Query 043269
Match_columns 191
No_of_seqs 192 out of 1470
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 03:13:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043269.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043269hhsearch_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 2.9E-37 6.4E-42 256.4 13.0 113 21-133 4-116 (238)
2 PLN03212 Transcription repress 100.0 3.4E-37 7.4E-42 252.5 12.9 118 21-138 20-137 (249)
3 PLN03091 hypothetical protein; 100.0 3.9E-35 8.6E-40 256.2 12.0 121 16-137 5-125 (459)
4 KOG0049 Transcription factor, 99.9 3E-21 6.5E-26 174.7 12.2 133 7-139 233-421 (939)
5 KOG0049 Transcription factor, 99.8 1.5E-21 3.3E-26 176.6 8.0 111 5-116 338-450 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.8 1.6E-18 3.5E-23 114.4 6.3 60 29-90 1-60 (60)
7 KOG0050 mRNA splicing protein 99.7 2.6E-17 5.7E-22 146.1 5.7 107 24-132 5-111 (617)
8 COG5147 REB1 Myb superfamily p 99.7 5.9E-17 1.3E-21 146.0 7.0 109 20-129 14-122 (512)
9 PF00249 Myb_DNA-binding: Myb- 99.6 2.2E-15 4.8E-20 95.3 3.7 48 26-73 1-48 (48)
10 PF00249 Myb_DNA-binding: Myb- 99.6 8.1E-15 1.8E-19 92.7 5.7 46 79-124 1-48 (48)
11 PLN03212 Transcription repress 99.6 8.3E-15 1.8E-19 120.7 7.0 79 56-142 10-90 (249)
12 KOG0051 RNA polymerase I termi 99.5 1.1E-14 2.5E-19 132.6 8.0 103 25-130 383-513 (607)
13 PF13921 Myb_DNA-bind_6: Myb-l 99.5 1.2E-14 2.6E-19 95.8 4.4 58 82-139 1-58 (60)
14 KOG0048 Transcription factor, 99.5 2E-14 4.3E-19 119.6 4.5 84 75-158 5-113 (238)
15 PLN03091 hypothetical protein; 99.4 2.1E-13 4.6E-18 120.1 5.3 68 75-142 10-79 (459)
16 smart00717 SANT SANT SWI3, AD 99.4 1E-12 2.2E-17 81.7 5.8 47 79-125 1-48 (49)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.3 9.1E-12 2E-16 76.1 5.8 44 81-124 1-45 (45)
18 KOG0051 RNA polymerase I termi 99.3 7.5E-12 1.6E-16 114.4 7.0 116 23-140 305-446 (607)
19 smart00717 SANT SANT SWI3, AD 99.3 8.1E-12 1.7E-16 77.5 4.6 48 26-74 1-48 (49)
20 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 6E-11 1.3E-15 72.4 4.2 45 28-73 1-45 (45)
21 COG5147 REB1 Myb superfamily p 98.6 4.1E-08 8.9E-13 89.2 4.4 117 7-126 52-169 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.3 8.2E-07 1.8E-11 58.1 4.3 49 25-73 2-54 (57)
23 KOG0457 Histone acetyltransfer 98.3 8E-07 1.7E-11 78.6 3.9 51 23-74 69-119 (438)
24 KOG0050 mRNA splicing protein 98.1 2.8E-06 6.2E-11 76.6 4.3 63 77-139 5-68 (617)
25 KOG0457 Histone acetyltransfer 98.1 7.4E-06 1.6E-10 72.6 5.9 50 76-125 69-119 (438)
26 TIGR01557 myb_SHAQKYF myb-like 98.0 1.9E-05 4.1E-10 51.6 6.0 47 79-125 3-55 (57)
27 PF13325 MCRS_N: N-terminal re 97.8 0.00018 3.8E-09 58.4 8.7 97 28-126 1-128 (199)
28 COG5259 RSC8 RSC chromatin rem 97.6 4.7E-05 1E-09 68.2 3.5 46 25-72 278-323 (531)
29 KOG1279 Chromatin remodeling f 97.6 0.00011 2.3E-09 67.3 5.3 46 78-123 252-297 (506)
30 PF13837 Myb_DNA-bind_4: Myb/S 97.5 9.4E-05 2E-09 51.8 3.5 49 80-128 2-68 (90)
31 KOG1279 Chromatin remodeling f 97.5 9.2E-05 2E-09 67.6 4.0 49 22-72 249-297 (506)
32 COG5259 RSC8 RSC chromatin rem 97.5 0.00012 2.7E-09 65.5 4.4 54 79-132 279-334 (531)
33 TIGR02894 DNA_bind_RsfA transc 97.5 0.00017 3.6E-09 56.4 4.4 49 78-127 3-58 (161)
34 PF08914 Myb_DNA-bind_2: Rap1 97.3 0.0005 1.1E-08 46.1 4.3 49 79-127 2-60 (65)
35 PF13873 Myb_DNA-bind_5: Myb/S 97.1 0.0013 2.9E-08 45.0 5.4 49 79-127 2-72 (78)
36 PF08914 Myb_DNA-bind_2: Rap1 97.1 0.0005 1.1E-08 46.1 2.7 51 26-76 2-60 (65)
37 PRK13923 putative spore coat p 96.9 0.0012 2.6E-08 52.3 4.1 50 77-127 3-59 (170)
38 TIGR02894 DNA_bind_RsfA transc 96.9 0.00064 1.4E-08 53.2 2.5 49 24-74 2-56 (161)
39 PF13837 Myb_DNA-bind_4: Myb/S 96.8 0.001 2.3E-08 46.4 2.6 48 26-73 1-64 (90)
40 COG5114 Histone acetyltransfer 96.7 0.00094 2E-08 57.5 2.4 48 26-74 63-110 (432)
41 PLN03142 Probable chromatin-re 96.6 0.012 2.6E-07 58.3 9.3 102 28-130 826-990 (1033)
42 COG5114 Histone acetyltransfer 96.5 0.0032 6.9E-08 54.3 4.3 47 79-125 63-110 (432)
43 PF13873 Myb_DNA-bind_5: Myb/S 96.2 0.0036 7.9E-08 42.8 2.3 49 25-73 1-69 (78)
44 PRK13923 putative spore coat p 95.9 0.0045 9.7E-08 49.0 1.8 49 24-74 3-57 (170)
45 COG5118 BDP1 Transcription ini 95.1 0.037 8E-07 48.9 4.9 47 80-126 366-412 (507)
46 KOG4282 Transcription factor G 94.8 0.069 1.5E-06 46.6 6.0 52 79-130 54-119 (345)
47 PF09111 SLIDE: SLIDE; InterP 94.1 0.13 2.7E-06 38.5 5.2 53 76-128 46-114 (118)
48 PF12776 Myb_DNA-bind_3: Myb/S 94.1 0.19 4E-06 35.3 5.8 46 81-126 1-64 (96)
49 KOG2656 DNA methyltransferase 93.8 0.082 1.8E-06 46.9 4.0 55 80-134 131-191 (445)
50 KOG1194 Predicted DNA-binding 93.3 0.37 7.9E-06 43.7 7.4 47 79-125 187-233 (534)
51 COG5118 BDP1 Transcription ini 91.6 0.19 4.2E-06 44.5 3.5 44 27-72 366-409 (507)
52 PF09111 SLIDE: SLIDE; InterP 91.6 0.22 4.8E-06 37.2 3.4 34 23-56 46-82 (118)
53 PF08281 Sigma70_r4_2: Sigma-7 91.0 0.9 1.9E-05 28.3 5.3 41 84-125 12-52 (54)
54 KOG4167 Predicted DNA-binding 90.9 1.2 2.7E-05 42.6 8.2 44 80-123 620-663 (907)
55 smart00595 MADF subfamily of S 90.6 0.43 9.4E-06 33.0 3.9 28 100-128 29-56 (89)
56 KOG4167 Predicted DNA-binding 90.0 0.3 6.5E-06 46.6 3.3 45 26-72 619-663 (907)
57 PF11626 Rap1_C: TRF2-interact 86.5 0.73 1.6E-05 32.3 2.8 25 22-46 43-75 (87)
58 KOG4282 Transcription factor G 86.3 0.88 1.9E-05 39.7 3.8 48 26-73 54-113 (345)
59 PF10545 MADF_DNA_bdg: Alcohol 83.1 1.1 2.5E-05 30.1 2.5 28 100-127 28-56 (85)
60 PF13404 HTH_AsnC-type: AsnC-t 82.1 4.2 9.1E-05 24.5 4.5 38 85-123 3-41 (42)
61 PF04545 Sigma70_r4: Sigma-70, 81.2 6.5 0.00014 24.0 5.3 41 85-126 7-47 (50)
62 KOG4468 Polycomb-group transcr 80.3 2.3 5E-05 40.0 4.0 46 26-73 88-143 (782)
63 PF12776 Myb_DNA-bind_3: Myb/S 80.1 2.9 6.2E-05 29.1 3.8 45 28-72 1-61 (96)
64 PF13325 MCRS_N: N-terminal re 78.6 4.7 0.0001 32.8 5.0 44 81-125 1-47 (199)
65 KOG4468 Polycomb-group transcr 78.6 4.2 9.1E-05 38.3 5.2 53 79-131 88-150 (782)
66 PF11035 SnAPC_2_like: Small n 77.8 11 0.00025 32.8 7.2 49 79-127 21-73 (344)
67 PRK09413 IS2 repressor TnpA; R 77.3 10 0.00023 27.9 6.2 45 26-74 10-54 (121)
68 PF11626 Rap1_C: TRF2-interact 76.8 2.5 5.4E-05 29.6 2.6 17 75-91 43-59 (87)
69 PF01388 ARID: ARID/BRIGHT DNA 76.7 7.2 0.00016 27.0 5.0 38 89-126 40-90 (92)
70 PF13404 HTH_AsnC-type: AsnC-t 76.0 3.7 7.9E-05 24.8 2.8 37 33-71 4-40 (42)
71 KOG1194 Predicted DNA-binding 75.9 4.5 9.7E-05 36.9 4.4 50 21-72 182-231 (534)
72 PRK11179 DNA-binding transcrip 75.8 7.8 0.00017 29.7 5.4 45 85-130 9-54 (153)
73 KOG4329 DNA-binding protein [G 74.6 8.9 0.00019 34.2 5.9 44 80-123 278-322 (445)
74 smart00501 BRIGHT BRIGHT, ARID 73.7 9.6 0.00021 26.6 5.0 39 89-127 36-87 (93)
75 cd08319 Death_RAIDD Death doma 73.7 5.5 0.00012 27.8 3.6 29 87-116 2-30 (83)
76 PF04504 DUF573: Protein of un 73.0 9.1 0.0002 27.5 4.7 49 80-128 5-66 (98)
77 KOG2009 Transcription initiati 72.6 4.3 9.3E-05 38.1 3.6 49 78-126 408-456 (584)
78 cd08803 Death_ank3 Death domai 72.6 7 0.00015 27.3 3.9 31 87-118 4-34 (84)
79 PF07750 GcrA: GcrA cell cycle 71.9 5.8 0.00013 31.1 3.8 40 81-121 2-41 (162)
80 TIGR02985 Sig70_bacteroi1 RNA 71.1 14 0.0003 27.4 5.7 39 87-126 118-156 (161)
81 PF01388 ARID: ARID/BRIGHT DNA 70.4 4.5 9.7E-05 28.1 2.6 39 36-74 40-89 (92)
82 PRK11169 leucine-responsive tr 68.9 12 0.00026 29.0 5.0 46 84-130 13-59 (164)
83 KOG2656 DNA methyltransferase 67.1 3.9 8.5E-05 36.5 2.1 49 23-72 127-180 (445)
84 cd08317 Death_ank Death domain 65.8 7.7 0.00017 26.7 3.0 30 87-117 4-33 (84)
85 cd08311 Death_p75NR Death doma 65.6 9.2 0.0002 26.2 3.3 33 84-118 2-34 (77)
86 smart00501 BRIGHT BRIGHT, ARID 64.7 5.5 0.00012 27.9 2.1 40 36-75 36-86 (93)
87 KOG0384 Chromodomain-helicase 63.9 11 0.00024 38.4 4.7 76 26-108 1133-1209(1373)
88 cd08804 Death_ank2 Death domai 63.5 11 0.00023 26.2 3.4 31 87-118 4-34 (84)
89 PRK09643 RNA polymerase sigma 63.2 26 0.00057 27.5 6.1 34 92-126 144-177 (192)
90 TIGR02937 sigma70-ECF RNA poly 61.7 24 0.00052 25.3 5.3 34 92-126 120-153 (158)
91 PF02954 HTH_8: Bacterial regu 61.6 24 0.00052 20.9 4.3 35 85-120 5-39 (42)
92 PRK11179 DNA-binding transcrip 61.1 10 0.00022 29.1 3.2 44 32-77 9-52 (153)
93 KOG2009 Transcription initiati 60.5 10 0.00022 35.7 3.6 56 14-71 397-452 (584)
94 PF09420 Nop16: Ribosome bioge 59.2 14 0.0003 28.9 3.7 48 24-72 112-162 (164)
95 PF08281 Sigma70_r4_2: Sigma-7 58.7 11 0.00023 23.3 2.5 38 31-71 12-49 (54)
96 PF07638 Sigma70_ECF: ECF sigm 58.2 31 0.00067 27.1 5.6 40 86-126 139-178 (185)
97 cd08318 Death_NMPP84 Death dom 57.9 16 0.00035 25.4 3.5 32 82-117 5-36 (86)
98 cd08805 Death_ank1 Death domai 56.8 16 0.00035 25.5 3.3 29 87-116 4-32 (84)
99 PF11035 SnAPC_2_like: Small n 56.4 26 0.00056 30.6 5.1 85 27-125 22-127 (344)
100 PF00196 GerE: Bacterial regul 55.5 16 0.00036 22.9 3.0 43 81-126 3-45 (58)
101 PF09420 Nop16: Ribosome bioge 55.3 29 0.00064 27.0 5.0 46 78-123 113-162 (164)
102 PRK09652 RNA polymerase sigma 55.2 35 0.00075 25.8 5.4 34 92-126 138-171 (182)
103 COG2197 CitB Response regulato 54.9 21 0.00046 28.8 4.2 44 80-126 147-190 (211)
104 smart00005 DEATH DEATH domain, 54.8 20 0.00044 24.3 3.6 29 87-116 5-34 (88)
105 PRK12512 RNA polymerase sigma 54.4 43 0.00093 25.8 5.8 33 96-129 145-177 (184)
106 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 54.1 39 0.00085 21.3 4.4 35 85-120 7-41 (50)
107 PF09197 Rap1-DNA-bind: Rap1, 54.0 18 0.0004 26.4 3.3 46 28-74 1-76 (105)
108 PRK04217 hypothetical protein; 53.9 54 0.0012 24.1 5.8 46 80-127 41-86 (110)
109 smart00344 HTH_ASNC helix_turn 53.8 33 0.00071 24.1 4.7 44 85-129 3-47 (108)
110 PRK12523 RNA polymerase sigma 53.2 53 0.0011 25.0 6.1 39 89-128 126-164 (172)
111 PRK11169 leucine-responsive tr 53.1 11 0.00023 29.3 2.1 45 31-77 13-57 (164)
112 cd08777 Death_RIP1 Death Domai 52.3 19 0.00041 25.1 3.1 29 89-118 4-32 (86)
113 cd06171 Sigma70_r4 Sigma70, re 51.9 46 0.00099 19.2 4.9 40 82-123 11-50 (55)
114 PRK11924 RNA polymerase sigma 51.8 40 0.00087 25.4 5.2 30 96-126 139-168 (179)
115 PF07750 GcrA: GcrA cell cycle 51.3 18 0.00039 28.4 3.2 39 28-69 2-40 (162)
116 PRK09641 RNA polymerase sigma 50.0 43 0.00094 25.6 5.2 29 97-126 151-179 (187)
117 TIGR02939 RpoE_Sigma70 RNA pol 47.1 41 0.00088 25.9 4.7 29 98-127 154-182 (190)
118 cd08779 Death_PIDD Death Domai 46.6 26 0.00056 24.3 3.1 32 88-120 3-37 (86)
119 TIGR02954 Sig70_famx3 RNA poly 46.3 59 0.0013 24.6 5.4 29 97-126 134-162 (169)
120 KOG3554 Histone deacetylase co 45.6 27 0.00059 32.2 3.7 41 81-121 287-328 (693)
121 KOG3841 TEF-1 and related tran 45.2 79 0.0017 28.5 6.4 54 77-130 74-148 (455)
122 TIGR02948 SigW_bacill RNA poly 44.8 55 0.0012 25.0 5.1 28 98-126 152-179 (187)
123 PF01710 HTH_Tnp_IS630: Transp 44.7 56 0.0012 23.9 4.8 55 33-90 58-112 (119)
124 KOG4329 DNA-binding protein [G 44.6 28 0.0006 31.2 3.5 43 28-72 279-322 (445)
125 PRK09642 RNA polymerase sigma 44.0 71 0.0015 23.9 5.5 30 96-126 120-149 (160)
126 PRK12529 RNA polymerase sigma 44.0 86 0.0019 24.1 6.0 36 93-129 138-173 (178)
127 PRK12515 RNA polymerase sigma 43.8 64 0.0014 25.0 5.3 29 97-126 146-174 (189)
128 PRK12547 RNA polymerase sigma 43.7 83 0.0018 23.7 5.9 31 96-127 126-156 (164)
129 PRK09648 RNA polymerase sigma 43.0 75 0.0016 24.5 5.6 30 96-126 153-182 (189)
130 PRK09047 RNA polymerase factor 43.0 71 0.0015 23.7 5.3 30 96-126 120-149 (161)
131 PRK09645 RNA polymerase sigma 42.9 75 0.0016 24.1 5.5 29 97-126 133-161 (173)
132 PRK09637 RNA polymerase sigma 42.6 72 0.0016 24.8 5.4 31 95-126 119-149 (181)
133 PRK01905 DNA-binding protein F 42.6 80 0.0017 21.3 5.0 35 84-119 36-70 (77)
134 KOG3554 Histone deacetylase co 42.5 26 0.00056 32.3 3.1 50 10-69 278-327 (693)
135 PF10440 WIYLD: Ubiquitin-bind 41.9 19 0.00041 24.0 1.7 19 88-106 30-48 (65)
136 PRK12536 RNA polymerase sigma 40.2 97 0.0021 23.8 5.8 31 96-127 143-173 (181)
137 PLN03142 Probable chromatin-re 39.8 63 0.0014 32.8 5.6 41 81-121 826-867 (1033)
138 PRK12531 RNA polymerase sigma 39.8 90 0.002 24.3 5.6 29 97-126 156-184 (194)
139 cd08306 Death_FADD Fas-associa 39.0 49 0.0011 22.9 3.5 27 91-118 6-32 (86)
140 PRK11923 algU RNA polymerase s 38.8 71 0.0015 24.7 4.9 28 98-126 154-181 (193)
141 PRK00430 fis global DNA-bindin 38.7 87 0.0019 22.2 4.8 34 85-119 55-88 (95)
142 PRK09649 RNA polymerase sigma 38.3 1E+02 0.0022 23.9 5.7 30 97-127 145-174 (185)
143 TIGR02999 Sig-70_X6 RNA polyme 37.6 1.1E+02 0.0024 23.3 5.7 29 97-126 149-177 (183)
144 TIGR02943 Sig70_famx1 RNA poly 37.2 1E+02 0.0022 24.0 5.5 35 91-126 140-174 (188)
145 cd01670 Death Death Domain: a 37.1 40 0.00088 22.2 2.8 26 90-116 2-27 (79)
146 PRK05602 RNA polymerase sigma 36.8 88 0.0019 24.1 5.1 29 97-126 143-171 (186)
147 PRK13919 putative RNA polymera 36.6 1.1E+02 0.0024 23.4 5.6 29 98-127 151-179 (186)
148 PRK12524 RNA polymerase sigma 36.4 88 0.0019 24.4 5.1 30 96-126 150-179 (196)
149 PRK12542 RNA polymerase sigma 35.7 1.2E+02 0.0025 23.4 5.6 31 96-127 136-166 (185)
150 TIGR02983 SigE-fam_strep RNA p 35.5 1.3E+02 0.0028 22.4 5.7 39 88-127 116-154 (162)
151 smart00344 HTH_ASNC helix_turn 35.5 50 0.0011 23.2 3.2 43 32-76 3-45 (108)
152 PRK15201 fimbriae regulatory p 35.4 1.4E+02 0.003 24.2 5.9 44 80-126 132-175 (198)
153 PF09905 DUF2132: Uncharacteri 34.9 49 0.0011 22.0 2.7 44 34-90 12-62 (64)
154 PRK12530 RNA polymerase sigma 34.8 1.1E+02 0.0024 23.7 5.5 29 97-126 149-177 (189)
155 PF08870 DUF1832: Domain of un 34.5 1.7E+02 0.0036 21.5 5.9 97 30-136 5-105 (113)
156 smart00351 PAX Paired Box doma 34.5 1.9E+02 0.0041 21.3 7.4 73 24-98 13-92 (125)
157 COG1522 Lrp Transcriptional re 33.9 74 0.0016 23.7 4.1 43 85-128 8-51 (154)
158 PRK12546 RNA polymerase sigma 33.5 1.2E+02 0.0026 23.7 5.5 35 92-127 123-157 (188)
159 PRK12527 RNA polymerase sigma 33.4 1.3E+02 0.0029 22.3 5.5 30 96-126 119-148 (159)
160 PF01527 HTH_Tnp_1: Transposas 33.3 40 0.00087 22.0 2.3 46 25-74 3-48 (76)
161 PF01466 Skp1: Skp1 family, di 33.1 51 0.0011 22.3 2.8 36 49-92 36-71 (78)
162 PF00531 Death: Death domain; 33.1 84 0.0018 20.6 3.9 27 90-117 3-30 (83)
163 TIGR02952 Sig70_famx2 RNA poly 33.1 1.4E+02 0.003 22.3 5.6 28 98-126 138-165 (170)
164 PRK00118 putative DNA-binding 33.1 1.3E+02 0.0028 21.8 5.1 40 84-124 19-58 (104)
165 PRK12516 RNA polymerase sigma 32.9 1.2E+02 0.0026 23.6 5.4 35 91-126 125-159 (187)
166 PRK06759 RNA polymerase factor 32.5 1.2E+02 0.0027 22.2 5.1 28 98-126 122-149 (154)
167 PRK09638 RNA polymerase sigma 32.0 57 0.0012 24.8 3.2 30 97-127 141-170 (176)
168 PRK12514 RNA polymerase sigma 31.6 1.4E+02 0.003 22.7 5.5 28 98-126 145-172 (179)
169 PF13936 HTH_38: Helix-turn-he 31.3 72 0.0016 19.0 3.0 36 81-118 4-39 (44)
170 KOG0384 Chromodomain-helicase 31.2 32 0.0007 35.3 2.0 25 80-104 1134-1159(1373)
171 PRK10100 DNA-binding transcrip 30.6 1.4E+02 0.003 24.1 5.5 43 81-126 155-197 (216)
172 PRK11922 RNA polymerase sigma 30.6 71 0.0015 25.9 3.7 29 98-127 165-193 (231)
173 PRK09646 RNA polymerase sigma 30.3 1.7E+02 0.0038 22.7 5.9 28 98-126 158-185 (194)
174 PRK09651 RNA polymerase sigma 30.0 1.1E+02 0.0024 23.3 4.6 29 97-126 134-162 (172)
175 PRK12532 RNA polymerase sigma 29.9 1.4E+02 0.003 23.2 5.2 30 96-126 150-179 (195)
176 TIGR02960 SigX5 RNA polymerase 29.9 1.3E+02 0.0028 25.5 5.3 31 97-128 157-187 (324)
177 PRK12528 RNA polymerase sigma 29.9 1.5E+02 0.0031 22.2 5.2 33 92-125 123-155 (161)
178 TIGR02950 SigM_subfam RNA poly 29.5 53 0.0011 24.2 2.6 28 98-126 121-148 (154)
179 COG2963 Transposase and inacti 29.3 1.9E+02 0.0042 20.5 5.6 46 79-126 5-51 (116)
180 TIGR02984 Sig-70_plancto1 RNA 29.3 1.7E+02 0.0036 22.2 5.6 30 96-126 154-183 (189)
181 COG1522 Lrp Transcriptional re 29.1 55 0.0012 24.4 2.7 43 32-76 8-50 (154)
182 PRK12537 RNA polymerase sigma 28.4 1.8E+02 0.0039 22.3 5.6 29 97-126 148-176 (182)
183 PRK09647 RNA polymerase sigma 28.3 1.6E+02 0.0034 23.4 5.3 29 97-126 153-181 (203)
184 cd08312 Death_MyD88 Death doma 27.8 50 0.0011 22.5 2.0 22 95-117 13-34 (79)
185 PRK06811 RNA polymerase factor 27.8 1.8E+02 0.0039 22.5 5.5 28 98-126 147-174 (189)
186 PRK15328 invasion protein IagB 27.5 1.1E+02 0.0023 24.0 4.0 43 89-131 98-142 (160)
187 COG5201 SKP1 SCF ubiquitin lig 27.2 76 0.0016 24.3 3.0 54 31-92 89-150 (158)
188 PF11216 DUF3012: Protein of u 27.1 40 0.00086 19.3 1.1 23 15-37 4-26 (32)
189 PRK12545 RNA polymerase sigma 26.1 1.9E+02 0.0041 22.7 5.5 29 97-126 154-182 (201)
190 PRK06986 fliA flagellar biosyn 25.8 1.7E+02 0.0038 23.6 5.3 31 96-127 198-228 (236)
191 PRK15411 rcsA colanic acid cap 25.5 1.3E+02 0.0027 24.1 4.3 43 81-126 137-179 (207)
192 PRK12520 RNA polymerase sigma 25.4 2.1E+02 0.0045 22.1 5.5 28 98-126 147-174 (191)
193 PRK06930 positive control sigm 25.0 2E+02 0.0043 22.5 5.2 35 92-127 124-158 (170)
194 PRK10360 DNA-binding transcrip 24.9 2.4E+02 0.0052 21.0 5.7 44 80-126 136-179 (196)
195 PRK12519 RNA polymerase sigma 23.6 1.8E+02 0.0039 22.4 4.8 28 98-126 157-184 (194)
196 PRK12526 RNA polymerase sigma 23.4 2.6E+02 0.0057 22.0 5.8 28 98-126 169-196 (206)
197 PRK09483 response regulator; P 23.2 1.4E+02 0.0031 22.7 4.1 43 81-126 148-190 (217)
198 PF07555 NAGidase: beta-N-acet 23.2 1.7E+02 0.0037 25.3 4.9 24 23-46 6-29 (306)
199 PRK12544 RNA polymerase sigma 22.7 2.2E+02 0.0048 22.6 5.3 29 97-126 163-191 (206)
200 PF13384 HTH_23: Homeodomain-l 22.7 1.3E+02 0.0027 17.9 3.0 29 88-118 8-36 (50)
201 PF11084 DUF2621: Protein of u 22.4 84 0.0018 24.0 2.4 65 39-106 19-83 (141)
202 TIGR02989 Sig-70_gvs1 RNA poly 22.4 2.4E+02 0.0051 20.7 5.1 28 97-125 126-153 (159)
203 TIGR01636 phage_rinA phage tra 22.3 3.3E+02 0.0072 20.2 6.2 46 82-129 83-130 (134)
204 PRK09636 RNA polymerase sigma 22.1 2.4E+02 0.0053 23.6 5.6 32 97-129 130-161 (293)
205 PRK09639 RNA polymerase sigma 22.1 2.1E+02 0.0046 21.2 4.8 29 97-126 126-154 (166)
206 PRK12538 RNA polymerase sigma 22.1 1.8E+02 0.004 23.7 4.7 28 98-126 187-214 (233)
207 PRK09415 RNA polymerase factor 22.0 2.5E+02 0.0053 21.5 5.3 28 98-126 143-170 (179)
208 TIGR02980 SigBFG RNA polymeras 21.8 2.6E+02 0.0056 22.3 5.5 29 97-126 193-221 (227)
209 PRK12540 RNA polymerase sigma 21.4 2.6E+02 0.0057 21.5 5.4 29 97-126 126-154 (182)
210 PRK08241 RNA polymerase factor 20.9 3.2E+02 0.0069 23.3 6.2 28 98-126 169-196 (339)
211 PF05263 DUF722: Protein of un 20.8 2.5E+02 0.0053 21.3 4.8 31 87-118 86-118 (130)
212 PRK12511 RNA polymerase sigma 20.0 3.1E+02 0.0067 21.2 5.5 29 97-126 126-154 (182)
No 1
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=2.9e-37 Score=256.43 Aligned_cols=113 Identities=49% Similarity=0.834 Sum_probs=108.3
Q ss_pred hcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHHHHHhcCCC
Q 043269 21 ILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILELHSRWGNR 100 (191)
Q Consensus 21 ~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~~v~~~G~~ 100 (191)
++.+.||+||+|||++|+++|.+||.++|..||+.+|++|++++||.||.|||+|++++|.||+|||.+|++++..||++
T Consensus 4 k~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 4 NPELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred CccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 34566899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHHhHHHHhhcCC
Q 043269 101 WSKIAQYLPGRTDNEIKNYWRTRVQKHAKQLKC 133 (191)
Q Consensus 101 W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~~~~~ 133 (191)
|+.||++|||||+++|||+|+..+++++.+...
T Consensus 84 Ws~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~ 116 (238)
T KOG0048|consen 84 WSLIAGRLPGRTDNEVKNHWNTHLKKKLLKMGI 116 (238)
T ss_pred HHHHHhhCCCcCHHHHHHHHHHHHHHHHHHcCC
Confidence 999999999999999999999999999888763
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=3.4e-37 Score=252.52 Aligned_cols=118 Identities=54% Similarity=1.036 Sum_probs=111.2
Q ss_pred hcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHHHHHhcCCC
Q 043269 21 ILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILELHSRWGNR 100 (191)
Q Consensus 21 ~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~~v~~~G~~ 100 (191)
++++++++||+|||++|+++|.+||..+|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++++..||++
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnK 99 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNR 99 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhcccc
Confidence 68999999999999999999999999899999999866899999999999999999999999999999999999999999
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHHhHHHHhhcCCCCCch
Q 043269 101 WSKIAQYLPGRTDNEIKNYWRTRVQKHAKQLKCDVNSK 138 (191)
Q Consensus 101 W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~~~~~~~~~~ 138 (191)
|..||++|||||+++|||||+.++++.+.+........
T Consensus 100 Ws~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~ 137 (249)
T PLN03212 100 WSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTH 137 (249)
T ss_pred HHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCC
Confidence 99999999999999999999999999887766555443
No 3
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=3.9e-35 Score=256.16 Aligned_cols=121 Identities=50% Similarity=0.900 Sum_probs=111.8
Q ss_pred chHhhhcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHHHHH
Q 043269 16 QSEEAILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILELHS 95 (191)
Q Consensus 16 ~~~~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~~v~ 95 (191)
.|+. +..++||+||+|||++|+++|.+||.++|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++++.
T Consensus 5 ~Cc~-KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k 83 (459)
T PLN03091 5 SCCY-KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHA 83 (459)
T ss_pred ccCc-CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHH
Confidence 3443 468999999999999999999999999999999998778999999999999999999999999999999999999
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHHHhhcCCCCCc
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQLKCDVNS 137 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~~~~~~~~~ 137 (191)
.||++|..||++|||||+++|||||+.++++++++.+.....
T Consensus 84 ~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t 125 (459)
T PLN03091 84 VLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNT 125 (459)
T ss_pred HhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCC
Confidence 999999999999999999999999999999988876655433
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.86 E-value=3e-21 Score=174.71 Aligned_cols=133 Identities=24% Similarity=0.365 Sum_probs=120.5
Q ss_pred CCCCCccccchH-hhhcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhh------------------
Q 043269 7 GFSSGNHRQQSE-EAILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRL------------------ 67 (191)
Q Consensus 7 ~~~~~~~~~~~~-~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~------------------ 67 (191)
.++...|+..|. +..|+++|..|++|||++|..+-..++..+|.+||..|+.+|+..||..
T Consensus 233 srS~~~~~~~W~n~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEe 312 (939)
T KOG0049|consen 233 SRSEWAVKSKWYNELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEE 312 (939)
T ss_pred cCCHHHHHHHHhhhcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhh
Confidence 355578999998 5799999999999999999999999999999999999997799999884
Q ss_pred ------------------------------------hhhhccCCCCcCCCCCHHHHHHHHHHHHhcC-CCHHHHhhhCCC
Q 043269 68 ------------------------------------RWLNYLRPDVRRGNITLQEQLMILELHSRWG-NRWSKIAQYLPG 110 (191)
Q Consensus 68 ------------------------------------rw~~~l~p~~~~~~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l~g 110 (191)
||...|+|.+++|+||.+||.+|+.+|.+|| ..|.+|-..+||
T Consensus 313 d~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPn 392 (939)
T KOG0049|consen 313 DTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPN 392 (939)
T ss_pred hHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCC
Confidence 4555588999999999999999999999999 579999999999
Q ss_pred CCHHHHHHHHHHHhHHHHhhcCCCCCchH
Q 043269 111 RTDNEIKNYWRTRVQKHAKQLKCDVNSKQ 139 (191)
Q Consensus 111 Rt~~~~k~rw~~~l~k~~~~~~~~~~~~~ 139 (191)
|++.||+.||.+.|...++...|...++.
T Consensus 393 RSdsQcR~RY~nvL~~s~K~~rW~l~ede 421 (939)
T KOG0049|consen 393 RSDSQCRERYTNVLNRSAKVERWTLVEDE 421 (939)
T ss_pred ccHHHHHHHHHHHHHHhhccCceeecchH
Confidence 99999999999999999999999877655
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.85 E-value=1.5e-21 Score=176.63 Aligned_cols=111 Identities=28% Similarity=0.442 Sum_probs=103.7
Q ss_pred CCCCCCCccccchHh-hhcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCC
Q 043269 5 VGGFSSGNHRQQSEE-AILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNIT 83 (191)
Q Consensus 5 ~~~~~~~~~~~~~~~-~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt 83 (191)
.+|++...-.-+|-. -+|++++|+||++||.+|+.+|.+||.++|.+|-+.+| ||+..|||+||.|.|+...+++.||
T Consensus 338 mpgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~ 416 (939)
T KOG0049|consen 338 MPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWT 416 (939)
T ss_pred cCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCcee
Confidence 357777777778774 69999999999999999999999999999999999998 9999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHH
Q 043269 84 LQEQLMILELHSRWG-NRWSKIAQYLPGRTDNEI 116 (191)
Q Consensus 84 ~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~ 116 (191)
-.||+.|+.+|.+|| ++|.+||..||+||..|.
T Consensus 417 l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~ 450 (939)
T KOG0049|consen 417 LVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQL 450 (939)
T ss_pred ecchHHHHHHHHHHccchHHHHHHHccccchhHH
Confidence 999999999999999 899999999999999554
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=99.76 E-value=1.6e-18 Score=114.44 Aligned_cols=60 Identities=47% Similarity=0.827 Sum_probs=55.3
Q ss_pred CCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHH
Q 043269 29 WTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMI 90 (191)
Q Consensus 29 WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L 90 (191)
||+|||++|+.+|..||. +|..||+.|| .|++.||+.||.++|.+.+++++||++||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999997 8999999997 89999999999999999999999999999987
No 7
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.68 E-value=2.6e-17 Score=146.14 Aligned_cols=107 Identities=23% Similarity=0.490 Sum_probs=101.1
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHHHHHhcCCCHHH
Q 043269 24 VRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILELHSRWGNRWSK 103 (191)
Q Consensus 24 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~~v~~~G~~W~~ 103 (191)
++.|.|+.-||+.|..+|.+||.+.|.+|++.+. -.+.+||+.||..+|+|.+++..|+.|||++|+.++..+...|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 5778999999999999999999999999999997 889999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHHhHHHHhhcC
Q 043269 104 IAQYLPGRTDNEIKNYWRTRVQKHAKQLK 132 (191)
Q Consensus 104 Ia~~l~gRt~~~~k~rw~~~l~k~~~~~~ 132 (191)
|+..| ||+.+||-.||.+++........
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~~ 111 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYHY 111 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhhc
Confidence 99999 99999999999999987655443
No 8
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.68 E-value=5.9e-17 Score=145.98 Aligned_cols=109 Identities=28% Similarity=0.463 Sum_probs=103.0
Q ss_pred hhcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHHHHHhcCC
Q 043269 20 AILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILELHSRWGN 99 (191)
Q Consensus 20 ~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~~v~~~G~ 99 (191)
....++.|.|+..||+.|..+|..||..+|..||..|. .++++||+.||.++++|.+++..|+.|||..|+.+..++|.
T Consensus 14 ~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~ 92 (512)
T COG5147 14 MQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT 92 (512)
T ss_pred ccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc
Confidence 34567889999999999999999999999999999998 69999999999999999999999999999999999999999
Q ss_pred CHHHHhhhCCCCCHHHHHHHHHHHhHHHHh
Q 043269 100 RWSKIAQYLPGRTDNEIKNYWRTRVQKHAK 129 (191)
Q Consensus 100 ~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~ 129 (191)
.|+.||.++++||..+|.++|...+.....
T Consensus 93 ~wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 93 QWSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 999999999999999999999988877554
No 9
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.56 E-value=2.2e-15 Score=95.28 Aligned_cols=48 Identities=42% Similarity=0.750 Sum_probs=43.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhcc
Q 043269 26 KGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYL 73 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l 73 (191)
|++||+|||++|+++|.+||.++|..||..|+.+|+..||+.||.++|
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 689999999999999999999669999999976999999999999875
No 10
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.56 E-value=8.1e-15 Score=92.69 Aligned_cols=46 Identities=33% Similarity=0.637 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCC-HHHHhhhCC-CCCHHHHHHHHHHHh
Q 043269 79 RGNITLQEQLMILELHSRWGNR-WSKIAQYLP-GRTDNEIKNYWRTRV 124 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G~~-W~~Ia~~l~-gRt~~~~k~rw~~~l 124 (191)
+++||+|||++|+++|.+||.+ |..||..|| |||..||++||.+++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999988 999999999 999999999999874
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.55 E-value=8.3e-15 Score=120.75 Aligned_cols=79 Identities=15% Similarity=0.325 Sum_probs=68.8
Q ss_pred cCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHHHHHhcC-CCHHHHhhhC-CCCCHHHHHHHHHHHhHHHHhhcCC
Q 043269 56 AGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILELHSRWG-NRWSKIAQYL-PGRTDNEIKNYWRTRVQKHAKQLKC 133 (191)
Q Consensus 56 l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l-~gRt~~~~k~rw~~~l~k~~~~~~~ 133 (191)
++ +|+..-|. .+.+++++||+|||++|+++|++|| ++|..||+.+ ++||+.||+.||.++|++.+++..+
T Consensus 10 ~~-~~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpW 81 (249)
T PLN03212 10 VS-KKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGI 81 (249)
T ss_pred CC-CCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCC
Confidence 44 56665553 3468999999999999999999999 6899999988 6999999999999999999999999
Q ss_pred CCCchHHHH
Q 043269 134 DVNSKQFRD 142 (191)
Q Consensus 134 ~~~~~~~~~ 142 (191)
+.+++.++.
T Consensus 82 T~EED~lLl 90 (249)
T PLN03212 82 TSDEEDLIL 90 (249)
T ss_pred ChHHHHHHH
Confidence 998877643
No 12
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.54 E-value=1.1e-14 Score=132.59 Aligned_cols=103 Identities=24% Similarity=0.522 Sum_probs=92.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCC--CcCCCCCHHHHHHHHHHHH-------
Q 043269 25 RKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPD--VRRGNITLQEQLMILELHS------- 95 (191)
Q Consensus 25 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~--~~~~~Wt~eEd~~L~~~v~------- 95 (191)
.+|.||+||++.|..+|..+|. .|..|+..|+ |.+..|++||++|.... .+++.||.||+++|+++|+
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 8999999999999999999998 8999999995 99999999999999887 4899999999999999995
Q ss_pred hcC-------------------CCHHHHhhhCCCCCHHHHHHHHHHHhHHHHhh
Q 043269 96 RWG-------------------NRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQ 130 (191)
Q Consensus 96 ~~G-------------------~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~~ 130 (191)
++- -.|..|++.+..|+..||+-+|..++......
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n 513 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFN 513 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhh
Confidence 341 16999999999999999999999998764433
No 13
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.52 E-value=1.2e-14 Score=95.80 Aligned_cols=58 Identities=31% Similarity=0.539 Sum_probs=48.3
Q ss_pred CCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHHHhhcCCCCCchH
Q 043269 82 ITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQLKCDVNSKQ 139 (191)
Q Consensus 82 Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~~~~~~~~~~~ 139 (191)
||+|||.+|+++|..||++|..||+.|+.||..+|++||...|++.+.+..++.+++.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~ 58 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQ 58 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHh
Confidence 9999999999999999999999999996699999999999988877777666665543
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.49 E-value=2e-14 Score=119.58 Aligned_cols=84 Identities=13% Similarity=0.295 Sum_probs=73.8
Q ss_pred CCCcCCCCCHHHHHHHHHHHHhcC-CCHHHHhhhCC-CCCHHHHHHHHHHHhHHHHhhcCCCCCchHH------------
Q 043269 75 PDVRRGNITLQEQLMILELHSRWG-NRWSKIAQYLP-GRTDNEIKNYWRTRVQKHAKQLKCDVNSKQF------------ 140 (191)
Q Consensus 75 p~~~~~~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l~-gRt~~~~k~rw~~~l~k~~~~~~~~~~~~~~------------ 140 (191)
+.+.+|+||+|||.+|+++|.+|| ++|..|++.++ +|++.+||.||.++|++.++++.++.+++.+
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 345579999999999999999999 67999999998 9999999999999999999999999998875
Q ss_pred -----------HHhhhhccccchHHHHhh
Q 043269 141 -----------RDAMRFVWVPRLIERIQA 158 (191)
Q Consensus 141 -----------~~~~~~~~~p~~~~~~~~ 158 (191)
...++.+|..++.+++..
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~ 113 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLK 113 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHH
Confidence 446678887777766654
No 15
>PLN03091 hypothetical protein; Provisional
Probab=99.41 E-value=2.1e-13 Score=120.14 Aligned_cols=68 Identities=15% Similarity=0.274 Sum_probs=62.4
Q ss_pred CCCcCCCCCHHHHHHHHHHHHhcC-CCHHHHhhhC-CCCCHHHHHHHHHHHhHHHHhhcCCCCCchHHHH
Q 043269 75 PDVRRGNITLQEQLMILELHSRWG-NRWSKIAQYL-PGRTDNEIKNYWRTRVQKHAKQLKCDVNSKQFRD 142 (191)
Q Consensus 75 p~~~~~~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l-~gRt~~~~k~rw~~~l~k~~~~~~~~~~~~~~~~ 142 (191)
..+++++||+|||++|+++|.+|| .+|..||+.+ +||++.||+.||.++|++.+++..++.+++.+..
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLL 79 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLII 79 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHH
Confidence 468999999999999999999999 6899999988 5999999999999999999999999998887533
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.38 E-value=1e-12 Score=81.65 Aligned_cols=47 Identities=36% Similarity=0.783 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHHhH
Q 043269 79 RGNITLQEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTRVQ 125 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~l~ 125 (191)
+++||++||.+|+.++..|| .+|..||..|++||+.+|+++|..+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 999999999999999999999998764
No 17
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.28 E-value=9.1e-12 Score=76.13 Aligned_cols=44 Identities=39% Similarity=0.740 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHHh
Q 043269 81 NITLQEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTRV 124 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~l 124 (191)
+||++|+..|+.++..|| .+|..||..|++||..+|+++|.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 99999999999999999999998763
No 18
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.27 E-value=7.5e-12 Score=114.35 Aligned_cols=116 Identities=22% Similarity=0.291 Sum_probs=96.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC-----------------------CChhhhhhhcCCCCCchhhhhhhhhccCCCC-c
Q 043269 23 GVRKGPWTVEEDSLLMNYVAIHGE-----------------------GRWNAVASSAGLNRTGKSCRLRWLNYLRPDV-R 78 (191)
Q Consensus 23 ~~~kg~WT~eED~~L~~~v~~~g~-----------------------~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~-~ 78 (191)
.++-+.|+++||..|...|..|-. +-|..|...|| .|+...++.+-++...|.- +
T Consensus 305 e~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~~ 383 (607)
T KOG0051|consen 305 EINLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFENK 383 (607)
T ss_pred hhhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCccccc
Confidence 456689999999999999988711 12788889998 6999999884444444433 9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH--HhhcCCCCCchHH
Q 043269 79 RGNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH--AKQLKCDVNSKQF 140 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~--~~~~~~~~~~~~~ 140 (191)
+|.||+||++.|..+|.++|+.|..|++.| ||.+.+|+++|+++++.. .++..++.++++.
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~ 446 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEK 446 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHH
Confidence 999999999999999999999999999999 999999999999999876 4777777777664
No 19
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.26 E-value=8.1e-12 Score=77.52 Aligned_cols=48 Identities=44% Similarity=0.846 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccC
Q 043269 26 KGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLR 74 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~ 74 (191)
++.||++||.+|..++..||..+|..||..|+ +|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 47899999999999999999559999999998 9999999999998764
No 20
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.14 E-value=6e-11 Score=72.43 Aligned_cols=45 Identities=47% Similarity=0.860 Sum_probs=41.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhcc
Q 043269 28 PWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYL 73 (191)
Q Consensus 28 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l 73 (191)
+||++||..|..++..||..+|..||..++ +|+..+|+.+|.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHhC
Confidence 599999999999999999559999999998 899999999998753
No 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.59 E-value=4.1e-08 Score=89.17 Aligned_cols=117 Identities=14% Similarity=0.170 Sum_probs=103.2
Q ss_pred CCCCCccccch-HhhhcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHH
Q 043269 7 GFSSGNHRQQS-EEAILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQ 85 (191)
Q Consensus 7 ~~~~~~~~~~~-~~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~e 85 (191)
.+++..|..+| ...+|.++++.|+.+||..|+.+-..+|. .|..||..++ +|+..+|++||.+.|.+..+ ..|+..
T Consensus 52 ~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~-~wstia~~~d-~rt~~~~~ery~~~~~~~~s-~~~s~~ 128 (512)
T COG5147 52 SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT-QWSTIADYKD-RRTAQQCVERYVNTLEDLSS-THDSKL 128 (512)
T ss_pred ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc-hhhhhccccC-ccchHHHHHHHHHHhhhhhc-cccccc
Confidence 36788999999 46899999999999999999999999999 6999999998 99999999999999987666 789999
Q ss_pred HHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 86 EQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 86 Ed~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
+....+.-+..|+..|..+....-.+-...|.|++.++...
T Consensus 129 ~~~~~f~k~d~f~~~~~~~~~~~~~~~~~~~~N~~~~~~~~ 169 (512)
T COG5147 129 QRRNEFDKIDPFNENSARRPDIYEDELLEREVNREASYRLR 169 (512)
T ss_pred cchhhccccCchhhhhhhhhhhhhcccchhhhhHHHHHHHH
Confidence 99998888999998888888777677778888888766544
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.32 E-value=8.2e-07 Score=58.08 Aligned_cols=49 Identities=14% Similarity=0.234 Sum_probs=43.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCh---hhhhhhcCCCC-Cchhhhhhhhhcc
Q 043269 25 RKGPWTVEEDSLLMNYVAIHGEGRW---NAVASSAGLNR-TGKSCRLRWLNYL 73 (191)
Q Consensus 25 ~kg~WT~eED~~L~~~v~~~g~~~W---~~Ia~~l~~~R-~~~qc~~rw~~~l 73 (191)
.+-.||+||...++++|..+|.++| ..|++.|...+ |..||+.+++.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3557999999999999999999999 99999987556 9999999998875
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.25 E-value=8e-07 Score=78.60 Aligned_cols=51 Identities=25% Similarity=0.588 Sum_probs=47.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccC
Q 043269 23 GVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLR 74 (191)
Q Consensus 23 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~ 74 (191)
.+-...||.+|+-+|++++..||.|||..||.++| .|+..+|+++|.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHHh
Confidence 45567799999999999999999999999999999 9999999999999863
No 24
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.10 E-value=2.8e-06 Score=76.57 Aligned_cols=63 Identities=21% Similarity=0.402 Sum_probs=58.3
Q ss_pred CcCCCCCHHHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHHhHHHHhhcCCCCCchH
Q 043269 77 VRRGNITLQEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQLKCDVNSKQ 139 (191)
Q Consensus 77 ~~~~~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~~~~~~~~~~~ 139 (191)
++.|-|+.-||++|--+|.+|| +.|+.|+..++-.|+.||++||..++.+.+++-.++..++.
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eede 68 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDE 68 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHH
Confidence 5778999999999999999999 78999999999999999999999999999999888876654
No 25
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.06 E-value=7.4e-06 Score=72.58 Aligned_cols=50 Identities=22% Similarity=0.419 Sum_probs=45.2
Q ss_pred CCcCCCCCHHHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHHhH
Q 043269 76 DVRRGNITLQEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTRVQ 125 (191)
Q Consensus 76 ~~~~~~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~l~ 125 (191)
.+-...||-+|+.+|++++..|| ++|..||.++..||..+|+.+|.+++-
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 34556899999999999999999 999999999988999999999987654
No 26
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=98.03 E-value=1.9e-05 Score=51.62 Aligned_cols=47 Identities=15% Similarity=0.198 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCC-CH---HHHhhhCC-CC-CHHHHHHHHHHHhH
Q 043269 79 RGNITLQEQLMILELHSRWGN-RW---SKIAQYLP-GR-TDNEIKNYWRTRVQ 125 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G~-~W---~~Ia~~l~-gR-t~~~~k~rw~~~l~ 125 (191)
+-.||+||...++++++.||. +| ..|+..|. .| |..||+.+...+..
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 347999999999999999995 99 99999874 35 99999998876653
No 27
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.77 E-value=0.00018 Score=58.37 Aligned_cols=97 Identities=22% Similarity=0.382 Sum_probs=73.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCC--CchhhhhhhhhccC-CCC--------------------cCCCCCH
Q 043269 28 PWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNR--TGKSCRLRWLNYLR-PDV--------------------RRGNITL 84 (191)
Q Consensus 28 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R--~~~qc~~rw~~~l~-p~~--------------------~~~~Wt~ 84 (191)
+|++++|-.|+.+|.... +-..|+..+++.| |...+.+||+..|. |.+ .+.+||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 599999999999998655 5788887665433 66778899998864 322 3568999
Q ss_pred HHHHHHHHHHHhcCC---CHHHHhh-----hCCCCCHHHHHHHHHHHhHH
Q 043269 85 QEQLMILELHSRWGN---RWSKIAQ-----YLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 85 eEd~~L~~~v~~~G~---~W~~Ia~-----~l~gRt~~~~k~rw~~~l~k 126 (191)
+|+++|......... .+.+|-. +-++||+.++.++|..+.+.
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy 128 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQY 128 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHh
Confidence 999999997765543 4666622 33789999999999966444
No 28
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.61 E-value=4.7e-05 Score=68.16 Aligned_cols=46 Identities=30% Similarity=0.669 Sum_probs=43.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhc
Q 043269 25 RKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNY 72 (191)
Q Consensus 25 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~ 72 (191)
....||.+|..+|++.|..||. +|.+||.+++ +|+..||..||.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVg-tKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVG-TKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhC-CCCHHHHHHHHHcC
Confidence 5668999999999999999999 8999999999 99999999999876
No 29
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.57 E-value=0.00011 Score=67.25 Aligned_cols=46 Identities=26% Similarity=0.403 Sum_probs=42.7
Q ss_pred cCCCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHH
Q 043269 78 RRGNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTR 123 (191)
Q Consensus 78 ~~~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~ 123 (191)
.++.||++|..+|+++++.||-+|.+||.++.+||..||-.+|..+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 4568999999999999999999999999999999999999998654
No 30
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=97.53 E-value=9.4e-05 Score=51.79 Aligned_cols=49 Identities=29% Similarity=0.482 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHHh------cC--C------CHHHHhhhC----CCCCHHHHHHHHHHHhHHHH
Q 043269 80 GNITLQEQLMILELHSR------WG--N------RWSKIAQYL----PGRTDNEIKNYWRTRVQKHA 128 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~------~G--~------~W~~Ia~~l----~gRt~~~~k~rw~~~l~k~~ 128 (191)
..||.+|...||+++.. ++ + -|..||..| ..||+.||+++|.++.+...
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 47999999999999987 21 1 399999976 46999999999999876643
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.50 E-value=9.2e-05 Score=67.64 Aligned_cols=49 Identities=29% Similarity=0.630 Sum_probs=45.2
Q ss_pred cCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhc
Q 043269 22 LGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNY 72 (191)
Q Consensus 22 ~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~ 72 (191)
....++.||.+|.-+|+++|..||. +|.+||.+++ +|+..||..++.+.
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 4566788999999999999999999 9999999999 99999999998775
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.48 E-value=0.00012 Score=65.48 Aligned_cols=54 Identities=20% Similarity=0.257 Sum_probs=45.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHH--hHHHHhhcC
Q 043269 79 RGNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTR--VQKHAKQLK 132 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~--l~k~~~~~~ 132 (191)
...||.+|..+|++.++.||-.|.+||+++..||..||.-||-++ ..+.+.++.
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~ 334 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGD 334 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhccc
Confidence 348999999999999999999999999999999999999999764 234444433
No 33
>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=97.47 E-value=0.00017 Score=56.39 Aligned_cols=49 Identities=24% Similarity=0.353 Sum_probs=43.2
Q ss_pred cCCCCCHHHHHHHHHHHHhcC---C----CHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 78 RRGNITLQEQLMILELHSRWG---N----RWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 78 ~~~~Wt~eEd~~L~~~v~~~G---~----~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
....||.|||.+|.+.|..|- + -..++++.| +||+.+|-=||+.++++.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkq 58 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQ 58 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHH
Confidence 456899999999999999883 2 378889999 999999999999999975
No 34
>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=97.26 E-value=0.0005 Score=46.10 Aligned_cols=49 Identities=14% Similarity=0.273 Sum_probs=32.3
Q ss_pred CCCCCHHHHHHHHHHHHhcC--------C-CHHHHhhhCC-CCCHHHHHHHHHHHhHHH
Q 043269 79 RGNITLQEQLMILELHSRWG--------N-RWSKIAQYLP-GRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G--------~-~W~~Ia~~l~-gRt~~~~k~rw~~~l~k~ 127 (191)
+-+||.|||..|++.|..+. + -|.++++.-+ .+|-.+.++||...|...
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 35899999999999996552 1 2999999877 899999999998887764
No 35
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=97.11 E-value=0.0013 Score=44.98 Aligned_cols=49 Identities=24% Similarity=0.481 Sum_probs=40.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCC-----------------CHHHHhhhC-----CCCCHHHHHHHHHHHhHHH
Q 043269 79 RGNITLQEQLMILELHSRWGN-----------------RWSKIAQYL-----PGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G~-----------------~W~~Ia~~l-----~gRt~~~~k~rw~~~l~k~ 127 (191)
...||.+|..+|++++.+|.. -|.+|+..| +.||..+++.+|.++....
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~ 72 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKA 72 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHH
Confidence 357999999999999998731 399998866 3699999999999887653
No 36
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=97.06 E-value=0.0005 Score=46.11 Aligned_cols=51 Identities=31% Similarity=0.529 Sum_probs=33.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------C--ChhhhhhhcCCCCCchhhhhhhhhccCCC
Q 043269 26 KGPWTVEEDSLLMNYVAIHGE------G--RWNAVASSAGLNRTGKSCRLRWLNYLRPD 76 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~~g~------~--~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~ 76 (191)
+-+||.+||..|+..|..+.. | =|.++++..+..++-.+-++||...|.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 457999999999999976632 2 29999988765789999999999998754
No 37
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.91 E-value=0.0012 Score=52.26 Aligned_cols=50 Identities=20% Similarity=0.278 Sum_probs=42.3
Q ss_pred CcCCCCCHHHHHHHHHHHHhcCC-------CHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 77 VRRGNITLQEQLMILELHSRWGN-------RWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 77 ~~~~~Wt~eEd~~L~~~v~~~G~-------~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
.+...||.|+|.+|-+.|..|+. -...++..| +||..+|..||+.++++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~ 59 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQ 59 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHH
Confidence 35678999999999999988873 256667788 999999999999999974
No 38
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.90 E-value=0.00064 Score=53.16 Aligned_cols=49 Identities=41% Similarity=0.733 Sum_probs=42.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC-C-----ChhhhhhhcCCCCCchhhhhhhhhccC
Q 043269 24 VRKGPWTVEEDSLLMNYVAIHGE-G-----RWNAVASSAGLNRTGKSCRLRWLNYLR 74 (191)
Q Consensus 24 ~~kg~WT~eED~~L~~~v~~~g~-~-----~W~~Ia~~l~~~R~~~qc~~rw~~~l~ 74 (191)
.++..||.|||.+|.+.|-+|-. | .+.+++..| +||...|.-||+.++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L--~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL--NRTAAACGFRWNAYVR 56 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH--cccHHHhcchHHHHHH
Confidence 46778999999999999999832 1 488899988 5999999999999876
No 39
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.78 E-value=0.001 Score=46.40 Aligned_cols=48 Identities=33% Similarity=0.621 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C--C-----CChhhhhhhc---CCCCCchhhhhhhhhcc
Q 043269 26 KGPWTVEEDSLLMNYVAI--H----G--E-----GRWNAVASSA---GLNRTGKSCRLRWLNYL 73 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~--~----g--~-----~~W~~Ia~~l---~~~R~~~qc~~rw~~~l 73 (191)
+-.||.+|...|++++.. + + . .-|..||..| |..|++.||+.+|.+..
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 357999999999999877 2 1 1 1499999776 55799999999998863
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.72 E-value=0.00094 Score=57.51 Aligned_cols=48 Identities=23% Similarity=0.551 Sum_probs=44.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccC
Q 043269 26 KGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLR 74 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~ 74 (191)
--.|+..|+-+|++...-.|-|||..||..+| .|....|+++|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 34599999999999999999999999999999 9999999999998876
No 41
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=96.59 E-value=0.012 Score=58.33 Aligned_cols=102 Identities=14% Similarity=0.269 Sum_probs=78.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhh-------hhhhc----------------------------
Q 043269 28 PWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRL-------RWLNY---------------------------- 72 (191)
Q Consensus 28 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~-------rw~~~---------------------------- 72 (191)
.|+..+=..++.+..+||-.+-..||..|. +++...++. ||..+
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 388888888888889999889999999997 888877752 11111
Q ss_pred --------------c-CCCCcCCCCCHHHHHHHHHHHHhcC-CCHHHHhh------------hCCCCCHHHHHHHHHHHh
Q 043269 73 --------------L-RPDVRRGNITLQEQLMILELHSRWG-NRWSKIAQ------------YLPGRTDNEIKNYWRTRV 124 (191)
Q Consensus 73 --------------l-~p~~~~~~Wt~eEd~~L~~~v~~~G-~~W~~Ia~------------~l~gRt~~~~k~rw~~~l 124 (191)
+ .+..++..+|+|||..|+-.+.+|| ++|..|-. +|..||+..|..|-..++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 0 1223445699999999999999999 88999832 236999999999999988
Q ss_pred HHHHhh
Q 043269 125 QKHAKQ 130 (191)
Q Consensus 125 ~k~~~~ 130 (191)
+-..+.
T Consensus 985 ~~~~~e 990 (1033)
T PLN03142 985 RLIEKE 990 (1033)
T ss_pred HHHHHH
Confidence 775443
No 42
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.52 E-value=0.0032 Score=54.30 Aligned_cols=47 Identities=26% Similarity=0.494 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHHhH
Q 043269 79 RGNITLQEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTRVQ 125 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~l~ 125 (191)
-..|+.+|+.+|++.....| ++|..||.++..|+...||.+|..+..
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 34799999999999999999 999999999988999999999876654
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=96.19 E-value=0.0036 Score=42.77 Aligned_cols=49 Identities=27% Similarity=0.469 Sum_probs=39.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------CChhhhhhhc----CCCCCchhhhhhhhhcc
Q 043269 25 RKGPWTVEEDSLLMNYVAIHGE----------------GRWNAVASSA----GLNRTGKSCRLRWLNYL 73 (191)
Q Consensus 25 ~kg~WT~eED~~L~~~v~~~g~----------------~~W~~Ia~~l----~~~R~~~qc~~rw~~~l 73 (191)
++..||++|.+.|+++|.+|.. .-|..|+..| +..|+..|++..|.++.
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 3567999999999999998822 1499999766 22599999999998864
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.89 E-value=0.0045 Score=49.02 Aligned_cols=49 Identities=33% Similarity=0.620 Sum_probs=40.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCC------ChhhhhhhcCCCCCchhhhhhhhhccC
Q 043269 24 VRKGPWTVEEDSLLMNYVAIHGEG------RWNAVASSAGLNRTGKSCRLRWLNYLR 74 (191)
Q Consensus 24 ~~kg~WT~eED~~L~~~v~~~g~~------~W~~Ia~~l~~~R~~~qc~~rw~~~l~ 74 (191)
.++..||.|||.+|.+.|..|+.. -...++..| +|+..+|..||.-++.
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHH
Confidence 467889999999999999998653 256666777 5999999999977665
No 45
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=95.10 E-value=0.037 Score=48.91 Aligned_cols=47 Identities=21% Similarity=0.304 Sum_probs=43.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 80 GNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.+|+.+|-+++.++..++|...+.|+..||.|...|||.+|.+--++
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 37999999999999999999999999999999999999999865443
No 46
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=94.84 E-value=0.069 Score=46.60 Aligned_cols=52 Identities=19% Similarity=0.316 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHhc----------CCCHHHHhhhC----CCCCHHHHHHHHHHHhHHHHhh
Q 043269 79 RGNITLQEQLMILELHSRW----------GNRWSKIAQYL----PGRTDNEIKNYWRTRVQKHAKQ 130 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~----------G~~W~~Ia~~l----~gRt~~~~k~rw~~~l~k~~~~ 130 (191)
...|+.+|-..||++.... +..|..||+.+ .-||+.+|+++|.++.++.-+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~ 119 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKE 119 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHH
Confidence 3689999999999998653 23599999954 4599999999999998875443
No 47
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=94.12 E-value=0.13 Score=38.51 Aligned_cols=53 Identities=21% Similarity=0.411 Sum_probs=41.2
Q ss_pred CCcCCCCCHHHHHHHHHHHHhcCC----CHHHHhh------------hCCCCCHHHHHHHHHHHhHHHH
Q 043269 76 DVRRGNITLQEQLMILELHSRWGN----RWSKIAQ------------YLPGRTDNEIKNYWRTRVQKHA 128 (191)
Q Consensus 76 ~~~~~~Wt~eEd~~L~~~v~~~G~----~W~~Ia~------------~l~gRt~~~~k~rw~~~l~k~~ 128 (191)
..++..||++||..|+-++.+||= .|..|-. +|..||+..|..|-..+++-..
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i~ 114 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLIE 114 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHHH
Confidence 556779999999999999999995 7988843 2378999999999988887643
No 48
>PF12776 Myb_DNA-bind_3: Myb/SANT-like DNA-binding domain; InterPro: IPR024752 This domain, found in a range of uncharacterised proteins, may be related to Myb/SANT-like DNA binding domains.
Probab=94.05 E-value=0.19 Score=35.29 Aligned_cols=46 Identities=28% Similarity=0.494 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHhc---CC----------CHHHHhhhC---C--CCCHHHHHHHHHHHhHH
Q 043269 81 NITLQEQLMILELHSRW---GN----------RWSKIAQYL---P--GRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~---G~----------~W~~Ia~~l---~--gRt~~~~k~rw~~~l~k 126 (191)
.||+++++.|++++.+. |+ .|..|+..| + ..|..||++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 49999999999998653 21 399998866 2 35778999999877665
No 49
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=93.76 E-value=0.082 Score=46.87 Aligned_cols=55 Identities=20% Similarity=0.229 Sum_probs=47.9
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHhhh-----CCC-CCHHHHHHHHHHHhHHHHhhcCCC
Q 043269 80 GNITLQEQLMILELHSRWGNRWSKIAQY-----LPG-RTDNEIKNYWRTRVQKHAKQLKCD 134 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~-----l~g-Rt~~~~k~rw~~~l~k~~~~~~~~ 134 (191)
..||.+|-.-|+++.+.|--+|--||.. ++. ||-.++|+||....++.++-....
T Consensus 131 n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 5799999999999999999999999875 555 999999999999998877665544
No 50
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=93.28 E-value=0.37 Score=43.66 Aligned_cols=47 Identities=19% Similarity=0.338 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhH
Q 043269 79 RGNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQ 125 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~ 125 (191)
...||.||--+|-+++..||.+..+|-+.||.|+-..|..+|....+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK 233 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKK 233 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHH
Confidence 45799999999999999999999999999999999999998876544
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=91.65 E-value=0.19 Score=44.47 Aligned_cols=44 Identities=18% Similarity=0.324 Sum_probs=40.3
Q ss_pred CCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhc
Q 043269 27 GPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNY 72 (191)
Q Consensus 27 g~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~ 72 (191)
-+||.+|-+++..++...|. ++..|+.++| +|..+|+...|.+-
T Consensus 366 ~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP-~R~RkqIKaKfi~E 409 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGT-DFSLISSLFP-NRERKQIKAKFIKE 409 (507)
T ss_pred CcccHHHHHHHHHHHHHhcc-hHHHHHHhcC-chhHHHHHHHHHHH
Confidence 35999999999999999999 8999999998 99999999988653
No 52
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=91.64 E-value=0.22 Score=37.21 Aligned_cols=34 Identities=24% Similarity=0.457 Sum_probs=28.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CChhhhhhhc
Q 043269 23 GVRKGPWTVEEDSLLMNYVAIHGE---GRWNAVASSA 56 (191)
Q Consensus 23 ~~~kg~WT~eED~~L~~~v~~~g~---~~W~~Ia~~l 56 (191)
..++..||.+||..|+-++.+||- +.|..|-..+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 556677999999999999999999 8999998766
No 53
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=90.99 E-value=0.9 Score=28.34 Aligned_cols=41 Identities=24% Similarity=0.302 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhH
Q 043269 84 LQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQ 125 (191)
Q Consensus 84 ~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~ 125 (191)
++++..++.++-..|-.+.+||..+ |.+...|+.+....++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 4677788888888899999999999 9999999988765544
No 54
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=90.90 E-value=1.2 Score=42.60 Aligned_cols=44 Identities=11% Similarity=0.151 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHH
Q 043269 80 GNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTR 123 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~ 123 (191)
..||+.|-.++-+++-.|..+.-.|++.++++|-.||-.+|...
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 47999999999999999999999999999999999998875443
No 55
>smart00595 MADF subfamily of SANT domain.
Probab=90.64 E-value=0.43 Score=32.97 Aligned_cols=28 Identities=29% Similarity=0.560 Sum_probs=23.7
Q ss_pred CHHHHhhhCCCCCHHHHHHHHHHHhHHHH
Q 043269 100 RWSKIAQYLPGRTDNEIKNYWRTRVQKHA 128 (191)
Q Consensus 100 ~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~ 128 (191)
-|.+||..| |-|..+|+.+|+++-....
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR~~y~ 56 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLRDRYR 56 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHHHHHH
Confidence 499999999 5599999999999876543
No 56
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=89.96 E-value=0.3 Score=46.60 Aligned_cols=45 Identities=16% Similarity=0.233 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhc
Q 043269 26 KGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNY 72 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~ 72 (191)
...||+.|-.++..++..|.. ++..|+++++ +++.+||-+-|+..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K-DF~~v~km~~-~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK-DFIFVQKMVK-SKTVAQCVEYYYTW 663 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc-cHHHHHHHhc-cccHHHHHHHHHHH
Confidence 346999999999999999998 8999999998 99999998876554
No 57
>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=86.51 E-value=0.73 Score=32.31 Aligned_cols=25 Identities=36% Similarity=0.605 Sum_probs=14.3
Q ss_pred cCCCCCCCCHHHHHHH--------HHHHHHhCC
Q 043269 22 LGVRKGPWTVEEDSLL--------MNYVAIHGE 46 (191)
Q Consensus 22 ~~~~kg~WT~eED~~L--------~~~v~~~g~ 46 (191)
|....|-||+|+|+.| ..++.+||.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 4566889999999999 355667764
No 58
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=86.27 E-value=0.88 Score=39.68 Aligned_cols=48 Identities=25% Similarity=0.412 Sum_probs=37.0
Q ss_pred CCCCCHHHHHHHHHHHHHh----CC-----CChhhhhhh---cCCCCCchhhhhhhhhcc
Q 043269 26 KGPWTVEEDSLLMNYVAIH----GE-----GRWNAVASS---AGLNRTGKSCRLRWLNYL 73 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~~----g~-----~~W~~Ia~~---l~~~R~~~qc~~rw~~~l 73 (191)
-..|+.+|-..|+++.... .. ..|..||.. .+..|++.||+.+|.+..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 3679999999999887542 11 259999973 345699999999998864
No 59
>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=83.13 E-value=1.1 Score=30.05 Aligned_cols=28 Identities=21% Similarity=0.447 Sum_probs=22.8
Q ss_pred CHHHHhhhCCC-CCHHHHHHHHHHHhHHH
Q 043269 100 RWSKIAQYLPG-RTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 100 ~W~~Ia~~l~g-Rt~~~~k~rw~~~l~k~ 127 (191)
-|..||..|.. -+..+|+.+|.++....
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~y 56 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDRY 56 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHHH
Confidence 49999999943 67889999999987654
No 60
>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=82.12 E-value=4.2 Score=24.51 Aligned_cols=38 Identities=21% Similarity=0.331 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHH
Q 043269 85 QEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTR 123 (191)
Q Consensus 85 eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~ 123 (191)
+=|..|+.+...-| -.+.+||+.+ |=+...|..|++.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 44778888888888 5799999999 99999999998754
No 61
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=81.20 E-value=6.5 Score=24.04 Aligned_cols=41 Identities=17% Similarity=0.269 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 85 QEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 85 eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
+++..++.++-..|-.+.+||..| |-+...|+.+-...+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 445555555555567899999999 99999998887776655
No 62
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=80.26 E-value=2.3 Score=39.96 Aligned_cols=46 Identities=20% Similarity=0.380 Sum_probs=36.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhhhh----------hhcCCCCCchhhhhhhhhcc
Q 043269 26 KGPWTVEEDSLLMNYVAIHGEGRWNAVA----------SSAGLNRTGKSCRLRWLNYL 73 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~~g~~~W~~Ia----------~~l~~~R~~~qc~~rw~~~l 73 (191)
|..||..|.+-+..++..+|. ++..|- ..+. -++-.|++.+|++.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~-~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQ-SKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchh-hhhhHHHHHHHHHHH
Confidence 667999999999999999998 898882 2222 356778888877654
No 63
>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=80.13 E-value=2.9 Score=29.08 Aligned_cols=45 Identities=31% Similarity=0.640 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHHHh---CC----C-----ChhhhhhhcC----CCCCchhhhhhhhhc
Q 043269 28 PWTVEEDSLLMNYVAIH---GE----G-----RWNAVASSAG----LNRTGKSCRLRWLNY 72 (191)
Q Consensus 28 ~WT~eED~~L~~~v~~~---g~----~-----~W~~Ia~~l~----~~R~~~qc~~rw~~~ 72 (191)
.||++++..|++++... |. + .|..|+..|. ...+..||..||...
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999998554 11 1 3888887663 234567788776553
No 64
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=78.62 E-value=4.7 Score=32.83 Aligned_cols=44 Identities=14% Similarity=0.157 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCHHHHhhh--C-CCCCHHHHHHHHHHHhH
Q 043269 81 NITLQEQLMILELHSRWGNRWSKIAQY--L-PGRTDNEIKNYWRTRVQ 125 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G~~W~~Ia~~--l-~gRt~~~~k~rw~~~l~ 125 (191)
.|++++|.+|+.+|. .|+.=..|+.. | -.-|-..|..||..+|-
T Consensus 1 rW~~~DDl~Li~av~-~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVE-QTNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHH-HhcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 499999999999995 46667777664 3 34688999999998873
No 65
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=78.61 E-value=4.2 Score=38.33 Aligned_cols=53 Identities=19% Similarity=0.374 Sum_probs=43.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCHHHH----------hhhCCCCCHHHHHHHHHHHhHHHHhhc
Q 043269 79 RGNITLQEQLMILELHSRWGNRWSKI----------AQYLPGRTDNEIKNYWRTRVQKHAKQL 131 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G~~W~~I----------a~~l~gRt~~~~k~rw~~~l~k~~~~~ 131 (191)
+..||-.|+.-+..+++++|.+...| -....-+|-.|++.+|...+.+..+-+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~ 150 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLL 150 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhh
Confidence 56899999999999999999999888 223345677899999988888765554
No 66
>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=77.76 E-value=11 Score=32.77 Aligned_cols=49 Identities=22% Similarity=0.404 Sum_probs=38.4
Q ss_pred CCCCCHHHHHHHHHHHHhc-CC---CHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 79 RGNITLQEQLMILELHSRW-GN---RWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~-G~---~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
-..||.-|...|+.+.... |. +=.+|++.++||+..+|++.-..+..+.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rv 73 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRV 73 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHH
Confidence 3479999999999988765 43 4578999999999999998665554443
No 67
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=77.34 E-value=10 Score=27.90 Aligned_cols=45 Identities=18% Similarity=0.200 Sum_probs=33.2
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccC
Q 043269 26 KGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLR 74 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~ 74 (191)
+..||.|+-..++..+...|. .-..||..++. +. +-..+|.+.+.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~-sv~evA~e~gI--s~-~tl~~W~r~y~ 54 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM-TVSLVARQHGV--AA-SQLFLWRKQYQ 54 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC-CHHHHHHHHCc--CH-HHHHHHHHHHh
Confidence 567999998888887777776 78899999983 43 44456776653
No 68
>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=76.85 E-value=2.5 Score=29.58 Aligned_cols=17 Identities=29% Similarity=0.337 Sum_probs=10.2
Q ss_pred CCCcCCCCCHHHHHHHH
Q 043269 75 PDVRRGNITLQEQLMIL 91 (191)
Q Consensus 75 p~~~~~~Wt~eEd~~L~ 91 (191)
|....|-||+|+|..|.
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 66778899999999993
No 69
>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=76.73 E-value=7.2 Score=27.02 Aligned_cols=38 Identities=13% Similarity=0.325 Sum_probs=27.9
Q ss_pred HHHHHHHhcCC--------CHHHHhhhCCC---CC--HHHHHHHHHHHhHH
Q 043269 89 MILELHSRWGN--------RWSKIAQYLPG---RT--DNEIKNYWRTRVQK 126 (191)
Q Consensus 89 ~L~~~v~~~G~--------~W~~Ia~~l~g---Rt--~~~~k~rw~~~l~k 126 (191)
.|..+|..+|+ +|..||+.|.- -+ ..+++..|..+|.+
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 37778888876 69999998822 12 36789999888754
No 70
>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=76.02 E-value=3.7 Score=24.78 Aligned_cols=37 Identities=16% Similarity=0.254 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhh
Q 043269 33 EDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLN 71 (191)
Q Consensus 33 ED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~ 71 (191)
=|..|+.+++.-+...+.+||+.+| =+...|..|+..
T Consensus 4 ~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 4 LDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 4788899999889889999999996 688889888754
No 71
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=75.91 E-value=4.5 Score=36.89 Aligned_cols=50 Identities=14% Similarity=0.200 Sum_probs=42.2
Q ss_pred hcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhc
Q 043269 21 ILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNY 72 (191)
Q Consensus 21 ~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~ 72 (191)
+-+-....||.||--+|.+++..||. ++.+|-+.|| .|+-.++..-|...
T Consensus 182 rr~~~~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~LP-~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 182 RRTEFPDEWTAEDIVLFEQAFQFFGK-DFHKIRQALP-HRSLASLVQYYYSW 231 (534)
T ss_pred hcCCCcccchHHHHHHHHHHHHHhcc-cHHHHHHHcc-CccHHHHHHHHHHH
Confidence 44556677999999999999999999 9999999998 99988887665443
No 72
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=75.82 E-value=7.8 Score=29.67 Aligned_cols=45 Identities=16% Similarity=0.071 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHHhHHHHhh
Q 043269 85 QEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQ 130 (191)
Q Consensus 85 eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~~ 130 (191)
+-|..|+.+..+-| -.|++||+.+ |-+...|..|++.+....+-+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 56888888888888 6899999999 999999999999998876543
No 73
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=74.64 E-value=8.9 Score=34.16 Aligned_cols=44 Identities=16% Similarity=0.151 Sum_probs=39.1
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHhh-hCCCCCHHHHHHHHHHH
Q 043269 80 GNITLQEQLMILELHSRWGNRWSKIAQ-YLPGRTDNEIKNYWRTR 123 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~G~~W~~Ia~-~l~gRt~~~~k~rw~~~ 123 (191)
..|+++|-..+-+.++.||.+...|.. .++.|+--.|-.+|...
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 379999999999999999999999955 79999999998877544
No 74
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=73.75 E-value=9.6 Score=26.63 Aligned_cols=39 Identities=15% Similarity=0.321 Sum_probs=29.1
Q ss_pred HHHHHHHhcCC--------CHHHHhhhCCCC-----CHHHHHHHHHHHhHHH
Q 043269 89 MILELHSRWGN--------RWSKIAQYLPGR-----TDNEIKNYWRTRVQKH 127 (191)
Q Consensus 89 ~L~~~v~~~G~--------~W~~Ia~~l~gR-----t~~~~k~rw~~~l~k~ 127 (191)
.|..+|...|+ .|..||..|.-- ...+++..|..+|.+.
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 37777888776 799999988222 3568888898888764
No 75
>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=73.65 E-value=5.5 Score=27.80 Aligned_cols=29 Identities=24% Similarity=0.496 Sum_probs=24.9
Q ss_pred HHHHHHHHHhcCCCHHHHhhhCCCCCHHHH
Q 043269 87 QLMILELHSRWGNRWSKIAQYLPGRTDNEI 116 (191)
Q Consensus 87 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~ 116 (191)
|+.|..+....|..|..+|..| |=|..+|
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I 30 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDI 30 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 4668889999999999999999 8777766
No 76
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=73.03 E-value=9.1 Score=27.45 Aligned_cols=49 Identities=12% Similarity=0.159 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHHHHHhc----C----CCHHHHhhhC-----CCCCHHHHHHHHHHHhHHHH
Q 043269 80 GNITLQEQLMILELHSRW----G----NRWSKIAQYL-----PGRTDNEIKNYWRTRVQKHA 128 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~----G----~~W~~Ia~~l-----~gRt~~~~k~rw~~~l~k~~ 128 (191)
.-||++++..||+.+..| | .+|..+...+ ..=+.+|+.++-+.+-++..
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~ 66 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYR 66 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHH
Confidence 369999999999999877 5 2455443333 22366788777777666543
No 77
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=72.63 E-value=4.3 Score=38.11 Aligned_cols=49 Identities=18% Similarity=0.306 Sum_probs=43.9
Q ss_pred cCCCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 78 RRGNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 78 ~~~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..+.|+.+|-++...+....|.+-+.|+..+|+|...|||.+|..--++
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE~r 456 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEEKR 456 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhhhc
Confidence 4568999999999999999999999999999999999999999754443
No 78
>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=72.55 E-value=7 Score=27.30 Aligned_cols=31 Identities=19% Similarity=0.403 Sum_probs=25.8
Q ss_pred HHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHH
Q 043269 87 QLMILELHSRWGNRWSKIAQYLPGRTDNEIKN 118 (191)
Q Consensus 87 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~ 118 (191)
|..|..+....|.+|.++|..| |=+...|.+
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 5678888899999999999999 777766543
No 79
>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=71.88 E-value=5.8 Score=31.14 Aligned_cols=40 Identities=23% Similarity=0.154 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHH
Q 043269 81 NITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWR 121 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~ 121 (191)
.||+|+.+.|.+|..+ |-.=++||..|.|.|.++|.-+-+
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhh
Confidence 5999999999998844 777799999997799999876544
No 80
>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=71.12 E-value=14 Score=27.39 Aligned_cols=39 Identities=18% Similarity=0.187 Sum_probs=28.9
Q ss_pred HHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 87 QLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 87 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
+..++.+.-..|-.+.+||+.+ |.+...|+.+....+++
T Consensus 118 ~r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 118 CRKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3344444334567899999999 99999999998876554
No 81
>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=70.35 E-value=4.5 Score=28.10 Aligned_cols=39 Identities=26% Similarity=0.448 Sum_probs=26.5
Q ss_pred HHHHHHHHhCC-------CChhhhhhhcCCCCC----chhhhhhhhhccC
Q 043269 36 LLMNYVAIHGE-------GRWNAVASSAGLNRT----GKSCRLRWLNYLR 74 (191)
Q Consensus 36 ~L~~~v~~~g~-------~~W~~Ia~~l~~~R~----~~qc~~rw~~~l~ 74 (191)
.|..+|...|. +.|..||..|+.... ..+++..|.++|.
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 46777777764 369999999975432 2456777777764
No 82
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=68.93 E-value=12 Score=29.04 Aligned_cols=46 Identities=13% Similarity=-0.015 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHHhHHHHhh
Q 043269 84 LQEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTRVQKHAKQ 130 (191)
Q Consensus 84 ~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~~ 130 (191)
.+-|.+|+.+...-| -.|.+||+.+ |=+...|..|++.+.+..+-+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeE
Confidence 456888888888877 5799999999 999999999999998876543
No 83
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=67.07 E-value=3.9 Score=36.54 Aligned_cols=49 Identities=18% Similarity=0.308 Sum_probs=42.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhh-----cCCCCCchhhhhhhhhc
Q 043269 23 GVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASS-----AGLNRTGKSCRLRWLNY 72 (191)
Q Consensus 23 ~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~-----l~~~R~~~qc~~rw~~~ 72 (191)
.++-..||.+|-+.|.++...|.- .|.-||.. ++..||....++||+..
T Consensus 127 ~l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 456678999999999999999998 89999966 66449999999999765
No 84
>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=65.77 E-value=7.7 Score=26.72 Aligned_cols=30 Identities=20% Similarity=0.608 Sum_probs=24.4
Q ss_pred HHHHHHHHHhcCCCHHHHhhhCCCCCHHHHH
Q 043269 87 QLMILELHSRWGNRWSKIAQYLPGRTDNEIK 117 (191)
Q Consensus 87 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k 117 (191)
|..|..+....|.+|.++|..| |=+..+|.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~ 33 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDID 33 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHH
Confidence 4567888889999999999999 77766553
No 85
>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=65.63 E-value=9.2 Score=26.24 Aligned_cols=33 Identities=33% Similarity=0.485 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHH
Q 043269 84 LQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKN 118 (191)
Q Consensus 84 ~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~ 118 (191)
.||.++|+.. -..|.+|..+|..| |=+...|.+
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5788888732 25678999999999 888887765
No 86
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=64.71 E-value=5.5 Score=27.90 Aligned_cols=40 Identities=28% Similarity=0.516 Sum_probs=26.6
Q ss_pred HHHHHHHHhCC-------CChhhhhhhcCCCC----CchhhhhhhhhccCC
Q 043269 36 LLMNYVAIHGE-------GRWNAVASSAGLNR----TGKSCRLRWLNYLRP 75 (191)
Q Consensus 36 ~L~~~v~~~g~-------~~W~~Ia~~l~~~R----~~~qc~~rw~~~l~p 75 (191)
.|..+|.+.|. ..|..||..|++.- ...+.+..|.++|.|
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 46777877764 46999999998432 234556666666643
No 87
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=63.87 E-value=11 Score=38.45 Aligned_cols=76 Identities=20% Similarity=0.236 Sum_probs=49.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHHHHHhc-CCCHHHH
Q 043269 26 KGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILELHSRW-GNRWSKI 104 (191)
Q Consensus 26 kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~~v~~~-G~~W~~I 104 (191)
-.-|..++|..|+-.|-+||.|+|..|-. .+.-|... ...+....-.+.+-..+-..|+.+...+ +.+|...
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGygswe~Ir~------Dp~L~l~d-Ki~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~~ 1205 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYGSWEAIRL------DPDLGLTD-KIFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPKK 1205 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccccHHHhcc------Cccccchh-hhcccccCCchHHHHHHHHHHHHHHhhcccCCCchh
Confidence 34599999999999999999999999941 11112111 1112222445566677777888888777 5667665
Q ss_pred hhhC
Q 043269 105 AQYL 108 (191)
Q Consensus 105 a~~l 108 (191)
.+..
T Consensus 1206 ~~~~ 1209 (1373)
T KOG0384|consen 1206 LKRE 1209 (1373)
T ss_pred hhcc
Confidence 5443
No 88
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=63.46 E-value=11 Score=26.22 Aligned_cols=31 Identities=19% Similarity=0.405 Sum_probs=25.8
Q ss_pred HHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHH
Q 043269 87 QLMILELHSRWGNRWSKIAQYLPGRTDNEIKN 118 (191)
Q Consensus 87 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~ 118 (191)
|..|..+....|.+|.++|+.| |=+...|.+
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~L-g~se~dI~~ 34 (84)
T cd08804 4 EERLAVIADHLGFSWTELAREL-DFTEEQIHQ 34 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 4567778889999999999999 888877755
No 89
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=63.20 E-value=26 Score=27.47 Aligned_cols=34 Identities=15% Similarity=0.132 Sum_probs=25.4
Q ss_pred HHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 92 ELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 92 ~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.+.-..|-...+||..| |-+...|+++.....++
T Consensus 144 ~l~~~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 144 VAVDMQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33334566899999999 99999999998555443
No 90
>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=61.67 E-value=24 Score=25.32 Aligned_cols=34 Identities=24% Similarity=0.260 Sum_probs=26.2
Q ss_pred HHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 92 ELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 92 ~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.++-..|-.+.+||+.+ |=+...|+++....+++
T Consensus 120 ~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 120 VLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34434577899999999 77999999888776555
No 91
>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=61.59 E-value=24 Score=20.89 Aligned_cols=35 Identities=26% Similarity=0.278 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHH
Q 043269 85 QEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYW 120 (191)
Q Consensus 85 eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw 120 (191)
=|...|.++...++++-.+.|+.| |=+...+..+-
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 377889999999999999999998 77776665543
No 92
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=61.13 E-value=10 Score=29.06 Aligned_cols=44 Identities=9% Similarity=0.123 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCC
Q 043269 32 EEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDV 77 (191)
Q Consensus 32 eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~ 77 (191)
+-|..|+.++++.|.-.|.+||+.++ -+...|+.|+.+.....+
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 56889999999999889999999996 799999999988765543
No 93
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=60.53 E-value=10 Score=35.70 Aligned_cols=56 Identities=11% Similarity=0.197 Sum_probs=48.2
Q ss_pred ccchHhhhcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhh
Q 043269 14 RQQSEEAILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLN 71 (191)
Q Consensus 14 ~~~~~~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~ 71 (191)
...|.........++|+.+|-++...+....|. +...|+..++ +|..+|++..|..
T Consensus 397 ~vn~~t~sk~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 397 PVNYATYSKKLETDKWDASETELFYKALSERGS-DFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred ccchhhccCccccCcccchhhHHhhhHHhhhcc-cccccccccc-cccHHHHHHHHhh
Confidence 344555566778889999999999999999999 8999999998 9999999987754
No 94
>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=59.17 E-value=14 Score=28.88 Aligned_cols=48 Identities=19% Similarity=0.257 Sum_probs=33.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCC---CCCchhhhhhhhhc
Q 043269 24 VRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGL---NRTGKSCRLRWLNY 72 (191)
Q Consensus 24 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~---~R~~~qc~~rw~~~ 72 (191)
.....-|..|..-|..||++||+ ++...+.-..+ -.|+.||+.+...|
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 45667899999999999999998 78777733221 24566665554443
No 95
>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=58.75 E-value=11 Score=23.27 Aligned_cols=38 Identities=13% Similarity=0.173 Sum_probs=24.9
Q ss_pred HHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhh
Q 043269 31 VEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLN 71 (191)
Q Consensus 31 ~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~ 71 (191)
++++..++.+.-..|. .+.+||..++ .+...++.+..+
T Consensus 12 ~~~~r~i~~l~~~~g~-s~~eIa~~l~--~s~~~v~~~l~r 49 (54)
T PF08281_consen 12 PERQREIFLLRYFQGM-SYAEIAEILG--ISESTVKRRLRR 49 (54)
T ss_dssp -HHHHHHHHHHHTS----HHHHHHHCT--S-HHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCc-CHHHHHHHHC--cCHHHHHHHHHH
Confidence 4566666666666676 8999999995 888888776554
No 96
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=58.22 E-value=31 Score=27.10 Aligned_cols=40 Identities=23% Similarity=0.209 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 86 EQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 86 Ed~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
+...++.+....|=.+.+||..| |-+...|+.+|......
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~~ 178 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARAW 178 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33445555555577899999999 99999999999877544
No 97
>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=57.89 E-value=16 Score=25.38 Aligned_cols=32 Identities=25% Similarity=0.510 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHH
Q 043269 82 ITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIK 117 (191)
Q Consensus 82 Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k 117 (191)
-|+++-.. +....|.+|..+|..| |-+..+|.
T Consensus 5 ~t~~~l~~---ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 5 VTGEQITV---FANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred CCHHHHHH---HHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 34444333 5677799999999999 88888773
No 98
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=56.83 E-value=16 Score=25.49 Aligned_cols=29 Identities=17% Similarity=0.414 Sum_probs=22.8
Q ss_pred HHHHHHHHHhcCCCHHHHhhhCCCCCHHHH
Q 043269 87 QLMILELHSRWGNRWSKIAQYLPGRTDNEI 116 (191)
Q Consensus 87 d~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~ 116 (191)
|..|..+....|.+|.++|..| |=+...|
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 5667788899999999999988 5555433
No 99
>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=56.39 E-value=26 Score=30.63 Aligned_cols=85 Identities=15% Similarity=0.265 Sum_probs=61.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCC---ChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHHHHHh-c-----
Q 043269 27 GPWTVEEDSLLMNYVAIHGEG---RWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILELHSR-W----- 97 (191)
Q Consensus 27 g~WT~eED~~L~~~v~~~g~~---~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~~v~~-~----- 97 (191)
..||..|...|+.+.+....+ +-.+|++.++ +|+..++++- .+.|. +..+.+++++ |
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~f-l~~LK------------~rvareaiqkv~~~g~~ 87 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRDF-LQQLK------------GRVAREAIQKVHPGGLK 87 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHHH-HHHHH------------HHHHHHHHHHhcccccc
Confidence 459999999999998766333 4568888997 9999998763 34333 2345555555 2
Q ss_pred CC------------CHHHHhhhCCCCCHHHHHHHHHHHhH
Q 043269 98 GN------------RWSKIAQYLPGRTDNEIKNYWRTRVQ 125 (191)
Q Consensus 98 G~------------~W~~Ia~~l~gRt~~~~k~rw~~~l~ 125 (191)
|. -|..+|+.+.|.-...+-.-|-.+|-
T Consensus 88 ~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 88 GPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred cccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 11 29999999999999999888876654
No 100
>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=55.53 E-value=16 Score=22.92 Aligned_cols=43 Identities=26% Similarity=0.305 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 81 NITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|+.|-+.|.-+.. |..=.+||..+ |.+...|+.+...+++|
T Consensus 3 ~LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 467777777655554 44557999999 99999999998888776
No 101
>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=55.27 E-value=29 Score=27.00 Aligned_cols=46 Identities=15% Similarity=0.182 Sum_probs=37.7
Q ss_pred cCCCCCHHHHHHHHHHHHhcCCCHHHHhhhC----CCCCHHHHHHHHHHH
Q 043269 78 RRGNITLQEQLMILELHSRWGNRWSKIAQYL----PGRTDNEIKNYWRTR 123 (191)
Q Consensus 78 ~~~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l----~gRt~~~~k~rw~~~ 123 (191)
....-|+.|...|..|+.+||.+...++.-. --.|..||+.+.+.+
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 4457899999999999999999999998733 248999998877654
No 102
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=55.23 E-value=35 Score=25.81 Aligned_cols=34 Identities=15% Similarity=0.164 Sum_probs=25.9
Q ss_pred HHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 92 ELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 92 ~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.+....|-.+.+||..| |-+...|+.+....+++
T Consensus 138 ~l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 138 TLREIEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 33334566899999999 99999999887765554
No 103
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=54.87 E-value=21 Score=28.82 Aligned_cols=44 Identities=20% Similarity=0.194 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 80 GNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
...|+.|-+.|.-+..=+.+ .+||..| +.+..-||+|..++++|
T Consensus 147 ~~LT~RE~eVL~lla~G~sn--keIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAEGLSN--KEIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHCCCCH--HHHHHHH-CCCHhHHHHHHHHHHHH
Confidence 36899999888666544444 6999999 99999999999999887
No 104
>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=54.75 E-value=20 Score=24.26 Aligned_cols=29 Identities=24% Similarity=0.515 Sum_probs=22.0
Q ss_pred HHHHHHHHHh-cCCCHHHHhhhCCCCCHHHH
Q 043269 87 QLMILELHSR-WGNRWSKIAQYLPGRTDNEI 116 (191)
Q Consensus 87 d~~L~~~v~~-~G~~W~~Ia~~l~gRt~~~~ 116 (191)
.+.|..++.. .|.+|..+|+.| |-+..+|
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 4566667777 899999999999 5566555
No 105
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=54.37 E-value=43 Score=25.77 Aligned_cols=33 Identities=12% Similarity=0.078 Sum_probs=25.4
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHHHh
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHAK 129 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~ 129 (191)
..|-.-.+||..| |-+...|+.+....+++...
T Consensus 145 ~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 145 VEGASIKETAAKL-SMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 3456789999999 99999999988777665433
No 106
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=54.11 E-value=39 Score=21.28 Aligned_cols=35 Identities=17% Similarity=0.394 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHH
Q 043269 85 QEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYW 120 (191)
Q Consensus 85 eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw 120 (191)
+.|+-.+.++.+.|-.=.+||+.+ ||+.+.|+++-
T Consensus 7 ~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 7 DAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred HHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 344555678888998899999999 99999887754
No 107
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=53.95 E-value=18 Score=26.42 Aligned_cols=46 Identities=17% Similarity=0.227 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHHHHHhCC------------C------------------ChhhhhhhcCCCCCchhhhhhhhhccC
Q 043269 28 PWTVEEDSLLMNYVAIHGE------------G------------------RWNAVASSAGLNRTGKSCRLRWLNYLR 74 (191)
Q Consensus 28 ~WT~eED~~L~~~v~~~g~------------~------------------~W~~Ia~~l~~~R~~~qc~~rw~~~l~ 74 (191)
+||++||-.|...|.+|-. . -....+...+ ..|..+=|+||+.++.
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p-~HT~~sWRDR~RKfv~ 76 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNP-RHTENSWRDRYRKFVS 76 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTT-TS-HHHHHHHHHHTHH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCC-ccchhHHHHHHHHHHH
Confidence 5899999999999977611 0 1344555555 6777777777777653
No 108
>PRK04217 hypothetical protein; Provisional
Probab=53.87 E-value=54 Score=24.08 Aligned_cols=46 Identities=15% Similarity=0.086 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 80 GNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
..-+.+| ..++.++...|-.-.+||+.+ |-+...|+.++....++.
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKKV 86 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 3466666 566777777778899999999 999999999998766553
No 109
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=53.85 E-value=33 Score=24.14 Aligned_cols=44 Identities=14% Similarity=0.104 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHHhHHHHh
Q 043269 85 QEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTRVQKHAK 129 (191)
Q Consensus 85 eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~ 129 (191)
+.|..|+.+....| -.+.+||+.+ |-+...|..+.+.+....+-
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i 47 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVI 47 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 46788888888877 5799999999 99999999999988876543
No 110
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=53.17 E-value=53 Score=25.03 Aligned_cols=39 Identities=15% Similarity=0.210 Sum_probs=28.4
Q ss_pred HHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHHH
Q 043269 89 MILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHA 128 (191)
Q Consensus 89 ~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~ 128 (191)
.++.+....|-...+||..| |-+...|+.+-..-+++-.
T Consensus 126 ~v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 126 AAFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 33344444566889999999 9999999998776666543
No 111
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=53.13 E-value=11 Score=29.32 Aligned_cols=45 Identities=16% Similarity=0.118 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCC
Q 043269 31 VEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDV 77 (191)
Q Consensus 31 ~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~ 77 (191)
.+-|.+|+.+.++.|.-.|.+||+.++ =+...|+.|+.+.....+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 456888999999999889999999996 788899999988866553
No 112
>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=52.30 E-value=19 Score=25.12 Aligned_cols=29 Identities=31% Similarity=0.577 Sum_probs=23.2
Q ss_pred HHHHHHHhcCCCHHHHhhhCCCCCHHHHHH
Q 043269 89 MILELHSRWGNRWSKIAQYLPGRTDNEIKN 118 (191)
Q Consensus 89 ~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~ 118 (191)
.|-.+....|.+|..+|+.| |=+..+|..
T Consensus 4 ~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 4 HLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 34455677899999999999 888888765
No 113
>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=51.90 E-value=46 Score=19.25 Aligned_cols=40 Identities=18% Similarity=0.259 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHH
Q 043269 82 ITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTR 123 (191)
Q Consensus 82 Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~ 123 (191)
.++++ ..++.++-..|-.+.+||..+ |=+...|+.+....
T Consensus 11 l~~~~-~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPERE-REVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHHH-HHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 34444 444455545677899999998 88888887665443
No 114
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=51.82 E-value=40 Score=25.36 Aligned_cols=30 Identities=27% Similarity=0.256 Sum_probs=24.2
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|-...+||..| |-+...|+++....+++
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466899999999 99999999987765544
No 115
>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=51.26 E-value=18 Score=28.36 Aligned_cols=39 Identities=21% Similarity=0.158 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhh
Q 043269 28 PWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRW 69 (191)
Q Consensus 28 ~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw 69 (191)
.||.|+.+.|.+|... |. .=.+||..|+ +.+...+.-+.
T Consensus 2 ~Wtde~~~~L~~lw~~-G~-SasqIA~~lg-~vsRnAViGk~ 40 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GL-SASQIARQLG-GVSRNAVIGKA 40 (162)
T ss_pred CCCHHHHHHHHHHHHc-CC-CHHHHHHHhC-Ccchhhhhhhh
Confidence 4999999999999964 33 5789999998 55555555443
No 116
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=49.99 E-value=43 Score=25.63 Aligned_cols=29 Identities=10% Similarity=0.010 Sum_probs=23.3
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-...+||..| |-+...|+++.....++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 99999998887665554
No 117
>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=47.14 E-value=41 Score=25.86 Aligned_cols=29 Identities=10% Similarity=0.115 Sum_probs=23.4
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
|-...+||..| |=+...|+++....+++.
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAREAI 182 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 55789999999 889999999887665553
No 118
>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=46.57 E-value=26 Score=24.35 Aligned_cols=32 Identities=31% Similarity=0.406 Sum_probs=24.3
Q ss_pred HHHHHHHHhcCCCHHHHhhhCCCCCHHH---HHHHH
Q 043269 88 LMILELHSRWGNRWSKIAQYLPGRTDNE---IKNYW 120 (191)
Q Consensus 88 ~~L~~~v~~~G~~W~~Ia~~l~gRt~~~---~k~rw 120 (191)
..|..+....|.+|..+|..| |=+..+ |+..+
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~~Id~Ie~~~ 37 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYRELQRIKYNN 37 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHHHHHHHHHHC
Confidence 457888999999999999998 655544 44455
No 119
>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=46.30 E-value=59 Score=24.58 Aligned_cols=29 Identities=17% Similarity=0.367 Sum_probs=22.8
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-...+||..| |-|...|+++....+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 455788899988 88999998888766555
No 120
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=45.61 E-value=27 Score=32.20 Aligned_cols=41 Identities=22% Similarity=0.437 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCHHHHhh-hCCCCCHHHHHHHHH
Q 043269 81 NITLQEQLMILELHSRWGNRWSKIAQ-YLPGRTDNEIKNYWR 121 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G~~W~~Ia~-~l~gRt~~~~k~rw~ 121 (191)
.|+--|-.++-++.++||.+...|-. +||-++-..|-.+|.
T Consensus 287 EWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIveyYY 328 (693)
T KOG3554|consen 287 EWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIVEYYY 328 (693)
T ss_pred hccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHHHHHH
Confidence 69999999999999999999999955 789999999987753
No 121
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=45.23 E-value=79 Score=28.45 Aligned_cols=54 Identities=15% Similarity=0.179 Sum_probs=40.7
Q ss_pred CcCCCCCHHHHHHHHHHHHhcCC----------------CHHHHhhhC-----CCCCHHHHHHHHHHHhHHHHhh
Q 043269 77 VRRGNITLQEQLMILELHSRWGN----------------RWSKIAQYL-----PGRTDNEIKNYWRTRVQKHAKQ 130 (191)
Q Consensus 77 ~~~~~Wt~eEd~~L~~~v~~~G~----------------~W~~Ia~~l-----~gRt~~~~k~rw~~~l~k~~~~ 130 (191)
..-|-|+++=|+-+.++...|.. +=..||+++ ..||..||-.|-.-+.++++++
T Consensus 74 daegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 74 DAEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred ccccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998842 357788876 4578889988766665655544
No 122
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=44.78 E-value=55 Score=25.02 Aligned_cols=28 Identities=11% Similarity=0.061 Sum_probs=22.3
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.-.+||..| |-+...|+++.....++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45788999999 88999999887666554
No 123
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=44.70 E-value=56 Score=23.89 Aligned_cols=55 Identities=15% Similarity=0.114 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHH
Q 043269 33 EDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMI 90 (191)
Q Consensus 33 ED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L 90 (191)
+.+.|.++|..++...-.+||+.++ ...+...++...|.-..++..|..++|..-
T Consensus 58 d~~~L~~~v~~~pd~tl~Ela~~l~---Vs~~ti~~~Lkrlg~t~KK~~~~~~~~~~~ 112 (119)
T PF01710_consen 58 DRDELKALVEENPDATLRELAERLG---VSPSTIWRALKRLGITRKKKTLHSEKDREK 112 (119)
T ss_pred cHHHHHHHHHHCCCcCHHHHHHHcC---CCHHHHHHHHHHcCchhccCcccchhHHHH
Confidence 5667999999999878889999997 466666777888888888888877666554
No 124
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=44.63 E-value=28 Score=31.16 Aligned_cols=43 Identities=12% Similarity=0.200 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCChhhhh-hhcCCCCCchhhhhhhhhc
Q 043269 28 PWTVEEDSLLMNYVAIHGEGRWNAVA-SSAGLNRTGKSCRLRWLNY 72 (191)
Q Consensus 28 ~WT~eED~~L~~~v~~~g~~~W~~Ia-~~l~~~R~~~qc~~rw~~~ 72 (191)
.|+.+|-..+.+.+..||. ++..|. ..|+ +|+...|..-|+..
T Consensus 279 ~wsEeEcr~FEegl~~yGK-DF~lIr~nkvr-tRsvgElVeyYYlW 322 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYGK-DFHLIRANKVR-TRSVGELVEYYYLW 322 (445)
T ss_pred cCCHHHHHHHHHHHHHhcc-cHHHHHhcccc-cchHHHHHHHHHHh
Confidence 4999999999999999999 888886 4565 89999998876543
No 125
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=44.04 E-value=71 Score=23.86 Aligned_cols=30 Identities=7% Similarity=-0.152 Sum_probs=23.5
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|-.-.+||..| |-+...|+++....+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3455788999999 99999999987665554
No 126
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=43.99 E-value=86 Score=24.12 Aligned_cols=36 Identities=19% Similarity=0.127 Sum_probs=27.2
Q ss_pred HHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHHHh
Q 043269 93 LHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHAK 129 (191)
Q Consensus 93 ~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~ 129 (191)
+....|-...+||..| |-+...|+.+...-+.+-..
T Consensus 138 L~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 138 MATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 3334466789999999 99999999998776665443
No 127
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=43.82 E-value=64 Score=24.98 Aligned_cols=29 Identities=10% Similarity=0.152 Sum_probs=23.8
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-...+||..| |-+...|++++...+++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 456789999999 88999999998776554
No 128
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=43.72 E-value=83 Score=23.74 Aligned_cols=31 Identities=16% Similarity=0.088 Sum_probs=23.8
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
..|-.-.+||..| |-+...|+++-...+++.
T Consensus 126 ~~g~s~~eIA~~l-gis~~tV~~~l~Rar~~L 156 (164)
T PRK12547 126 ASGFSYEDAAAIC-GCAVGTIKSRVSRARNRL 156 (164)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 3455789999999 899999988876665553
No 129
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=42.99 E-value=75 Score=24.54 Aligned_cols=30 Identities=13% Similarity=0.126 Sum_probs=23.7
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|-...+||..| |-+...|+.+....+++
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 88999998887666554
No 130
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=42.99 E-value=71 Score=23.74 Aligned_cols=30 Identities=10% Similarity=0.071 Sum_probs=23.9
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|-.-.+||..| |-+...|+.+....+++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 120 WEDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred HhcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3455789999999 99999999987766554
No 131
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=42.91 E-value=75 Score=24.05 Aligned_cols=29 Identities=21% Similarity=0.240 Sum_probs=23.2
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.-.+||..| |.+...|+.+....+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355678999999 99999999987766554
No 132
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=42.61 E-value=72 Score=24.77 Aligned_cols=31 Identities=23% Similarity=0.073 Sum_probs=24.4
Q ss_pred HhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 95 SRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 95 ~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
...|-...+||..| |-+...|+.+....+++
T Consensus 119 ~~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 119 ELEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred HhcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 34466899999999 99999999987665544
No 133
>PRK01905 DNA-binding protein Fis; Provisional
Probab=42.56 E-value=80 Score=21.27 Aligned_cols=35 Identities=23% Similarity=0.301 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHH
Q 043269 84 LQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNY 119 (191)
Q Consensus 84 ~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~r 119 (191)
.-|...|.+++..+|+++.+.|+.+ |=+...++.+
T Consensus 36 ~~E~~~i~~aL~~~~gn~s~aAr~L-GIsrstL~rk 70 (77)
T PRK01905 36 CVEKPLLEVVMEQAGGNQSLAAEYL-GINRNTLRKK 70 (77)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHH
Confidence 4467788899999999999999988 6666655444
No 134
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=42.51 E-value=26 Score=32.33 Aligned_cols=50 Identities=18% Similarity=0.202 Sum_probs=37.3
Q ss_pred CCccccchHhhhcCCCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhh
Q 043269 10 SGNHRQQSEEAILGVRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRW 69 (191)
Q Consensus 10 ~~~~~~~~~~~~~~~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw 69 (191)
.-.|++...+ |+.-|-.++.+++.+||. ++..|-..+-+-++-.++.+-|
T Consensus 278 PvLCRDemEE---------WSasEanLFEeALeKyGK-DFndIrqdfLPWKSl~sIveyY 327 (693)
T KOG3554|consen 278 PVLCRDEMEE---------WSASEANLFEEALEKYGK-DFNDIRQDFLPWKSLTSIVEYY 327 (693)
T ss_pred ceeehhhhhh---------ccchhhHHHHHHHHHhcc-cHHHHHHhhcchHHHHHHHHHH
Confidence 3456665554 999999999999999998 8888875543366766665544
No 135
>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=41.87 E-value=19 Score=24.05 Aligned_cols=19 Identities=16% Similarity=0.419 Sum_probs=15.1
Q ss_pred HHHHHHHHhcCCCHHHHhh
Q 043269 88 LMILELHSRWGNRWSKIAQ 106 (191)
Q Consensus 88 ~~L~~~v~~~G~~W~~Ia~ 106 (191)
..|.+|.+.||++|.-|-.
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3577888899999999864
No 136
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=40.20 E-value=97 Score=23.79 Aligned_cols=31 Identities=16% Similarity=0.088 Sum_probs=24.6
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
..|-...+||..| |-+...|+++-...+++.
T Consensus 143 ~~g~s~~EIA~~l-~is~~tV~~~l~rar~~L 173 (181)
T PRK12536 143 LEGLSVAETAQLT-GLSESAVKVGIHRGLKAL 173 (181)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3456789999999 999999999877665553
No 137
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=39.79 E-value=63 Score=32.78 Aligned_cols=41 Identities=20% Similarity=0.406 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHH
Q 043269 81 NITLQEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWR 121 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~ 121 (191)
.|+.-+=..++.+..+|| .+-..||..|.|+|...|+.+.+
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~ 867 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAK 867 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHH
Confidence 588888888999999999 78999999999999999987543
No 138
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=39.76 E-value=90 Score=24.32 Aligned_cols=29 Identities=17% Similarity=0.126 Sum_probs=22.4
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-...+||..| |-+...|+.+....+++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 355778999999 99999998887665554
No 139
>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=38.99 E-value=49 Score=22.90 Aligned_cols=27 Identities=26% Similarity=0.523 Sum_probs=20.5
Q ss_pred HHHHHhcCCCHHHHhhhCCCCCHHHHHH
Q 043269 91 LELHSRWGNRWSKIAQYLPGRTDNEIKN 118 (191)
Q Consensus 91 ~~~v~~~G~~W~~Ia~~l~gRt~~~~k~ 118 (191)
--+....|.+|..+|+.| |=|..+|..
T Consensus 6 ~~i~~~lG~~Wk~laR~L-Glse~~Id~ 32 (86)
T cd08306 6 DVICENVGRDWRKLARKL-GLSETKIES 32 (86)
T ss_pred HHHHHHHhhhHHHHHHHc-CCCHHHHHH
Confidence 334566799999999999 778777643
No 140
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=38.82 E-value=71 Score=24.71 Aligned_cols=28 Identities=11% Similarity=0.112 Sum_probs=22.3
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-...+||..| |-+...|+++....+++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45688999999 88999999887766554
No 141
>PRK00430 fis global DNA-binding transcriptional dual regulator Fis; Provisional
Probab=38.69 E-value=87 Score=22.20 Aligned_cols=34 Identities=12% Similarity=0.086 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHH
Q 043269 85 QEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNY 119 (191)
Q Consensus 85 eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~r 119 (191)
-|...|..++..++++..+.|+.+ |=+...++.+
T Consensus 55 ~Er~~i~~aL~~~~gn~s~AAr~L-GIsRsTL~rK 88 (95)
T PRK00430 55 VEAPLLDMVMQYTRGNQTRAALML-GINRGTLRKK 88 (95)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHh-CCCHHHHHHH
Confidence 477788899999999999999998 6666655443
No 142
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=38.26 E-value=1e+02 Score=23.88 Aligned_cols=30 Identities=13% Similarity=0.086 Sum_probs=23.9
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
.|-.-.+||..| |-+...|+.+....+++.
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 174 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARARDAL 174 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 345689999999 999999999887665553
No 143
>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=37.56 E-value=1.1e+02 Score=23.32 Aligned_cols=29 Identities=24% Similarity=0.304 Sum_probs=22.9
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-...+||..| |-+...|+.+....+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 177 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFARAW 177 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 345789999999 99999999887765544
No 144
>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=37.17 E-value=1e+02 Score=24.01 Aligned_cols=35 Identities=11% Similarity=0.024 Sum_probs=25.9
Q ss_pred HHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 91 LELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 91 ~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
+.+.-..|-.-.+||..| |-+...|+.+....+++
T Consensus 140 ~~l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 140 FMMREVLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HHHHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 333334466789999999 99999999887666554
No 145
>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=37.05 E-value=40 Score=22.15 Aligned_cols=26 Identities=38% Similarity=0.732 Sum_probs=19.1
Q ss_pred HHHHHHhcCCCHHHHhhhCCCCCHHHH
Q 043269 90 ILELHSRWGNRWSKIAQYLPGRTDNEI 116 (191)
Q Consensus 90 L~~~v~~~G~~W~~Ia~~l~gRt~~~~ 116 (191)
|..+....|++|..+|..| |=+..+|
T Consensus 2 ~~~ia~~lg~~W~~la~~L-gl~~~~I 27 (79)
T cd01670 2 LDKLAKKLGKDWKKLARKL-GLSDGEI 27 (79)
T ss_pred HHHHHHHHhhHHHHHHHHh-CCCHHHH
Confidence 3456677899999999998 5555544
No 146
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=36.84 E-value=88 Score=24.07 Aligned_cols=29 Identities=7% Similarity=-0.002 Sum_probs=21.7
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.-.+||+.| |-+...|+.+....+++
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRA 171 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 455778888888 88888888876655544
No 147
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=36.65 E-value=1.1e+02 Score=23.44 Aligned_cols=29 Identities=24% Similarity=0.256 Sum_probs=22.8
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
|-.=.+||..| |-+...|+.+....+++.
T Consensus 151 ~~s~~eIA~~l-gis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 151 GYTHREAAQLL-GLPLGTLKTRARRALSRL 179 (186)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 44678999999 999999998877665553
No 148
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=36.44 E-value=88 Score=24.43 Aligned_cols=30 Identities=10% Similarity=-0.025 Sum_probs=23.2
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|-.+.+||+.| |=+...|+++-...+++
T Consensus 150 ~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~~ 179 (196)
T PRK12524 150 IEGLSNPEIAEVM-EIGVEAVESLTARGKRA 179 (196)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3456899999999 88999998877655444
No 149
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=35.71 E-value=1.2e+02 Score=23.42 Aligned_cols=31 Identities=10% Similarity=0.312 Sum_probs=24.4
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
..|-.-.+||..| |-+...|+.+....+++.
T Consensus 136 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~L 166 (185)
T PRK12542 136 FYNLTYQEISSVM-GITEANVRKQFERARKRV 166 (185)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3455789999999 999999999876665553
No 150
>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=35.49 E-value=1.3e+02 Score=22.41 Aligned_cols=39 Identities=13% Similarity=0.089 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 88 LMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 88 ~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
..++.+.-..|-.=.+||..| |-+...|+.+....+++.
T Consensus 116 r~i~~l~~~~g~s~~eIA~~l-gis~~tV~~~l~ra~~~L 154 (162)
T TIGR02983 116 RAVVVLRYYEDLSEAQVAEAL-GISVGTVKSRLSRALARL 154 (162)
T ss_pred HHHhhhHHHhcCCHHHHHHHh-CCCHHHHHHHHHHHHHHH
Confidence 334444334455678999999 899999999887766553
No 151
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=35.46 E-value=50 Score=23.16 Aligned_cols=43 Identities=12% Similarity=0.062 Sum_probs=34.9
Q ss_pred HHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCC
Q 043269 32 EEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPD 76 (191)
Q Consensus 32 eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~ 76 (191)
+.|..|+.++...+.-.+.+||+.++ -+...|+.+........
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g 45 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEG 45 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 46888889998888778999999996 78888888877765544
No 152
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=35.35 E-value=1.4e+02 Score=24.23 Aligned_cols=44 Identities=20% Similarity=0.333 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 80 GNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
...|+.|-+.|.-+.+ |-...+||..| +-+...|+++-..+++|
T Consensus 132 ~~LSpRErEVLrLLAq--GkTnKEIAe~L-~IS~rTVkth~srImkK 175 (198)
T PRK15201 132 RHFSVTERHLLKLIAS--GYHLSETAALL-SLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3588888888755554 77789999999 99999999888777766
No 153
>PF09905 DUF2132: Uncharacterized conserved protein (DUF2132); InterPro: IPR018668 This entry contains proteins that have no known function. ; PDB: 2JVW_A.
Probab=34.89 E-value=49 Score=21.96 Aligned_cols=44 Identities=16% Similarity=0.350 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCC-------CcCCCCCHHHHHHH
Q 043269 34 DSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPD-------VRRGNITLQEQLMI 90 (191)
Q Consensus 34 D~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~-------~~~~~Wt~eEd~~L 90 (191)
+.+|.++|+.|| |..+++.+. -| |+. -+|+ +.+.+|-.+..+.|
T Consensus 12 e~il~~Lv~~yG---W~~L~~~i~-i~----CF~-----~~PsikSSLkFLRkTpWAR~KVE~l 62 (64)
T PF09905_consen 12 ETILTELVEHYG---WEELGERIN-IN----CFK-----NNPSIKSSLKFLRKTPWAREKVENL 62 (64)
T ss_dssp HHHHHHHHHHT----HHHHHHHTT-SS----STT-----SS--HHHHHHHHHHSHHHHHHHHHH
T ss_pred HHHHHHHHHHhC---HHHHHhhcc-cc----cCC-----CCCchHHHHHHHhcCHhHHHHHHHh
Confidence 467889999997 999998886 33 221 2443 34667877766655
No 154
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=34.79 E-value=1.1e+02 Score=23.73 Aligned_cols=29 Identities=7% Similarity=-0.072 Sum_probs=23.1
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-...+||..| |-+...|+.+....+++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 177 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARLQ 177 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355789999999 99999999987655443
No 155
>PF08870 DUF1832: Domain of unknown function (DUF1832); InterPro: IPR014969 This entry describes the DndE protein encoded by an operon associated with a sulphur-containing modification to DNA []. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases.
Probab=34.49 E-value=1.7e+02 Score=21.48 Aligned_cols=97 Identities=15% Similarity=0.082 Sum_probs=61.3
Q ss_pred CHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhh--hhhhhccC--CCCcCCCCCHHHHHHHHHHHHhcCCCHHHHh
Q 043269 30 TVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCR--LRWLNYLR--PDVRRGNITLQEQLMILELHSRWGNRWSKIA 105 (191)
Q Consensus 30 T~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~--~rw~~~l~--p~~~~~~Wt~eEd~~L~~~v~~~G~~W~~Ia 105 (191)
|++-++.|..+-.+.|-..|..+++.-- .++-..=. .......+ -.++...|+-|-+..+..++.++-
T Consensus 5 S~~~~~~L~~Lk~~tgi~~~Nil~R~A~-~~SL~~~~~~~~~~~~~d~g~e~~~~t~~Ge~~~~~~~ll~q~~------- 76 (113)
T PF08870_consen 5 SKKAKEQLKKLKRRTGITPWNILCRIAF-CRSLEEPSIPSDEDIKDDSGLELNWKTFTGEYDDIYEALLKQRY------- 76 (113)
T ss_pred CHHHHHHHHHHHHhcCCCcccHHHHHHH-HHHHccCCCCCCCccCCCCCeEEeeeeecCchHHHHHHHHHHHh-------
Confidence 6777889999999999989988875431 23221110 00000011 124555788888877777766543
Q ss_pred hhCCCCCHHHHHHHHHHHhHHHHhhcCCCCC
Q 043269 106 QYLPGRTDNEIKNYWRTRVQKHAKQLKCDVN 136 (191)
Q Consensus 106 ~~l~gRt~~~~k~rw~~~l~k~~~~~~~~~~ 136 (191)
-++-++..+...|+.++.+.+.-+....+
T Consensus 77 --g~~~d~~~l~~~~~~Hl~rGi~~L~~~~~ 105 (113)
T PF08870_consen 77 --GPELDDEELPKYFKLHLDRGIEYLSNDKN 105 (113)
T ss_pred --CCCCCHHHHHHHHHHHHHHhHHHHhcccc
Confidence 23558889999999999987766554433
No 156
>smart00351 PAX Paired Box domain.
Probab=34.48 E-value=1.9e+02 Score=21.29 Aligned_cols=73 Identities=15% Similarity=0.134 Sum_probs=44.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCC-chhhhhhhhhc--cCCCC----cCCCCCHHHHHHHHHHHHh
Q 043269 24 VRKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRT-GKSCRLRWLNY--LRPDV----RRGNITLQEQLMILELHSR 96 (191)
Q Consensus 24 ~~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~-~~qc~~rw~~~--l~p~~----~~~~Wt~eEd~~L~~~v~~ 96 (191)
....+.+.++-..++.++. -|. .-..||+.|+..+. ...+..||... +.|.- ....-+.+++..|++++..
T Consensus 13 ~~~~~~s~~~R~riv~~~~-~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~ 90 (125)
T smart00351 13 VNGRPLPDEERQRIVELAQ-NGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQE 90 (125)
T ss_pred cCCCCCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHH
Confidence 4455689999999988886 454 68999999984432 33344444332 33321 1223556666667766665
Q ss_pred cC
Q 043269 97 WG 98 (191)
Q Consensus 97 ~G 98 (191)
.+
T Consensus 91 ~p 92 (125)
T smart00351 91 NP 92 (125)
T ss_pred CC
Confidence 54
No 157
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=33.93 E-value=74 Score=23.66 Aligned_cols=43 Identities=12% Similarity=0.064 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhcC-CCHHHHhhhCCCCCHHHHHHHHHHHhHHHH
Q 043269 85 QEQLMILELHSRWG-NRWSKIAQYLPGRTDNEIKNYWRTRVQKHA 128 (191)
Q Consensus 85 eEd~~L~~~v~~~G-~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~ 128 (191)
+-|.+|+++.+.-+ -.+..||+.+ |-+...|.+|=+.+.+..+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCc
Confidence 45777778877777 5799999999 9999999999988887754
No 158
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=33.46 E-value=1.2e+02 Score=23.71 Aligned_cols=35 Identities=14% Similarity=0.085 Sum_probs=25.9
Q ss_pred HHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 92 ELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 92 ~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
.+....|-...+||..| |-+...|+.+-...+++.
T Consensus 123 ~L~~~~g~s~~EIA~~L-giS~~tVk~~l~Rar~~L 157 (188)
T PRK12546 123 ILVGASGFSYEEAAEMC-GVAVGTVKSRANRARARL 157 (188)
T ss_pred hhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 33334566789999999 999999999877665543
No 159
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=33.40 E-value=1.3e+02 Score=22.34 Aligned_cols=30 Identities=17% Similarity=0.157 Sum_probs=22.8
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|-.=.+||..| |-+...|+.+....++.
T Consensus 119 ~~~~s~~eIA~~l-gis~~tv~~~l~ra~~~ 148 (159)
T PRK12527 119 LEGLSHQQIAEHL-GISRSLVEKHIVNAMKH 148 (159)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3455678999999 99999999887665554
No 160
>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=33.25 E-value=40 Score=21.98 Aligned_cols=46 Identities=20% Similarity=0.243 Sum_probs=32.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccC
Q 043269 25 RKGPWTVEEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLR 74 (191)
Q Consensus 25 ~kg~WT~eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~ 74 (191)
++..||+|+-..++..+...|. .-..|+..++. ..+...+|...+.
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~-sv~~va~~~gi---~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGE-SVSEVAREYGI---SPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHC-HHHHHHHHHTS----HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCC-ceEeeeccccc---ccccccHHHHHHh
Confidence 3567999999999999976776 79999999983 5556667877663
No 161
>PF01466 Skp1: Skp1 family, dimerisation domain; InterPro: IPR016072 SKP1 (together with SKP2) was identified as an essential component of the cyclin A-CDK2 S phase kinase complex []. It was found to bind several F-box containing proteins (e.g., Cdc4, Skp2, cyclin F) and to be involved in the ubiquitin protein degradation pathway. A yeast homologue of SKP1 (P52286) was identified in the centromere bound kinetochore complex [] and is also involved in the ubiquitin pathway []. In Dictyostelium discoideum (Slime mold) FP21 was shown to be glycosylated in the cytosol and has homology to SKP1 []. This entry represents a dimerisation domain found at the C-terminal of SKP1 proteins [], as well as in subunit D of the centromere DNA-binding protein complex Cbf3 []. This domain is multi-helical in structure, and consists of an interlocked herterodimer in F-box proteins.; GO: 0006511 ubiquitin-dependent protein catabolic process; PDB: 2P1O_A 3OGL_G 3OGM_A 3C6O_A 2P1N_A 2P1Q_A 3OGK_I 3C6N_A 3C6P_A 2P1P_A ....
Probab=33.13 E-value=51 Score=22.26 Aligned_cols=36 Identities=14% Similarity=0.213 Sum_probs=25.4
Q ss_pred hhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHH
Q 043269 49 WNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILE 92 (191)
Q Consensus 49 W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~ 92 (191)
-..||..+. |+++.++|..+ ++ ...+|+||+..|.+
T Consensus 36 ~~~iA~~i~-gks~eeir~~f------gi-~~d~t~eee~~i~~ 71 (78)
T PF01466_consen 36 CKYIANMIK-GKSPEEIRKYF------GI-ENDLTPEEEEEIRK 71 (78)
T ss_dssp HHHHHHHHT-TS-HHHHHHHH------T----TSSHHHHHHHHH
T ss_pred HHHHHHHhc-CCCHHHHHHHc------CC-CCCCCHHHHHHHHH
Confidence 568899997 99999998865 23 33689998887643
No 162
>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=33.12 E-value=84 Score=20.62 Aligned_cols=27 Identities=30% Similarity=0.740 Sum_probs=18.5
Q ss_pred HHHHH-HhcCCCHHHHhhhCCCCCHHHHH
Q 043269 90 ILELH-SRWGNRWSKIAQYLPGRTDNEIK 117 (191)
Q Consensus 90 L~~~v-~~~G~~W~~Ia~~l~gRt~~~~k 117 (191)
|.+++ ...|++|..+|..| |=+..+|.
T Consensus 3 l~~~l~~~~~~~Wk~La~~L-g~~~~~i~ 30 (83)
T PF00531_consen 3 LFDLLAEDLGSDWKRLARKL-GLSESEIE 30 (83)
T ss_dssp HHHHHHHSHSTCHHHHHHHT-TS-HHHHH
T ss_pred HHHHHhhcchhhHHHHHHHh-CcCHHHHH
Confidence 33444 55679999999999 77766553
No 163
>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=33.11 E-value=1.4e+02 Score=22.28 Aligned_cols=28 Identities=21% Similarity=0.321 Sum_probs=20.8
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.-.+||+.| |-+...|+.+-...+++
T Consensus 138 g~s~~eIA~~l-~is~~tv~~~l~ra~~~ 165 (170)
T TIGR02952 138 NLPIAEVARIL-GKTEGAVKILQFRAIKK 165 (170)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 55678889988 88888888876555443
No 164
>PRK00118 putative DNA-binding protein; Validated
Probab=33.08 E-value=1.3e+02 Score=21.81 Aligned_cols=40 Identities=13% Similarity=0.049 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHh
Q 043269 84 LQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRV 124 (191)
Q Consensus 84 ~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l 124 (191)
++.+..++.+....|-...+||+.+ |-+...|+.+-....
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RAr 58 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRTE 58 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3455666677777788999999999 999999988765443
No 165
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=32.89 E-value=1.2e+02 Score=23.61 Aligned_cols=35 Identities=20% Similarity=0.165 Sum_probs=24.9
Q ss_pred HHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 91 LELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 91 ~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
+.|....|-...+||..| |-+...|+.+-...+++
T Consensus 125 ~~L~~~~g~s~~EIA~~L-gis~~tVk~~l~Rar~~ 159 (187)
T PRK12516 125 IILVGASGFAYEEAAEIC-GCAVGTIKSRVNRARQR 159 (187)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333334466789999999 89999998886655444
No 166
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=32.52 E-value=1.2e+02 Score=22.25 Aligned_cols=28 Identities=21% Similarity=0.270 Sum_probs=20.6
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.-.+||..| |-+...|+.+-...+++
T Consensus 122 ~~s~~EIA~~l-~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 122 GKTMGEIALET-EMTYYQVRWIYRQALEK 149 (154)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45678888888 88888888876554443
No 167
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=31.97 E-value=57 Score=24.78 Aligned_cols=30 Identities=17% Similarity=0.376 Sum_probs=22.9
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
+|-...+||..| |-+...|+.+....+.+.
T Consensus 141 ~g~s~~eIA~~l-~is~~~V~~~l~ra~~~l 170 (176)
T PRK09638 141 YGYTYEEIAKML-NIPEGTVKSRVHHGIKQL 170 (176)
T ss_pred cCCCHHHHHHHH-CCChhHHHHHHHHHHHHH
Confidence 355789999999 889999988776655543
No 168
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=31.64 E-value=1.4e+02 Score=22.69 Aligned_cols=28 Identities=18% Similarity=0.319 Sum_probs=22.3
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.-.+||..| |.+...|+.+....+++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~~ 172 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLLK 172 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHHH
Confidence 55678999999 99999998887665544
No 169
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=31.30 E-value=72 Score=19.01 Aligned_cols=36 Identities=28% Similarity=0.356 Sum_probs=17.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHH
Q 043269 81 NITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKN 118 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~ 118 (191)
.+|.+|-..|..++ .-|-.=.+||+.| ||+..-|.+
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHH
Confidence 46777777766664 5677778999999 999988754
No 170
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=31.17 E-value=32 Score=35.33 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=23.4
Q ss_pred CCCCHHHHHHHHHHHHhcC-CCHHHH
Q 043269 80 GNITLQEQLMILELHSRWG-NRWSKI 104 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~G-~~W~~I 104 (191)
..|..++|..|+-.|-+|| ++|.+|
T Consensus 1134 ~~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1134 CDWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred cCCCchhhhhHhhhhhhcccccHHHh
Confidence 3599999999999999999 999998
No 171
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=30.61 E-value=1.4e+02 Score=24.12 Aligned_cols=43 Identities=23% Similarity=0.239 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 81 NITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|+.|-+.|.-++. |-.-.+||+.| +-+...++++-.++++|
T Consensus 155 ~Lt~rE~~Vl~l~~~--G~s~~eIA~~L-~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 155 LLTHREKEILNKLRI--GASNNEIARSL-FISENTVKTHLYNLFKK 197 (216)
T ss_pred CCCHHHHHHHHHHHc--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 478877777655554 87789999999 99999999998888776
No 172
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=30.57 E-value=71 Score=25.86 Aligned_cols=29 Identities=17% Similarity=0.102 Sum_probs=23.5
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
|-.-.+||..| |-+...|+++....+++.
T Consensus 165 g~s~~EIAe~l-gis~~tVk~~l~Rar~kL 193 (231)
T PRK11922 165 ELSVEETAQAL-GLPEETVKTRLHRARRLL 193 (231)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 44789999999 999999999887665543
No 173
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=30.32 E-value=1.7e+02 Score=22.66 Aligned_cols=28 Identities=18% Similarity=0.277 Sum_probs=21.1
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.-.+||+.| |-+...|+.+-...+++
T Consensus 158 ~~s~~EIA~~L-gis~~tVk~~l~ra~~~ 185 (194)
T PRK09646 158 GLTYREVAERL-AVPLGTVKTRMRDGLIR 185 (194)
T ss_pred CCCHHHHHHHh-CCChHhHHHHHHHHHHH
Confidence 44678999998 77888888876655544
No 174
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=29.99 E-value=1.1e+02 Score=23.32 Aligned_cols=29 Identities=28% Similarity=0.381 Sum_probs=23.2
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.-.+||+.| |-+...|+++....++.
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 162 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKATEH 162 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 355789999999 99999999987665544
No 175
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=29.95 E-value=1.4e+02 Score=23.18 Aligned_cols=30 Identities=13% Similarity=0.104 Sum_probs=23.0
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|-.-.+||..| |-+...|+.+....+++
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~ 179 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARES 179 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3455789999999 99999999887665443
No 176
>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=29.88 E-value=1.3e+02 Score=25.47 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=24.3
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHHHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHA 128 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~ 128 (191)
+|-.-.+||..| |.+...|+.+....+++..
T Consensus 157 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr 187 (324)
T TIGR02960 157 LGWRAAETAELL-GTSTASVNSALQRARATLD 187 (324)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 355689999999 9999999998776655433
No 177
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=29.87 E-value=1.5e+02 Score=22.17 Aligned_cols=33 Identities=24% Similarity=0.237 Sum_probs=23.8
Q ss_pred HHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhH
Q 043269 92 ELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQ 125 (191)
Q Consensus 92 ~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~ 125 (191)
.+.-..|-.-.+||..+ |-+...|+.+....++
T Consensus 123 ~L~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 123 LLAQVDGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred HHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 33334466789999999 8899889887765543
No 178
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=29.53 E-value=53 Score=24.25 Aligned_cols=28 Identities=14% Similarity=0.143 Sum_probs=22.9
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.+.+||..| |=+...|+++.....++
T Consensus 121 g~s~~eIA~~l-gis~~tv~~~l~Ra~~~ 148 (154)
T TIGR02950 121 EFSYKEIAELL-NLSLAKVKSNLFRARKE 148 (154)
T ss_pred cCcHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 34789999999 99999999988766554
No 179
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.34 E-value=1.9e+02 Score=20.53 Aligned_cols=46 Identities=26% Similarity=0.400 Sum_probs=35.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCC-CHHHHHHHHHHHhHH
Q 043269 79 RGNITLQEQLMILELHSRWGNRWSKIAQYLPGR-TDNEIKNYWRTRVQK 126 (191)
Q Consensus 79 ~~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gR-t~~~~k~rw~~~l~k 126 (191)
+..||+|.-..+++++..-|..=+.||+.+ |- ..++++ +|...+..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~-~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLY-KWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHH-HHHHHHHH
Confidence 457999999999999999888788999999 76 555554 45544443
No 180
>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=29.26 E-value=1.7e+02 Score=22.24 Aligned_cols=30 Identities=13% Similarity=0.409 Sum_probs=22.8
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|-.-.+||..| |-+...|+.+....+++
T Consensus 154 ~~g~s~~eIA~~l-gis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 154 LEGLSFAEVAERM-DRSEGAVSMLWVRGLAR 183 (189)
T ss_pred hcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3456788899988 88998888887666554
No 181
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=29.12 E-value=55 Score=24.39 Aligned_cols=43 Identities=9% Similarity=0.033 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCC
Q 043269 32 EEDSLLMNYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPD 76 (191)
Q Consensus 32 eED~~L~~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~ 76 (191)
+-|.+++++.+..+...+..||+.++ -+...|..|-.+..+..
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEG 50 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCC
Confidence 45788889999888889999999996 78888988877775544
No 182
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.45 E-value=1.8e+02 Score=22.29 Aligned_cols=29 Identities=24% Similarity=0.325 Sum_probs=21.9
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.=.+||..| |-+...|+.+....+++
T Consensus 148 ~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 176 (182)
T PRK12537 148 DGCSHAEIAQRL-GAPLGTVKAWIKRSLKA 176 (182)
T ss_pred cCCCHHHHHHHH-CCChhhHHHHHHHHHHH
Confidence 345678888888 88888888887766554
No 183
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=28.25 E-value=1.6e+02 Score=23.41 Aligned_cols=29 Identities=21% Similarity=0.216 Sum_probs=22.7
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.=.+||..| |-+...|+++....+++
T Consensus 153 ~g~s~~EIA~~L-gis~~tV~~~l~RArk~ 181 (203)
T PRK09647 153 EGLSYEEIAATL-GVKLGTVRSRIHRGRQQ 181 (203)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 345678899999 99999999888766554
No 184
>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=27.85 E-value=50 Score=22.50 Aligned_cols=22 Identities=23% Similarity=0.383 Sum_probs=17.3
Q ss_pred HhcCCCHHHHhhhCCCCCHHHHH
Q 043269 95 SRWGNRWSKIAQYLPGRTDNEIK 117 (191)
Q Consensus 95 ~~~G~~W~~Ia~~l~gRt~~~~k 117 (191)
..+|++|..+|..| |-+...|+
T Consensus 13 ~~~g~DWr~LA~~L-g~~~~~I~ 34 (79)
T cd08312 13 RVVAADWTALAEEM-GFEYLEIR 34 (79)
T ss_pred CCcccCHHHHHHHc-CCCHHHHH
Confidence 45789999999999 76665654
No 185
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=27.83 E-value=1.8e+02 Score=22.48 Aligned_cols=28 Identities=32% Similarity=0.408 Sum_probs=21.4
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.=.+||+.| |-+...|+++-...+++
T Consensus 147 g~s~~EIAe~l-gis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 147 GEKIEEIAKKL-GLTRSAIDNRLSRGRKK 174 (189)
T ss_pred cCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44568899999 99999998886655444
No 186
>PRK15328 invasion protein IagB; Provisional
Probab=27.46 E-value=1.1e+02 Score=24.01 Aligned_cols=43 Identities=12% Similarity=0.468 Sum_probs=30.9
Q ss_pred HHHHHHHhcCCCHHHHhhhC--CCCCHHHHHHHHHHHhHHHHhhc
Q 043269 89 MILELHSRWGNRWSKIAQYL--PGRTDNEIKNYWRTRVQKHAKQL 131 (191)
Q Consensus 89 ~L~~~v~~~G~~W~~Ia~~l--~gRt~~~~k~rw~~~l~k~~~~~ 131 (191)
.|..++..||+.|..|+.+= +++.....+.+|...+.+...++
T Consensus 98 ~L~~~~~~~g~~~~alaaYNaG~~~~~~~~~~~Y~~kV~~~y~~l 142 (160)
T PRK15328 98 ILSDMMKIYGYSWEAVGAYNAGTSPKRSDIRKRYAKKIWENYRKL 142 (160)
T ss_pred HHHHHHHHcCChHHhhhhccCCCCCCCCHHHHHHHHHHHHHHHHH
Confidence 67788899999999999875 34444456677777666655554
No 187
>COG5201 SKP1 SCF ubiquitin ligase, SKP1 component [Posttranslational modification, protein turnover, chaperones]
Probab=27.24 E-value=76 Score=24.33 Aligned_cols=54 Identities=15% Similarity=0.136 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHHhC--C------CChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHH
Q 043269 31 VEEDSLLMNYVAIHG--E------GRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILE 92 (191)
Q Consensus 31 ~eED~~L~~~v~~~g--~------~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~ 92 (191)
.=+.+.|.+++..-. . -.-+.||..+. +|++..++.-+ .--..||+||+..+.+
T Consensus 89 ~vDqemL~eI~laaNYL~ikpLLd~gCKivaemir-gkSpeeir~tf-------ni~ndfTpEEe~~irk 150 (158)
T COG5201 89 EVDQEMLLEICLAANYLEIKPLLDLGCKIVAEMIR-GKSPEEIRETF-------NIENDFTPEEERRIRK 150 (158)
T ss_pred HhhHHHHHHHHHhhccccchHHHHHHHHHHHHHHc-cCCHHHHHHHh-------CCCCCCCHHHHHHHHH
Confidence 345566776664321 1 02578889997 99999998764 1234799999998754
No 188
>PF11216 DUF3012: Protein of unknown function (DUF3012); InterPro: IPR021379 This family of proteins with unknown function is restricted to Gammaproteobacteria.
Probab=27.13 E-value=40 Score=19.31 Aligned_cols=23 Identities=26% Similarity=0.359 Sum_probs=17.8
Q ss_pred cchHhhhcCCCCCCCCHHHHHHH
Q 043269 15 QQSEEAILGVRKGPWTVEEDSLL 37 (191)
Q Consensus 15 ~~~~~~~~~~~kg~WT~eED~~L 37 (191)
..|+..-....||-||.+|-...
T Consensus 4 e~WC~~m~~kpK~dWtanea~~f 26 (32)
T PF11216_consen 4 EAWCEDMKEKPKGDWTANEAADF 26 (32)
T ss_pred HHHHHHHhhCCcccCcHhHHHHH
Confidence 46777777888999999986544
No 189
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=26.06 E-value=1.9e+02 Score=22.69 Aligned_cols=29 Identities=14% Similarity=-0.009 Sum_probs=22.2
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.-.+||..| |-+...|+.+....+++
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~~ 182 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRARTR 182 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 345688999999 99999999886654443
No 190
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=25.83 E-value=1.7e+02 Score=23.58 Aligned_cols=31 Identities=10% Similarity=0.202 Sum_probs=23.9
Q ss_pred hcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 96 RWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 96 ~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
..|-.-.+||..| |-+...|+.+-...+++.
T Consensus 198 ~~g~s~~EIA~~l-gis~~tV~~~~~ra~~~L 228 (236)
T PRK06986 198 QEELNLKEIGAVL-GVSESRVSQIHSQAIKRL 228 (236)
T ss_pred ccCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 3455789999999 999999988877666553
No 191
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=25.47 E-value=1.3e+02 Score=24.07 Aligned_cols=43 Identities=12% Similarity=0.105 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 81 NITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|+-|-+.|.-+++ |..-.+||+.| +-+..-++++-.++++|
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 489999988865554 44558999999 99999999988888777
No 192
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=25.36 E-value=2.1e+02 Score=22.07 Aligned_cols=28 Identities=14% Similarity=-0.079 Sum_probs=22.1
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.-.+||..| |-+...|+.+....+++
T Consensus 147 g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 174 (191)
T PRK12520 147 ELETEEICQEL-QITATNAWVLLYRARMR 174 (191)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 45678999999 99999999987665544
No 193
>PRK06930 positive control sigma-like factor; Validated
Probab=25.00 E-value=2e+02 Score=22.52 Aligned_cols=35 Identities=23% Similarity=0.401 Sum_probs=26.0
Q ss_pred HHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHHH
Q 043269 92 ELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQKH 127 (191)
Q Consensus 92 ~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~ 127 (191)
.++...|-.-.+||..| |-+...|+.+....+++.
T Consensus 124 ~L~~~eg~s~~EIA~~l-giS~~tVk~~l~Ra~~kL 158 (170)
T PRK06930 124 LMHRGYGLSYSEIADYL-NIKKSTVQSMIERAEKKI 158 (170)
T ss_pred HHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHHH
Confidence 34344567789999999 889999988877665553
No 194
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=24.92 E-value=2.4e+02 Score=21.00 Aligned_cols=44 Identities=20% Similarity=0.213 Sum_probs=34.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 80 GNITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 80 ~~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
...|+.|-++|.-+.. |-.-.+||..+ +-+...++.+..++++|
T Consensus 136 ~~Lt~~E~~il~~l~~--g~~~~~Ia~~l-~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ--GMAVKEIAAEL-GLSPKTVHVHRANLMEK 179 (196)
T ss_pred cCCCHHHHHHHHHHHC--CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 4688888888766664 44678999999 78999998888777666
No 195
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=23.59 E-value=1.8e+02 Score=22.40 Aligned_cols=28 Identities=32% Similarity=0.269 Sum_probs=20.6
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.=.+||..| |-+...|+.+-...+++
T Consensus 157 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 184 (194)
T PRK12519 157 GLSQSEIAKRL-GIPLGTVKARARQGLLK 184 (194)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 44668888888 88888888876655444
No 196
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=23.38 E-value=2.6e+02 Score=21.97 Aligned_cols=28 Identities=21% Similarity=0.148 Sum_probs=21.7
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.=.+||..| |-+...|+.+....+++
T Consensus 169 g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 196 (206)
T PRK12526 169 ELSQEQLAQQL-NVPLGTVKSRLRLALAK 196 (206)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44678999999 99999998887665554
No 197
>PRK09483 response regulator; Provisional
Probab=23.18 E-value=1.4e+02 Score=22.75 Aligned_cols=43 Identities=16% Similarity=0.307 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 81 NITLQEQLMILELHSRWGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 81 ~Wt~eEd~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
..|+-|-+.|.-++ .|..=.+||..| +-+...++++-+++++|
T Consensus 148 ~Lt~rE~~vl~~~~--~G~~~~~Ia~~l-~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 148 SLSERELQIMLMIT--KGQKVNEISEQL-NLSPKTVNSYRYRMFSK 190 (217)
T ss_pred ccCHHHHHHHHHHH--CCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 58999999885443 454456999999 77999998887777666
No 198
>PF07555 NAGidase: beta-N-acetylglucosaminidase ; InterPro: IPR011496 This family consists of both eukaryotic and prokaryotic hyaluronidases. Human Q9HAR0 from SWISSPROT is expressed during meningioma []. Clostridium perfringens, P26831 from SWISSPROT, is involved in pathogenesis and is likely to act on connectivity tissue during gas gangrene []. It catalyses the random hydrolysis of 1->4-linkages between N-acetyl-beta-D-glucosamine and D-glucuronate residues in hyaluronate.; PDB: 2WB5_B 2V5C_B 2VUR_A 2V5D_A 2YDS_A 2CBI_A 2XPK_A 2CBJ_B 2J62_A 2X0Y_A ....
Probab=23.16 E-value=1.7e+02 Score=25.35 Aligned_cols=24 Identities=21% Similarity=0.425 Sum_probs=16.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC
Q 043269 23 GVRKGPWTVEEDSLLMNYVAIHGE 46 (191)
Q Consensus 23 ~~~kg~WT~eED~~L~~~v~~~g~ 46 (191)
|.-..+||.|+-..|++.+.+|+-
T Consensus 6 GFYG~PWs~e~R~~l~~f~~~~km 29 (306)
T PF07555_consen 6 GFYGRPWSHEDRLDLIRFLGRYKM 29 (306)
T ss_dssp -SSSS---HHHHHHHHHHHHHTT-
T ss_pred CcCCCCCCHHHHHHHHHHHHHcCC
Confidence 344559999999999999999876
No 199
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.72 E-value=2.2e+02 Score=22.59 Aligned_cols=29 Identities=3% Similarity=-0.064 Sum_probs=22.9
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.=.+||..| |-+...++.+....+++
T Consensus 163 ~g~s~~EIAe~l-gis~~tV~~~l~RAr~~ 191 (206)
T PRK12544 163 IELETNEICHAV-DLSVSNLNVLLYRARLR 191 (206)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 355678999999 99999999987666554
No 200
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=22.66 E-value=1.3e+02 Score=17.86 Aligned_cols=29 Identities=24% Similarity=0.315 Sum_probs=18.9
Q ss_pred HHHHHHHHhcCCCHHHHhhhCCCCCHHHHHH
Q 043269 88 LMILELHSRWGNRWSKIAQYLPGRTDNEIKN 118 (191)
Q Consensus 88 ~~L~~~v~~~G~~W~~Ia~~l~gRt~~~~k~ 118 (191)
..++.++.. |-...+||+.+ |-+...|.+
T Consensus 8 ~~ii~l~~~-G~s~~~ia~~l-gvs~~Tv~~ 36 (50)
T PF13384_consen 8 AQIIRLLRE-GWSIREIAKRL-GVSRSTVYR 36 (50)
T ss_dssp --HHHHHHH-T--HHHHHHHH-TS-HHHHHH
T ss_pred HHHHHHHHC-CCCHHHHHHHH-CcCHHHHHH
Confidence 345666666 88899999999 888877755
No 201
>PF11084 DUF2621: Protein of unknown function (DUF2621); InterPro: IPR020203 This entry represents a group of uncharacterised proteins.
Probab=22.40 E-value=84 Score=23.98 Aligned_cols=65 Identities=22% Similarity=0.210 Sum_probs=40.1
Q ss_pred HHHHHhCCCChhhhhhhcCCCCCchhhhhhhhhccCCCCcCCCCCHHHHHHHHHHHHhcCCCHHHHhh
Q 043269 39 NYVAIHGEGRWNAVASSAGLNRTGKSCRLRWLNYLRPDVRRGNITLQEQLMILELHSRWGNRWSKIAQ 106 (191)
Q Consensus 39 ~~v~~~g~~~W~~Ia~~l~~~R~~~qc~~rw~~~l~p~~~~~~Wt~eEd~~L~~~v~~~G~~W~~Ia~ 106 (191)
-++...|.-=..+.-+.|| ...+++.-+ |++|.-. -.+.-||+|+-.+|-+||.-...-...||+
T Consensus 19 ~l~~IGGfFMFRKFLK~lP-KeDGkS~LD-Wq~~yi~-~trhlW~de~K~lL~eLV~PVPelFRdvAk 83 (141)
T PF11084_consen 19 GLMAIGGFFMFRKFLKRLP-KEDGKSILD-WQEYYIE-KTRHLWTDEQKALLEELVSPVPELFRDVAK 83 (141)
T ss_pred HHHHHhHHHHHHHHHHhCC-cccCccccc-HHHHHHH-HhHhhcCHHHHHHHHHHhhcCcHHHHHHHH
Confidence 3444444323455556676 555655544 4444321 245579999999999999887766666655
No 202
>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=22.38 E-value=2.4e+02 Score=20.74 Aligned_cols=28 Identities=25% Similarity=0.236 Sum_probs=18.5
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQ 125 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~ 125 (191)
.|-.=.+||..| |=+...|+.+.....+
T Consensus 126 ~g~~~~eIA~~l-~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 126 RGVSLTALAEQL-GRTVNAVYKALSRLRV 153 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 344567778877 7777777776554433
No 203
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=22.31 E-value=3.3e+02 Score=20.19 Aligned_cols=46 Identities=17% Similarity=0.063 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHHhcCC--CHHHHhhhCCCCCHHHHHHHHHHHhHHHHh
Q 043269 82 ITLQEQLMILELHSRWGN--RWSKIAQYLPGRTDNEIKNYWRTRVQKHAK 129 (191)
Q Consensus 82 Wt~eEd~~L~~~v~~~G~--~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~ 129 (191)
.+++|-++|...+ ..+. .|..||..| |=+...|..+=+..+.+...
T Consensus 83 Ld~~er~II~~rY-~~~~~~t~~~Ia~~l-~iS~~t~~r~r~~~l~kla~ 130 (134)
T TIGR01636 83 ADEQTRVIIQELY-MKKRPLTLVGLAQQL-FISKSTAYRLRNHIIEAVAE 130 (134)
T ss_pred CCHHHHHHHHHHH-ccCCCCCHHHHHHHh-CCCHHHHHHHHHHHHHHHHH
Confidence 3444444443333 2233 799999998 88888886554444444433
No 204
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=22.14 E-value=2.4e+02 Score=23.58 Aligned_cols=32 Identities=19% Similarity=0.290 Sum_probs=24.7
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHHHHh
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQKHAK 129 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k~~~ 129 (191)
+|-.-.+||+.| |.+...|+.+...-.++...
T Consensus 130 ~g~s~~EIA~~l-g~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 130 FGVPFDEIASTL-GRSPAACRQLASRARKHVRA 161 (293)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHh
Confidence 345679999999 99999999988766555333
No 205
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=22.11 E-value=2.1e+02 Score=21.25 Aligned_cols=29 Identities=21% Similarity=0.307 Sum_probs=21.9
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.=.+||..| |-+...|+++....+++
T Consensus 126 ~g~s~~eIA~~l-gis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 126 SGYSYKEIAEAL-GIKESSVGTTLARAKKK 154 (166)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 555678899998 88898888887655444
No 206
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=22.09 E-value=1.8e+02 Score=23.66 Aligned_cols=28 Identities=14% Similarity=0.159 Sum_probs=22.2
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.-.+||..| |-+...|+.+....+++
T Consensus 187 g~s~~EIA~~L-gis~~tVk~~l~RAr~k 214 (233)
T PRK12538 187 NMSNGEIAEVM-DTTVAAVESLLKRGRQQ 214 (233)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 44678999999 99999998887665554
No 207
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=22.04 E-value=2.5e+02 Score=21.47 Aligned_cols=28 Identities=18% Similarity=0.206 Sum_probs=20.6
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.=.+||..| |-+...|+.+....+++
T Consensus 143 g~s~~EIA~~l-~is~~tv~~~l~Ra~~~ 170 (179)
T PRK09415 143 ELSIKEIAEVT-GVNENTVKTRLKKAKEL 170 (179)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 44667888888 77888888877666544
No 208
>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=21.80 E-value=2.6e+02 Score=22.27 Aligned_cols=29 Identities=24% Similarity=0.294 Sum_probs=22.0
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.-.+||+.+ |-+...|+.+....+++
T Consensus 193 ~~~s~~eIA~~l-gis~~~v~~~~~ra~~~ 221 (227)
T TIGR02980 193 EDKTQSEIAERL-GISQMHVSRLLRRALKK 221 (227)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 455788999999 88998888776665554
No 209
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=21.36 E-value=2.6e+02 Score=21.55 Aligned_cols=29 Identities=21% Similarity=0.128 Sum_probs=20.4
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.-.+||..| |-+...|+.+-...+++
T Consensus 126 ~g~s~~EIA~~L-gis~~tV~~~l~RAr~~ 154 (182)
T PRK12540 126 SGFSYEDAAAIC-GCAVGTIKSRVNRARSK 154 (182)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 345678888888 88888887776554443
No 210
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=20.94 E-value=3.2e+02 Score=23.27 Aligned_cols=28 Identities=11% Similarity=0.138 Sum_probs=22.8
Q ss_pred CCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 98 GNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 98 G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
|-.-.+||..| |-+...|+.+....+++
T Consensus 169 g~s~~EIA~~l-gis~~tVk~~l~RAr~~ 196 (339)
T PRK08241 169 GWSAAEVAELL-DTSVAAVNSALQRARAT 196 (339)
T ss_pred CCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 44679999999 99999999987666554
No 211
>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=20.79 E-value=2.5e+02 Score=21.27 Aligned_cols=31 Identities=26% Similarity=0.414 Sum_probs=19.2
Q ss_pred HHHHHHHHH-hc-CCCHHHHhhhCCCCCHHHHHH
Q 043269 87 QLMILELHS-RW-GNRWSKIAQYLPGRTDNEIKN 118 (191)
Q Consensus 87 d~~L~~~v~-~~-G~~W~~Ia~~l~gRt~~~~k~ 118 (191)
++.++++.- .+ |..|-.||..| +-+..+|+.
T Consensus 86 ~k~Ii~lry~~r~~~TW~~IA~~l-~i~erta~r 118 (130)
T PF05263_consen 86 EKRIIKLRYDRRSRRTWYQIAQKL-HISERTARR 118 (130)
T ss_pred HHHHHHHHHcccccchHHHHHHHh-CccHHHHHH
Confidence 444544442 23 35799999988 566666654
No 212
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=20.04 E-value=3.1e+02 Score=21.20 Aligned_cols=29 Identities=14% Similarity=0.048 Sum_probs=21.9
Q ss_pred cCCCHHHHhhhCCCCCHHHHHHHHHHHhHH
Q 043269 97 WGNRWSKIAQYLPGRTDNEIKNYWRTRVQK 126 (191)
Q Consensus 97 ~G~~W~~Ia~~l~gRt~~~~k~rw~~~l~k 126 (191)
.|-.-.+||..| |-+...|+.+....+++
T Consensus 126 eg~s~~EIA~~l-gis~~tV~~~l~Rar~~ 154 (182)
T PRK12511 126 EGLSYQEAAAVL-GIPIGTLMSRIGRARAA 154 (182)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 355678999999 88999998887555443
Done!