REAIILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQ 158 (187)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334444455577899999998 7888999988765443
No 121
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.82 E-value=2e+02 Score=20.67 Aligned_cols=44 Identities=14% Similarity=0.206 Sum_probs=34.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChHHHhhhCCCC-CHHHHHHHHHHH
Q 038824 37 HESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGR-TDNDVKNYWNTK 81 (187)
Q Consensus 37 k~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgR-t~~q~k~rw~~~ 81 (187)
+..||+|.-..+++++..-|..=+.||+.+ |- ..+++...+..+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~~~ 49 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRIQL 49 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHHHH
Confidence 568999999999999999998889999998 54 555555444333
No 122
>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=29.81 E-value=41 Score=24.98 Aligned_cols=27 Identities=19% Similarity=0.080 Sum_probs=21.7
Q ss_pred CCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 56 GSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 56 G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
|-.+.+||..| |-+...|+++.....+
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~ 147 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARK 147 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 45789999998 8889999998876544
No 123
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=29.51 E-value=1.4e+02 Score=22.56 Aligned_cols=33 Identities=18% Similarity=0.066 Sum_probs=23.8
Q ss_pred HHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 50 RLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 50 ~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.+....|-...+||..| |-+...|+.+-...++
T Consensus 122 ~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Rar~ 154 (164)
T PRK12547 122 ILIGASGFSYEDAAAIC-GCAVGTIKSRVSRARN 154 (164)
T ss_pred HHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 34344566789999998 7788888887765544
No 124
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=29.33 E-value=43 Score=22.68 Aligned_cols=19 Identities=16% Similarity=0.450 Sum_probs=15.0
Q ss_pred HHHHHHHHHhCCChHHHhh
Q 038824 46 EMIIRLHAAIGSRWSIIAQ 64 (187)
Q Consensus 46 ~~Ll~~v~~~G~~W~~Ia~ 64 (187)
..|.+|...||++|..|-.
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3566788999988998864
No 125
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=29.27 E-value=1.3e+02 Score=23.18 Aligned_cols=32 Identities=13% Similarity=0.261 Sum_probs=23.8
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+....|-.-.+||..| |-+...|+.+....++
T Consensus 133 l~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar~ 164 (185)
T PRK12542 133 YKVFYNLTYQEISSVM-GITEANVRKQFERARK 164 (185)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3334567789999998 8899999998765443
No 126
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=29.12 E-value=1.4e+02 Score=22.99 Aligned_cols=29 Identities=24% Similarity=0.149 Sum_probs=21.8
Q ss_pred hCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 55 IGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 55 ~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
.|-.-.+||..| |-+...|+.+.+..+++
T Consensus 150 ~~~s~~eIA~~l-gis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 150 QGYTHREAAQLL-GLPLGTLKTRARRALSR 178 (186)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355678999988 88888999887765543
No 127
>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=29.07 E-value=1.3e+02 Score=22.45 Aligned_cols=40 Identities=18% Similarity=0.184 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 44 EEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 44 ED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
++..++.+.-..|-.-.+||..| |-+...|+.+....+++
T Consensus 114 ~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~ 153 (162)
T TIGR02983 114 RQRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALAR 153 (162)
T ss_pred HHHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 44444555555567789999988 88899999988765543
No 128
>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=28.99 E-value=1.4e+02 Score=22.88 Aligned_cols=34 Identities=24% Similarity=0.433 Sum_probs=24.4
Q ss_pred HHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 49 IRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 49 l~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+.++-..|....+||..| |-|...|+.+....++
T Consensus 149 i~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Ra~~ 182 (189)
T TIGR02984 149 ILLRHLEGLSFAEVAERM-DRSEGAVSMLWVRGLA 182 (189)
T ss_pred HHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 334344567789999887 8888888888765544
No 129
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=28.99 E-value=1.7e+02 Score=24.06 Aligned_cols=43 Identities=21% Similarity=0.315 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
..|+.|-+.|.-+.. |....+||..| +-+...|+++-...+++
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkK 175 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 588888877665443 88899999998 88999999977766654
No 130
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=28.97 E-value=2.8e+02 Score=23.34 Aligned_cols=31 Identities=13% Similarity=0.282 Sum_probs=24.3
Q ss_pred HHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 53 AAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 53 ~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
..+|-.-.+||..| |.|...|+.+.+...++
T Consensus 121 ~~~g~s~~EIA~~l-g~s~~tVr~~l~RAr~~ 151 (281)
T TIGR02957 121 EVFDYPYEEIASIV-GKSEANCRQLVSRARRH 151 (281)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34566789999998 79999999988755443
No 131
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=28.55 E-value=1.6e+02 Score=23.85 Aligned_cols=43 Identities=35% Similarity=0.373 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
..|+.|-+.|.-+ ..|-.=.+||..| +.+.+.||+|..++++|
T Consensus 148 ~LT~RE~eVL~ll--a~G~snkeIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 148 LLTPRELEVLRLL--AEGLSNKEIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCHHHHHHHHHH--HCCCCHHHHHHHH-CCCHhHHHHHHHHHHHH
Confidence 6898888887654 3466678999998 89999999999998886
No 132
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.49 E-value=1.4e+02 Score=23.10 Aligned_cols=30 Identities=30% Similarity=0.369 Sum_probs=22.4
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
..|-.-.+||..| |-+...|+.+....+++
T Consensus 147 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 147 VDGCSHAEIAQRL-GAPLGTVKAWIKRSLKA 176 (182)
T ss_pred HcCCCHHHHHHHH-CCChhhHHHHHHHHHHH
Confidence 3456678888888 78888888888766543
No 133
>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=28.35 E-value=1.2e+02 Score=21.17 Aligned_cols=21 Identities=19% Similarity=0.540 Sum_probs=18.7
Q ss_pred HHHHHHHHHhCCChHHHhhhC
Q 038824 46 EMIIRLHAAIGSRWSIIAQQL 66 (187)
Q Consensus 46 ~~Ll~~v~~~G~~W~~Ia~~l 66 (187)
+.|..+....|..|..+|..|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L 23 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL 23 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc
Confidence 457888899999999999998
No 134
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=27.72 E-value=1.5e+02 Score=23.02 Aligned_cols=29 Identities=14% Similarity=-0.079 Sum_probs=22.4
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|-.-.+||..| |-+...|+.|....++
T Consensus 145 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 173 (191)
T PRK12520 145 WLELETEEICQEL-QITATNAWVLLYRARM 173 (191)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3456679999998 8899999998875543
No 135
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=27.19 E-value=1.3e+02 Score=23.64 Aligned_cols=36 Identities=22% Similarity=0.112 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 47 MIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 47 ~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.++.++...|-...+||..| |-+...|+.+-...++
T Consensus 120 ~v~~L~~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~ 155 (188)
T PRK12546 120 EALILVGASGFSYEEAAEMC-GVAVGTVKSRANRARA 155 (188)
T ss_pred HHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 33444455677899999998 7888899988775544
No 136
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=27.03 E-value=1.9e+02 Score=21.72 Aligned_cols=44 Identities=23% Similarity=0.288 Sum_probs=33.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 38 ESFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 38 ~~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
...|+.|-++|.-+.. |-...+||..+ +-+.+.++.|...+.++
T Consensus 136 ~~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHRANLMEK 179 (196)
T ss_pred cCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 4688888877765554 56789999998 67899998888776654
No 137
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=26.88 E-value=1.2e+02 Score=23.27 Aligned_cols=45 Identities=27% Similarity=0.429 Sum_probs=25.2
Q ss_pred HHHHHHHHhhhCCCCCCCCCCHHHHHHHHHHHHHh--CCChHHHhhhCCCCCHHHHHH
Q 038824 21 KSCRLRWTNYLRPDLKHESFTPQEEEMIIRLHAAI--GSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 21 ~qCr~RW~~~L~P~l~k~~wT~eED~~Ll~~v~~~--G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
+.+-++|... ++++ +..++.+.-.- |..|-.||..|. -+..+|+.
T Consensus 72 k~~id~~~~~---------l~de-~k~Ii~lry~~r~~~TW~~IA~~l~-i~erta~r 118 (130)
T PF05263_consen 72 KEAIDRWLET---------LIDE-EKRIIKLRYDRRSRRTWYQIAQKLH-ISERTARR 118 (130)
T ss_pred HHHHHHHHHh---------hCHH-HHHHHHHHHcccccchHHHHHHHhC-ccHHHHHH
Confidence 3455566653 4444 55555554322 366999999883 34444443
No 138
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=26.54 E-value=1.5e+02 Score=22.11 Aligned_cols=45 Identities=13% Similarity=0.116 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHhC-CChHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 038824 43 QEEEMIIRLHAAIG-SRWSIIAQQLPGRTDNDVKNYWNTKLRKKLTE 88 (187)
Q Consensus 43 eED~~Ll~~v~~~G-~~W~~Ia~~lpgRt~~q~k~rw~~~l~~~~~~ 88 (187)
+-|.+|+++...-| -.+..||+.+ |-+...|++|=..+.+..+.+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCcee
Confidence 55778888877777 5699999998 899999999998887766544
No 139
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=24.95 E-value=1.8e+02 Score=22.60 Aligned_cols=29 Identities=24% Similarity=0.374 Sum_probs=21.6
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|-.-.+||..| |.|...|+++-+..++
T Consensus 145 ~~g~s~~EIAe~l-gis~~~V~~~l~Ra~~ 173 (189)
T PRK06811 145 LLGEKIEEIAKKL-GLTRSAIDNRLSRGRK 173 (189)
T ss_pred HccCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3456678899888 8888888888765544
No 140
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=24.91 E-value=2e+02 Score=23.42 Aligned_cols=43 Identities=26% Similarity=0.250 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
..|+.|-+.|. ++.. |....+||+.| +-+...|+.+-...+++
T Consensus 155 ~Lt~rE~~Vl~-l~~~-G~s~~eIA~~L-~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 155 LLTHREKEILN-KLRI-GASNNEIARSL-FISENTVKTHLYNLFKK 197 (216)
T ss_pred CCCHHHHHHHH-HHHc-CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 47876655554 4444 98899999998 78999999988777665
No 141
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=24.45 E-value=87 Score=25.48 Aligned_cols=27 Identities=26% Similarity=0.198 Sum_probs=21.2
Q ss_pred CCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 56 GSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 56 G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
|-...+||..| |-+...|+.+....+.
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~ 191 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARR 191 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 45689999998 8889999998875443
No 142
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=23.68 E-value=1.7e+02 Score=22.54 Aligned_cols=28 Identities=21% Similarity=0.122 Sum_probs=20.4
Q ss_pred hCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 55 IGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 55 ~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.|..-.+||..| |-+...|+.|....++
T Consensus 142 ~g~s~~EIA~~l-~is~~tv~~~l~Ra~~ 169 (179)
T PRK09415 142 EELSIKEIAEVT-GVNENTVKTRLKKAKE 169 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 355678888888 6688888888775554
No 143
>PRK00118 putative DNA-binding protein; Validated
Probab=23.43 E-value=2.3e+02 Score=20.74 Aligned_cols=38 Identities=11% Similarity=0.067 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHH
Q 038824 42 PQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNT 80 (187)
Q Consensus 42 ~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~ 80 (187)
++.+..++.+....|-...+||..+ |-|...|+.+-..
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~R 56 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKR 56 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 4556677777777788999999998 8888888887654
No 144
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=23.35 E-value=2e+02 Score=21.49 Aligned_cols=33 Identities=21% Similarity=0.277 Sum_probs=23.2
Q ss_pred HHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 49 IRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 49 l~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
+.+.- .|-.-.+||..| |-+...|+++....++
T Consensus 121 l~l~~-~g~s~~eIA~~l-gis~~tV~~~i~ra~~ 153 (166)
T PRK09639 121 LLLRF-SGYSYKEIAEAL-GIKESSVGTTLARAKK 153 (166)
T ss_pred HHHHH-cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 33444 566678889887 7888888888765443
No 145
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=23.18 E-value=2e+02 Score=22.44 Aligned_cols=29 Identities=21% Similarity=0.135 Sum_probs=20.4
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|-...+||..| |-+...|+.+-...++
T Consensus 156 ~~~~s~~EIA~~L-gis~~tVk~~l~ra~~ 184 (194)
T PRK09646 156 YGGLTYREVAERL-AVPLGTVKTRMRDGLI 184 (194)
T ss_pred HcCCCHHHHHHHh-CCChHhHHHHHHHHHH
Confidence 3456688999988 6688888887654443
No 146
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=23.13 E-value=57 Score=33.97 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHHHHHHHhC-CChHHHhh
Q 038824 38 ESFTPQEEEMIIRLHAAIG-SRWSIIAQ 64 (187)
Q Consensus 38 ~~wT~eED~~Ll~~v~~~G-~~W~~Ia~ 64 (187)
..|..++|..|+--|-.|| ++|..|-.
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~Ir~ 1161 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAIRL 1161 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHhcc
Confidence 4799999999999999999 89998863
No 147
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=22.97 E-value=94 Score=23.65 Aligned_cols=27 Identities=22% Similarity=-0.001 Sum_probs=20.4
Q ss_pred CCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 56 GSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 56 G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
|-.-.+||..| |-+...|+.+....++
T Consensus 136 g~s~~eIA~~l-g~s~~tv~~~l~Rar~ 162 (175)
T PRK12518 136 DLPQKEIAEIL-NIPVGTVKSRLFYARR 162 (175)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 44578999988 7788889988865443
No 148
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=22.60 E-value=2.1e+02 Score=22.70 Aligned_cols=28 Identities=25% Similarity=0.087 Sum_probs=21.3
Q ss_pred hCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 55 IGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 55 ~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.|-.-.+||..| |.+.+.|+.+....++
T Consensus 168 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~ 195 (206)
T PRK12526 168 QELSQEQLAQQL-NVPLGTVKSRLRLALA 195 (206)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 356678999988 8889999888765444
No 149
>PRK01905 DNA-binding protein Fis; Provisional
Probab=22.58 E-value=2.5e+02 Score=18.95 Aligned_cols=55 Identities=20% Similarity=0.265 Sum_probs=37.1
Q ss_pred ChHHH-HHHHHhhhCCCCCCC---CC----CHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHH
Q 038824 19 CGKSC-RLRWTNYLRPDLKHE---SF----TPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDV 74 (187)
Q Consensus 19 t~~qC-r~RW~~~L~P~l~k~---~w----T~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~ 74 (187)
+-.|| +.+-.+++.+-+-.+ +| ..-|...+.+++..+|.++...|+.+ |=+...+
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL 67 (77)
T PRK01905 5 NIEQCIRDSLDQYFRDLDGSNPHDVYDMVLSCVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTL 67 (77)
T ss_pred cHHHHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHH
Confidence 44566 667777776654432 33 44577788899999999999999887 4344433
No 150
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=22.47 E-value=1.2e+02 Score=18.25 Aligned_cols=33 Identities=30% Similarity=0.358 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHH
Q 038824 42 PQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 42 ~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
.++-..++.++.. |.....||+.+ |-+...|.+
T Consensus 4 ~~~R~~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~ 36 (50)
T PF13384_consen 4 EERRAQIIRLLRE-GWSIREIAKRL-GVSRSTVYR 36 (50)
T ss_dssp ------HHHHHHH-T--HHHHHHHH-TS-HHHHHH
T ss_pred hhHHHHHHHHHHC-CCCHHHHHHHH-CcCHHHHHH
Confidence 3444556677776 98999999998 666666554
No 151
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=22.39 E-value=1.9e+02 Score=20.72 Aligned_cols=18 Identities=11% Similarity=0.218 Sum_probs=15.6
Q ss_pred CCCCHHHHHHHHHHHHHh
Q 038824 38 ESFTPQEEEMIIRLHAAI 55 (187)
Q Consensus 38 ~~wT~eED~~Ll~~v~~~ 55 (187)
.-||+|++-.||+.+..|
T Consensus 5 R~WS~eDEi~iL~gl~~~ 22 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDF 22 (98)
T ss_pred CCCCchHHHHHHHHHHHH
Confidence 359999999999988777
No 152
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.35 E-value=2.2e+02 Score=22.81 Aligned_cols=29 Identities=7% Similarity=-0.065 Sum_probs=22.5
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|-.-.+||..| |-|...|+.|.+..++
T Consensus 162 ~~g~s~~EIAe~l-gis~~tV~~~l~RAr~ 190 (206)
T PRK12544 162 FIELETNEICHAV-DLSVSNLNVLLYRARL 190 (206)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3456679999998 8899999998875444
No 153
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=22.14 E-value=1.7e+02 Score=22.73 Aligned_cols=29 Identities=31% Similarity=0.142 Sum_probs=20.4
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|-.-.+||..| |-+...|+.+-...++
T Consensus 155 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~ 183 (194)
T PRK12519 155 YEGLSQSEIAKRL-GIPLGTVKARARQGLL 183 (194)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3455678888888 6688888887655443
No 154
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=21.97 E-value=47 Score=30.91 Aligned_cols=41 Identities=20% Similarity=0.458 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHH
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNT 80 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~ 80 (187)
.||++|-. +++...-||.+...||..+.-.|+.|++.+|..
T Consensus 472 ~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~~ 512 (534)
T KOG1194|consen 472 GWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYMD 512 (534)
T ss_pred CCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhcC
Confidence 69999988 777888999999999999999999999999953
No 155
>PF09019 EcoRII-C: EcoRII C terminal; InterPro: IPR015109 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents the C-terminal catalytic domain of the type II restriction endonuclease EcoRII, which has a restriction endonuclease-like fold with a central five-stranded mixed beta-sheet surrounded on both sides by alpha-helices. EcoRII cleaves DNA specifically at single 5' CCWGG sites []. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 3HQG_A 1NA6_A 2GB7_C 2FQZ_A 3BM3_B.
Probab=21.65 E-value=20 Score=28.72 Aligned_cols=10 Identities=30% Similarity=0.700 Sum_probs=7.5
Q ss_pred HHHHHHHhhh
Q 038824 22 SCRLRWTNYL 31 (187)
Q Consensus 22 qCr~RW~~~L 31 (187)
-||+||+.+|
T Consensus 97 TlkdRWrQVl 106 (164)
T PF09019_consen 97 TLKDRWRQVL 106 (164)
T ss_dssp S-TTGCGHHH
T ss_pred cHHHHHHHHH
Confidence 4999999876
No 156
>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=21.64 E-value=1.5e+02 Score=20.62 Aligned_cols=28 Identities=18% Similarity=0.531 Sum_probs=20.1
Q ss_pred HHHHHHHhCCChHHHhhhCCCCCHHHHHH
Q 038824 48 IIRLHAAIGSRWSIIAQQLPGRTDNDVKN 76 (187)
Q Consensus 48 Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~ 76 (187)
+--+....|..|..+|+.| |=|+.+|..
T Consensus 5 f~~i~~~lG~~Wk~laR~L-Glse~~Id~ 32 (86)
T cd08306 5 FDVICENVGRDWRKLARKL-GLSETKIES 32 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 3345567799999999998 566665543
No 157
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.39 E-value=2.3e+02 Score=22.59 Aligned_cols=29 Identities=21% Similarity=0.189 Sum_probs=21.4
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|..-.+||..| |-+...|+.+....++
T Consensus 152 ~~g~s~~EIA~~L-gis~~tV~~~l~RArk 180 (203)
T PRK09647 152 IEGLSYEEIAATL-GVKLGTVRSRIHRGRQ 180 (203)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3456678888888 7888888888775543
No 158
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=21.30 E-value=2e+02 Score=23.39 Aligned_cols=33 Identities=15% Similarity=0.188 Sum_probs=23.9
Q ss_pred HHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 51 LHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 51 ~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
++-..|-...+||..| |-+...|+.+....+++
T Consensus 195 l~~~~g~s~~EIA~~l-gis~~tV~~~~~ra~~~ 227 (236)
T PRK06986 195 LYYQEELNLKEIGAVL-GVSESRVSQIHSQAIKR 227 (236)
T ss_pred hHhccCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334456789999988 88888898887655543
No 159
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=21.20 E-value=3.4e+02 Score=21.69 Aligned_cols=43 Identities=21% Similarity=0.165 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHHhCCChHHHhhhCCCCCHHHHHHHHHHHhhh
Q 038824 39 SFTPQEEEMIIRLHAAIGSRWSIIAQQLPGRTDNDVKNYWNTKLRK 84 (187)
Q Consensus 39 ~wT~eED~~Ll~~v~~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~~ 84 (187)
..|+-|-+.|.-++ -|....+||+.| +-+.+.|++|-...++|
T Consensus 137 ~LT~RE~eVL~lla--~G~snkeIA~~L-~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 137 SLSRTESSMLRMWM--AGQGTIQISDQM-NIKAKTVSSHKGNIKRK 179 (207)
T ss_pred cCCHHHHHHHHHHH--cCCCHHHHHHHc-CCCHHHHHHHHHHHHHH
Confidence 48998888776543 466789999999 78999999988777665
No 160
>COG4628 Uncharacterized conserved protein [Function unknown]
Probab=20.82 E-value=95 Score=23.56 Aligned_cols=22 Identities=23% Similarity=0.459 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHhCCChHHHhhhCC
Q 038824 44 EEEMIIRLHAAIGSRWSIIAQQLP 67 (187)
Q Consensus 44 ED~~Ll~~v~~~G~~W~~Ia~~lp 67 (187)
-+.+|-++|..|| |..++..++
T Consensus 20 LE~llt~Lvd~YG--Wd~L~~ri~ 41 (136)
T COG4628 20 LETLLTELVDFYG--WDGLATRIR 41 (136)
T ss_pred HHHHHHHHHHHhC--hHHHHhhce
Confidence 4678899999999 988888763
No 161
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=20.73 E-value=95 Score=23.65 Aligned_cols=29 Identities=21% Similarity=0.274 Sum_probs=20.8
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
.+|-...+||..| |-+...|+.+....+.
T Consensus 140 ~~g~s~~eIA~~l-~is~~~V~~~l~ra~~ 168 (176)
T PRK09638 140 YYGYTYEEIAKML-NIPEGTVKSRVHHGIK 168 (176)
T ss_pred hcCCCHHHHHHHH-CCChhHHHHHHHHHHH
Confidence 3466789999988 6688888877765443
No 162
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.45 E-value=1.9e+02 Score=23.78 Aligned_cols=29 Identities=14% Similarity=0.018 Sum_probs=22.1
Q ss_pred HhCCChHHHhhhCCCCCHHHHHHHHHHHhh
Q 038824 54 AIGSRWSIIAQQLPGRTDNDVKNYWNTKLR 83 (187)
Q Consensus 54 ~~G~~W~~Ia~~lpgRt~~q~k~rw~~~l~ 83 (187)
..|-.-.+||..| |-+...|+.+.+..++
T Consensus 185 ~eg~s~~EIA~~L-gis~~tVk~~l~RAr~ 213 (233)
T PRK12538 185 HENMSNGEIAEVM-DTTVAAVESLLKRGRQ 213 (233)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3356679999998 8889999888775544
No 163
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=20.34 E-value=2.7e+02 Score=20.54 Aligned_cols=24 Identities=38% Similarity=0.464 Sum_probs=15.5
Q ss_pred CCChHHHhhhCCCCCHHHHHHHHHH
Q 038824 56 GSRWSIIAQQLPGRTDNDVKNYWNT 80 (187)
Q Consensus 56 G~~W~~Ia~~lpgRt~~q~k~rw~~ 80 (187)
|-.=.+||..| |=+...|+.+...
T Consensus 127 g~~~~eIA~~l-~is~~tv~~~l~R 150 (159)
T TIGR02989 127 GVSLTALAEQL-GRTVNAVYKALSR 150 (159)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHH
Confidence 45567777776 6666777766543
Done!