Query 034546
Match_columns 91
No_of_seqs 136 out of 1016
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 03:58:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034546.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034546hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0048 Transcription factor, 100.0 6.8E-29 1.5E-33 183.0 7.3 74 3-81 42-115 (238)
2 PLN03212 Transcription repress 99.9 1.4E-27 3.1E-32 178.2 5.4 80 2-86 57-136 (249)
3 PLN03091 hypothetical protein; 99.9 1.9E-25 4.1E-30 177.3 6.5 81 2-87 46-126 (459)
4 PF00249 Myb_DNA-binding: Myb- 99.6 7.1E-16 1.5E-20 88.6 5.2 46 28-73 1-48 (48)
5 smart00717 SANT SANT SWI3, AD 99.5 3.4E-14 7.5E-19 78.7 5.8 47 28-74 1-48 (49)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.5 8.3E-14 1.8E-18 82.6 5.2 45 31-75 1-45 (60)
7 PLN03212 Transcription repress 99.5 1.4E-13 3.1E-18 103.1 6.3 68 12-79 9-78 (249)
8 cd00167 SANT 'SWI3, ADA2, N-Co 99.4 4.3E-13 9.3E-18 73.4 5.8 43 30-72 1-44 (45)
9 KOG0048 Transcription factor, 99.3 6.9E-13 1.5E-17 97.9 3.9 55 24-78 5-61 (238)
10 PLN03091 hypothetical protein; 99.2 2.2E-11 4.7E-16 97.5 5.0 61 18-78 4-66 (459)
11 KOG0049 Transcription factor, 99.1 6.8E-11 1.5E-15 98.7 6.0 72 1-77 338-410 (939)
12 COG5147 REB1 Myb superfamily p 99.0 3.8E-10 8.3E-15 91.8 4.8 70 4-78 53-122 (512)
13 KOG0049 Transcription factor, 98.7 1.9E-08 4.2E-13 84.3 4.2 62 1-67 390-452 (939)
14 KOG0050 mRNA splicing protein 98.7 1.2E-08 2.6E-13 83.5 2.7 69 4-78 40-108 (617)
15 PF13921 Myb_DNA-bind_6: Myb-l 98.4 1.4E-07 3E-12 55.6 2.1 34 1-39 27-60 (60)
16 KOG0051 RNA polymerase I termi 98.0 1.1E-05 2.5E-10 67.0 4.8 49 27-76 383-431 (607)
17 COG5147 REB1 Myb superfamily p 97.9 6E-06 1.3E-10 67.6 2.2 55 25-79 17-72 (512)
18 PF08914 Myb_DNA-bind_2: Rap1 97.8 2.6E-05 5.7E-10 47.9 3.8 48 29-76 3-60 (65)
19 KOG0050 mRNA splicing protein 97.8 3.2E-05 7E-10 63.7 4.4 55 25-79 4-59 (617)
20 KOG0457 Histone acetyltransfer 97.6 0.00015 3.2E-09 58.5 6.0 46 27-72 71-117 (438)
21 TIGR01557 myb_SHAQKYF myb-like 97.5 0.00035 7.6E-09 41.8 5.5 44 29-72 4-53 (57)
22 TIGR02894 DNA_bind_RsfA transc 97.5 0.00018 4E-09 51.3 4.9 52 28-80 4-62 (161)
23 KOG0051 RNA polymerase I termi 97.5 0.00013 2.9E-09 60.8 4.1 78 1-81 412-515 (607)
24 PF13837 Myb_DNA-bind_4: Myb/S 97.3 0.00036 7.9E-09 43.3 3.6 47 29-75 2-66 (90)
25 PRK13923 putative spore coat p 96.7 0.0053 1.1E-07 44.2 5.5 52 27-79 4-62 (170)
26 KOG1279 Chromatin remodeling f 96.6 0.0041 8.8E-08 51.2 5.3 48 25-72 250-297 (506)
27 COG5114 Histone acetyltransfer 96.6 0.0041 8.9E-08 49.3 5.0 51 23-73 58-109 (432)
28 COG5259 RSC8 RSC chromatin rem 96.6 0.0033 7.2E-08 51.5 4.6 43 29-71 280-322 (531)
29 PF13873 Myb_DNA-bind_5: Myb/S 96.2 0.021 4.6E-07 34.8 5.6 47 28-74 2-70 (78)
30 PF09111 SLIDE: SLIDE; InterP 95.5 0.039 8.5E-07 37.4 4.9 51 25-75 46-112 (118)
31 PF08281 Sigma70_r4_2: Sigma-7 94.6 0.15 3.2E-06 28.8 5.0 40 33-73 12-51 (54)
32 PF12776 Myb_DNA-bind_3: Myb/S 94.5 0.16 3.4E-06 31.7 5.5 45 30-74 1-63 (96)
33 PF00249 Myb_DNA-binding: Myb- 94.3 0.007 1.5E-07 34.1 -1.0 17 1-17 31-48 (48)
34 PF13325 MCRS_N: N-terminal re 93.8 0.18 4E-06 37.1 5.5 56 18-73 63-126 (199)
35 COG5118 BDP1 Transcription ini 92.2 0.33 7.2E-06 39.5 5.1 56 16-71 349-408 (507)
36 PF07750 GcrA: GcrA cell cycle 92.2 0.2 4.4E-06 35.4 3.5 39 30-69 2-40 (162)
37 PLN03142 Probable chromatin-re 91.4 0.62 1.3E-05 41.5 6.3 54 23-76 921-987 (1033)
38 KOG1194 Predicted DNA-binding 90.8 1.1 2.4E-05 37.1 6.8 44 29-72 188-231 (534)
39 KOG4282 Transcription factor G 90.3 1.2 2.5E-05 34.3 6.3 48 29-76 55-116 (345)
40 KOG2656 DNA methyltransferase 90.0 0.33 7.1E-06 39.4 3.2 53 26-78 128-186 (445)
41 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 86.5 1.6 3.4E-05 25.5 3.7 39 30-70 4-42 (50)
42 PF04545 Sigma70_r4: Sigma-70, 85.7 3.1 6.7E-05 23.0 4.7 42 31-74 5-46 (50)
43 TIGR02985 Sig70_bacteroi1 RNA 85.5 3 6.4E-05 27.2 5.2 38 35-73 117-154 (161)
44 PF10545 MADF_DNA_bdg: Alcohol 82.0 3.5 7.5E-05 24.4 4.1 34 48-82 27-61 (85)
45 PF13936 HTH_38: Helix-turn-he 81.3 1.9 4E-05 23.9 2.5 38 29-68 3-40 (44)
46 PF13325 MCRS_N: N-terminal re 79.4 5.5 0.00012 29.4 5.1 44 31-75 2-48 (199)
47 smart00595 MADF subfamily of S 79.4 7.2 0.00016 23.7 5.0 25 49-74 29-53 (89)
48 TIGR02937 sigma70-ECF RNA poly 78.1 7.1 0.00015 24.5 4.8 42 30-73 110-151 (158)
49 cd08319 Death_RAIDD Death doma 78.0 4.8 0.0001 25.5 3.9 32 36-68 2-33 (83)
50 PRK09652 RNA polymerase sigma 76.3 8.4 0.00018 25.6 5.0 41 31-73 129-169 (182)
51 PRK11924 RNA polymerase sigma 75.7 8.5 0.00018 25.5 4.9 34 39-73 133-166 (179)
52 PRK09641 RNA polymerase sigma 74.1 9.8 0.00021 25.7 4.9 35 37-72 142-176 (187)
53 PRK09643 RNA polymerase sigma 73.8 10 0.00023 26.3 5.1 36 35-71 138-173 (192)
54 PRK12512 RNA polymerase sigma 73.5 13 0.00028 25.3 5.4 38 37-75 137-174 (184)
55 PF07638 Sigma70_ECF: ECF sigm 73.3 9.2 0.0002 26.7 4.7 40 33-73 137-176 (185)
56 KOG2009 Transcription initiati 72.2 4.7 0.0001 34.1 3.4 52 19-70 396-451 (584)
57 cd08803 Death_ank3 Death domai 71.4 9.8 0.00021 24.1 4.1 32 36-68 4-35 (84)
58 PF11035 SnAPC_2_like: Small n 71.2 20 0.00043 28.6 6.5 44 29-72 22-69 (344)
59 TIGR02939 RpoE_Sigma70 RNA pol 70.0 10 0.00022 25.7 4.3 33 39-72 146-178 (190)
60 cd08317 Death_ank Death domain 69.9 7.8 0.00017 24.0 3.4 34 36-70 4-37 (84)
61 cd08318 Death_NMPP84 Death dom 69.7 11 0.00025 23.6 4.1 35 30-68 4-38 (86)
62 PF00196 GerE: Bacterial regul 69.7 13 0.00028 21.1 4.1 44 30-76 3-46 (58)
63 PRK09047 RNA polymerase factor 69.7 17 0.00037 23.9 5.2 34 39-73 114-147 (161)
64 PRK12514 RNA polymerase sigma 69.5 15 0.00033 24.8 5.1 32 39-71 137-168 (179)
65 PRK04217 hypothetical protein; 69.3 27 0.00058 23.3 6.0 49 25-75 37-85 (110)
66 PRK12529 RNA polymerase sigma 68.9 17 0.00037 24.8 5.2 37 38-75 134-170 (178)
67 TIGR02948 SigW_bacill RNA poly 68.7 14 0.0003 25.0 4.7 31 41-72 146-176 (187)
68 PRK12515 RNA polymerase sigma 68.5 17 0.00037 24.9 5.2 35 38-73 138-172 (189)
69 cd08311 Death_p75NR Death doma 67.8 8.3 0.00018 24.0 3.1 34 33-68 2-35 (77)
70 COG2197 CitB Response regulato 67.4 17 0.00037 26.1 5.1 46 29-77 147-192 (211)
71 smart00005 DEATH DEATH domain, 67.0 11 0.00024 22.8 3.6 32 36-68 5-37 (88)
72 PRK09637 RNA polymerase sigma 66.8 18 0.00039 25.0 5.0 37 36-73 111-147 (181)
73 PRK09642 RNA polymerase sigma 66.6 21 0.00045 23.6 5.1 35 37-72 112-146 (160)
74 PRK12530 RNA polymerase sigma 66.6 19 0.00041 24.9 5.1 36 36-72 139-174 (189)
75 cd06171 Sigma70_r4 Sigma70, re 66.5 17 0.00036 18.8 4.8 39 31-71 11-49 (55)
76 PRK12523 RNA polymerase sigma 66.3 21 0.00045 24.1 5.2 39 36-75 124-162 (172)
77 PF11626 Rap1_C: TRF2-interact 65.9 4.3 9.2E-05 25.6 1.5 17 24-40 43-59 (87)
78 cd08804 Death_ank2 Death domai 65.8 12 0.00025 23.5 3.6 32 36-68 4-35 (84)
79 PRK11179 DNA-binding transcrip 65.4 20 0.00042 24.4 4.9 41 34-75 9-50 (153)
80 TIGR02954 Sig70_famx3 RNA poly 65.1 20 0.00044 24.0 4.9 33 40-73 128-160 (169)
81 PRK09645 RNA polymerase sigma 64.8 23 0.00049 23.8 5.1 35 38-73 125-159 (173)
82 PRK12527 RNA polymerase sigma 64.6 25 0.00054 23.3 5.3 34 38-72 112-145 (159)
83 PRK12536 RNA polymerase sigma 64.0 23 0.00051 24.1 5.1 34 38-72 136-169 (181)
84 COG5352 Uncharacterized protei 63.7 11 0.00023 27.0 3.3 36 30-66 2-37 (169)
85 PRK11923 algU RNA polymerase s 63.2 21 0.00046 24.4 4.8 33 39-72 146-178 (193)
86 cd08777 Death_RIP1 Death Domai 62.7 14 0.0003 23.4 3.5 27 42-69 8-34 (86)
87 PRK12528 RNA polymerase sigma 62.3 29 0.00062 23.0 5.2 37 36-73 118-154 (161)
88 PRK09649 RNA polymerase sigma 62.0 24 0.00052 24.3 4.9 37 36-73 135-171 (185)
89 TIGR02983 SigE-fam_strep RNA p 61.0 27 0.00058 23.1 4.9 39 34-73 113-151 (162)
90 TIGR02999 Sig-70_X6 RNA polyme 60.7 30 0.00066 23.3 5.2 33 38-71 141-173 (183)
91 PRK13919 putative RNA polymera 60.4 30 0.00064 23.5 5.1 31 41-72 145-175 (186)
92 cd08306 Death_FADD Fas-associa 59.9 20 0.00043 22.5 3.8 34 38-72 4-37 (86)
93 TIGR02952 Sig70_famx2 RNA poly 59.9 31 0.00067 22.8 5.0 30 40-70 131-160 (170)
94 PRK12520 RNA polymerase sigma 59.5 31 0.00067 23.6 5.1 34 39-73 139-172 (191)
95 PRK09648 RNA polymerase sigma 59.4 32 0.0007 23.5 5.2 34 38-72 146-179 (189)
96 PRK12531 RNA polymerase sigma 59.1 44 0.00095 23.0 5.9 34 39-73 149-182 (194)
97 PRK12532 RNA polymerase sigma 59.0 51 0.0011 22.6 6.2 33 38-71 143-175 (195)
98 PRK12537 RNA polymerase sigma 58.9 31 0.00067 23.5 5.0 34 39-73 141-174 (182)
99 TIGR02943 Sig70_famx1 RNA poly 58.7 34 0.00073 23.7 5.2 34 39-73 139-172 (188)
100 PRK09651 RNA polymerase sigma 58.5 25 0.00055 23.8 4.5 35 38-73 126-160 (172)
101 KOG4167 Predicted DNA-binding 58.3 23 0.0005 31.3 5.0 43 29-71 620-662 (907)
102 PF13404 HTH_AsnC-type: AsnC-t 58.1 30 0.00064 18.9 4.6 37 34-71 3-40 (42)
103 PRK10100 DNA-binding transcrip 57.2 37 0.0008 24.5 5.4 49 29-80 154-202 (216)
104 PRK06759 RNA polymerase factor 57.2 39 0.00085 22.0 5.1 29 42-71 117-145 (154)
105 PRK15411 rcsA colanic acid cap 56.9 38 0.00083 24.0 5.3 43 30-75 137-179 (207)
106 TIGR02950 SigM_subfam RNA poly 56.8 10 0.00022 24.8 2.2 25 47-72 121-145 (154)
107 COG2963 Transposase and inacti 56.2 48 0.001 21.2 5.3 42 28-70 5-47 (116)
108 PF13384 HTH_23: Homeodomain-l 55.8 19 0.00042 19.5 3.0 34 33-68 4-37 (50)
109 PRK12547 RNA polymerase sigma 54.5 46 0.00099 22.3 5.2 34 38-72 119-152 (164)
110 TIGR02984 Sig-70_plancto1 RNA 54.3 43 0.00092 22.5 5.1 34 39-73 148-181 (189)
111 TIGR02960 SigX5 RNA polymerase 54.1 33 0.00072 25.5 4.9 33 39-72 150-182 (324)
112 cd08779 Death_PIDD Death Domai 53.9 19 0.00041 22.6 3.0 29 38-67 4-32 (86)
113 PRK12543 RNA polymerase sigma 53.5 68 0.0015 21.7 6.7 46 39-85 125-173 (179)
114 PRK05602 RNA polymerase sigma 53.4 40 0.00087 22.9 4.9 32 39-71 136-167 (186)
115 PRK11169 leucine-responsive tr 53.2 35 0.00076 23.4 4.5 42 33-75 13-55 (164)
116 PRK12545 RNA polymerase sigma 53.1 44 0.00095 23.3 5.1 32 39-71 147-178 (201)
117 PRK12516 RNA polymerase sigma 53.1 45 0.00097 23.1 5.1 37 35-72 120-156 (187)
118 PRK15201 fimbriae regulatory p 53.0 50 0.0011 24.4 5.4 46 30-78 133-178 (198)
119 PRK09647 RNA polymerase sigma 52.5 46 0.001 23.5 5.2 32 41-73 148-179 (203)
120 cd08805 Death_ank1 Death domai 51.3 26 0.00057 22.2 3.4 29 36-65 4-32 (84)
121 PRK10360 DNA-binding transcrip 51.2 61 0.0013 21.3 5.3 45 29-76 136-180 (196)
122 PRK09646 RNA polymerase sigma 51.1 51 0.0011 22.7 5.1 31 39-70 150-180 (194)
123 PRK09639 RNA polymerase sigma 51.0 52 0.0011 21.7 5.0 31 39-71 120-150 (166)
124 TIGR02989 Sig-70_gvs1 RNA poly 50.4 58 0.0013 21.2 5.1 28 42-70 122-149 (159)
125 PRK06811 RNA polymerase factor 50.2 55 0.0012 22.5 5.1 34 37-71 137-170 (189)
126 PRK12524 RNA polymerase sigma 50.2 53 0.0012 22.7 5.1 32 39-71 144-175 (196)
127 KOG4468 Polycomb-group transcr 49.8 38 0.00082 29.4 4.9 50 26-75 86-145 (782)
128 PF00531 Death: Death domain; 49.8 40 0.00086 19.8 3.9 25 43-68 8-32 (83)
129 PRK12546 RNA polymerase sigma 49.8 47 0.001 23.1 4.8 35 37-72 119-153 (188)
130 PF00046 Homeobox: Homeobox do 49.7 44 0.00096 18.4 4.5 43 28-71 4-50 (57)
131 smart00501 BRIGHT BRIGHT, ARID 49.6 60 0.0013 20.1 4.9 38 38-75 36-86 (93)
132 PRK12542 RNA polymerase sigma 49.2 57 0.0012 22.2 5.1 33 38-71 129-161 (185)
133 PRK11922 RNA polymerase sigma 48.8 25 0.00054 25.2 3.3 34 39-73 157-190 (231)
134 PRK09636 RNA polymerase sigma 48.8 52 0.0011 24.4 5.2 31 40-71 124-154 (293)
135 PRK09638 RNA polymerase sigma 48.4 20 0.00044 24.0 2.7 31 40-71 135-165 (176)
136 PRK12544 RNA polymerase sigma 48.2 60 0.0013 23.0 5.2 33 40-73 157-189 (206)
137 PRK12526 RNA polymerase sigma 47.5 62 0.0013 22.7 5.2 33 39-72 161-193 (206)
138 PRK12511 RNA polymerase sigma 47.5 61 0.0013 22.4 5.1 33 40-73 120-152 (182)
139 PRK09415 RNA polymerase factor 47.1 55 0.0012 22.3 4.7 31 41-72 137-167 (179)
140 cd01670 Death Death Domain: a 46.0 28 0.00061 20.4 2.8 28 40-68 3-30 (79)
141 TIGR02959 SigZ RNA polymerase 45.3 77 0.0017 21.4 5.2 33 38-71 107-139 (170)
142 PRK12535 RNA polymerase sigma 45.3 64 0.0014 22.6 4.9 33 40-73 142-174 (196)
143 cd00569 HTH_Hin_like Helix-tur 44.7 33 0.00072 15.6 4.9 36 30-67 5-40 (42)
144 PRK12538 RNA polymerase sigma 44.5 53 0.0012 23.8 4.5 34 39-73 179-212 (233)
145 PRK00118 putative DNA-binding 44.1 91 0.002 20.5 5.2 38 33-71 19-56 (104)
146 PRK06986 fliA flagellar biosyn 44.0 64 0.0014 23.1 4.9 37 37-74 190-226 (236)
147 TIGR02957 SigX4 RNA polymerase 43.8 68 0.0015 23.8 5.1 32 40-72 117-148 (281)
148 PF01388 ARID: ARID/BRIGHT DNA 43.1 77 0.0017 19.3 5.1 37 38-74 40-89 (92)
149 PRK12518 RNA polymerase sigma 43.1 25 0.00054 23.5 2.5 27 46-73 135-161 (175)
150 PRK12519 RNA polymerase sigma 43.0 60 0.0013 22.1 4.4 32 39-71 149-180 (194)
151 PRK12513 RNA polymerase sigma 42.9 28 0.00061 23.9 2.8 26 45-71 153-178 (194)
152 PRK08241 RNA polymerase factor 42.8 57 0.0012 24.5 4.6 34 39-73 161-194 (339)
153 PRK12525 RNA polymerase sigma 41.8 95 0.0021 20.8 5.2 34 38-72 125-158 (168)
154 smart00344 HTH_ASNC helix_turn 41.4 64 0.0014 20.0 4.1 43 34-77 3-46 (108)
155 PRK09483 response regulator; P 40.7 99 0.0021 20.6 5.2 44 29-75 147-190 (217)
156 PRK06930 positive control sigm 40.3 91 0.002 21.9 5.0 43 30-74 114-156 (170)
157 PRK06288 RNA polymerase sigma 39.6 1.2E+02 0.0026 22.2 5.9 24 46-70 227-250 (268)
158 TIGR03001 Sig-70_gmx1 RNA poly 37.6 1.6E+02 0.0035 21.5 7.1 36 37-73 167-202 (244)
159 TIGR02980 SigBFG RNA polymeras 37.4 1E+02 0.0022 21.7 5.0 28 45-73 192-219 (227)
160 PRK07037 extracytoplasmic-func 37.4 1.2E+02 0.0026 19.9 6.2 22 46-68 124-145 (163)
161 PRK12522 RNA polymerase sigma 36.9 1.1E+02 0.0024 20.4 5.0 24 46-70 134-157 (173)
162 PRK07670 RNA polymerase sigma 36.6 1E+02 0.0022 22.3 5.0 36 36-72 206-241 (251)
163 PRK09644 RNA polymerase sigma 36.6 1.1E+02 0.0024 20.2 4.9 28 42-70 119-146 (165)
164 PRK12540 RNA polymerase sigma 36.3 1.1E+02 0.0025 20.9 5.0 31 39-70 119-149 (182)
165 PF05263 DUF722: Protein of un 35.1 37 0.00081 23.3 2.3 28 30-57 81-109 (130)
166 PRK11475 DNA-binding transcrip 34.9 1.3E+02 0.0028 21.5 5.3 45 29-76 133-177 (207)
167 PRK08301 sporulation sigma fac 34.4 1.1E+02 0.0023 21.8 4.7 25 46-71 197-221 (234)
168 TIGR02479 FliA_WhiG RNA polyme 34.0 1.3E+02 0.0028 21.2 5.1 24 47-71 191-214 (224)
169 TIGR02947 SigH_actino RNA poly 33.9 53 0.0011 22.5 3.0 32 39-71 139-170 (193)
170 PF09846 DUF2073: Uncharacteri 33.5 38 0.00082 22.7 2.1 15 29-43 27-41 (104)
171 PRK12541 RNA polymerase sigma 33.2 1.3E+02 0.0028 19.8 4.8 23 46-69 127-149 (161)
172 KOG1194 Predicted DNA-binding 31.9 38 0.00083 28.3 2.3 41 29-70 471-511 (534)
173 PRK07122 RNA polymerase sigma 31.9 1.2E+02 0.0025 22.5 4.7 35 39-74 223-257 (264)
174 PF10440 WIYLD: Ubiquitin-bind 31.8 40 0.00086 20.7 1.8 26 30-55 22-48 (65)
175 cd08780 Death_TRADD Death Doma 31.7 86 0.0019 20.5 3.5 33 42-75 8-45 (90)
176 PRK13719 conjugal transfer tra 31.6 1.7E+02 0.0037 21.9 5.5 44 29-75 142-185 (217)
177 PRK08295 RNA polymerase factor 31.2 1.5E+02 0.0033 20.2 5.0 24 46-70 169-192 (208)
178 KOG3200 Uncharacterized conser 31.1 39 0.00085 25.1 2.0 27 30-56 20-47 (224)
179 PRK10840 transcriptional regul 31.0 1.7E+02 0.0036 20.1 5.2 44 29-75 149-192 (216)
180 PRK09413 IS2 repressor TnpA; R 30.6 58 0.0013 21.3 2.6 24 37-60 95-119 (121)
181 cd07316 terB_like_DjlA N-termi 29.9 65 0.0014 19.8 2.7 19 29-47 88-106 (106)
182 cd07176 terB tellurite resista 29.9 66 0.0014 19.8 2.7 19 29-47 92-110 (111)
183 PRK08583 RNA polymerase sigma 29.4 1.7E+02 0.0036 21.2 5.2 35 39-74 213-247 (257)
184 PRK12517 RNA polymerase sigma 29.1 1.9E+02 0.0042 19.8 7.0 30 42-72 139-168 (188)
185 PRK09635 sigI RNA polymerase s 29.0 1.5E+02 0.0032 22.4 4.9 32 39-71 126-157 (290)
186 PRK12533 RNA polymerase sigma 29.0 1.5E+02 0.0032 21.2 4.8 34 37-71 140-173 (216)
187 PRK07408 RNA polymerase sigma 28.0 1.7E+02 0.0037 21.4 5.0 26 47-73 219-244 (256)
188 KOG4329 DNA-binding protein [G 27.9 1.5E+02 0.0033 24.3 5.0 43 29-71 278-321 (445)
189 PRK12534 RNA polymerase sigma 27.7 2E+02 0.0042 19.4 5.0 28 42-70 148-175 (187)
190 PRK09191 two-component respons 27.3 1.9E+02 0.0042 20.1 5.0 36 35-71 92-127 (261)
191 PF06628 Catalase-rel: Catalas 27.0 1.4E+02 0.0031 17.6 5.7 43 31-83 20-62 (68)
192 cd08312 Death_MyD88 Death doma 26.8 73 0.0016 19.6 2.4 23 44-67 13-35 (79)
193 PRK05911 RNA polymerase sigma 26.6 1.9E+02 0.0041 21.2 5.1 27 46-73 220-246 (257)
194 PLN03142 Probable chromatin-re 26.2 1.4E+02 0.003 27.2 4.8 39 30-68 826-865 (1033)
195 PF04504 DUF573: Protein of un 25.3 64 0.0014 20.8 2.1 18 29-46 5-22 (98)
196 PF09420 Nop16: Ribosome bioge 25.3 2.4E+02 0.0051 19.5 5.1 44 27-70 113-160 (164)
197 PRK12539 RNA polymerase sigma 25.0 2.2E+02 0.0049 19.2 4.9 24 46-70 146-169 (184)
198 PRK09640 RNA polymerase sigma 24.2 71 0.0015 21.8 2.3 23 47-70 150-172 (188)
199 PRK15328 invasion protein IagB 24.1 1.9E+02 0.004 20.3 4.4 42 38-79 98-141 (160)
200 PRK02866 cyanate hydratase; Va 24.1 1.3E+02 0.0029 21.1 3.6 36 37-73 8-43 (147)
201 PF01527 HTH_Tnp_1: Transposas 24.1 1.5E+02 0.0032 17.0 3.4 38 29-67 5-42 (76)
202 PF05176 ATP-synt_10: ATP10 pr 22.4 81 0.0018 23.7 2.4 27 7-45 225-251 (252)
203 cd00086 homeodomain Homeodomai 22.3 1.4E+02 0.0031 16.0 4.8 43 28-71 4-50 (59)
204 TIGR02941 Sigma_B RNA polymera 22.0 2.4E+02 0.0053 20.3 4.8 24 46-70 220-243 (255)
205 PF09905 DUF2132: Uncharacteri 21.5 1.3E+02 0.0029 18.4 2.8 31 35-67 11-44 (64)
206 PRK05572 sporulation sigma fac 21.2 2.7E+02 0.0059 20.1 5.0 23 47-70 218-240 (252)
207 PF02954 HTH_8: Bacterial regu 20.9 1.5E+02 0.0033 15.7 4.1 33 34-67 5-37 (42)
208 COG2992 Bax Uncharacterized Fl 20.6 50 0.0011 25.3 0.9 43 23-75 90-132 (262)
209 PRK00430 fis global DNA-bindin 20.2 2.5E+02 0.0054 17.9 4.4 34 33-67 54-87 (95)
210 PF13725 tRNA_bind_2: Possible 20.1 46 0.00099 20.8 0.6 24 33-57 70-93 (101)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.95 E-value=6.8e-29 Score=182.98 Aligned_cols=74 Identities=32% Similarity=0.627 Sum_probs=70.4
Q ss_pred ccchhhhhccccccCCccccCCCcccCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHHHHHHH
Q 034546 3 KRRRKQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQAFADRR 81 (91)
Q Consensus 3 ~~~~~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~~~~ 81 (91)
+|.+|+||.||.+||.|.|. +|+||+|||++||++|..+||+|+.||++|||||||+|||+|++++++++....
T Consensus 42 ~R~GKSCRlRW~NyLrP~ik-----rg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~ 115 (238)
T KOG0048|consen 42 RRCGKSCRLRWTNYLRPDLK-----RGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMG 115 (238)
T ss_pred CccchHHHHHhhcccCCCcc-----CCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcC
Confidence 79999999999999987766 599999999999999999999999999999999999999999999999998766
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.94 E-value=1.4e-27 Score=178.16 Aligned_cols=80 Identities=31% Similarity=0.573 Sum_probs=73.5
Q ss_pred CccchhhhhccccccCCccccCCCcccCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHHHHHHH
Q 034546 2 DKRRRKQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQAFADRR 81 (91)
Q Consensus 2 ~~~~~~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~~~~ 81 (91)
++|++||||+||.+||+|.|.. ++||+|||++|+++|..+|++|+.||++|||||+++|||||++++++.+...+
T Consensus 57 ~gRT~KQCReRW~N~L~P~I~k-----gpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~ 131 (249)
T PLN03212 57 LLRCGKSCRLRWMNYLRPSVKR-----GGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQG 131 (249)
T ss_pred cCCCcchHHHHHHHhhchhccc-----CCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcC
Confidence 5899999999999999887665 99999999999999999999999999999999999999999999999888766
Q ss_pred HHHHh
Q 034546 82 RELRI 86 (91)
Q Consensus 82 ~~~~~ 86 (91)
..+..
T Consensus 132 i~p~~ 136 (249)
T PLN03212 132 IDPQT 136 (249)
T ss_pred CCCCC
Confidence 55443
No 3
>PLN03091 hypothetical protein; Provisional
Probab=99.92 E-value=1.9e-25 Score=177.31 Aligned_cols=81 Identities=25% Similarity=0.457 Sum_probs=73.6
Q ss_pred CccchhhhhccccccCCccccCCCcccCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHHHHHHH
Q 034546 2 DKRRRKQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQAFADRR 81 (91)
Q Consensus 2 ~~~~~~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~~~~ 81 (91)
.+|+.||||+||.+||+|.|.. |+||+|||++|+++|..+|++|+.||.+||||||++|||||+..+++.+...+
T Consensus 46 ~gRT~KQCRERW~NyLdP~IkK-----gpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~ 120 (459)
T PLN03091 46 LQRCGKSCRLRWINYLRPDLKR-----GTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRG 120 (459)
T ss_pred cCcCcchHhHHHHhccCCcccC-----CCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcC
Confidence 4899999999999999887654 99999999999999999999999999999999999999999999999888766
Q ss_pred HHHHhh
Q 034546 82 RELRIY 87 (91)
Q Consensus 82 ~~~~~~ 87 (91)
..+..+
T Consensus 121 I~p~t~ 126 (459)
T PLN03091 121 IDPNTH 126 (459)
T ss_pred CCCCCC
Confidence 555443
No 4
>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=99.62 E-value=7.1e-16 Score=88.57 Aligned_cols=46 Identities=26% Similarity=0.382 Sum_probs=41.8
Q ss_pred cCCCCHHHHHHHHHHHHHhCCc-HHHHhhhCC-CCCHHHHHHHHHHHh
Q 034546 28 FINMSEQEEDLIYRMYKLVGDR-WALIAGRIP-GRKAEEIERFWIMRH 73 (91)
Q Consensus 28 kg~wT~eED~lLi~l~~~~G~k-W~~Ia~~lp-GRt~n~vKnrw~~~l 73 (91)
+++||+|||++|++++.++|.. |..||..|| |||+.+|+++|+.++
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 5899999999999999999988 999999999 999999999998764
No 5
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.52 E-value=3.4e-14 Score=78.74 Aligned_cols=47 Identities=30% Similarity=0.519 Sum_probs=44.0
Q ss_pred cCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHHhh
Q 034546 28 FINMSEQEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIMRHG 74 (91)
Q Consensus 28 kg~wT~eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~~l~ 74 (91)
+++||++||.+|+.++..+| ..|..||..||+||+.+|+++|+..++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999987654
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.47 E-value=8.3e-14 Score=82.57 Aligned_cols=45 Identities=20% Similarity=0.451 Sum_probs=39.3
Q ss_pred CCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 31 MSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 31 wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
||+|||++|+.++..+|+.|..||..|+.||+.+|++||+.+|.+
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~ 45 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRP 45 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTST
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcc
Confidence 999999999999999999999999999669999999999996654
No 7
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.45 E-value=1.4e-13 Score=103.15 Aligned_cols=68 Identities=12% Similarity=0.164 Sum_probs=61.0
Q ss_pred cccccCCccccCCCcccCCCCHHHHHHHHHHHHHhC-CcHHHHhhhC-CCCCHHHHHHHHHHHhhHHHHH
Q 034546 12 TTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYKLVG-DRWALIAGRI-PGRKAEEIERFWIMRHGQAFAD 79 (91)
Q Consensus 12 ~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~~~G-~kW~~Ia~~l-pGRt~n~vKnrw~~~l~k~~~~ 79 (91)
--....+|++..+.+++++||+|||++|+.++..+| ++|..||+.+ +|||+.||+.||..+|...+..
T Consensus 9 ~~~~~~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~k 78 (249)
T PLN03212 9 PVSKKTTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKR 78 (249)
T ss_pred CCCCCCCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhccc
Confidence 344667899999999999999999999999999999 5799999998 6999999999999999876553
No 8
>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=99.43 E-value=4.3e-13 Score=73.39 Aligned_cols=43 Identities=28% Similarity=0.583 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 30 NMSEQEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
+||++||.+|+.++..+| ..|..||..||+||+.+|+++|+.+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 699999999999999999 8999999999999999999999765
No 9
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.35 E-value=6.9e-13 Score=97.92 Aligned_cols=55 Identities=13% Similarity=0.007 Sum_probs=50.2
Q ss_pred CCcccCCCCHHHHHHHHHHHHHhCCc-HHHHhhhCC-CCCHHHHHHHHHHHhhHHHH
Q 034546 24 IEWEFINMSEQEEDLIYRMYKLVGDR-WALIAGRIP-GRKAEEIERFWIMRHGQAFA 78 (91)
Q Consensus 24 ~~lkkg~wT~eED~lLi~l~~~~G~k-W~~Ia~~lp-GRt~n~vKnrw~~~l~k~~~ 78 (91)
+++.+||||+|||++|+.++..+|.. |..||+.++ ||++.+|+-||..+|+..+.
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ik 61 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLK 61 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCcc
Confidence 44567999999999999999999965 999999999 99999999999999998664
No 10
>PLN03091 hypothetical protein; Provisional
Probab=99.19 E-value=2.2e-11 Score=97.52 Aligned_cols=61 Identities=13% Similarity=0.127 Sum_probs=53.6
Q ss_pred CccccCCCcccCCCCHHHHHHHHHHHHHhCC-cHHHHhhhC-CCCCHHHHHHHHHHHhhHHHH
Q 034546 18 SEEVSSIEWEFINMSEQEEDLIYRMYKLVGD-RWALIAGRI-PGRKAEEIERFWIMRHGQAFA 78 (91)
Q Consensus 18 s~~v~s~~lkkg~wT~eED~lLi~l~~~~G~-kW~~Ia~~l-pGRt~n~vKnrw~~~l~k~~~ 78 (91)
.+++....+++|+||+|||++|+.++..+|. .|..||+.+ +||++.+|+.||..+|...+.
T Consensus 4 ~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~Ik 66 (459)
T PLN03091 4 HSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLK 66 (459)
T ss_pred CccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCccc
Confidence 3455667899999999999999999999995 699999988 599999999999999887653
No 11
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.14 E-value=6.8e-11 Score=98.70 Aligned_cols=72 Identities=19% Similarity=0.258 Sum_probs=66.5
Q ss_pred CCccchhhhhccccccCCccccCCCcccCCCCHHHHHHHHHHHHHhCCc-HHHHhhhCCCCCHHHHHHHHHHHhhHHH
Q 034546 1 MDKRRRKQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYKLVGDR-WALIAGRIPGRKAEEIERFWIMRHGQAF 77 (91)
Q Consensus 1 ~~~~~~~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~~~G~k-W~~Ia~~lpGRt~n~vKnrw~~~l~k~~ 77 (91)
|++|+.-|-=.||+..|+|+|. +|+||++||-+|+.++.+||.+ |..|...+|||++.||+.||...|....
T Consensus 338 mpgr~~~qLI~R~~~~LdPsik-----hg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~ 410 (939)
T KOG0049|consen 338 MPGRTRQQLITRFSHTLDPSVK-----HGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSA 410 (939)
T ss_pred cCCcchhhhhhhheeccCcccc-----CCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhh
Confidence 8999999999999999998775 4999999999999999999987 9999999999999999999998876544
No 12
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.00 E-value=3.8e-10 Score=91.84 Aligned_cols=70 Identities=19% Similarity=0.264 Sum_probs=63.2
Q ss_pred cchhhhhccccccCCccccCCCcccCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHHHH
Q 034546 4 RRRKQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQAFA 78 (91)
Q Consensus 4 ~~~~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~ 78 (91)
++++||+.||.+|+.|.+.- ++|+.+||..|+.++.++|+.|+.||..+||||+.+|.++|...+.....
T Consensus 53 ~~~kq~~~rw~~~lnp~lk~-----~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 53 STGKQSSNRWNNHLNPQLKK-----KNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred cccccccchhhhhhchhccc-----ccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 67899999999988766555 99999999999999999999999999999999999999999987765444
No 13
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=98.67 E-value=1.9e-08 Score=84.30 Aligned_cols=62 Identities=18% Similarity=0.306 Sum_probs=54.2
Q ss_pred CCccchhhhhccccccCCccccCCCcccCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHH
Q 034546 1 MDKRRRKQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIER 67 (91)
Q Consensus 1 ~~~~~~~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKn 67 (91)
.+||+--|||+||.+.|--+ +|++-||-.||+.||.++.+|| +.|..||..||.+|..+...
T Consensus 390 vPnRSdsQcR~RY~nvL~~s-----~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~r 452 (939)
T KOG0049|consen 390 VPNRSDSQCRERYTNVLNRS-----AKVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRR 452 (939)
T ss_pred cCCccHHHHHHHHHHHHHHh-----hccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHH
Confidence 47999999999999877554 5569999999999999999999 78999999999999955433
No 14
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.66 E-value=1.2e-08 Score=83.46 Aligned_cols=69 Identities=16% Similarity=0.251 Sum_probs=61.0
Q ss_pred cchhhhhccccccCCccccCCCcccCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHHHH
Q 034546 4 RRRKQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQAFA 78 (91)
Q Consensus 4 ~~~~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~ 78 (91)
.++|||+-||..+++|.|. +..|+.+||+.||++...+...|..||..| |||+++|-.||+.++-....
T Consensus 40 kt~rqC~~rw~e~ldp~i~-----~tews~eederlLhlakl~p~qwrtIa~i~-gr~~~qc~eRy~~ll~~~~s 108 (617)
T KOG0050|consen 40 KTARQCKARWEEWLDPAIK-----KTEWSREEDERLLHLAKLEPTQWRTIADIM-GRTSQQCLERYNNLLDVYVS 108 (617)
T ss_pred cchhHHHHHHHHHhCHHHh-----hhhhhhhHHHHHHHHHHhcCCccchHHHHh-hhhHHHHHHHHHHHHHHHHh
Confidence 5789999999977776654 599999999999999999999999999999 99999999999987765443
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=98.42 E-value=1.4e-07 Score=55.59 Aligned_cols=34 Identities=15% Similarity=0.216 Sum_probs=27.9
Q ss_pred CCccchhhhhccccccCCccccCCCcccCCCCHHHHHHH
Q 034546 1 MDKRRRKQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLI 39 (91)
Q Consensus 1 ~~~~~~~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lL 39 (91)
|++|++.||+.||..+|.+.+. +++||++||+.|
T Consensus 27 l~~Rt~~~~~~r~~~~l~~~~~-----~~~wt~eEd~~L 60 (60)
T PF13921_consen 27 LGNRTPKQCRNRWRNHLRPKIS-----RGPWTKEEDQRL 60 (60)
T ss_dssp STTS-HHHHHHHHHHTTSTTST-----SSSSSHHHHHHH
T ss_pred HCcCCHHHHHHHHHHHCccccc-----CCCcCHHHHhcC
Confidence 5569999999999998876544 499999999976
No 16
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=97.95 E-value=1.1e-05 Score=67.02 Aligned_cols=49 Identities=16% Similarity=0.257 Sum_probs=45.4
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHH
Q 034546 27 EFINMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQA 76 (91)
Q Consensus 27 kkg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~ 76 (91)
.+|.||++|++.|..+|.++|+.|..|+..| ||.+.+|+.+|..+....
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g 431 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCG 431 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccc
Confidence 6799999999999999999999999999999 999999999998766543
No 17
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=97.90 E-value=6e-06 Score=67.62 Aligned_cols=55 Identities=11% Similarity=0.224 Sum_probs=49.1
Q ss_pred CcccCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHHhhHHHHH
Q 034546 25 EWEFINMSEQEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIMRHGQAFAD 79 (91)
Q Consensus 25 ~lkkg~wT~eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~~ 79 (91)
.++.|+|+..||+.+..++..+| +.|+.||..|.-+++++|++||+.++.+.+..
T Consensus 17 ~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~ 72 (512)
T COG5147 17 KRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKK 72 (512)
T ss_pred eecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhccc
Confidence 45678999999999999999999 56999999999999999999999888776553
No 18
>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=97.83 E-value=2.6e-05 Score=47.91 Aligned_cols=48 Identities=10% Similarity=0.262 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHHHHHHh--------CCc-HHHHhhhCC-CCCHHHHHHHHHHHhhHH
Q 034546 29 INMSEQEEDLIYRMYKLV--------GDR-WALIAGRIP-GRKAEEIERFWIMRHGQA 76 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~--------G~k-W~~Ia~~lp-GRt~n~vKnrw~~~l~k~ 76 (91)
.+||.+||.+|+..+..+ ||+ |..++..-| ..|-.+.++||...|...
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 589999999999999542 344 999999988 999999999998777654
No 19
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.77 E-value=3.2e-05 Score=63.70 Aligned_cols=55 Identities=16% Similarity=0.227 Sum_probs=49.8
Q ss_pred CcccCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHHhhHHHHH
Q 034546 25 EWEFINMSEQEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIMRHGQAFAD 79 (91)
Q Consensus 25 ~lkkg~wT~eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~~ 79 (91)
.++-|.|+.-||++|-..+..+| +.|+.|++.|+--|..+|+++|+..+...+..
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~ 59 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKK 59 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhh
Confidence 45678999999999999999999 77999999999999999999999988876653
No 20
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.61 E-value=0.00015 Score=58.47 Aligned_cols=46 Identities=22% Similarity=0.294 Sum_probs=42.4
Q ss_pred ccCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 27 EFINMSEQEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 27 kkg~wT~eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
-.+.||.+||-+||++...+| +.|..||.++..+|..+|+.+|..+
T Consensus 71 ~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~ 117 (438)
T KOG0457|consen 71 LDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKH 117 (438)
T ss_pred CCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHH
Confidence 346899999999999999999 8999999999999999999999864
No 21
>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=97.53 E-value=0.00035 Score=41.83 Aligned_cols=44 Identities=14% Similarity=0.242 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHHhCC-cH---HHHhhhCC--CCCHHHHHHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGD-RW---ALIAGRIP--GRKAEEIERFWIMR 72 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~-kW---~~Ia~~lp--GRt~n~vKnrw~~~ 72 (91)
-.||+||....++.+..+|. .| ..|+..|. +.|..+|+.+.+.+
T Consensus 4 ~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy 53 (57)
T TIGR01557 4 VVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKY 53 (57)
T ss_pred CCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 47999999999999999996 99 99999874 33999999987654
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=97.52 E-value=0.00018 Score=51.30 Aligned_cols=52 Identities=12% Similarity=0.139 Sum_probs=42.6
Q ss_pred cCCCCHHHHHHHHHHHHHh---CCc----HHHHhhhCCCCCHHHHHHHHHHHhhHHHHHH
Q 034546 28 FINMSEQEEDLIYRMYKLV---GDR----WALIAGRIPGRKAEEIERFWIMRHGQAFADR 80 (91)
Q Consensus 28 kg~wT~eED~lLi~l~~~~---G~k----W~~Ia~~lpGRt~n~vKnrw~~~l~k~~~~~ 80 (91)
...||.|||.+|.+.+-.+ |+. ...++..| +||+-+|.=|||+.+++++...
T Consensus 4 QDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 4 QDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred ccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 4589999999988766554 432 56788888 9999999999999999987753
No 23
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=97.46 E-value=0.00013 Score=60.78 Aligned_cols=78 Identities=12% Similarity=0.130 Sum_probs=64.6
Q ss_pred CCccchhhhhccccccCCccccCCCcccCCCCHHHHHHHHHHHH-------Hh-----------C-C-------cHHHHh
Q 034546 1 MDKRRRKQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYK-------LV-----------G-D-------RWALIA 54 (91)
Q Consensus 1 ~~~~~~~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~-------~~-----------G-~-------kW~~Ia 54 (91)
|-+|.+--|+++|..|....-. .++|+||-||++.|+.+++ ++ - + .|+.|+
T Consensus 412 ~lgr~P~~crd~wr~~~~~g~~---~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vs 488 (607)
T KOG0051|consen 412 ALGRMPMDCRDRWRQYVKCGSK---RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVS 488 (607)
T ss_pred HHccCcHHHHHHHHHhhccccc---cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhh
Confidence 3578999999999999887654 5779999999999999995 22 1 1 499999
Q ss_pred hhCCCCCHHHHHHHHHHHhhHHHHHHH
Q 034546 55 GRIPGRKAEEIERFWIMRHGQAFADRR 81 (91)
Q Consensus 55 ~~lpGRt~n~vKnrw~~~l~k~~~~~~ 81 (91)
..+..|+--+|+-.|+.++.......+
T Consensus 489 e~~~TR~~~qCr~Kw~kl~~~~s~n~~ 515 (607)
T KOG0051|consen 489 EMLGTRSRIQCRYKWYKLTTSPSFNKR 515 (607)
T ss_pred HhhcCCCcchHHHHHHHHHhhHHhhcc
Confidence 999999999999999988877655444
No 24
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.28 E-value=0.00036 Score=43.32 Aligned_cols=47 Identities=21% Similarity=0.405 Sum_probs=33.9
Q ss_pred CCCCHHHHHHHHHHHHH------hCC--------cHHHHhhhC----CCCCHHHHHHHHHHHhhH
Q 034546 29 INMSEQEEDLIYRMYKL------VGD--------RWALIAGRI----PGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~------~G~--------kW~~Ia~~l----pGRt~n~vKnrw~~~l~k 75 (91)
-.||++|..+||.++.. +++ -|..||..| ..||+.+|++.|..+.+.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~ 66 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKK 66 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHH
Confidence 47999999999999887 321 399999997 479999999999885544
No 25
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.66 E-value=0.0053 Score=44.22 Aligned_cols=52 Identities=8% Similarity=0.101 Sum_probs=40.4
Q ss_pred ccCCCCHHHHHHHHHHHHHhC----Cc---HHHHhhhCCCCCHHHHHHHHHHHhhHHHHH
Q 034546 27 EFINMSEQEEDLIYRMYKLVG----DR---WALIAGRIPGRKAEEIERFWIMRHGQAFAD 79 (91)
Q Consensus 27 kkg~wT~eED~lLi~l~~~~G----~k---W~~Ia~~lpGRt~n~vKnrw~~~l~k~~~~ 79 (91)
....||.|||.+|-+.+-.++ -+ -..++..| +||..+|.-|||+.+++++..
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 457899999999866666554 22 34566777 899999999999999986654
No 26
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.62 E-value=0.0041 Score=51.20 Aligned_cols=48 Identities=23% Similarity=0.306 Sum_probs=42.9
Q ss_pred CcccCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 25 EWEFINMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 25 ~lkkg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
+--.+.||.+|..+|++.+..||..|..||.++..||-.+|=-++..+
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 344579999999999999999999999999999999999998887643
No 27
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.61 E-value=0.0041 Score=49.27 Aligned_cols=51 Identities=25% Similarity=0.293 Sum_probs=44.0
Q ss_pred CCCcccCCCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 23 SIEWEFINMSEQEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 23 s~~lkkg~wT~eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
|-.+--..|+.+|+.+||+.-..+| +.|.-||.++..|+...||.+|....
T Consensus 58 sypI~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 58 SYPIGEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred CccccCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 3333345899999999999999999 89999999999999999999987543
No 28
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.60 E-value=0.0033 Score=51.54 Aligned_cols=43 Identities=23% Similarity=0.342 Sum_probs=40.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
-+||.+|..+|++.+..||..|..||.++..+|..+|=-+|..
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~ 322 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQ 322 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHc
Confidence 4999999999999999999999999999999999999888864
No 29
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.19 E-value=0.021 Score=34.82 Aligned_cols=47 Identities=19% Similarity=0.372 Sum_probs=38.0
Q ss_pred cCCCCHHHHHHHHHHHHHh-----C------------CcHHHHhhhC-----CCCCHHHHHHHHHHHhh
Q 034546 28 FINMSEQEEDLIYRMYKLV-----G------------DRWALIAGRI-----PGRKAEEIERFWIMRHG 74 (91)
Q Consensus 28 kg~wT~eED~lLi~l~~~~-----G------------~kW~~Ia~~l-----pGRt~n~vKnrw~~~l~ 74 (91)
...||.+|..+|+.++..+ | .-|..|+..| +.||..+++..|.....
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~ 70 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKS 70 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Confidence 3589999999999997775 2 1299999986 47999999999986543
No 30
>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=95.46 E-value=0.039 Score=37.38 Aligned_cols=51 Identities=20% Similarity=0.203 Sum_probs=39.7
Q ss_pred CcccCCCCHHHHHHHHHHHHHhCC----cHHHHhhh------------CCCCCHHHHHHHHHHHhhH
Q 034546 25 EWEFINMSEQEEDLIYRMYKLVGD----RWALIAGR------------IPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 25 ~lkkg~wT~eED~lLi~l~~~~G~----kW~~Ia~~------------lpGRt~n~vKnrw~~~l~k 75 (91)
.-++..||++||..|+.+...+|- .|..|... |..||+..|..|.+++++-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 344569999999999999999996 69877654 4789999999999888753
No 31
>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=94.60 E-value=0.15 Score=28.83 Aligned_cols=40 Identities=18% Similarity=0.210 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 33 EQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 33 ~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
++++..++.++-..|-.|..||..+ |.|.+.|+++.+...
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRAR 51 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 4567778888888899999999999 999999999765443
No 32
>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=94.48 E-value=0.16 Score=31.67 Aligned_cols=45 Identities=16% Similarity=0.367 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHHh---CCc----------HHHHhhhC---CCC--CHHHHHHHHHHHhh
Q 034546 30 NMSEQEEDLIYRMYKLV---GDR----------WALIAGRI---PGR--KAEEIERFWIMRHG 74 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~---G~k----------W~~Ia~~l---pGR--t~n~vKnrw~~~l~ 74 (91)
.||++++.+|+++..+. |+. |..|+..| +|. |..+|+|+|..+-+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 49999999999887554 322 88899887 333 67899999865443
No 33
>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=94.31 E-value=0.007 Score=34.08 Aligned_cols=17 Identities=24% Similarity=0.343 Sum_probs=14.5
Q ss_pred CC-ccchhhhhccccccC
Q 034546 1 MD-KRRRKQAKTTTTTFY 17 (91)
Q Consensus 1 ~~-~~~~~q~~~~~~~~~ 17 (91)
|+ +|+..||+.+|.+++
T Consensus 31 ~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 31 MPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp HSSSSTHHHHHHHHHHHT
T ss_pred cCCCCCHHHHHHHHHhhC
Confidence 45 899999999998764
No 34
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=93.85 E-value=0.18 Score=37.08 Aligned_cols=56 Identities=16% Similarity=0.204 Sum_probs=38.0
Q ss_pred CccccCCCcccCCCCHHHHHHHHHHHHHhCCc---HHHHhh-----hCCCCCHHHHHHHHHHHh
Q 034546 18 SEEVSSIEWEFINMSEQEEDLIYRMYKLVGDR---WALIAG-----RIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 18 s~~v~s~~lkkg~wT~eED~lLi~l~~~~G~k---W~~Ia~-----~lpGRt~n~vKnrw~~~l 73 (91)
.|+....--.+.+||.+||++|...-....+. +..|=. +-++||+..+.++|....
T Consensus 63 ~p~~~~~iq~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmk 126 (199)
T PF13325_consen 63 HPELIAAIQSKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMK 126 (199)
T ss_pred CcchhhcccccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHH
Confidence 34433334456799999999999876555443 433321 238999999999998543
No 35
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=92.18 E-value=0.33 Score=39.46 Aligned_cols=56 Identities=21% Similarity=0.373 Sum_probs=47.0
Q ss_pred cCCccccCCCcccC----CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 16 FYSEEVSSIEWEFI----NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 16 ~~s~~v~s~~lkkg----~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
.++.-|.+..+-++ +||.+|-++...+-..+|-..+.|+..||.|.-.+||.-|..
T Consensus 349 ~~ar~vts~t~g~~~~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 349 PFARIVTSSTFGKKKGALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred chhheeecccccCCCCCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHH
Confidence 34444666666444 899999999999999999999999999999999999997754
No 36
>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=92.16 E-value=0.2 Score=35.42 Aligned_cols=39 Identities=10% Similarity=0.147 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHH
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFW 69 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw 69 (91)
.||+|+.+.|-+|.. -|-.-++||..|.|.|-|+|-..-
T Consensus 2 ~Wtde~~~~L~~lw~-~G~SasqIA~~lg~vsRnAViGk~ 40 (162)
T PF07750_consen 2 SWTDERVERLRKLWA-EGLSASQIARQLGGVSRNAVIGKA 40 (162)
T ss_pred CCCHHHHHHHHHHHH-cCCCHHHHHHHhCCcchhhhhhhh
Confidence 599999999999997 488899999999889999987643
No 37
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=91.36 E-value=0.62 Score=41.51 Aligned_cols=54 Identities=13% Similarity=0.117 Sum_probs=43.7
Q ss_pred CCCcccCCCCHHHHHHHHHHHHHhC-CcHHHHhhh------------CCCCCHHHHHHHHHHHhhHH
Q 034546 23 SIEWEFINMSEQEEDLIYRMYKLVG-DRWALIAGR------------IPGRKAEEIERFWIMRHGQA 76 (91)
Q Consensus 23 s~~lkkg~wT~eED~lLi~l~~~~G-~kW~~Ia~~------------lpGRt~n~vKnrw~~~l~k~ 76 (91)
.+.-+...||++||..|+.+...+| ..|..|... |..||+..|..|.+++++-.
T Consensus 921 ~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~ 987 (1033)
T PLN03142 921 YGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLI 987 (1033)
T ss_pred cCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHH
Confidence 3444556799999999999999999 779888443 47999999999999877653
No 38
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=90.79 E-value=1.1 Score=37.09 Aligned_cols=44 Identities=11% Similarity=0.291 Sum_probs=39.9
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
..||.||--++-..|..||...+.|-+.||.|+-..|..+|++.
T Consensus 188 d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 188 DEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSW 231 (534)
T ss_pred ccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHH
Confidence 37999988888899999999999999999999999999888753
No 39
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=90.35 E-value=1.2 Score=34.32 Aligned_cols=48 Identities=15% Similarity=0.124 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHHHHh----------CCcHHHHhhhC----CCCCHHHHHHHHHHHhhHH
Q 034546 29 INMSEQEEDLIYRMYKLV----------GDRWALIAGRI----PGRKAEEIERFWIMRHGQA 76 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~----------G~kW~~Ia~~l----pGRt~n~vKnrw~~~l~k~ 76 (91)
..|+.+|=..||+++..+ ++-|..||..+ --||+.+|++.|....++-
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Y 116 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKY 116 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 579999999999988765 23499999964 4699999999998766553
No 40
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=90.04 E-value=0.33 Score=39.37 Aligned_cols=53 Identities=19% Similarity=0.265 Sum_probs=46.7
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCcHHHHhhh-----CCC-CCHHHHHHHHHHHhhHHHH
Q 034546 26 WEFINMSEQEEDLIYRMYKLVGDRWALIAGR-----IPG-RKAEEIERFWIMRHGQAFA 78 (91)
Q Consensus 26 lkkg~wT~eED~lLi~l~~~~G~kW~~Ia~~-----lpG-Rt~n~vKnrw~~~l~k~~~ 78 (91)
++-..||.+|-+-|+.|...|-=+|..||.. ++- ||-..+|.||++..++-+.
T Consensus 128 l~dn~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~k 186 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLK 186 (445)
T ss_pred hccccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHH
Confidence 3446899999999999999999999999988 666 9999999999998887554
No 41
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=86.49 E-value=1.6 Score=25.48 Aligned_cols=39 Identities=28% Similarity=0.372 Sum_probs=25.6
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
..|++|...|.-++ ++|-+-.+||+.+ ||+-+.|+++-+
T Consensus 4 ~Lt~~Eqaqid~m~-qlG~s~~~isr~i-~RSr~~Ir~yl~ 42 (50)
T PF11427_consen 4 TLTDAEQAQIDVMH-QLGMSLREISRRI-GRSRTCIRRYLK 42 (50)
T ss_dssp ---HHHHHHHHHHH-HTT--HHHHHHHH-T--HHHHHHHHH
T ss_pred cCCHHHHHHHHHHH-HhchhHHHHHHHh-CccHHHHHHHhc
Confidence 45777777766555 4899999999999 999999998743
No 42
>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=85.70 E-value=3.1 Score=23.02 Aligned_cols=42 Identities=21% Similarity=0.286 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhh
Q 034546 31 MSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHG 74 (91)
Q Consensus 31 wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~ 74 (91)
-+++|-++|...| .-|-.+..||..| |-|...|+.+-...+.
T Consensus 5 L~~~er~vi~~~y-~~~~t~~eIa~~l-g~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 5 LPPREREVIRLRY-FEGLTLEEIAERL-GISRSTVRRILKRALK 46 (50)
T ss_dssp S-HHHHHHHHHHH-TST-SHHHHHHHH-TSCHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHh-cCCCCHHHHHHHH-CCcHHHHHHHHHHHHH
Confidence 3455555555444 4566799999999 8899999987665543
No 43
>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=85.49 E-value=3 Score=27.20 Aligned_cols=38 Identities=16% Similarity=0.231 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 35 EEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 35 ED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
++..|+.++-..|-.+..||..| |.+...|+++.+...
T Consensus 117 ~~r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~ 154 (161)
T TIGR02985 117 QCRKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKAL 154 (161)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 33445555445688899999998 899999999887643
No 44
>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=82.00 E-value=3.5 Score=24.42 Aligned_cols=34 Identities=12% Similarity=0.331 Sum_probs=24.2
Q ss_pred CcHHHHhhhCCC-CCHHHHHHHHHHHhhHHHHHHHH
Q 034546 48 DRWALIAGRIPG-RKAEEIERFWIMRHGQAFADRRR 82 (91)
Q Consensus 48 ~kW~~Ia~~lpG-Rt~n~vKnrw~~~l~k~~~~~~~ 82 (91)
.-|..||..|.+ -+...|+.+|.+ |+..+....+
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~-Lr~~y~~~~~ 61 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKN-LRDRYRRELK 61 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHH-HHHHHHHHHH
Confidence 349999999953 577889999987 4455554433
No 45
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=81.33 E-value=1.9 Score=23.89 Aligned_cols=38 Identities=24% Similarity=0.338 Sum_probs=19.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
..+|++|-..|..++. -|-.=..||+.| |++...|.+.
T Consensus 3 ~~Lt~~eR~~I~~l~~-~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 3 KHLTPEERNQIEALLE-QGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp ---------HHHHHHC-S---HHHHHHHT-T--HHHHHHH
T ss_pred cchhhhHHHHHHHHHH-cCCCHHHHHHHH-CcCcHHHHHH
Confidence 3678888888888875 677788999999 9999888763
No 46
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=79.40 E-value=5.5 Score=29.36 Aligned_cols=44 Identities=11% Similarity=0.087 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHHhCCcHHHHhhhC---CCCCHHHHHHHHHHHhhH
Q 034546 31 MSEQEEDLIYRMYKLVGDRWALIAGRI---PGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 31 wT~eED~lLi~l~~~~G~kW~~Ia~~l---pGRt~n~vKnrw~~~l~k 75 (91)
|++++|-+||..+. .|+.-..|+..+ -.-|-..|..||+..|-.
T Consensus 2 W~~~DDl~Li~av~-~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd 48 (199)
T PF13325_consen 2 WKPEDDLLLINAVE-QTNDLESVHLGVKFSCKFTLQEIEERWYALLYD 48 (199)
T ss_pred CCchhhHHHHHHHH-HhcCHHHHHccCCcCCcCcHHHHHHHHHHHHcC
Confidence 99999999998887 477767766653 345889999999987754
No 47
>smart00595 MADF subfamily of SANT domain.
Probab=79.38 E-value=7.2 Score=23.75 Aligned_cols=25 Identities=24% Similarity=0.417 Sum_probs=20.9
Q ss_pred cHHHHhhhCCCCCHHHHHHHHHHHhh
Q 034546 49 RWALIAGRIPGRKAEEIERFWIMRHG 74 (91)
Q Consensus 49 kW~~Ia~~lpGRt~n~vKnrw~~~l~ 74 (91)
-|..||..|. -|...|+.+|+++-.
T Consensus 29 aW~~Ia~~l~-~~~~~~~~kw~~LR~ 53 (89)
T smart00595 29 AWEEIAEELG-LSVEECKKRWKNLRD 53 (89)
T ss_pred HHHHHHHHHC-cCHHHHHHHHHHHHH
Confidence 5999999994 499999999987543
No 48
>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=78.15 E-value=7.1 Score=24.55 Aligned_cols=42 Identities=19% Similarity=0.268 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
..++.|-.+| .++-..|-.+..||..| |=+...|.++.....
T Consensus 110 ~L~~~~~~ii-~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 110 KLPEREREVL-VLRYLEGLSYKEIAEIL-GISVGTVKRRLKRAR 151 (158)
T ss_pred hCCHHHHHHH-hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3455555554 44444688899999999 779999999876644
No 49
>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=77.95 E-value=4.8 Score=25.52 Aligned_cols=32 Identities=16% Similarity=0.368 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
|.-|..+...+|..|..+|.+| |=|+.+|...
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~~i 33 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIYRC 33 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHHHH
Confidence 3456677899999999999999 8888887654
No 50
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=76.34 E-value=8.4 Score=25.62 Aligned_cols=41 Identities=12% Similarity=0.137 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 31 MSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 31 wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
.++++-+ ++.++-..|-.+..||..| |-+...|+++....+
T Consensus 129 L~~~~r~-vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~ 169 (182)
T PRK09652 129 LPEELRT-AITLREIEGLSYEEIAEIM-GCPIGTVRSRIFRAR 169 (182)
T ss_pred CCHHHHH-HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3444434 3344445678899999999 899999999876433
No 51
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=75.74 E-value=8.5 Score=25.51 Aligned_cols=34 Identities=12% Similarity=0.131 Sum_probs=26.0
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
++.++-..|-....||..| |-+...|+++.....
T Consensus 133 i~~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~ 166 (179)
T PRK11924 133 VFLLRYVEGLSYREIAEIL-GVPVGTVKSRLRRAR 166 (179)
T ss_pred HhhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3445445678899999999 899999999877533
No 52
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=74.07 E-value=9.8 Score=25.73 Aligned_cols=35 Identities=3% Similarity=-0.133 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 37 DLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 37 ~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
..++.+.-..|-.+..||..| |-|...|+++.+..
T Consensus 142 r~il~l~~~~~~s~~eIA~~l-gis~~~v~~~l~Ra 176 (187)
T PRK09641 142 RTVIVLKYIEDLSLKEISEIL-DLPVGTVKTRIHRG 176 (187)
T ss_pred HHHhhhHHhhCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 344445555677889999998 88999998877543
No 53
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=73.78 E-value=10 Score=26.29 Aligned_cols=36 Identities=14% Similarity=0.028 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 35 EEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 35 ED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
++..|+.++-..|-....||..| |-+.+.|+++...
T Consensus 138 ~~r~i~~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~r 173 (192)
T PRK09643 138 EQRAALVAVDMQGYSVADAARML-GVAEGTVKSRCAR 173 (192)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 34455666666778899999999 8999999999854
No 54
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=73.53 E-value=13 Score=25.29 Aligned_cols=38 Identities=5% Similarity=-0.032 Sum_probs=27.1
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 37 DLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 37 ~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
..|+.++-..|-....||..| |-+.+.|+.+....+++
T Consensus 137 r~v~~l~~~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 137 RDVVQSISVEGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred HHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 334445544577788999998 89999999987655443
No 55
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=73.27 E-value=9.2 Score=26.68 Aligned_cols=40 Identities=15% Similarity=0.145 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 33 EQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 33 ~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
+++...++.+....|-.+.+||..| |-+...|+++|...-
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 3445566667776788999999999 999999999997643
No 56
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=72.19 E-value=4.7 Score=34.14 Aligned_cols=52 Identities=19% Similarity=0.314 Sum_probs=43.9
Q ss_pred ccccCCCccc----CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 19 EEVSSIEWEF----INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 19 ~~v~s~~lkk----g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
..|+++.+.+ +.||.+|=++-...-..+|..-+.|+..+|+|+..+||.-+.
T Consensus 396 ~~vn~~t~sk~~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~ 451 (584)
T KOG2009|consen 396 RPVNYATYSKKLETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFK 451 (584)
T ss_pred cccchhhccCccccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHh
Confidence 3455555443 589999999999999999999999999999999999998664
No 57
>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=71.44 E-value=9.8 Score=24.06 Aligned_cols=32 Identities=16% Similarity=0.286 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
|..|..+-..+|..|..+|..| |=+...|.+.
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~i 35 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQI 35 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHHH
Confidence 4566677788999999999999 8888777665
No 58
>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=71.20 E-value=20 Score=28.58 Aligned_cols=44 Identities=27% Similarity=0.387 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHHHh-CCc---HHHHhhhCCCCCHHHHHHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLV-GDR---WALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~-G~k---W~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
..||.-|...|+.+-... |.. -..|++.|+||+..+|.++-+.+
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~L 69 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQL 69 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHH
Confidence 379999988887766554 533 57899999999999999976543
No 59
>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=70.03 E-value=10 Score=25.69 Aligned_cols=33 Identities=12% Similarity=0.044 Sum_probs=23.4
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
++.++-..|-....||..| |=|.+.|+++.+..
T Consensus 146 v~~l~~~~~~s~~EIA~~l-gis~~tv~~~l~ra 178 (190)
T TIGR02939 146 AITLRELEGLSYEDIARIM-DCPVGTVRSRIFRA 178 (190)
T ss_pred hhhhhhhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3344444566788888888 88889998887543
No 60
>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=69.86 E-value=7.8 Score=23.99 Aligned_cols=34 Identities=18% Similarity=0.392 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
|..|..+...+|..|..+|..| |=++..|...=.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~~i~~ 37 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDIDLIKA 37 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHHHHHH
Confidence 4456667788999999999999 788877766543
No 61
>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=69.74 E-value=11 Score=23.56 Aligned_cols=35 Identities=17% Similarity=0.404 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
|-|.++=++ +-..+|..|..+|..| |=++.+|...
T Consensus 4 ~~t~~~l~~---ia~~iG~~Wk~Lar~L-Gls~~dI~~i 38 (86)
T cd08318 4 PVTGEQITV---FANKLGEDWKTLAPHL-EMKDKEIRAI 38 (86)
T ss_pred CCCHHHHHH---HHHHHhhhHHHHHHHc-CCCHHHHHHH
Confidence 445555554 3488999999999999 8898888653
No 62
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=69.72 E-value=13 Score=21.08 Aligned_cols=44 Identities=14% Similarity=0.139 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHH
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQA 76 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~ 76 (91)
.+|+.|-++|..+. -|..=..||..+ |.+...|+.+....+++-
T Consensus 3 ~LT~~E~~vl~~l~--~G~~~~eIA~~l-~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLA--QGMSNKEIAEEL-GISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHH--TTS-HHHHHHHH-TSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHH--hcCCcchhHHhc-CcchhhHHHHHHHHHHHh
Confidence 57888888665443 377788999999 999999999988777663
No 63
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=69.71 E-value=17 Score=23.88 Aligned_cols=34 Identities=9% Similarity=-0.008 Sum_probs=25.7
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
++.++-..|-....||..| |-+.+.|+++.+..+
T Consensus 114 v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~ 147 (161)
T PRK09047 114 AFLLRYWEDMDVAETAAAM-GCSEGSVKTHCSRAT 147 (161)
T ss_pred HHHHHHHhcCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3445555577789999999 899999999876543
No 64
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=69.47 E-value=15 Score=24.80 Aligned_cols=32 Identities=16% Similarity=0.083 Sum_probs=24.1
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
++.+.-..|-.-..||..| |.+.+.|+++.+-
T Consensus 137 i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~R 168 (179)
T PRK12514 137 AVRRAYLEGLSYKELAERH-DVPLNTMRTWLRR 168 (179)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCChHHHHHHHHH
Confidence 3444444577788999999 9999999998764
No 65
>PRK04217 hypothetical protein; Provisional
Probab=69.27 E-value=27 Score=23.28 Aligned_cols=49 Identities=16% Similarity=0.021 Sum_probs=36.6
Q ss_pred CcccCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 25 EWEFINMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 25 ~lkkg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
++.-...|++| ..++.+...-|-....||..| |-+.+.|+++++...++
T Consensus 37 ~~p~~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 37 PKPPIFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred CCCcccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33344566766 456667766788899999999 99999999999864433
No 66
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=68.87 E-value=17 Score=24.83 Aligned_cols=37 Identities=14% Similarity=0.066 Sum_probs=29.3
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
.++.|+..-|-...+||..| |-+.+.|+.+.+..+..
T Consensus 134 ~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~ 170 (178)
T PRK12529 134 QAFLMATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVT 170 (178)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44666666688899999999 99999999988755544
No 67
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=68.72 E-value=14 Score=25.00 Aligned_cols=31 Identities=3% Similarity=-0.159 Sum_probs=21.7
Q ss_pred HHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 41 RMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 41 ~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
.+.-..|-....||..| |-+.+.|+++.+-.
T Consensus 146 ~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Ra 176 (187)
T TIGR02948 146 VLKYMEDLSLKEISEIL-DLPVGTVKTRIHRG 176 (187)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 33333466678888888 88888888876543
No 68
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=68.51 E-value=17 Score=24.90 Aligned_cols=35 Identities=6% Similarity=0.001 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
.++.++-..|-....||..| |-+.+.|+++.+...
T Consensus 138 ~vl~l~~~~~~s~~eIA~~l-gis~~tV~~~l~Rar 172 (189)
T PRK12515 138 EIIDLVYYHEKSVEEVGEIV-GIPESTVKTRMFYAR 172 (189)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 34445555678889999999 889999999886533
No 69
>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=67.82 E-value=8.3 Score=24.03 Aligned_cols=34 Identities=26% Similarity=0.566 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 034546 33 EQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 33 ~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
+||-+.|+.. ..+|..|...|..| |=++..|.+.
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~i 35 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDTF 35 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHHH
Confidence 5777777732 24788899999999 8999999885
No 70
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=67.44 E-value=17 Score=26.06 Aligned_cols=46 Identities=9% Similarity=-0.045 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQAF 77 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~ 77 (91)
..+|+.|-++|-.+- -|-.=.+||..| +.+..-||+|....++|--
T Consensus 147 ~~LT~RE~eVL~lla--~G~snkeIA~~L-~iS~~TVk~h~~~i~~KL~ 192 (211)
T COG2197 147 ELLTPRELEVLRLLA--EGLSNKEIAEEL-NLSEKTVKTHVSNILRKLG 192 (211)
T ss_pred CCCCHHHHHHHHHHH--CCCCHHHHHHHH-CCCHhHHHHHHHHHHHHcC
Confidence 378999988765443 377778999999 9999999999999988743
No 71
>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=66.97 E-value=11 Score=22.79 Aligned_cols=32 Identities=16% Similarity=0.487 Sum_probs=22.7
Q ss_pred HHHHHHHHHH-hCCcHHHHhhhCCCCCHHHHHHH
Q 034546 36 EDLIYRMYKL-VGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 36 D~lLi~l~~~-~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
++.|..+... +|+.|..+|..| |=++..|...
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i~~i 37 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADIDQI 37 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHHHHH
Confidence 3445555566 899999999999 5566666553
No 72
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=66.83 E-value=18 Score=24.97 Aligned_cols=37 Identities=16% Similarity=0.030 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
+..++.+.-..|-....||..| |-+.+.|+++.....
T Consensus 111 ~r~i~~l~~~~g~~~~EIA~~l-gis~~tV~~~l~Rar 147 (181)
T PRK09637 111 YAEALRLTELEGLSQKEIAEKL-GLSLSGAKSRVQRGR 147 (181)
T ss_pred HHHHHHHHHhcCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 3444555555678889999999 899999999876443
No 73
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=66.60 E-value=21 Score=23.64 Aligned_cols=35 Identities=11% Similarity=-0.084 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 37 DLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 37 ~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
..++.++-..|-.-..||..| |-+.+.|+++-+..
T Consensus 112 r~v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra 146 (160)
T PRK09642 112 RDVVLAHYLEEKSYQEIALQE-KIEVKTVEMKLYRA 146 (160)
T ss_pred HHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 344445555577778899998 89999999987643
No 74
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=66.59 E-value=19 Score=24.92 Aligned_cols=36 Identities=6% Similarity=0.031 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
+..++.++-..|-....||..| |-+.+.|+.+.+..
T Consensus 139 ~R~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~RA 174 (189)
T PRK12530 139 QARVFMMREYLELSSEQICQEC-DISTSNLHVLLYRA 174 (189)
T ss_pred HHHHHhHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 3445555555678889999999 99999999986643
No 75
>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=66.47 E-value=17 Score=18.83 Aligned_cols=39 Identities=15% Similarity=0.139 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 31 MSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 31 wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
.++++-.+ +.++-..|-.+..||..+ |=+...|+.+.+.
T Consensus 11 l~~~~~~~-~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~ 49 (55)
T cd06171 11 LPEREREV-ILLRFGEGLSYEEIAEIL-GISRSTVRQRLHR 49 (55)
T ss_pred CCHHHHHH-HHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 45555444 445445677899999998 7888888776544
No 76
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=66.29 E-value=21 Score=24.08 Aligned_cols=39 Identities=21% Similarity=0.250 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
+..++.|+-..|-....||..| |-+.+.|+++-...+++
T Consensus 124 ~r~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 162 (172)
T PRK12523 124 ARAAFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQ 162 (172)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4455666666678899999999 99999999987654443
No 77
>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=65.88 E-value=4.3 Score=25.56 Aligned_cols=17 Identities=0% Similarity=-0.056 Sum_probs=9.7
Q ss_pred CCcccCCCCHHHHHHHH
Q 034546 24 IEWEFINMSEQEEDLIY 40 (91)
Q Consensus 24 ~~lkkg~wT~eED~lLi 40 (91)
|.-..|-||+++|+.|.
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 55556899999999984
No 78
>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=65.76 E-value=12 Score=23.53 Aligned_cols=32 Identities=19% Similarity=0.354 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
|..|-.+-..+|..|..+|..| |=++..|.+.
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~i 35 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQI 35 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHHH
Confidence 3445566688999999999999 8899888874
No 79
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=65.43 E-value=20 Score=24.39 Aligned_cols=41 Identities=12% Similarity=-0.019 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 34 QEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 34 eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
+-|..|+.+-..-| -.|+.||..+ |-+...|.+|+..+...
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence 45666666655555 5699999999 99999999999765544
No 80
>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=65.13 E-value=20 Score=23.97 Aligned_cols=33 Identities=6% Similarity=-0.053 Sum_probs=21.9
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 40 YRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 40 i~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
+.++-..|-....||..| |=|.+.|+++.+..+
T Consensus 128 ~~l~~~~g~s~~eiA~~l-gis~~tv~~~l~Ra~ 160 (169)
T TIGR02954 128 IILRYYHDLTIKEIAEVM-NKPEGTVKTYLHRAL 160 (169)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 334444466677788877 778888888776443
No 81
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=64.80 E-value=23 Score=23.77 Aligned_cols=35 Identities=14% Similarity=-0.015 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
.++.|+-..|-.-..||..| |-+.+.|+.+.+..+
T Consensus 125 ~vl~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~ 159 (173)
T PRK09645 125 AVLVRSYYRGWSTAQIAADL-GIPEGTVKSRLHYAL 159 (173)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 34445555567778899988 889999999876433
No 82
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=64.61 E-value=25 Score=23.26 Aligned_cols=34 Identities=21% Similarity=0.209 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
.|+.++-..|-.-..||..| |-+.+.|+++....
T Consensus 112 ~v~~l~~~~~~s~~eIA~~l-gis~~tv~~~l~ra 145 (159)
T PRK12527 112 DSFLLRKLEGLSHQQIAEHL-GISRSLVEKHIVNA 145 (159)
T ss_pred HHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHH
Confidence 34445444566678899988 89999999987643
No 83
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=63.99 E-value=23 Score=24.10 Aligned_cols=34 Identities=21% Similarity=-0.055 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
.++.++-..|-...+||..| |-+...|+++-+..
T Consensus 136 ~v~~l~~~~g~s~~EIA~~l-~is~~tV~~~l~ra 169 (181)
T PRK12536 136 LPIVHVKLEGLSVAETAQLT-GLSESAVKVGIHRG 169 (181)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 34556666788899999999 99999999986543
No 84
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=63.73 E-value=11 Score=26.99 Aligned_cols=36 Identities=14% Similarity=0.275 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHH
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIE 66 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vK 66 (91)
.||+|--++|..|..+ |=.=++||..|.|=+-|+|=
T Consensus 2 nWtdERve~LkKLWse-GLSASQIAaQLGGVsRnAVI 37 (169)
T COG5352 2 NWTDERVETLKKLWSE-GLSASQIAAQLGGVSRNAVI 37 (169)
T ss_pred CchHHHHHHHHHHHHc-ccCHHHHHHHhcCcchhhhh
Confidence 6999999999988875 66779999999998888863
No 85
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=63.18 E-value=21 Score=24.42 Aligned_cols=33 Identities=9% Similarity=0.028 Sum_probs=22.8
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
++.+.-..|-....||..| |-+.+.|+++.+..
T Consensus 146 v~~l~~~~g~s~~eIA~~l-gis~~tv~~~l~Ra 178 (193)
T PRK11923 146 ALTLREFDGLSYEDIASVM-QCPVGTVRSRIFRA 178 (193)
T ss_pred HHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 4444444566678888888 78888888877643
No 86
>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=62.71 E-value=14 Score=23.39 Aligned_cols=27 Identities=26% Similarity=0.486 Sum_probs=23.3
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHH
Q 034546 42 MYKLVGDRWALIAGRIPGRKAEEIERFW 69 (91)
Q Consensus 42 l~~~~G~kW~~Ia~~lpGRt~n~vKnrw 69 (91)
+...+|..|..+|..| |=+++.|.+.=
T Consensus 8 l~~~lG~~Wk~lar~L-G~s~~eI~~ie 34 (86)
T cd08777 8 LRENLGKKWKRCARKL-GFTESEIEEID 34 (86)
T ss_pred HHHHHHHHHHHHHHHc-CCCHHHHHHHH
Confidence 4478899999999999 89999998853
No 87
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=62.26 E-value=29 Score=23.03 Aligned_cols=37 Identities=14% Similarity=0.202 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
+..++.++-..|-....||..| |-+.+.|+++....+
T Consensus 118 ~r~v~~L~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~ 154 (161)
T PRK12528 118 VKRAFLLAQVDGLGYGEIATEL-GISLATVKRYLNKAA 154 (161)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3445556666677788898888 888888888765443
No 88
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=61.98 E-value=24 Score=24.31 Aligned_cols=37 Identities=16% Similarity=0.062 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
...++.|.-..|-...+||..| |-+.+.|+++.+..+
T Consensus 135 ~r~v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~Rar 171 (185)
T PRK09649 135 QREALLLTQLLGLSYADAAAVC-GCPVGTIRSRVARAR 171 (185)
T ss_pred HhHHhhhHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3445556666677788999999 899999999875433
No 89
>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=61.02 E-value=27 Score=23.07 Aligned_cols=39 Identities=8% Similarity=-0.045 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 34 QEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 34 eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
+++..++.++-..|-.-..||..| |-+...|+++.....
T Consensus 113 ~~~r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~ 151 (162)
T TIGR02983 113 ARQRAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRAL 151 (162)
T ss_pred HHHHHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 344555666666677788899988 889999999876544
No 90
>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=60.67 E-value=30 Score=23.29 Aligned_cols=33 Identities=21% Similarity=0.284 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
.++.++-.-|-....||..| |-+...|+++.+.
T Consensus 141 ~v~~l~~~~g~s~~EIA~~l-gis~~tVk~~l~R 173 (183)
T TIGR02999 141 EVVELRFFAGLTVEEIAELL-GVSVRTVERDWRF 173 (183)
T ss_pred HHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHH
Confidence 34445555567788899988 8999999998754
No 91
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=60.45 E-value=30 Score=23.46 Aligned_cols=31 Identities=10% Similarity=-0.072 Sum_probs=21.9
Q ss_pred HHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 41 RMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 41 ~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
.++-..|-.-..||..| |-+.+.|+++.+..
T Consensus 145 ~l~~~~~~s~~eIA~~l-gis~~~V~~~l~ra 175 (186)
T PRK13919 145 EVLYYQGYTHREAAQLL-GLPLGTLKTRARRA 175 (186)
T ss_pred HHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 33344466678888888 88888888876643
No 92
>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=59.89 E-value=20 Score=22.48 Aligned_cols=34 Identities=21% Similarity=0.322 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
.+--+...+|..|..+|..| |=|+++|...=..+
T Consensus 4 ~f~~i~~~lG~~Wk~laR~L-Glse~~Id~i~~~~ 37 (86)
T cd08306 4 AFDVICENVGRDWRKLARKL-GLSETKIESIEEAH 37 (86)
T ss_pred HHHHHHHHHhhhHHHHHHHc-CCCHHHHHHHHHHC
Confidence 33345567899999999999 88888877654433
No 93
>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=59.86 E-value=31 Score=22.77 Aligned_cols=30 Identities=10% Similarity=-0.003 Sum_probs=19.6
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 40 YRMYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 40 i~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
+.++-..|-....||..| |-+.+.|+++-.
T Consensus 131 l~l~~~~g~s~~eIA~~l-~is~~tv~~~l~ 160 (170)
T TIGR02952 131 IALRFGQNLPIAEVARIL-GKTEGAVKILQF 160 (170)
T ss_pred HHHHHhcCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 334333466667788887 777888877653
No 94
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=59.49 E-value=31 Score=23.63 Aligned_cols=34 Identities=9% Similarity=-0.007 Sum_probs=24.7
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
++.++-..|-.-..||..| |-+.+.|+++.+...
T Consensus 139 v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Rar 172 (191)
T PRK12520 139 VFMMREWLELETEEICQEL-QITATNAWVLLYRAR 172 (191)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 4444444566778899988 899999999876443
No 95
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=59.37 E-value=32 Score=23.47 Aligned_cols=34 Identities=15% Similarity=0.010 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
.|+.++-..|-...+||..| |-+.+.|+.+.+..
T Consensus 146 ~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra 179 (189)
T PRK09648 146 EILILRVVVGLSAEETAEAV-GSTPGAVRVAQHRA 179 (189)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 34445444577788899988 88888888876543
No 96
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=59.10 E-value=44 Score=23.04 Aligned_cols=34 Identities=6% Similarity=-0.080 Sum_probs=23.9
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
|+.++-.-|-...+||..| |-+.+.|+++.+..+
T Consensus 149 v~~l~~~eg~s~~EIA~~l-gis~~tVk~rl~ra~ 182 (194)
T PRK12531 149 VLQAVYLEELPHQQVAEMF-DIPLGTVKSRLRLAV 182 (194)
T ss_pred HHHHHHHcCCCHHHHHHHh-CcCHHHHHHHHHHHH
Confidence 4445444566778888888 888888888765433
No 97
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=59.00 E-value=51 Score=22.60 Aligned_cols=33 Identities=9% Similarity=0.097 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
.++.++-..|-.-..||..| |-+.+.|+++.+.
T Consensus 143 ~i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~R 175 (195)
T PRK12532 143 RVFTLKEILGFSSDEIQQMC-GISTSNYHTIMHR 175 (195)
T ss_pred HHhhhHHHhCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 34445555677788999999 9999999998775
No 98
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=58.90 E-value=31 Score=23.50 Aligned_cols=34 Identities=18% Similarity=0.072 Sum_probs=24.2
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
|+.++-..|-.-..||..| |-+.+.|+++.+..+
T Consensus 141 i~~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~ 174 (182)
T PRK12537 141 CILHAYVDGCSHAEIAQRL-GAPLGTVKAWIKRSL 174 (182)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCChhhHHHHHHHHH
Confidence 3455544566678888888 888888888876544
No 99
>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=58.67 E-value=34 Score=23.65 Aligned_cols=34 Identities=9% Similarity=0.114 Sum_probs=25.2
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
++.++-.-|-....||..| |-+.+.|+.+.....
T Consensus 139 v~~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar 172 (188)
T TIGR02943 139 VFMMREVLGFESDEICQEL-EISTSNCHVLLYRAR 172 (188)
T ss_pred HHHHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 4455555577788899998 899999988876443
No 100
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=58.53 E-value=25 Score=23.76 Aligned_cols=35 Identities=14% Similarity=0.284 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
.|+.++-..|-...+||..| |-+.+.|+++....+
T Consensus 126 ~i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra~ 160 (172)
T PRK09651 126 EAFLLSQLDGLTYSEIAHKL-GVSVSSVKKYVAKAT 160 (172)
T ss_pred HHhhhhhccCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 34445555577789999999 999999999876443
No 101
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=58.34 E-value=23 Score=31.26 Aligned_cols=43 Identities=5% Similarity=0.152 Sum_probs=39.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
..||+.|-.+.-.++-.+....-.|++.++|.|-.+|-.+|++
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 4799999999988888888899999999999999999998775
No 102
>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=58.11 E-value=30 Score=18.94 Aligned_cols=37 Identities=19% Similarity=0.250 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 34 QEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 34 eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
+-|..|+.+...-| -.|..||..+ |=|...|.+|+..
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHH
Confidence 44667777666666 4599999999 9999999998753
No 103
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=57.24 E-value=37 Score=24.47 Aligned_cols=49 Identities=8% Similarity=0.089 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQAFADR 80 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~~~ 80 (91)
...|+.|-++|..+.. |-...+||..| +-+...|+++-...++|--...
T Consensus 154 ~~Lt~rE~~Vl~l~~~--G~s~~eIA~~L-~iS~~TVk~~~~~i~~Kl~v~n 202 (216)
T PRK10100 154 ALLTHREKEILNKLRI--GASNNEIARSL-FISENTVKTHLYNLFKKIAVKN 202 (216)
T ss_pred CCCCHHHHHHHHHHHc--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHhCCCC
Confidence 3589888887765544 88899999999 8999999999888777644333
No 104
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=57.20 E-value=39 Score=22.01 Aligned_cols=29 Identities=14% Similarity=0.022 Sum_probs=18.5
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 42 MYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 42 l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
++-.-|-....||..| |-+.+.|+++-..
T Consensus 117 l~~~~~~s~~EIA~~l-~is~~tV~~~~~r 145 (154)
T PRK06759 117 ERFFVGKTMGEIALET-EMTYYQVRWIYRQ 145 (154)
T ss_pred HHHhcCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 3333455667777777 7777777776443
No 105
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=56.85 E-value=38 Score=24.00 Aligned_cols=43 Identities=14% Similarity=0.135 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
..|+.|-++|-.+.. |....+||..| |-+..-|+++-...++|
T Consensus 137 ~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 137 SLSRTESSMLRMWMA--GQGTIQISDQM-NIKAKTVSSHKGNIKRK 179 (207)
T ss_pred cCCHHHHHHHHHHHc--CCCHHHHHHHc-CCCHHHHHHHHHHHHHH
Confidence 499999988754443 88889999999 89999999998777766
No 106
>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=56.77 E-value=10 Score=24.85 Aligned_cols=25 Identities=8% Similarity=-0.012 Sum_probs=19.0
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 47 GDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 47 G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
|-.+..||..| |=+...|+++.+..
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra 145 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRA 145 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHH
Confidence 55678888888 78888888877644
No 107
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.23 E-value=48 Score=21.17 Aligned_cols=42 Identities=19% Similarity=0.157 Sum_probs=34.8
Q ss_pred cCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCC-CHHHHHHHHH
Q 034546 28 FINMSEQEEDLIYRMYKLVGDRWALIAGRIPGR-KAEEIERFWI 70 (91)
Q Consensus 28 kg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGR-t~n~vKnrw~ 70 (91)
.-.||+|+-.-|+.++..-|..=+.||..+ |- ..+.+...+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHH
Confidence 358999999999999999888888999999 75 7777776544
No 108
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=55.83 E-value=19 Score=19.48 Aligned_cols=34 Identities=26% Similarity=0.360 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 034546 33 EQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 33 ~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
.++-..++.++.. |-....||..| |-+.+.|.+.
T Consensus 4 ~~~R~~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~w 37 (50)
T PF13384_consen 4 EERRAQIIRLLRE-GWSIREIAKRL-GVSRSTVYRW 37 (50)
T ss_dssp ------HHHHHHH-T--HHHHHHHH-TS-HHHHHHH
T ss_pred hhHHHHHHHHHHC-CCCHHHHHHHH-CcCHHHHHHH
Confidence 3445567777777 98999999999 8888888764
No 109
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=54.53 E-value=46 Score=22.26 Aligned_cols=34 Identities=12% Similarity=-0.085 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
.++.++..-|-....||..| |-+...|+++-+..
T Consensus 119 ~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~Ra 152 (164)
T PRK12547 119 EAIILIGASGFSYEDAAAIC-GCAVGTIKSRVSRA 152 (164)
T ss_pred HHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHHHH
Confidence 34555555677788888888 88888888876543
No 110
>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=54.33 E-value=43 Score=22.50 Aligned_cols=34 Identities=21% Similarity=0.411 Sum_probs=22.9
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
++.++-..|-....||..| |-|.+.|+++.+..+
T Consensus 148 vi~l~~~~g~s~~eIA~~l-gis~~~v~~~l~Ra~ 181 (189)
T TIGR02984 148 VILLRHLEGLSFAEVAERM-DRSEGAVSMLWVRGL 181 (189)
T ss_pred HHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3344444566778888887 888888888765433
No 111
>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=54.10 E-value=33 Score=25.47 Aligned_cols=33 Identities=15% Similarity=0.140 Sum_probs=25.7
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
++.|+...|-.-..||..| |-+.+.|+++-+..
T Consensus 150 v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra 182 (324)
T TIGR02960 150 VLLLRDVLGWRAAETAELL-GTSTASVNSALQRA 182 (324)
T ss_pred HhhhHHHhCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 3445555677789999999 99999999987643
No 112
>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=53.85 E-value=19 Score=22.61 Aligned_cols=29 Identities=21% Similarity=0.375 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIER 67 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKn 67 (91)
-|..+-..+|..|..+|.+| |=++..|..
T Consensus 4 ~l~~ia~~LG~~Wk~lar~L-Glse~~Id~ 32 (86)
T cd08779 4 NLLSIAGRLGLDWQAIGLHL-GLSYRELQR 32 (86)
T ss_pred HHHHHHHHHhHHHHHHHHHc-CCCHHHHHH
Confidence 35667789999999999998 666665433
No 113
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=53.47 E-value=68 Score=21.72 Aligned_cols=46 Identities=11% Similarity=-0.142 Sum_probs=28.9
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH---HHhhHHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWI---MRHGQAFADRRRELR 85 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~---~~l~k~~~~~~~~~~ 85 (91)
|+.+.-..|-.-.+||..| |-+...|+++-+ ..|++.+.....+..
T Consensus 125 i~~l~~~e~~s~~EIA~~l-gis~~tV~~~l~ra~~~Lr~~l~~~~~~~~ 173 (179)
T PRK12543 125 VIILRYLHDYSQEEIAQLL-QIPIGTVKSRIHAALKKLRQKEQIEEIFLG 173 (179)
T ss_pred HHHHHHHccCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4444444566677888888 788888888755 344455555555444
No 114
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=53.43 E-value=40 Score=22.91 Aligned_cols=32 Identities=9% Similarity=-0.024 Sum_probs=21.8
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
|+.+.-..|-....||..| |-+.+.|+++.+.
T Consensus 136 i~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~R 167 (186)
T PRK05602 136 AIVLQYYQGLSNIEAAAVM-DISVDALESLLAR 167 (186)
T ss_pred HhhHHHhcCCCHHHHHHHh-CcCHHHHHHHHHH
Confidence 3444444566677888887 7888888887654
No 115
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=53.24 E-value=35 Score=23.42 Aligned_cols=42 Identities=12% Similarity=-0.019 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 33 EQEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 33 ~eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
++-|..||.+-..-| -.|+.||..+ |=+...|.+|+..+...
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQ 55 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHC
Confidence 345666665555444 5699999999 99999999999766544
No 116
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=53.11 E-value=44 Score=23.34 Aligned_cols=32 Identities=9% Similarity=0.075 Sum_probs=23.5
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
++.|+-..|-.-..||..| |-+.+.|+++.+.
T Consensus 147 v~~L~~~eg~s~~EIA~~l-gis~~tVk~~l~R 178 (201)
T PRK12545 147 VFMMREFLDFEIDDICTEL-TLTANHCSVLLYR 178 (201)
T ss_pred HHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 3344444566778899998 8999999998653
No 117
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=53.06 E-value=45 Score=23.12 Aligned_cols=37 Identities=11% Similarity=-0.058 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 35 EEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 35 ED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
++..++.|+...|-...+||..| |-+.+.|+++-+..
T Consensus 120 ~~r~i~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Ra 156 (187)
T PRK12516 120 DQREAIILVGASGFAYEEAAEIC-GCAVGTIKSRVNRA 156 (187)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 34556667666788899999999 89999999986643
No 118
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=52.97 E-value=50 Score=24.43 Aligned_cols=46 Identities=13% Similarity=0.086 Sum_probs=37.2
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHHHH
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQAFA 78 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~ 78 (91)
..|+.|-++|.-+.. |-...+||..| |-+...|+++-...+.|--.
T Consensus 133 ~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkKLgV 178 (198)
T PRK15201 133 HFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRKLHV 178 (198)
T ss_pred CCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHhCC
Confidence 589999887754443 88899999999 99999999998887776433
No 119
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=52.48 E-value=46 Score=23.49 Aligned_cols=32 Identities=16% Similarity=0.154 Sum_probs=23.1
Q ss_pred HHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 41 RMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 41 ~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
.++-..|-.-..||..| |-+...|+++.....
T Consensus 148 ~L~~~~g~s~~EIA~~L-gis~~tV~~~l~RAr 179 (203)
T PRK09647 148 VLCDIEGLSYEEIAATL-GVKLGTVRSRIHRGR 179 (203)
T ss_pred HHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 34444566678888888 889999999876543
No 120
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=51.32 E-value=26 Score=22.16 Aligned_cols=29 Identities=24% Similarity=0.329 Sum_probs=21.3
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHH
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEI 65 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~v 65 (91)
|-.|-.+-+.+|..|..+|..| |=++..|
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~dI 32 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVEDI 32 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHHHH
Confidence 3445566788999999999998 5555543
No 121
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=51.21 E-value=61 Score=21.27 Aligned_cols=45 Identities=11% Similarity=0.123 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQA 76 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~ 76 (91)
.+.|+.|-+++.-+.. |-....||..| +-+++.|+++.....+|-
T Consensus 136 ~~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHRANLMEKL 180 (196)
T ss_pred cCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHHh
Confidence 3689988887765443 66788999999 789999999988776663
No 122
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=51.06 E-value=51 Score=22.71 Aligned_cols=31 Identities=10% Similarity=0.010 Sum_probs=21.0
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
++.++-..|-...+||..| |-+...|+++-+
T Consensus 150 vl~l~~~~~~s~~EIA~~L-gis~~tVk~~l~ 180 (194)
T PRK09646 150 SVTLAYYGGLTYREVAERL-AVPLGTVKTRMR 180 (194)
T ss_pred HHHHHHHcCCCHHHHHHHh-CCChHhHHHHHH
Confidence 3344444566678888888 778888877654
No 123
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=50.97 E-value=52 Score=21.70 Aligned_cols=31 Identities=16% Similarity=0.157 Sum_probs=22.6
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
++.++- .|-.-..||..| |-+.+.|+++...
T Consensus 120 il~l~~-~g~s~~eIA~~l-gis~~tV~~~i~r 150 (166)
T PRK09639 120 VLLLRF-SGYSYKEIAEAL-GIKESSVGTTLAR 150 (166)
T ss_pred HHHHHH-cCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 333444 677778888888 8888999888754
No 124
>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=50.44 E-value=58 Score=21.23 Aligned_cols=28 Identities=14% Similarity=0.203 Sum_probs=16.6
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 42 MYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 42 l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
++-..|-.-..||..| |=+.+.|+++.+
T Consensus 122 l~~~~g~~~~eIA~~l-~is~~tv~~~l~ 149 (159)
T TIGR02989 122 LRYQRGVSLTALAEQL-GRTVNAVYKALS 149 (159)
T ss_pred HHHhcCCCHHHHHHHh-CCCHHHHHHHHH
Confidence 3333455556666666 666677776543
No 125
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=50.22 E-value=55 Score=22.46 Aligned_cols=34 Identities=21% Similarity=0.254 Sum_probs=22.7
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 37 DLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 37 ~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
..|+.++-.-|-.-..||..| |-|.+.|+++-+.
T Consensus 137 r~i~~l~~~~g~s~~EIAe~l-gis~~~V~~~l~R 170 (189)
T PRK06811 137 REIFIRRYLLGEKIEEIAKKL-GLTRSAIDNRLSR 170 (189)
T ss_pred HHHHHHHHHccCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 334444444466677888888 8888888887543
No 126
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=50.18 E-value=53 Score=22.66 Aligned_cols=32 Identities=16% Similarity=0.033 Sum_probs=24.0
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
|+.++-..|-.+..||..| |=+.+.|+++-.-
T Consensus 144 i~~L~~~~g~s~~eIA~~l-gis~~tV~~~l~R 175 (196)
T PRK12524 144 AVVLRHIEGLSNPEIAEVM-EIGVEAVESLTAR 175 (196)
T ss_pred HHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 4555555677788999988 8888888887653
No 127
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=49.83 E-value=38 Score=29.41 Aligned_cols=50 Identities=14% Similarity=0.418 Sum_probs=36.3
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCcHHHH-hhhCCCC---------CHHHHHHHHHHHhhH
Q 034546 26 WEFINMSEQEEDLIYRMYKLVGDRWALI-AGRIPGR---------KAEEIERFWIMRHGQ 75 (91)
Q Consensus 26 lkkg~wT~eED~lLi~l~~~~G~kW~~I-a~~lpGR---------t~n~vKnrw~~~l~k 75 (91)
+.+..||-+|++-.+....++|.....| -..+..| |-.+|+.+||..+.+
T Consensus 86 ~~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~ 145 (782)
T KOG4468|consen 86 WAKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRR 145 (782)
T ss_pred ccccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHH
Confidence 4566899999999999999999998776 2223333 455677777765554
No 128
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=49.82 E-value=40 Score=19.79 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=19.7
Q ss_pred HHHhCCcHHHHhhhCCCCCHHHHHHH
Q 034546 43 YKLVGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 43 ~~~~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
-...|+.|..+|..| |=+...|.+.
T Consensus 8 ~~~~~~~Wk~La~~L-g~~~~~i~~i 32 (83)
T PF00531_consen 8 AEDLGSDWKRLARKL-GLSESEIENI 32 (83)
T ss_dssp HHSHSTCHHHHHHHT-TS-HHHHHHH
T ss_pred hhcchhhHHHHHHHh-CcCHHHHHHH
Confidence 455789999999999 8888887764
No 129
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=49.77 E-value=47 Score=23.14 Aligned_cols=35 Identities=9% Similarity=-0.103 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 37 DLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 37 ~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
..++.|+...|-....||..| |-+...|+++-+..
T Consensus 119 r~v~~L~~~~g~s~~EIA~~L-giS~~tVk~~l~Ra 153 (188)
T PRK12546 119 REALILVGASGFSYEEAAEMC-GVAVGTVKSRANRA 153 (188)
T ss_pred hHHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 334556656788889999999 88999999976643
No 130
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=49.68 E-value=44 Score=18.44 Aligned_cols=43 Identities=5% Similarity=0.164 Sum_probs=34.0
Q ss_pred cCCCCHHHHHHHHHHHHHhC-C---cHHHHhhhCCCCCHHHHHHHHHH
Q 034546 28 FINMSEQEEDLIYRMYKLVG-D---RWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 28 kg~wT~eED~lLi~l~~~~G-~---kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
+..||++.-..|-..|.... + .-..||..| |=+..+|.+.|..
T Consensus 4 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~n 50 (57)
T PF00046_consen 4 RTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQN 50 (57)
T ss_dssp SSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHH
Confidence 45799999999999999733 1 146788888 9999999998754
No 131
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=49.64 E-value=60 Score=20.12 Aligned_cols=38 Identities=18% Similarity=0.292 Sum_probs=25.4
Q ss_pred HHHHHHHHhCC--------cHHHHhhhCCCC-----CHHHHHHHHHHHhhH
Q 034546 38 LIYRMYKLVGD--------RWALIAGRIPGR-----KAEEIERFWIMRHGQ 75 (91)
Q Consensus 38 lLi~l~~~~G~--------kW~~Ia~~lpGR-----t~n~vKnrw~~~l~k 75 (91)
.|..++..+|+ .|..||..|.-- .+..++..|..+|..
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 35555555553 699999998332 356788888877643
No 132
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=49.17 E-value=57 Score=22.18 Aligned_cols=33 Identities=6% Similarity=0.179 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
.++.+.-..|-....||..| |-+...|+++.+.
T Consensus 129 ~i~~l~~~~g~s~~EIA~~l-gis~~tVk~~l~R 161 (185)
T PRK12542 129 QVFKYKVFYNLTYQEISSVM-GITEANVRKQFER 161 (185)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 34445555677788999998 8999999997653
No 133
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=48.79 E-value=25 Score=25.22 Aligned_cols=34 Identities=9% Similarity=0.018 Sum_probs=24.3
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
|+.++-..|-....||..| |-+...|+++.+...
T Consensus 157 i~~l~~~~g~s~~EIAe~l-gis~~tVk~~l~Rar 190 (231)
T PRK11922 157 VFVLRVVEELSVEETAQAL-GLPEETVKTRLHRAR 190 (231)
T ss_pred hheeehhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3444444466778899998 899999999876433
No 134
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=48.77 E-value=52 Score=24.41 Aligned_cols=31 Identities=16% Similarity=0.281 Sum_probs=24.0
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 40 YRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 40 i~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
+.|+...|-.-.+||..| |.+...|+++.+.
T Consensus 124 ~~L~~~~g~s~~EIA~~l-g~s~~tVk~~l~R 154 (293)
T PRK09636 124 FLLHDVFGVPFDEIASTL-GRSPAACRQLASR 154 (293)
T ss_pred HHHHHHhCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 345555677778999999 9999999998754
No 135
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=48.43 E-value=20 Score=24.01 Aligned_cols=31 Identities=10% Similarity=-0.005 Sum_probs=21.8
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 40 YRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 40 i~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
+.++-..|-....||..| |-+...|+++.+.
T Consensus 135 ~~l~~~~g~s~~eIA~~l-~is~~~V~~~l~r 165 (176)
T PRK09638 135 VILKHYYGYTYEEIAKML-NIPEGTVKSRVHH 165 (176)
T ss_pred eeehhhcCCCHHHHHHHH-CCChhHHHHHHHH
Confidence 344444577788888888 7788888876653
No 136
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=48.23 E-value=60 Score=22.97 Aligned_cols=33 Identities=6% Similarity=0.069 Sum_probs=24.1
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 40 YRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 40 i~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
+.++-..|-.-..||..| |-|.+.|+++.+-.+
T Consensus 157 ~~L~~~~g~s~~EIAe~l-gis~~tV~~~l~RAr 189 (206)
T PRK12544 157 FMMREFIELETNEICHAV-DLSVSNLNVLLYRAR 189 (206)
T ss_pred HHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 334444566678999999 999999999876433
No 137
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=47.49 E-value=62 Score=22.65 Aligned_cols=33 Identities=3% Similarity=-0.064 Sum_probs=23.2
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
++.++-..|-.-..||..| |-+.+.|+++.+..
T Consensus 161 vl~l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra 193 (206)
T PRK12526 161 VVKGVYFQELSQEQLAQQL-NVPLGTVKSRLRLA 193 (206)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 3444444466678888888 88999998876543
No 138
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=47.49 E-value=61 Score=22.37 Aligned_cols=33 Identities=9% Similarity=0.008 Sum_probs=23.1
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 40 YRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 40 i~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
+.++-..|-....||..| |-+...|+++.....
T Consensus 120 ~~L~~~eg~s~~EIA~~l-gis~~tV~~~l~Rar 152 (182)
T PRK12511 120 LHLVAIEGLSYQEAAAVL-GIPIGTLMSRIGRAR 152 (182)
T ss_pred HHHHHHcCCCHHHHHHHh-CcCHHHHHHHHHHHH
Confidence 334444566678888888 888888888875433
No 139
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=47.13 E-value=55 Score=22.25 Aligned_cols=31 Identities=10% Similarity=-0.025 Sum_probs=19.1
Q ss_pred HHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 41 RMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 41 ~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
.++-..|-.-..||..| |-+.+.|+++....
T Consensus 137 ~l~~~~g~s~~EIA~~l-~is~~tv~~~l~Ra 167 (179)
T PRK09415 137 YLFYYEELSIKEIAEVT-GVNENTVKTRLKKA 167 (179)
T ss_pred HhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 34444455667777777 66777777766543
No 140
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (DDs) are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=46.02 E-value=28 Score=20.45 Aligned_cols=28 Identities=25% Similarity=0.570 Sum_probs=20.9
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHH
Q 034546 40 YRMYKLVGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 40 i~l~~~~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
..+...+|+.|..+|..| |=++..|...
T Consensus 3 ~~ia~~lg~~W~~la~~L-gl~~~~I~~i 30 (79)
T cd01670 3 DKLAKKLGKDWKKLARKL-GLSDGEIDQI 30 (79)
T ss_pred HHHHHHHhhHHHHHHHHh-CCCHHHHHHH
Confidence 345577899999999999 5666666653
No 141
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=45.25 E-value=77 Score=21.37 Aligned_cols=33 Identities=18% Similarity=0.062 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
.++.++-..|-.-.+||..| |-+...|+++...
T Consensus 107 ~v~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~R 139 (170)
T TIGR02959 107 EAIRLTELEGLSQQEIAEKL-GLSLSGAKSRVQR 139 (170)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 34445555566678888888 8888888887654
No 142
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=45.25 E-value=64 Score=22.56 Aligned_cols=33 Identities=9% Similarity=0.020 Sum_probs=23.4
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 40 YRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 40 i~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
+.+.-..|-.-..||..| |-+.+.|+++.+..+
T Consensus 142 ~~l~~~~g~s~~EIAe~l-gis~~tV~~~l~Rar 174 (196)
T PRK12535 142 LILTQVLGYTYEEAAKIA-DVRVGTIRSRVARAR 174 (196)
T ss_pred hhhHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 334444455668889888 899999999876433
No 143
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=44.69 E-value=33 Score=15.56 Aligned_cols=36 Identities=22% Similarity=0.351 Sum_probs=23.7
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIER 67 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKn 67 (91)
.+++++-..|+.++. -|..+..||..+ |.+...|.+
T Consensus 5 ~~~~~~~~~i~~~~~-~~~s~~~ia~~~-~is~~tv~~ 40 (42)
T cd00569 5 KLTPEQIEEARRLLA-AGESVAEIARRL-GVSRSTLYR 40 (42)
T ss_pred cCCHHHHHHHHHHHH-cCCCHHHHHHHH-CCCHHHHHH
Confidence 456655556666654 466788899887 667666654
No 144
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=44.49 E-value=53 Score=23.83 Aligned_cols=34 Identities=9% Similarity=-0.078 Sum_probs=24.8
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
++.|+-..|-.-..||..| |-+.+.|+++-+..+
T Consensus 179 v~~L~~~eg~s~~EIA~~L-gis~~tVk~~l~RAr 212 (233)
T PRK12538 179 AVILSYHENMSNGEIAEVM-DTTVAAVESLLKRGR 212 (233)
T ss_pred HhhhHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3445555566778899998 899999998876433
No 145
>PRK00118 putative DNA-binding protein; Validated
Probab=44.13 E-value=91 Score=20.50 Aligned_cols=38 Identities=11% Similarity=0.024 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 33 EQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 33 ~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
++.+..++.++-..|-....||..+ |-|.+.|+++-..
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 4556666677777789999999999 9999999987654
No 146
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=44.00 E-value=64 Score=23.09 Aligned_cols=37 Identities=11% Similarity=0.127 Sum_probs=24.5
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhh
Q 034546 37 DLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHG 74 (91)
Q Consensus 37 ~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~ 74 (91)
..++.++-..|-....||..| |-+...|+++-+..++
T Consensus 190 r~vl~l~~~~g~s~~EIA~~l-gis~~tV~~~~~ra~~ 226 (236)
T PRK06986 190 QLVLSLYYQEELNLKEIGAVL-GVSESRVSQIHSQAIK 226 (236)
T ss_pred HHHHHhHhccCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334444444566678888888 8888888887654443
No 147
>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=43.78 E-value=68 Score=23.76 Aligned_cols=32 Identities=9% Similarity=0.198 Sum_probs=25.0
Q ss_pred HHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 40 YRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 40 i~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
+.|+..+|-.-.+||..| |.|...|+.+.+..
T Consensus 117 ~~L~~~~g~s~~EIA~~l-g~s~~tVr~~l~RA 148 (281)
T TIGR02957 117 FVLREVFDYPYEEIASIV-GKSEANCRQLVSRA 148 (281)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 445566677789999999 89999999987543
No 148
>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=43.10 E-value=77 Score=19.35 Aligned_cols=37 Identities=14% Similarity=0.271 Sum_probs=24.4
Q ss_pred HHHHHHHHhC--------CcHHHHhhhCCC---CC--HHHHHHHHHHHhh
Q 034546 38 LIYRMYKLVG--------DRWALIAGRIPG---RK--AEEIERFWIMRHG 74 (91)
Q Consensus 38 lLi~l~~~~G--------~kW~~Ia~~lpG---Rt--~n~vKnrw~~~l~ 74 (91)
.|..++...| ..|..||..|.- -+ ..++++.|..+|-
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 4455555555 359999999822 12 3678888887764
No 149
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=43.07 E-value=25 Score=23.54 Aligned_cols=27 Identities=7% Similarity=-0.108 Sum_probs=20.3
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 46 VGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
.|-.-..||..| |-+.+.|+++.+...
T Consensus 135 ~g~s~~eIA~~l-g~s~~tv~~~l~Rar 161 (175)
T PRK12518 135 EDLPQKEIAEIL-NIPVGTVKSRLFYAR 161 (175)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 355568888888 888999999876433
No 150
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=43.04 E-value=60 Score=22.14 Aligned_cols=32 Identities=16% Similarity=0.064 Sum_probs=21.1
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
++.++-..|-.-..||..| |-+.+.|+++-..
T Consensus 149 v~~l~~~~g~s~~EIA~~l-gis~~tV~~~l~R 180 (194)
T PRK12519 149 VLELAYYEGLSQSEIAKRL-GIPLGTVKARARQ 180 (194)
T ss_pred hhhhhhhcCCCHHHHHHHh-CCCHHHHHHHHHH
Confidence 3334444466667888888 7788888886543
No 151
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=42.87 E-value=28 Score=23.86 Aligned_cols=26 Identities=15% Similarity=-0.052 Sum_probs=19.9
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 45 LVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 45 ~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
..|-....||..| |-+...|+++.+.
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~r 178 (194)
T PRK12513 153 HGDLELEEIAELT-GVPEETVKSRLRY 178 (194)
T ss_pred ccCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 3466678888888 7888899887653
No 152
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=42.82 E-value=57 Score=24.54 Aligned_cols=34 Identities=9% Similarity=0.057 Sum_probs=23.8
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
++.|+...|-.-.+||..| |-+.+.|+++-+...
T Consensus 161 v~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~RAr 194 (339)
T PRK08241 161 VLILRDVLGWSAAEVAELL-DTSVAAVNSALQRAR 194 (339)
T ss_pred hhhhHHhhCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 3344445566678888888 889999998765433
No 153
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=41.83 E-value=95 Score=20.76 Aligned_cols=34 Identities=21% Similarity=0.359 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
.++.|+-.-|-...+||..| |-+.+.|+++-...
T Consensus 125 ~v~~L~~~eg~s~~EIA~~l-~is~~tV~~~l~ra 158 (168)
T PRK12525 125 AAFLMSQLEGLTYVEIGERL-GVSLSRIHQYMVEA 158 (168)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 34445555566788899888 88888888865433
No 154
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=41.39 E-value=64 Score=20.04 Aligned_cols=43 Identities=9% Similarity=0.020 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHHHHHHhhHHH
Q 034546 34 QEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERFWIMRHGQAF 77 (91)
Q Consensus 34 eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~ 77 (91)
+.|..|+.+...-| -.++.||..+ |-+...|..+........+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 45666776666655 4699999999 9999999999877665543
No 155
>PRK09483 response regulator; Provisional
Probab=40.73 E-value=99 Score=20.59 Aligned_cols=44 Identities=11% Similarity=0.237 Sum_probs=35.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
..+|+.|-++|.- .. -|-.-..||..| +-+.+-|+++-+..++|
T Consensus 147 ~~Lt~rE~~vl~~-~~-~G~~~~~Ia~~l-~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 147 ASLSERELQIMLM-IT-KGQKVNEISEQL-NLSPKTVNSYRYRMFSK 190 (217)
T ss_pred cccCHHHHHHHHH-HH-CCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3599999998753 33 576677999999 77999999988877776
No 156
>PRK06930 positive control sigma-like factor; Validated
Probab=40.30 E-value=91 Score=21.88 Aligned_cols=43 Identities=16% Similarity=0.211 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhh
Q 034546 30 NMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHG 74 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~ 74 (91)
..++.|-++++ ++-..|-....||..| |-+.+.|+.+.....+
T Consensus 114 ~L~~rer~V~~-L~~~eg~s~~EIA~~l-giS~~tVk~~l~Ra~~ 156 (170)
T PRK06930 114 VLTEREKEVYL-MHRGYGLSYSEIADYL-NIKKSTVQSMIERAEK 156 (170)
T ss_pred hCCHHHHHHHH-HHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 45555555443 4445678889999998 8899999987664433
No 157
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=39.58 E-value=1.2e+02 Score=22.20 Aligned_cols=24 Identities=13% Similarity=0.084 Sum_probs=16.2
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 46 VGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
-|-.-..||..| |-+.+.|+.+-.
T Consensus 227 ~~~s~~eIA~~l-gis~~tV~~~~~ 250 (268)
T PRK06288 227 EDLTLKEIGKVL-GVTESRISQLHT 250 (268)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHH
Confidence 355567777777 777777776554
No 158
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=37.59 E-value=1.6e+02 Score=21.53 Aligned_cols=36 Identities=11% Similarity=0.070 Sum_probs=26.5
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 37 DLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 37 ~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
..++.++-.-|-....||..| |=+.+.|+.+-+..+
T Consensus 167 R~v~~L~~~eg~S~~EIA~~L-gis~~TVk~rl~RAr 202 (244)
T TIGR03001 167 RHLLRLHFVDGLSMDRIGAMY-QVHRSTVSRWVAQAR 202 (244)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 334555555677789999998 899999999876443
No 159
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=37.41 E-value=1e+02 Score=21.72 Aligned_cols=28 Identities=18% Similarity=0.173 Sum_probs=19.2
Q ss_pred HhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 45 LVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 45 ~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
..|-.-..||..| |-+.+.|+.+-+..+
T Consensus 192 ~~~~s~~eIA~~l-gis~~~v~~~~~ra~ 219 (227)
T TIGR02980 192 FEDKTQSEIAERL-GISQMHVSRLLRRAL 219 (227)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3466677888887 778888877655433
No 160
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=37.39 E-value=1.2e+02 Score=19.89 Aligned_cols=22 Identities=18% Similarity=0.200 Sum_probs=13.7
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHH
Q 034546 46 VGDRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnr 68 (91)
.|-.-..||..| |-+.+.|+.+
T Consensus 124 ~~~s~~EIA~~l-gis~~tV~~~ 145 (163)
T PRK07037 124 HGETQKDIAREL-GVSPTLVNFM 145 (163)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHH
Confidence 355556666666 6666666664
No 161
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=36.88 E-value=1.1e+02 Score=20.39 Aligned_cols=24 Identities=0% Similarity=-0.140 Sum_probs=15.1
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 46 VGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
-|-.-..||..| |-+...|+.+-.
T Consensus 134 ~~~s~~EIA~~l-gis~~tV~~~l~ 157 (173)
T PRK12522 134 EQYSYKEMSEIL-NIPIGTVKYRLN 157 (173)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHH
Confidence 344556667666 677777776644
No 162
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=36.60 E-value=1e+02 Score=22.31 Aligned_cols=36 Identities=11% Similarity=0.099 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 36 EDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 36 D~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
+..|+.+.-.-|-....||..| |-|...|+++-+..
T Consensus 206 ~r~vl~l~~~~~~s~~EIA~~l-gis~~tV~~~~~ra 241 (251)
T PRK07670 206 EQLVISLFYKEELTLTEIGQVL-NLSTSRISQIHSKA 241 (251)
T ss_pred HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3444444444456677888888 78888888766543
No 163
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=36.57 E-value=1.1e+02 Score=20.25 Aligned_cols=28 Identities=7% Similarity=0.037 Sum_probs=18.6
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 42 MYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 42 l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
++...|-.-.+||..| |-+.+.|+.+-+
T Consensus 119 l~~~~g~s~~eIA~~l-gis~~tv~~~l~ 146 (165)
T PRK09644 119 LCDVHELTYEEAASVL-DLKLNTYKSHLF 146 (165)
T ss_pred hHHHhcCCHHHHHHHH-CCCHHHHHHHHH
Confidence 3344455667788877 778888877644
No 164
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=36.29 E-value=1.1e+02 Score=20.94 Aligned_cols=31 Identities=13% Similarity=-0.047 Sum_probs=21.8
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
++.++-..|-...+||..| |-+.+.|+.+-+
T Consensus 119 v~~L~~~~g~s~~EIA~~L-gis~~tV~~~l~ 149 (182)
T PRK12540 119 ALILVGASGFSYEDAAAIC-GCAVGTIKSRVN 149 (182)
T ss_pred HhhHHHHcCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 4444445566778888888 788888888755
No 165
>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=35.13 E-value=37 Score=23.32 Aligned_cols=28 Identities=21% Similarity=0.419 Sum_probs=17.6
Q ss_pred CCCHHHHHHHHHHHHHh-CCcHHHHhhhC
Q 034546 30 NMSEQEEDLIYRMYKLV-GDRWALIAGRI 57 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~-G~kW~~Ia~~l 57 (91)
++++++-.+|.--|... |..|..||..|
T Consensus 81 ~l~de~k~Ii~lry~~r~~~TW~~IA~~l 109 (130)
T PF05263_consen 81 TLIDEEKRIIKLRYDRRSRRTWYQIAQKL 109 (130)
T ss_pred hhCHHHHHHHHHHHcccccchHHHHHHHh
Confidence 45555555554444443 46799999987
No 166
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=34.91 E-value=1.3e+02 Score=21.49 Aligned_cols=45 Identities=18% Similarity=0.186 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQA 76 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~ 76 (91)
...|+-|-++|-.+.. |-.-.+||..| +-+..-|+++-.+.++|-
T Consensus 133 ~~LT~RE~eVL~ll~~--G~snkeIA~~L-~iS~~TV~~h~~~I~~KL 177 (207)
T PRK11475 133 RMLSPTEREILRFMSR--GYSMPQIAEQL-ERNIKTIRAHKFNVMSKL 177 (207)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHHHHHHHHHHHHHHc
Confidence 3699999988765444 77889999999 899999999988887773
No 167
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=34.44 E-value=1.1e+02 Score=21.81 Aligned_cols=25 Identities=16% Similarity=0.040 Sum_probs=18.9
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 46 VGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
-|-....||..| |-+.+.|+++-+.
T Consensus 197 eg~s~~EIA~~l-gis~~tVk~~~~r 221 (234)
T PRK08301 197 EEKTQKEVADML-GISQSYISRLEKR 221 (234)
T ss_pred CCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 366788888888 8888888886543
No 168
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=34.03 E-value=1.3e+02 Score=21.23 Aligned_cols=24 Identities=8% Similarity=0.050 Sum_probs=13.9
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 47 GDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 47 G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
|-.-..||..| |-+...|+.+.+.
T Consensus 191 ~~s~~eIA~~l-gis~~tV~~~~~r 214 (224)
T TIGR02479 191 ELNLKEIGEVL-GLTESRVSQIHSQ 214 (224)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHH
Confidence 44455666666 6666666665543
No 169
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 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 (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=33.86 E-value=53 Score=22.51 Aligned_cols=32 Identities=13% Similarity=0.030 Sum_probs=22.7
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
++.++-..|-.-..||..| |-+...|+++-..
T Consensus 139 i~~L~~~~g~s~~EIA~~l-gis~~tVk~~l~R 170 (193)
T TIGR02947 139 AVYLADVEGFAYKEIAEIM-GTPIGTVMSRLHR 170 (193)
T ss_pred heeehhhcCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 3334444466678888888 8899999998664
No 170
>PF09846 DUF2073: Uncharacterized protein conserved in archaea (DUF2073); InterPro: IPR012017 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=33.53 E-value=38 Score=22.70 Aligned_cols=15 Identities=20% Similarity=0.306 Sum_probs=13.0
Q ss_pred CCCCHHHHHHHHHHH
Q 034546 29 INMSEQEEDLIYRMY 43 (91)
Q Consensus 29 g~wT~eED~lLi~l~ 43 (91)
+.|||+|+..||+.-
T Consensus 27 ~GLtPeEe~~LIE~T 41 (104)
T PF09846_consen 27 EGLTPEEESKLIEMT 41 (104)
T ss_pred CCCChHHHHHHHHHH
Confidence 589999999999764
No 171
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=33.22 E-value=1.3e+02 Score=19.78 Aligned_cols=23 Identities=17% Similarity=0.101 Sum_probs=14.3
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHH
Q 034546 46 VGDRWALIAGRIPGRKAEEIERFW 69 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnrw 69 (91)
.|-...+||..| |=+...|+.+-
T Consensus 127 ~~~s~~eIA~~l-gis~~tv~~~l 149 (161)
T PRK12541 127 YGFSYKEIAEMT-GLSLAKVKIEL 149 (161)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHH
Confidence 344556677766 66666666654
No 172
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=31.88 E-value=38 Score=28.33 Aligned_cols=41 Identities=24% Similarity=0.489 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
-.||++|-. +++.+..||...-.||..+...|+.||+.+|-
T Consensus 471 ~~wSp~e~s-~ircf~~y~~~fe~ia~l~~tktp~Q~~~fy~ 511 (534)
T KOG1194|consen 471 YGWSPEEKS-AIRCFHWYKDNFELIAELMATKTPEQIKKFYM 511 (534)
T ss_pred CCCCCcccc-cccCchhhccchHHHHHHhcCCCHHHHHHHhc
Confidence 379999988 77888889999999999999999999999985
No 173
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=31.88 E-value=1.2e+02 Score=22.50 Aligned_cols=35 Identities=14% Similarity=0.134 Sum_probs=22.5
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHG 74 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~ 74 (91)
++.++-.-|-....||..| |-+...|+.+....+.
T Consensus 223 vl~l~y~~~~t~~EIA~~l-gis~~~V~~~~~ral~ 257 (264)
T PRK07122 223 VLVLRFFESMTQTQIAERV-GISQMHVSRLLAKTLA 257 (264)
T ss_pred HHHHHhcCCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 3344433456677888888 8888888876654443
No 174
>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=31.83 E-value=40 Score=20.66 Aligned_cols=26 Identities=23% Similarity=0.509 Sum_probs=17.4
Q ss_pred CCCHHHH-HHHHHHHHHhCCcHHHHhh
Q 034546 30 NMSEQEE-DLIYRMYKLVGDRWALIAG 55 (91)
Q Consensus 30 ~wT~eED-~lLi~l~~~~G~kW~~Ia~ 55 (91)
+|+.+.- ..|..|...||+.|..|-.
T Consensus 22 G~~~~~v~~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 22 GFSKKQVRPVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred CCCHHHHHHHHHHHHHHHcCCchhhhc
Confidence 3444433 3566788889988998863
No 175
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. 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 s
Probab=31.74 E-value=86 Score=20.45 Aligned_cols=33 Identities=15% Similarity=0.316 Sum_probs=24.5
Q ss_pred HHHHhCCcHHHHhhhCCC-----CCHHHHHHHHHHHhhH
Q 034546 42 MYKLVGDRWALIAGRIPG-----RKAEEIERFWIMRHGQ 75 (91)
Q Consensus 42 l~~~~G~kW~~Ia~~lpG-----Rt~n~vKnrw~~~l~k 75 (91)
+-..+|-+|..+|..| | =++.+|-+.=+.+.+.
T Consensus 8 ~~~nvGr~WK~laR~L-g~~cral~d~~ID~I~~~y~r~ 45 (90)
T cd08780 8 FAKSVGKKWKPVGRSL-QKNCRALRDPAIDNLAYEYDRE 45 (90)
T ss_pred HHHHHhHHHHHHHHHH-cccccccchhHHHHHHhhcccc
Confidence 4477899999999999 6 5788887765544444
No 176
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=31.63 E-value=1.7e+02 Score=21.87 Aligned_cols=44 Identities=11% Similarity=0.065 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
.+.|+.|-++|. ++. -|-....||..| +-+...|+++=...++|
T Consensus 142 ~~LS~RE~eVL~-Lia-~G~SnkEIA~~L-~IS~~TVk~hvs~I~~K 185 (217)
T PRK13719 142 NKVTKYQNDVFI-LYS-FGFSHEYIAQLL-NITVGSSKNKISEILKF 185 (217)
T ss_pred CCCCHHHHHHHH-HHH-CCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 378998888765 444 388899999999 99999999987776666
No 177
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=31.24 E-value=1.5e+02 Score=20.25 Aligned_cols=24 Identities=21% Similarity=0.324 Sum_probs=17.4
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 46 VGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
.|-....||..| |-+.+.|+++-.
T Consensus 169 e~~s~~EIA~~l-gis~~tV~~~l~ 192 (208)
T PRK08295 169 DGKSYQEIAEEL-NRHVKSIDNALQ 192 (208)
T ss_pred ccCCHHHHHHHH-CCCHHHHHHHHH
Confidence 455667788877 788888887654
No 178
>KOG3200 consensus Uncharacterized conserved protein [Function unknown]
Probab=31.14 E-value=39 Score=25.09 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=17.8
Q ss_pred CCCHHHHHHHH-HHHHHhCCcHHHHhhh
Q 034546 30 NMSEQEEDLIY-RMYKLVGDRWALIAGR 56 (91)
Q Consensus 30 ~wT~eED~lLi-~l~~~~G~kW~~Ia~~ 56 (91)
-.|+||+.+++ ..+..-|++|..++..
T Consensus 20 fIt~EEe~~~lshIe~ap~pkW~~L~NR 47 (224)
T KOG3200|consen 20 FITEEEENLYLSHIENAPQPKWRVLANR 47 (224)
T ss_pred ccChHHHHHHHHHHhcCCCchhHHHHhh
Confidence 35677777666 4445567899887653
No 179
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=30.99 E-value=1.7e+02 Score=20.06 Aligned_cols=44 Identities=16% Similarity=0.097 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
.+.|+-|-++|-.+ . -|..=.+||..| +-+..-|++|=...++|
T Consensus 149 ~~Lt~rE~evl~~~-~-~G~s~~eIA~~l-~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 149 KRLSPKESEVLRLF-A-EGFLVTEIAKKL-NRSIKTISSQKKSAMMK 192 (216)
T ss_pred ccCCHHHHHHHHHH-H-CCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 35899998776544 3 477889999999 89999999988777766
No 180
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=30.59 E-value=58 Score=21.31 Aligned_cols=24 Identities=21% Similarity=0.437 Sum_probs=15.8
Q ss_pred HHHHHHHHHhC-CcHHHHhhhCCCC
Q 034546 37 DLIYRMYKLVG-DRWALIAGRIPGR 60 (91)
Q Consensus 37 ~lLi~l~~~~G-~kW~~Ia~~lpGR 60 (91)
++|-.....++ .+|...+.++||-
T Consensus 95 diLKKa~~~~~~~~~~~~~~~~~~~ 119 (121)
T PRK09413 95 ELLKEAVEYGRAKKWIAHAPLLPGD 119 (121)
T ss_pred HHHHHHHHHhchhhhhhcCCCCCCC
Confidence 44444455555 4599999999874
No 181
>cd07316 terB_like_DjlA N-terminal tellurium resistance protein terB-like domain of heat shock DnaJ-like proteins. Tellurium resistance terB-like domain of the DnaJ-like DjlA proteins. This family represents the terB-like domain of DjlA-like proteins, a subgroup of heat shock DnaJ-like proteins. Escherichia coli DjlA is a type III membrane protein with a small N-terminal transmembrane region and DnaJ-like domain on the extreme C-terminus. Overproduction has been shown to activate the RcsC pathway, which regulates the production of the capsular exopolysaccharide colanic acid. The specific function of this domain is unknown.
Probab=29.92 E-value=65 Score=19.82 Aligned_cols=19 Identities=37% Similarity=0.642 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHHHHHHHhC
Q 034546 29 INMSEQEEDLIYRMYKLVG 47 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G 47 (91)
|..++.|+.+|-++...+|
T Consensus 88 G~~~~~E~~~l~~ia~~Lg 106 (106)
T cd07316 88 GELSEAERELLRRIARLLG 106 (106)
T ss_pred CCCCHHHHHHHHHHHHHcC
Confidence 7899999999988887766
No 182
>cd07176 terB tellurite resistance protein terB. This family contains uncharacterized bacterial proteins involved in tellurium resistance. The prototype of this CD is the Kp-terB protein from Klebsiella pneumoniae, whose 3D structure was recently determined. The biological function of terB and the mechanism responsible for tellurium resistance are unknown.
Probab=29.91 E-value=66 Score=19.76 Aligned_cols=19 Identities=16% Similarity=0.501 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHHHHHHhC
Q 034546 29 INMSEQEEDLIYRMYKLVG 47 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G 47 (91)
|..++.|..+|-++...+|
T Consensus 92 G~~~~~E~~~L~~l~~~Lg 110 (111)
T cd07176 92 GEVDPEERAVLEKLYRALG 110 (111)
T ss_pred CCCCHHHHHHHHHHHHHhC
Confidence 8899999999998888776
No 183
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=29.42 E-value=1.7e+02 Score=21.18 Aligned_cols=35 Identities=11% Similarity=-0.007 Sum_probs=23.6
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhh
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHG 74 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~ 74 (91)
++.++-..|-....||..| |=+...|+.+.+..++
T Consensus 213 vl~l~~~~g~s~~eIA~~l-~is~~tV~~~~~ra~~ 247 (257)
T PRK08583 213 IIQCTFIENLSQKETGERL-GISQMHVSRLQRQAIK 247 (257)
T ss_pred HHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3444444566788888888 7888888877654443
No 184
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=29.14 E-value=1.9e+02 Score=19.83 Aligned_cols=30 Identities=10% Similarity=-0.055 Sum_probs=21.2
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHHHHH
Q 034546 42 MYKLVGDRWALIAGRIPGRKAEEIERFWIMR 72 (91)
Q Consensus 42 l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~ 72 (91)
++-..|-.-..||..| |-+.+.|+.+-+..
T Consensus 139 l~~~~g~s~~EIA~~l-gis~~tV~~~l~Ra 168 (188)
T PRK12517 139 LQVIGGFSGEEIAEIL-DLNKNTVMTRLFRA 168 (188)
T ss_pred HHHHhCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 3434455668888888 88888888876543
No 185
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=29.04 E-value=1.5e+02 Score=22.39 Aligned_cols=32 Identities=19% Similarity=0.311 Sum_probs=25.9
Q ss_pred HHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 39 IYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 39 Li~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
++.|+..+|-.-.+||..| |.|.+.|+.+-+.
T Consensus 126 vf~L~~~~g~s~~EIA~~L-gis~~tVr~~l~R 157 (290)
T PRK09635 126 VFVLHEIFGLPYQQIATTI-GSQASTCRQLAHR 157 (290)
T ss_pred HhhHHHHhCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 3456677788889999999 9999999987653
No 186
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=28.97 E-value=1.5e+02 Score=21.25 Aligned_cols=34 Identities=9% Similarity=-0.048 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 37 DLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 37 ~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
..|+.++-..|-.-.+||..| |=+.+.|+.+-+.
T Consensus 140 R~v~~L~y~eg~s~~EIAe~L-giS~~tVk~~L~R 173 (216)
T PRK12533 140 REVLVLRELEDMSYREIAAIA-DVPVGTVMSRLAR 173 (216)
T ss_pred HhHhhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 344445555566678888888 8888888887653
No 187
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=28.02 E-value=1.7e+02 Score=21.39 Aligned_cols=26 Identities=15% Similarity=-0.040 Sum_probs=16.2
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 47 GDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 47 G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
|-.-..||..| |-+...|+.+....+
T Consensus 219 ~~s~~eIA~~l-gvs~~~V~~~~~ra~ 244 (256)
T PRK07408 219 DLTQKEAAERL-GISPVTVSRRVKKGL 244 (256)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 44566677776 667777776655433
No 188
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=27.87 E-value=1.5e+02 Score=24.31 Aligned_cols=43 Identities=21% Similarity=0.319 Sum_probs=37.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhh-CCCCCHHHHHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGR-IPGRKAEEIERFWIM 71 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~-lpGRt~n~vKnrw~~ 71 (91)
..||++|=.-.-+....||.....|... ++-|+-..|-.+|+.
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH
Confidence 5899999998889999999999998766 899999998887763
No 189
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=27.73 E-value=2e+02 Score=19.40 Aligned_cols=28 Identities=11% Similarity=0.107 Sum_probs=17.7
Q ss_pred HHHHhCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 42 MYKLVGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 42 l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
++-..|-....||..| |=+...|+++-+
T Consensus 148 l~~~~g~s~~eIA~~l-gis~~~v~~~l~ 175 (187)
T PRK12534 148 TAFFEGITYEELAART-DTPIGTVKSWIR 175 (187)
T ss_pred HHHHcCCCHHHHHHHh-CCChhHHHHHHH
Confidence 3333456667777777 667777777544
No 190
>PRK09191 two-component response regulator; Provisional
Probab=27.26 E-value=1.9e+02 Score=20.09 Aligned_cols=36 Identities=17% Similarity=0.029 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHH
Q 034546 35 EEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 35 ED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
+...++.++..-|-....||..| |-+.+.|+.+-..
T Consensus 92 ~~r~v~~l~~~~~~s~~eIA~~l-~~s~~tV~~~l~r 127 (261)
T PRK09191 92 LPRQAFLLTALEGFSVEEAAEIL-GVDPAEAEALLDD 127 (261)
T ss_pred HHhHHHHHHHHhcCCHHHHHHHH-CCCHHHHHHHHHH
Confidence 45556667777788899999988 8999999987653
No 191
>PF06628 Catalase-rel: Catalase-related immune-responsive; InterPro: IPR010582 Catalases (1.11.1.6 from EC) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects []. Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (IPR000763 from INTERPRO) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (IPR007760 from INTERPRO) that are found in bacteria []. This entry represents a small conserved region within catalase enzymes that carries the immune-responsive amphipathic octa-peptide that is recognised by T cells [].; PDB: 2CAH_A 1NM0_A 1H7K_A 1E93_A 1H6N_A 3HB6_A 2CAG_A 1M85_A 1MQF_A 1A4E_C ....
Probab=26.98 E-value=1.4e+02 Score=17.63 Aligned_cols=43 Identities=23% Similarity=0.298 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhHHHHHHHHH
Q 034546 31 MSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQAFADRRRE 83 (91)
Q Consensus 31 wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k~~~~~~~~ 83 (91)
++++|-+.|+ ..||.+|.+=++..|+.++..++.+.-..-+..
T Consensus 20 l~~~er~~lv----------~nia~~l~~v~~~~i~~r~l~~f~~vd~~lg~~ 62 (68)
T PF06628_consen 20 LSDEERERLV----------ENIAGHLSGVSDEEIQERVLAYFYKVDPDLGQR 62 (68)
T ss_dssp SSHHHHHHHH----------HHHHHHHTTSSHHHHHHHHHHHHHHH-HHHHHH
T ss_pred CCHHHHHHHH----------HHHHHHHccCChhhHHHHHHHHHHHhCHHHHHH
Confidence 4666777666 467888877777779999988887765554443
No 192
>cd08312 Death_MyD88 Death domain of Myeloid Differentation primary response protein MyD88. Death Domain (DD) of Myeloid Differentiation primary response protein 88 (MyD88). MyD88 is an adaptor protein involved in interleukin-1 receptor (IL-1R)- and Toll-like receptor (TLR)-induced activation of nuclear factor-kappaB (NF-kB) and mitogen activated protein kinase pathways that lead to the induction of proinflammatory cytokines. It is a key component in the signaling pathway of pathogen recognition in the innate immune system. MyD88 contains an N-terminal DD and a C-terminal Toll/IL-1 Receptor (TIR) homology domain that mediates interaction with TLRs and IL-1R. 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
Probab=26.78 E-value=73 Score=19.57 Aligned_cols=23 Identities=26% Similarity=0.531 Sum_probs=17.7
Q ss_pred HHhCCcHHHHhhhCCCCCHHHHHH
Q 034546 44 KLVGDRWALIAGRIPGRKAEEIER 67 (91)
Q Consensus 44 ~~~G~kW~~Ia~~lpGRt~n~vKn 67 (91)
...|+.|..+|..| |=+...|.+
T Consensus 13 ~~~g~DWr~LA~~L-g~~~~~I~~ 35 (79)
T cd08312 13 RVVAADWTALAEEM-GFEYLEIRN 35 (79)
T ss_pred CCcccCHHHHHHHc-CCCHHHHHH
Confidence 34688999999999 666666665
No 193
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=26.59 E-value=1.9e+02 Score=21.19 Aligned_cols=27 Identities=7% Similarity=-0.049 Sum_probs=17.4
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 46 VGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
-|-....||..| |-+...|+.+....+
T Consensus 220 e~~t~~EIA~~l-gis~~~V~~~~~ral 246 (257)
T PRK05911 220 EELVLKEIGKIL-GVSESRVSQIHSKAL 246 (257)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 345567777777 677777777655433
No 194
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=26.15 E-value=1.4e+02 Score=27.21 Aligned_cols=39 Identities=26% Similarity=0.443 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHHHHhC-CcHHHHhhhCCCCCHHHHHHH
Q 034546 30 NMSEQEEDLIYRMYKLVG-DRWALIAGRIPGRKAEEIERF 68 (91)
Q Consensus 30 ~wT~eED~lLi~l~~~~G-~kW~~Ia~~lpGRt~n~vKnr 68 (91)
.||.-+=...|.....|| ..-..||..+.|.|...|+.+
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y 865 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERY 865 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHH
Confidence 344444444555555566 446789999999999999976
No 195
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=25.34 E-value=64 Score=20.78 Aligned_cols=18 Identities=22% Similarity=0.028 Sum_probs=15.0
Q ss_pred CCCCHHHHHHHHHHHHHh
Q 034546 29 INMSEQEEDLIYRMYKLV 46 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~ 46 (91)
.-||+++|-.||+....|
T Consensus 5 R~WS~eDEi~iL~gl~~~ 22 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDF 22 (98)
T ss_pred CCCCchHHHHHHHHHHHH
Confidence 369999999999887766
No 196
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=25.32 E-value=2.4e+02 Score=19.52 Aligned_cols=44 Identities=18% Similarity=0.163 Sum_probs=32.8
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCcHHHHhhhC----CCCCHHHHHHHHH
Q 034546 27 EFINMSEQEEDLIYRMYKLVGDRWALIAGRI----PGRKAEEIERFWI 70 (91)
Q Consensus 27 kkg~wT~eED~lLi~l~~~~G~kW~~Ia~~l----pGRt~n~vKnrw~ 70 (91)
....-|+.|...|..|+..+|..+..+|.=. ---|..+|+....
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~ 160 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIR 160 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHH
Confidence 3457899999999999999999999988732 2345666655443
No 197
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=25.04 E-value=2.2e+02 Score=19.19 Aligned_cols=24 Identities=21% Similarity=0.014 Sum_probs=14.0
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 46 VGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
.|-.-..||..| |-+.+.|+++-+
T Consensus 146 ~g~s~~eIA~~l-gis~~tV~~~l~ 169 (184)
T PRK12539 146 EGLSVAEAATRS-GMSESAVKVSVH 169 (184)
T ss_pred cCCcHHHHHHHH-CcCHHHHHHHHH
Confidence 344556666666 556666666543
No 198
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=24.19 E-value=71 Score=21.81 Aligned_cols=23 Identities=9% Similarity=-0.065 Sum_probs=17.3
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 47 GDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 47 G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
|-...+||..| |-+...|+++-.
T Consensus 150 g~s~~EIA~~l-gis~~tV~~~l~ 172 (188)
T PRK09640 150 ELEFQEIADIM-HMGLSATKMRYK 172 (188)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHH
Confidence 44567888888 888888888754
No 199
>PRK15328 invasion protein IagB; Provisional
Probab=24.13 E-value=1.9e+02 Score=20.34 Aligned_cols=42 Identities=17% Similarity=0.388 Sum_probs=27.9
Q ss_pred HHHHHHHHhCCcHHHHhhhCCC--CCHHHHHHHHHHHhhHHHHH
Q 034546 38 LIYRMYKLVGDRWALIAGRIPG--RKAEEIERFWIMRHGQAFAD 79 (91)
Q Consensus 38 lLi~l~~~~G~kW~~Ia~~lpG--Rt~n~vKnrw~~~l~k~~~~ 79 (91)
+|..++..+|+.|..|+.+=-| +.....+.+|-..+-+.+..
T Consensus 98 ~L~~~~~~~g~~~~alaaYNaG~~~~~~~~~~~Y~~kV~~~y~~ 141 (160)
T PRK15328 98 ILSDMMKIYGYSWEAVGAYNAGTSPKRSDIRKRYAKKIWENYRK 141 (160)
T ss_pred HHHHHHHHcCChHHhhhhccCCCCCCCCHHHHHHHHHHHHHHHH
Confidence 5667888899999999988644 33334555665555554443
No 200
>PRK02866 cyanate hydratase; Validated
Probab=24.12 E-value=1.3e+02 Score=21.08 Aligned_cols=36 Identities=25% Similarity=0.197 Sum_probs=29.9
Q ss_pred HHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHh
Q 034546 37 DLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRH 73 (91)
Q Consensus 37 ~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l 73 (91)
+.|+..-..-|=.|..||..+ |++..-+-...++..
T Consensus 8 e~Ll~AK~~kGLTw~~IA~~i-G~S~v~vaaa~lGQ~ 43 (147)
T PRK02866 8 EKILAAKKEKGLTWADIAEAI-GLSEVWVTAALLGQM 43 (147)
T ss_pred HHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHHHhCCC
Confidence 467778888899999999999 999998888777643
No 201
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=24.09 E-value=1.5e+02 Score=17.04 Aligned_cols=38 Identities=16% Similarity=0.087 Sum_probs=27.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 034546 29 INMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIER 67 (91)
Q Consensus 29 g~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKn 67 (91)
..||+|+-.-|+..+..-|..-..||..+ |=+...+.+
T Consensus 5 ~~ys~e~K~~~v~~~~~~g~sv~~va~~~-gi~~~~l~~ 42 (76)
T PF01527_consen 5 RRYSPEFKLQAVREYLESGESVSEVAREY-GISPSTLYN 42 (76)
T ss_dssp ----HHHHHHHHHHHHHHHCHHHHHHHHH-TS-HHHHHH
T ss_pred CCCCHHHHHHHHHHHHHCCCceEeeeccc-ccccccccH
Confidence 57999999999999977788889999887 556666665
No 202
>PF05176 ATP-synt_10: ATP10 protein; InterPro: IPR007849 This entry represents the ATPase assembly factor ATP10 found in mitochondria, which is essential for the assembly of the mitochondrial F1-F0 complex. A yeast nuclear gene (ATP10) encodes a product that is essential for the assembly of a functional mitochondrial ATPase complex. Mutations in ATP10 induce a loss of rutamycin sensitivity in the mitochondrial ATPase, but do not affect the respiratory enzymes. ATP10 has an Mr of 30,293 and its primary structure is not related to any known subunit of the yeast or mammalian mitochondrial ATPase complexes. ATP10 is associated with the mitochondrial membrane. It is suggested that the ATP10 product is not a subunit of the ATPase complex but rather a protein required for the assembly of the F0 sector of the complex [].; GO: 0033615 mitochondrial proton-transporting ATP synthase complex assembly, 0005743 mitochondrial inner membrane
Probab=22.36 E-value=81 Score=23.71 Aligned_cols=27 Identities=7% Similarity=0.004 Sum_probs=20.3
Q ss_pred hhhhccccccCCccccCCCcccCCCCHHHHHHHHHHHHH
Q 034546 7 KQAKTTTTTFYSEEVSSIEWEFINMSEQEEDLIYRMYKL 45 (91)
Q Consensus 7 ~q~~~~~~~~~s~~v~s~~lkkg~wT~eED~lLi~l~~~ 45 (91)
.+||+||-.. |.=|++|-+.|......
T Consensus 225 ~~grIRWags------------G~At~~E~~~L~k~~~~ 251 (252)
T PF05176_consen 225 PNGRIRWAGS------------GPATPEELESLWKCVKG 251 (252)
T ss_pred CCCeEEeCcc------------CCCCHHHHHHHHHHHhc
Confidence 3678887653 88999999988876653
No 203
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=22.30 E-value=1.4e+02 Score=16.00 Aligned_cols=43 Identities=5% Similarity=0.114 Sum_probs=33.0
Q ss_pred cCCCCHHHHHHHHHHHHHhC-Cc---HHHHhhhCCCCCHHHHHHHHHH
Q 034546 28 FINMSEQEEDLIYRMYKLVG-DR---WALIAGRIPGRKAEEIERFWIM 71 (91)
Q Consensus 28 kg~wT~eED~lLi~l~~~~G-~k---W~~Ia~~lpGRt~n~vKnrw~~ 71 (91)
...||++...+|-..|.... +. =..||..+ |-+..+|.+.|..
T Consensus 4 r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~-~l~~~qV~~WF~n 50 (59)
T cd00086 4 RTRFTPEQLEELEKEFEKNPYPSREEREELAKEL-GLTERQVKIWFQN 50 (59)
T ss_pred CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHH-CcCHHHHHHHHHH
Confidence 46899999999999888855 23 24577777 8999999997644
No 204
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=22.03 E-value=2.4e+02 Score=20.29 Aligned_cols=24 Identities=13% Similarity=0.036 Sum_probs=13.8
Q ss_pred hCCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 46 VGDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 46 ~G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
.|-.-..||..| |-+...|+.+-+
T Consensus 220 ~g~s~~eIA~~l-gis~~~V~~~~~ 243 (255)
T TIGR02941 220 ENLSQKETGERL-GISQMHVSRLQR 243 (255)
T ss_pred CCCCHHHHHHHH-CcCHHHHHHHHH
Confidence 344456666666 666666655543
No 205
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=21.54 E-value=1.3e+02 Score=18.39 Aligned_cols=31 Identities=19% Similarity=0.368 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHhCCcHHHHhhhCCCC---CHHHHHH
Q 034546 35 EEDLIYRMYKLVGDRWALIAGRIPGR---KAEEIER 67 (91)
Q Consensus 35 ED~lLi~l~~~~G~kW~~Ia~~lpGR---t~n~vKn 67 (91)
-+.+|-+|+..+| |..++..++=| ++..||-
T Consensus 11 Le~il~~Lv~~yG--W~~L~~~i~i~CF~~~PsikS 44 (64)
T PF09905_consen 11 LETILTELVEHYG--WEELGERININCFKNNPSIKS 44 (64)
T ss_dssp HHHHHHHHHHHT---HHHHHHHTTSSSTTSS--HHH
T ss_pred HHHHHHHHHHHhC--HHHHHhhcccccCCCCCchHH
Confidence 3678889999996 99999887544 3344554
No 206
>PRK05572 sporulation sigma factor SigF; Validated
Probab=21.21 E-value=2.7e+02 Score=20.09 Aligned_cols=23 Identities=17% Similarity=0.225 Sum_probs=14.1
Q ss_pred CCcHHHHhhhCCCCCHHHHHHHHH
Q 034546 47 GDRWALIAGRIPGRKAEEIERFWI 70 (91)
Q Consensus 47 G~kW~~Ia~~lpGRt~n~vKnrw~ 70 (91)
|-.-..||..| |-|.+.|..+-.
T Consensus 218 ~~s~~eIA~~l-gis~~~V~~~~~ 240 (252)
T PRK05572 218 DKTQSEVAKRL-GISQVQVSRLEK 240 (252)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHH
Confidence 44556677776 667776665433
No 207
>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=20.91 E-value=1.5e+02 Score=15.70 Aligned_cols=33 Identities=21% Similarity=0.229 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 034546 34 QEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIER 67 (91)
Q Consensus 34 eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKn 67 (91)
-|.++|......+|+.-+..|..| |=+...+..
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 478889999999999999999887 555554443
No 208
>COG2992 Bax Uncharacterized FlgJ-related protein [General function prediction only]
Probab=20.57 E-value=50 Score=25.29 Aligned_cols=43 Identities=12% Similarity=0.136 Sum_probs=31.1
Q ss_pred CCCcccCCCCHHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHHHHHHHhhH
Q 034546 23 SIEWEFINMSEQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIERFWIMRHGQ 75 (91)
Q Consensus 23 s~~lkkg~wT~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKnrw~~~l~k 75 (91)
+.+.-++.||++|-..|-++...+.-+|+. |.+++.|+.++.+
T Consensus 90 ~kd~~k~~~s~~e~a~l~~lat~ykv~~~e----------N~~~~~wnel~~R 132 (262)
T COG2992 90 SKDYQKEQLSPSERARLKDLATRYKVKWSE----------NTRKIPWNELLHR 132 (262)
T ss_pred HHHhhhccCCHHHHHHHHHHHHHHHhhhcc----------ccccccHHHHHHH
Confidence 345566889999999888888877766655 6777778755443
No 209
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=20.20 E-value=2.5e+02 Score=17.89 Aligned_cols=34 Identities=15% Similarity=0.130 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhCCCCCHHHHHH
Q 034546 33 EQEEDLIYRMYKLVGDRWALIAGRIPGRKAEEIER 67 (91)
Q Consensus 33 ~eED~lLi~l~~~~G~kW~~Ia~~lpGRt~n~vKn 67 (91)
+-|..+|..+...+|+..+..|+.| |=+.+.+..
T Consensus 54 ~~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~r 87 (95)
T PRK00430 54 EVEAPLLDMVMQYTRGNQTRAALML-GINRGTLRK 87 (95)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHH
Confidence 3577888899999999999999888 666555443
No 210
>PF13725 tRNA_bind_2: Possible tRNA binding domain; PDB: 2ZPA_B.
Probab=20.08 E-value=46 Score=20.77 Aligned_cols=24 Identities=25% Similarity=0.468 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHhCCcHHHHhhhC
Q 034546 33 EQEEDLIYRMYKLVGDRWALIAGRI 57 (91)
Q Consensus 33 ~eED~lLi~l~~~~G~kW~~Ia~~l 57 (91)
..+..+|+... .-+..|..||+.|
T Consensus 70 ~~q~~lLi~k~-LQ~ksw~~~a~~l 93 (101)
T PF13725_consen 70 ELQQALLIAKG-LQGKSWEEVAKEL 93 (101)
T ss_dssp -S--HHHHHHH-CS---HHHHHHHC
T ss_pred HHHHHHHHHHH-HCCCCHHHHHHHc
Confidence 34444444333 2456688888775
Done!