Query 037352
Match_columns 189
No_of_seqs 230 out of 1412
Neff 7.4
Searched_HMMs 46136
Date Fri Mar 29 11:23:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037352.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/037352hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03212 Transcription repress 100.0 7.3E-40 1.6E-44 266.6 9.8 131 6-142 10-141 (249)
2 PLN03091 hypothetical protein; 100.0 5.6E-37 1.2E-41 266.2 10.4 125 9-139 2-127 (459)
3 KOG0048 Transcription factor, 100.0 5.4E-36 1.2E-40 247.6 9.0 113 21-137 7-120 (238)
4 KOG0049 Transcription factor, 99.8 4.6E-20 9.9E-25 166.1 3.6 115 8-123 287-406 (939)
5 KOG0049 Transcription factor, 99.8 1.2E-19 2.5E-24 163.6 4.1 117 3-123 336-458 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 1.3E-18 2.8E-23 114.3 2.2 60 26-90 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 3.5E-16 7.6E-21 140.2 5.6 100 20-123 17-117 (512)
8 KOG0050 mRNA splicing protein 99.6 1.3E-16 2.7E-21 141.0 1.2 98 21-123 5-103 (617)
9 KOG0051 RNA polymerase I termi 99.5 4.2E-15 9E-20 134.7 4.2 100 22-128 383-511 (607)
10 PF00249 Myb_DNA-binding: Myb- 99.5 5.7E-15 1.2E-19 92.9 -0.2 48 23-73 1-48 (48)
11 PF00249 Myb_DNA-binding: Myb- 99.5 4.4E-14 9.6E-19 88.8 3.2 45 79-123 1-48 (48)
12 PLN03212 Transcription repress 99.4 5.4E-13 1.2E-17 109.4 4.9 98 59-175 12-112 (249)
13 PF13921 Myb_DNA-bind_6: Myb-l 99.3 2.2E-12 4.8E-17 84.5 3.5 42 82-123 1-43 (60)
14 smart00717 SANT SANT SWI3, AD 99.2 1.1E-11 2.4E-16 76.6 4.1 45 79-123 1-47 (49)
15 PLN03091 hypothetical protein; 99.2 1.3E-11 2.9E-16 108.3 4.6 92 74-177 9-103 (459)
16 KOG0048 Transcription factor, 99.2 1.9E-11 4.2E-16 101.1 5.4 93 75-179 5-100 (238)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 5E-11 1.1E-15 72.4 3.9 42 81-122 1-44 (45)
18 smart00717 SANT SANT SWI3, AD 99.1 1.4E-11 3E-16 76.1 1.0 48 23-74 1-48 (49)
19 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 1.3E-10 2.8E-15 70.6 0.8 44 25-72 1-44 (45)
20 KOG0051 RNA polymerase I termi 98.8 4.8E-09 1E-13 95.7 3.4 101 21-123 306-428 (607)
21 COG5147 REB1 Myb superfamily p 98.4 9.6E-09 2.1E-13 92.7 -4.1 99 19-123 287-396 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.0 2.5E-06 5.5E-11 55.4 1.1 49 22-73 2-54 (57)
23 KOG0457 Histone acetyltransfer 97.8 5.1E-06 1.1E-10 73.1 0.6 50 20-73 69-118 (438)
24 TIGR02894 DNA_bind_RsfA transc 97.8 1.4E-05 3E-10 62.0 2.1 50 78-129 3-60 (161)
25 KOG0050 mRNA splicing protein 97.6 2.9E-06 6.3E-11 76.1 -3.6 63 5-73 37-103 (617)
26 KOG0457 Histone acetyltransfer 97.6 8.1E-05 1.8E-09 65.7 4.2 48 76-123 69-118 (438)
27 TIGR01557 myb_SHAQKYF myb-like 97.5 0.00016 3.4E-09 47.0 4.4 45 79-123 3-54 (57)
28 COG5259 RSC8 RSC chromatin rem 97.4 3.6E-05 7.9E-10 68.4 0.3 46 22-72 278-323 (531)
29 KOG1279 Chromatin remodeling f 97.4 5.8E-05 1.3E-09 68.6 0.9 47 21-72 251-297 (506)
30 PF13325 MCRS_N: N-terminal re 97.3 0.00044 9.6E-09 55.7 5.2 94 25-123 1-126 (199)
31 KOG1279 Chromatin remodeling f 97.0 0.00062 1.3E-08 62.0 3.8 46 78-123 252-298 (506)
32 PF08914 Myb_DNA-bind_2: Rap1 97.0 0.00053 1.1E-08 45.7 2.4 45 79-123 2-57 (65)
33 COG5259 RSC8 RSC chromatin rem 96.9 0.00058 1.3E-08 61.0 2.6 44 80-123 280-324 (531)
34 TIGR02894 DNA_bind_RsfA transc 96.8 0.00026 5.6E-09 55.0 -0.2 52 21-74 2-56 (161)
35 PF13837 Myb_DNA-bind_4: Myb/S 96.5 0.0023 4.9E-08 44.4 2.7 49 80-130 2-69 (90)
36 PRK13923 putative spore coat p 96.4 0.0016 3.5E-08 51.2 1.7 47 77-124 3-57 (170)
37 PF13837 Myb_DNA-bind_4: Myb/S 96.4 0.00042 9.1E-09 48.2 -1.6 49 24-72 2-63 (90)
38 PF08914 Myb_DNA-bind_2: Rap1 96.0 0.0011 2.3E-08 44.2 -1.0 54 23-76 2-60 (65)
39 COG5114 Histone acetyltransfer 95.9 0.0016 3.5E-08 55.7 -0.7 51 20-74 60-110 (432)
40 PRK13923 putative spore coat p 95.8 0.0012 2.6E-08 51.9 -1.8 53 21-75 3-58 (170)
41 COG5114 Histone acetyltransfer 95.6 0.023 4.9E-07 48.9 4.9 45 79-123 63-109 (432)
42 PF13873 Myb_DNA-bind_5: Myb/S 95.2 0.029 6.3E-07 38.0 3.6 45 79-123 2-69 (78)
43 PF13873 Myb_DNA-bind_5: Myb/S 95.0 0.0041 8.9E-08 42.3 -1.0 51 23-73 2-69 (78)
44 KOG2656 DNA methyltransferase 94.7 0.054 1.2E-06 47.7 4.9 75 48-123 75-181 (445)
45 KOG4282 Transcription factor G 92.4 0.13 2.7E-06 44.7 3.3 54 79-132 54-122 (345)
46 PLN03142 Probable chromatin-re 92.2 0.23 5E-06 49.3 5.1 95 25-123 826-984 (1033)
47 COG5118 BDP1 Transcription ini 90.6 0.25 5.5E-06 43.5 3.2 44 80-123 366-410 (507)
48 PF09111 SLIDE: SLIDE; InterP 90.0 0.18 3.8E-06 37.5 1.6 48 76-123 46-110 (118)
49 PF12776 Myb_DNA-bind_3: Myb/S 88.8 0.48 1E-05 33.0 3.0 43 81-123 1-62 (96)
50 PF11626 Rap1_C: TRF2-interact 86.7 0.69 1.5E-05 32.3 2.7 23 21-43 45-75 (87)
51 COG5118 BDP1 Transcription ini 85.7 0.34 7.4E-06 42.7 0.9 63 22-89 364-434 (507)
52 KOG4282 Transcription factor G 85.3 0.27 5.8E-06 42.7 0.1 50 24-73 55-113 (345)
53 PF08281 Sigma70_r4_2: Sigma-7 85.3 1.2 2.6E-05 27.6 3.1 39 84-123 12-51 (54)
54 PF13325 MCRS_N: N-terminal re 83.5 1.5 3.3E-05 35.5 3.6 43 81-123 1-46 (199)
55 KOG1194 Predicted DNA-binding 82.7 1.6 3.5E-05 39.4 3.8 45 79-123 187-232 (534)
56 PF09111 SLIDE: SLIDE; InterP 81.5 1.2 2.7E-05 33.0 2.3 37 20-56 46-82 (118)
57 PF04545 Sigma70_r4: Sigma-70, 77.4 3.2 6.9E-05 25.3 2.9 38 85-123 7-45 (50)
58 PF07750 GcrA: GcrA cell cycle 75.8 1.9 4.2E-05 33.7 1.9 40 81-120 2-41 (162)
59 PF11035 SnAPC_2_like: Small n 72.6 9.6 0.00021 33.0 5.5 49 79-129 21-74 (344)
60 KOG4167 Predicted DNA-binding 68.4 1.8 3.9E-05 41.3 0.3 44 23-71 619-662 (907)
61 KOG4167 Predicted DNA-binding 66.7 5.8 0.00013 38.1 3.2 44 79-122 619-663 (907)
62 KOG2009 Transcription initiati 64.8 9.9 0.00022 35.6 4.3 46 78-123 408-454 (584)
63 smart00595 MADF subfamily of S 63.9 3.4 7.3E-05 28.2 0.9 23 100-123 30-52 (89)
64 PF13936 HTH_38: Helix-turn-he 62.7 4.2 9E-05 24.5 1.0 36 81-117 4-39 (44)
65 KOG4468 Polycomb-group transcr 61.7 10 0.00022 35.7 3.7 45 79-123 88-143 (782)
66 KOG2656 DNA methyltransferase 61.2 3.8 8.3E-05 36.4 0.9 48 21-72 128-180 (445)
67 PF07750 GcrA: GcrA cell cycle 59.1 6.7 0.00015 30.6 1.9 33 25-62 2-35 (162)
68 TIGR02985 Sig70_bacteroi1 RNA 59.1 13 0.00027 27.5 3.4 35 88-123 119-154 (161)
69 PF13404 HTH_AsnC-type: AsnC-t 56.6 11 0.00023 22.5 2.1 36 85-121 3-40 (42)
70 cd08311 Death_p75NR Death doma 50.3 12 0.00026 25.5 1.8 33 84-117 2-34 (77)
71 PRK11179 DNA-binding transcrip 45.4 23 0.00049 26.9 2.9 38 85-123 9-48 (153)
72 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 45.4 17 0.00037 22.8 1.7 38 81-119 4-41 (50)
73 PF02954 HTH_8: Bacterial regu 42.3 11 0.00025 22.2 0.6 29 29-61 5-33 (42)
74 KOG4329 DNA-binding protein [G 42.0 32 0.00069 30.6 3.5 43 80-122 278-322 (445)
75 cd08319 Death_RAIDD Death doma 39.3 20 0.00043 24.8 1.5 28 87-115 2-30 (83)
76 TIGR02937 sigma70-ECF RNA poly 38.9 35 0.00075 24.4 2.9 27 96-123 125-151 (158)
77 cd08803 Death_ank3 Death domai 38.3 26 0.00057 24.2 2.0 30 87-117 4-34 (84)
78 PF10545 MADF_DNA_bdg: Alcohol 37.6 14 0.00031 24.4 0.6 24 100-123 29-53 (85)
79 PRK11169 leucine-responsive tr 37.6 36 0.00077 26.2 2.9 39 84-123 13-53 (164)
80 PF07638 Sigma70_ECF: ECF sigm 36.7 35 0.00075 26.7 2.8 35 88-123 141-176 (185)
81 PRK11179 DNA-binding transcrip 36.3 9.5 0.00021 29.0 -0.5 42 29-75 9-50 (153)
82 PRK09652 RNA polymerase sigma 35.7 42 0.00091 25.2 3.0 27 96-123 143-169 (182)
83 PF09420 Nop16: Ribosome bioge 35.7 16 0.00035 28.4 0.7 31 22-56 113-143 (164)
84 PRK09643 RNA polymerase sigma 34.6 46 0.00099 25.9 3.2 27 96-123 149-175 (192)
85 KOG1194 Predicted DNA-binding 33.3 15 0.00033 33.4 0.2 43 23-70 187-229 (534)
86 PRK04217 hypothetical protein; 33.2 55 0.0012 23.9 3.1 41 81-123 42-83 (110)
87 COG5352 Uncharacterized protei 32.7 29 0.00063 26.7 1.6 37 81-117 2-38 (169)
88 PF01388 ARID: ARID/BRIGHT DNA 31.6 46 0.00099 22.7 2.4 35 89-123 40-88 (92)
89 PRK11924 RNA polymerase sigma 31.6 51 0.0011 24.6 2.9 27 96-123 140-166 (179)
90 PF09420 Nop16: Ribosome bioge 31.6 81 0.0017 24.4 4.0 45 79-123 114-163 (164)
91 PRK09641 RNA polymerase sigma 30.8 53 0.0012 25.0 2.9 27 96-123 151-177 (187)
92 KOG2009 Transcription initiati 30.2 29 0.00063 32.6 1.5 48 19-71 405-452 (584)
93 PRK11169 leucine-responsive tr 30.0 11 0.00024 29.0 -1.1 44 28-76 13-56 (164)
94 cd08317 Death_ank Death domain 29.0 28 0.00061 23.7 0.9 29 87-116 4-33 (84)
95 TIGR02939 RpoE_Sigma70 RNA pol 28.8 50 0.0011 25.2 2.5 26 97-123 154-179 (190)
96 PRK09648 RNA polymerase sigma 28.0 71 0.0015 24.5 3.2 27 96-123 154-180 (189)
97 KOG4468 Polycomb-group transcr 27.8 18 0.0004 34.0 -0.2 46 23-72 88-142 (782)
98 PLN03142 Probable chromatin-re 27.7 46 0.00099 33.6 2.4 33 21-56 924-956 (1033)
99 cd08804 Death_ank2 Death domai 27.6 36 0.00079 23.4 1.3 30 87-117 4-34 (84)
100 smart00501 BRIGHT BRIGHT, ARID 27.5 68 0.0015 22.1 2.7 35 89-123 36-84 (93)
101 KOG0384 Chromodomain-helicase 27.4 30 0.00066 35.3 1.1 75 22-106 1132-1208(1373)
102 PRK12523 RNA polymerase sigma 27.3 94 0.002 23.5 3.7 33 90-123 127-160 (172)
103 PRK09637 RNA polymerase sigma 27.2 72 0.0016 24.6 3.1 27 96-123 121-147 (181)
104 PRK09413 IS2 repressor TnpA; R 27.2 69 0.0015 23.3 2.8 46 21-73 8-53 (121)
105 COG2197 CitB Response regulato 27.2 69 0.0015 25.6 3.1 42 80-123 147-188 (211)
106 PRK09047 RNA polymerase factor 27.1 76 0.0017 23.4 3.2 27 96-123 121-147 (161)
107 PRK09645 RNA polymerase sigma 27.1 76 0.0016 23.9 3.2 27 96-123 133-159 (173)
108 PRK12512 RNA polymerase sigma 27.1 75 0.0016 24.3 3.2 27 96-123 146-172 (184)
109 TIGR02954 Sig70_famx3 RNA poly 26.7 71 0.0015 24.0 3.0 27 96-123 134-160 (169)
110 PF09197 Rap1-DNA-bind: Rap1, 26.5 61 0.0013 23.5 2.3 23 101-123 53-75 (105)
111 PRK12531 RNA polymerase sigma 25.5 84 0.0018 24.4 3.2 27 96-123 156-182 (194)
112 PRK09642 RNA polymerase sigma 25.4 85 0.0018 23.3 3.1 27 96-123 121-147 (160)
113 TIGR02943 Sig70_famx1 RNA poly 25.1 86 0.0019 24.3 3.2 27 96-123 146-172 (188)
114 PRK06759 RNA polymerase factor 24.8 94 0.002 22.8 3.3 27 96-123 121-147 (154)
115 TIGR02952 Sig70_famx2 RNA poly 24.6 88 0.0019 23.3 3.1 27 96-123 137-163 (170)
116 PRK11923 algU RNA polymerase s 24.6 79 0.0017 24.4 2.9 26 97-123 154-179 (193)
117 PRK12530 RNA polymerase sigma 24.5 87 0.0019 24.3 3.1 27 96-123 149-175 (189)
118 TIGR02948 SigW_bacill RNA poly 24.4 75 0.0016 24.1 2.7 27 96-123 151-177 (187)
119 cd08318 Death_NMPP84 Death dom 23.8 49 0.0011 22.7 1.4 22 93-115 13-35 (86)
120 PRK06811 RNA polymerase factor 23.5 1.1E+02 0.0025 23.5 3.6 35 96-133 146-180 (189)
121 cd00569 HTH_Hin_like Helix-tur 22.9 1.2E+02 0.0026 15.2 3.1 34 82-116 6-39 (42)
122 PRK12524 RNA polymerase sigma 22.9 99 0.0021 24.0 3.2 27 96-123 151-177 (196)
123 PRK12514 RNA polymerase sigma 22.8 98 0.0021 23.5 3.1 27 96-123 144-170 (179)
124 cd08777 Death_RIP1 Death Domai 22.4 46 0.001 23.0 1.0 27 90-117 5-32 (86)
125 smart00351 PAX Paired Box doma 22.1 1.2E+02 0.0026 22.2 3.3 72 19-95 11-89 (125)
126 cd06171 Sigma70_r4 Sigma70, re 22.1 1.2E+02 0.0025 17.3 2.7 35 87-122 15-50 (55)
127 PRK12536 RNA polymerase sigma 21.7 1.1E+02 0.0024 23.4 3.2 27 96-123 144-170 (181)
128 PRK12515 RNA polymerase sigma 21.7 1.1E+02 0.0024 23.5 3.2 27 96-123 146-172 (189)
129 TIGR02999 Sig-70_X6 RNA polyme 21.6 1.1E+02 0.0025 23.1 3.2 27 96-123 149-175 (183)
130 PRK15411 rcsA colanic acid cap 21.5 1.1E+02 0.0024 24.3 3.3 41 81-123 137-177 (207)
131 PRK12527 RNA polymerase sigma 21.5 1.2E+02 0.0026 22.5 3.3 27 96-123 120-146 (159)
132 PRK09651 RNA polymerase sigma 21.5 72 0.0016 24.2 2.1 27 96-123 134-160 (172)
133 cd08805 Death_ank1 Death domai 21.0 60 0.0013 22.5 1.4 26 87-113 4-30 (84)
134 PF00531 Death: Death domain; 20.6 71 0.0015 20.9 1.7 27 89-116 2-30 (83)
135 PRK09649 RNA polymerase sigma 20.2 1.1E+02 0.0024 23.5 3.0 27 96-123 145-171 (185)
136 PRK12529 RNA polymerase sigma 20.1 1.6E+02 0.0034 22.5 3.7 27 96-123 142-168 (178)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=7.3e-40 Score=266.62 Aligned_cols=131 Identities=44% Similarity=0.835 Sum_probs=122.1
Q ss_pred cccCCCcccccCCCCcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCCccCCCCCHH
Q 037352 6 MEKMCPSCVSKDHHMIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPNIRRGDFTLE 85 (189)
Q Consensus 6 ~~~~~~~~~~~~~~~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~~~~~WT~e 85 (189)
+.+.+++||.|.+ +++++||+|||++|+++|++||. . +|..||..++++|+++||++||.++|+|.+++++||.|
T Consensus 10 ~~~~~~pcc~K~g--lKRg~WT~EEDe~L~~lV~kyG~-~--nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~E 84 (249)
T PLN03212 10 VSKKTTPCCTKMG--MKRGPWTVEEDEILVSFIKKEGE-G--RWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSD 84 (249)
T ss_pred CCCCCCCCcccCC--CcCCCCCHHHHHHHHHHHHHhCc-c--cHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChH
Confidence 3456899999999 99999999999999999999997 5 99999999977899999999999999999999999999
Q ss_pred HHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhhhhhhhhhcCCCCcccCCCC
Q 037352 86 EDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSYMRNKMSNRGVDLLLISDRE 142 (189)
Q Consensus 86 Ed~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l~k~~~~~~~~~~~~~~~~~ 142 (189)
||++|++++. +|++|+.||+.|||||+++|||||+.++ ++++...++++.......
T Consensus 85 ED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~L-rK~l~r~~i~p~~~kp~~ 141 (249)
T PLN03212 85 EEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHL-RKKLLRQGIDPQTHKPLD 141 (249)
T ss_pred HHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHH-hHHHHhcCCCCCCCCCCC
Confidence 9999999999 9999999999999999999999999999 888888898887765433
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=5.6e-37 Score=266.16 Aligned_cols=125 Identities=42% Similarity=0.841 Sum_probs=118.5
Q ss_pred CCCcccccCCCCcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCCccCCCCCHHHHH
Q 037352 9 MCPSCVSKDHHMIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPNIRRGDFTLEEDE 88 (189)
Q Consensus 9 ~~~~~~~~~~~~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~~~~~WT~eEd~ 88 (189)
.+++||.|.+ ++||+||+|||++|+++|.+||. . +|..||..++++|+++||++||.++|+|.+++++||.|||+
T Consensus 2 gr~~Cc~Kqk--lrKg~WTpEEDe~L~~~V~kyG~-~--nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~ 76 (459)
T PLN03091 2 GRHSCCYKQK--LRKGLWSPEEDEKLLRHITKYGH-G--CWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEEN 76 (459)
T ss_pred CCCccCcCCC--CcCCCCCHHHHHHHHHHHHHhCc-C--CHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHH
Confidence 5789999999 99999999999999999999998 6 99999999987899999999999999999999999999999
Q ss_pred HHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhhhhhhhhhcCCCCcccC
Q 037352 89 LIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSYMRNKMSNRGVDLLLIS 139 (189)
Q Consensus 89 ~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l~k~~~~~~~~~~~~~~ 139 (189)
+|+++|. +|++|..||+.|||||+++|||||+.++ +++++..++++....
T Consensus 77 lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslL-KKklr~~~I~p~t~k 127 (459)
T PLN03091 77 LIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCL-KKKLRQRGIDPNTHK 127 (459)
T ss_pred HHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHH-HHHHHHcCCCCCCCC
Confidence 9999999 9999999999999999999999999999 888888888877543
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=5.4e-36 Score=247.57 Aligned_cols=113 Identities=42% Similarity=0.693 Sum_probs=107.0
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCCccCCCCCHHHHHHHHHHhh-cCCc
Q 037352 21 IRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPNIRRGDFTLEEDELIINLCR-AGSK 99 (189)
Q Consensus 21 lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~-~g~~ 99 (189)
+.||+||+|||++|+++|.+||. + +|..||+.+|.+|++++||.||.|||+|++++|.||+|||.+|++|+. +|++
T Consensus 7 ~~kGpWt~EED~~L~~~V~~~G~-~--~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNr 83 (238)
T KOG0048|consen 7 LVKGPWTQEEDLTQIRSIKSFGK-H--NGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNR 83 (238)
T ss_pred ccCCCCChHHHHHHHHHHHHhCC-C--CcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcH
Confidence 55799999999999999999999 7 999999999889999999999999999999999999999999999999 9999
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhhhhhhhcCCCCcc
Q 037352 100 WTNIGLLLPGRTHKDVMNYCKTSYMRNKMSNRGVDLLL 137 (189)
Q Consensus 100 W~~Ia~~l~gRt~~q~k~rw~~~l~k~~~~~~~~~~~~ 137 (189)
|+.||++|||||++.|||+|+..+ |+|+...+.++..
T Consensus 84 Ws~IA~~LPGRTDNeIKN~Wnt~l-kkkl~~~~~~~~~ 120 (238)
T KOG0048|consen 84 WSLIAGRLPGRTDNEVKNHWNTHL-KKKLLKMGIDPST 120 (238)
T ss_pred HHHHHhhCCCcCHHHHHHHHHHHH-HHHHHHcCCCCCc
Confidence 999999999999999999999999 8888887755544
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.79 E-value=4.6e-20 Score=166.14 Aligned_cols=115 Identities=19% Similarity=0.404 Sum_probs=106.3
Q ss_pred cCCCcccccCC---CCcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCCccCCCCCH
Q 037352 8 KMCPSCVSKDH---HMIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPNIRRGDFTL 84 (189)
Q Consensus 8 ~~~~~~~~~~~---~~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~~~~~WT~ 84 (189)
++..||-.+.+ ..++...||.|||.+|+.+|.....+.-|+|.+|...| +||+..|..-||...|+|.+++|+||.
T Consensus 287 RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ym-pgr~~~qLI~R~~~~LdPsikhg~wt~ 365 (939)
T KOG0049|consen 287 RSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYM-PGRTRQQLITRFSHTLDPSVKHGRWTD 365 (939)
T ss_pred cchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhc-CCcchhhhhhhheeccCccccCCCCCC
Confidence 66778887766 45778999999999999999999776788999999999 599999999999999999999999999
Q ss_pred HHHHHHHHHhh-cCC-ccccccccCCCCCHHHHHHHHHHhh
Q 037352 85 EEDELIINLCR-AGS-KWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 85 eEd~~L~~~v~-~g~-~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
+||.+|+.+|. ||. .|.+|-..||||++.|||.||.+.|
T Consensus 366 ~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL 406 (939)
T KOG0049|consen 366 QEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVL 406 (939)
T ss_pred HHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHH
Confidence 99999999999 865 5999999999999999999999988
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.77 E-value=1.2e-19 Score=163.57 Aligned_cols=117 Identities=22% Similarity=0.420 Sum_probs=101.9
Q ss_pred ccccccCCCccccc----CCCCcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCCcc
Q 037352 3 EHIMEKMCPSCVSK----DHHMIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPNIR 78 (189)
Q Consensus 3 ~~~~~~~~~~~~~~----~~~~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~~ 78 (189)
++|..++.++-..+ .+|.|++|+||++||.+|..+|.+||. . +|.+|-+.+ |||+..|||+||.+.|+...+
T Consensus 336 ~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~-k--dw~k~R~~v-PnRSdsQcR~RY~nvL~~s~K 411 (939)
T KOG0049|consen 336 QYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGA-K--DWAKVRQAV-PNRSDSQCRERYTNVLNRSAK 411 (939)
T ss_pred HhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCc-c--chhhHHHhc-CCccHHHHHHHHHHHHHHhhc
Confidence 56777877765543 337799999999999999999999998 7 999999999 599999999999999999999
Q ss_pred CCCCCHHHHHHHHHHhh-cC-CccccccccCCCCCHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-AG-SKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~g-~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.+.||-.||+.|+.+|. || ++|.+||..||.||..|...|=...+
T Consensus 412 ~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~ 458 (939)
T KOG0049|consen 412 VERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLI 458 (939)
T ss_pred cCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHHH
Confidence 99999999999999999 97 56999999999999966544443333
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=99.72 E-value=1.3e-18 Score=114.29 Aligned_cols=60 Identities=43% Similarity=0.844 Sum_probs=55.1
Q ss_pred CCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCCccCCCCCHHHHHHH
Q 037352 26 WTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPNIRRGDFTLEEDELI 90 (189)
Q Consensus 26 WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~~~~~WT~eEd~~L 90 (189)
||+|||++|+.+|..||. +|..||..|| .|++.+|+.||.++|.|.+++++||.+||+.|
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 999999999999999998 9999999996 79999999999999999999999999999987
No 7
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.62 E-value=3.5e-16 Score=140.23 Aligned_cols=100 Identities=31% Similarity=0.570 Sum_probs=96.3
Q ss_pred CcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCCccCCCCCHHHHHHHHHHhh-cCC
Q 037352 20 MIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPNIRRGDFTLEEDELIINLCR-AGS 98 (189)
Q Consensus 20 ~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~-~g~ 98 (189)
.++.|.|+..||+.|..+|+.+|. . +|..||+.++ .++++||+.||.++++|.+++..|+.+||..|+.+.. +|.
T Consensus 17 ~~k~gsw~~~EDe~l~~~vk~l~~-n--nws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~ 92 (512)
T COG5147 17 KRKGGSWKRTEDEDLKALVKKLGP-N--NWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT 92 (512)
T ss_pred eecCCCCCCcchhHHHHHHhhccc-c--cHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc
Confidence 488999999999999999999999 5 8999999997 4999999999999999999999999999999999999 999
Q ss_pred ccccccccCCCCCHHHHHHHHHHhh
Q 037352 99 KWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 99 ~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|..||..++||+..+|.+||...+
T Consensus 93 ~wstia~~~d~rt~~~~~ery~~~~ 117 (512)
T COG5147 93 QWSTIADYKDRRTAQQCVERYVNTL 117 (512)
T ss_pred hhhhhccccCccchHHHHHHHHHHh
Confidence 9999999999999999999999888
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.61 E-value=1.3e-16 Score=141.04 Aligned_cols=98 Identities=27% Similarity=0.645 Sum_probs=94.7
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCCccCCCCCHHHHHHHHHHhh-cCCc
Q 037352 21 IRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPNIRRGDFTLEEDELIINLCR-AGSK 99 (189)
Q Consensus 21 lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~-~g~~ 99 (189)
++-|.|+.-||+.|..+|.+||. + .|..|++.+. ..+++||+.||..+|+|.+++..|+.|||+.||.+.. ....
T Consensus 5 ~kggvwrntEdeilkaav~kyg~-n--qws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~q 80 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGK-N--QWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQ 80 (617)
T ss_pred EecceecccHHHHHHHHHHHcch-H--HHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCc
Confidence 78899999999999999999999 5 8999999995 6899999999999999999999999999999999999 9999
Q ss_pred cccccccCCCCCHHHHHHHHHHhh
Q 037352 100 WTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 100 W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
|..|+..| ||+.+||-.||+.++
T Consensus 81 wrtIa~i~-gr~~~qc~eRy~~ll 103 (617)
T KOG0050|consen 81 WRTIADIM-GRTSQQCLERYNNLL 103 (617)
T ss_pred cchHHHHh-hhhHHHHHHHHHHHH
Confidence 99999999 999999999999998
No 9
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.53 E-value=4.2e-15 Score=134.67 Aligned_cols=100 Identities=26% Similarity=0.554 Sum_probs=90.7
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCC--ccCCCCCHHHHHHHHHHhh----
Q 037352 22 RRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPN--IRRGDFTLEEDELIINLCR---- 95 (189)
Q Consensus 22 kkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~--~~~~~WT~eEd~~L~~~v~---- 95 (189)
++|.||+||++.|..+|.++|. +|..|+..|| |.+..|++||+++..+. .+++.||.||++.|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~----~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~ 456 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN----DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIR 456 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc----cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHH
Confidence 8999999999999999999998 9999999996 99999999999999887 4899999999999999992
Q ss_pred ----c-------------------CCccccccccCCCCCHHHHHHHHHHhhhhhhh
Q 037352 96 ----A-------------------GSKWTNIGLLLPGRTHKDVMNYCKTSYMRNKM 128 (189)
Q Consensus 96 ----~-------------------g~~W~~Ia~~l~gRt~~q~k~rw~~~l~k~~~ 128 (189)
+ +-.|+.|++.+..|+..||+.+|+.++ ....
T Consensus 457 ~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~-~~~s 511 (607)
T KOG0051|consen 457 EALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLT-TSPS 511 (607)
T ss_pred HhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHH-hhHH
Confidence 1 114999999999999999999999999 4443
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=99.47 E-value=5.7e-15 Score=92.89 Aligned_cols=48 Identities=38% Similarity=0.648 Sum_probs=42.1
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccC
Q 037352 23 RGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHL 73 (189)
Q Consensus 23 kg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L 73 (189)
|++||+|||++|+++|.+||. + +|..||..|+.+||+.||+.||.++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~-~--~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGK-D--NWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTT-T--HHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCC-c--HHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 689999999999999999999 3 49999999965899999999998864
No 11
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.46 E-value=4.4e-14 Score=88.81 Aligned_cols=45 Identities=33% Similarity=0.592 Sum_probs=40.7
Q ss_pred CCCCCHHHHHHHHHHhh-cCCc-cccccccCC-CCCHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-AGSK-WTNIGLLLP-GRTHKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~g~~-W~~Ia~~l~-gRt~~q~k~rw~~~l 123 (189)
+++||+|||++|+++|. +|.. |..||..|| |||..||++||+.++
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 57999999999999999 9998 999999999 999999999998864
No 12
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.37 E-value=5.4e-13 Score=109.42 Aligned_cols=98 Identities=20% Similarity=0.305 Sum_probs=74.4
Q ss_pred ccCCCcccccccccCCCCccCCCCCHHHHHHHHHHhh-cC-CccccccccC-CCCCHHHHHHHHHHhhhhhhhhhcCCCC
Q 037352 59 LRCGKSCHDRWFNHLNPNIRRGDFTLEEDELIINLCR-AG-SKWTNIGLLL-PGRTHKDVMNYCKTSYMRNKMSNRGVDL 135 (189)
Q Consensus 59 ~Rt~~qc~~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~-~g-~~W~~Ia~~l-~gRt~~q~k~rw~~~l~k~~~~~~~~~~ 135 (189)
+|++.-|. ++.+++++||+|||++|+++|+ || .+|..||+.+ +|||+.||+.||.++| +..+
T Consensus 12 ~~~~pcc~-------K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L-~P~I------- 76 (249)
T PLN03212 12 KKTTPCCT-------KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYL-RPSV------- 76 (249)
T ss_pred CCCCCCcc-------cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhh-chhc-------
Confidence 46665554 3578899999999999999999 98 5799999988 6999999999999999 3333
Q ss_pred cccCCCCCCCCCcchHHHHHHhhhccccccccCCcccccc
Q 037352 136 LLISDREGSHQQPHHLLLLLLLKRKTSFKKSLRPKFRRTN 175 (189)
Q Consensus 136 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 175 (189)
.......+.+.+........+..|..++...+.+++
T Consensus 77 ----~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTD 112 (249)
T PLN03212 77 ----KRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTD 112 (249)
T ss_pred ----ccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCH
Confidence 223444555666666666777778777776666654
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=99.29 E-value=2.2e-12 Score=84.46 Aligned_cols=42 Identities=36% Similarity=0.578 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 82 FTLEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 82 WT~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
||.|||++|+.+|. ||++|..||..|+.||..+|++||...|
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l 43 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHL 43 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTT
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHC
Confidence 99999999999999 9999999999996699999999999977
No 14
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.23 E-value=1.1e-11 Score=76.57 Aligned_cols=45 Identities=38% Similarity=0.682 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHhh-cC-CccccccccCCCCCHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-AG-SKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~g-~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
+++||++||.+|+.++. +| .+|..||..|++||..+|++||+.++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 36899999999999999 99 99999999999999999999999876
No 15
>PLN03091 hypothetical protein; Provisional
Probab=99.20 E-value=1.3e-11 Score=108.29 Aligned_cols=92 Identities=20% Similarity=0.202 Sum_probs=73.5
Q ss_pred CCCccCCCCCHHHHHHHHHHhh-cCC-ccccccccC-CCCCHHHHHHHHHHhhhhhhhhhcCCCCcccCCCCCCCCCcch
Q 037352 74 NPNIRRGDFTLEEDELIINLCR-AGS-KWTNIGLLL-PGRTHKDVMNYCKTSYMRNKMSNRGVDLLLISDREGSHQQPHH 150 (189)
Q Consensus 74 ~p~~~~~~WT~eEd~~L~~~v~-~g~-~W~~Ia~~l-~gRt~~q~k~rw~~~l~k~~~~~~~~~~~~~~~~~~~~~~~~~ 150 (189)
++.+++++||+|||++|+++|. ||. +|..||+.+ +||++.|||.||.++| ...+ .......+.+.
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyL-dP~I-----------kKgpWT~EED~ 76 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYL-RPDL-----------KRGTFSQQEEN 76 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhcc-CCcc-----------cCCCCCHHHHH
Confidence 3578899999999999999999 985 699999988 5999999999999999 3332 23345666666
Q ss_pred HHHHHHhhhccccccccCCcccccccc
Q 037352 151 LLLLLLLKRKTSFKKSLRPKFRRTNWM 177 (189)
Q Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 177 (189)
....+....+..|..++.....+++-.
T Consensus 77 lLLeL~k~~GnKWskIAk~LPGRTDnq 103 (459)
T PLN03091 77 LIIELHAVLGNRWSQIAAQLPGRTDNE 103 (459)
T ss_pred HHHHHHHHhCcchHHHHHhcCCCCHHH
Confidence 777777778888888887777776654
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.20 E-value=1.9e-11 Score=101.15 Aligned_cols=93 Identities=19% Similarity=0.137 Sum_probs=75.6
Q ss_pred CCccCCCCCHHHHHHHHHHhh-cCCc-cccccccCC-CCCHHHHHHHHHHhhhhhhhhhcCCCCcccCCCCCCCCCcchH
Q 037352 75 PNIRRGDFTLEEDELIINLCR-AGSK-WTNIGLLLP-GRTHKDVMNYCKTSYMRNKMSNRGVDLLLISDREGSHQQPHHL 151 (189)
Q Consensus 75 p~~~~~~WT~eEd~~L~~~v~-~g~~-W~~Ia~~l~-gRt~~q~k~rw~~~l~k~~~~~~~~~~~~~~~~~~~~~~~~~~ 151 (189)
+.+.+||||.|||++|+++|+ ||.. |..|++.++ ||++++||-||.++| +..+++ .....+.+.+
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyL-rP~ikr-----------g~fT~eEe~~ 72 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYL-RPDLKR-----------GNFSDEEEDL 72 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhccc-CCCccC-----------CCCCHHHHHH
Confidence 345579999999999999999 9865 999999998 999999999999999 555543 3344556667
Q ss_pred HHHHHhhhccccccccCCcccccccccc
Q 037352 152 LLLLLLKRKTSFKKSLRPKFRRTNWMEK 179 (189)
Q Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 179 (189)
...+....+.-++.+|.-.+.+||=..|
T Consensus 73 Ii~lH~~~GNrWs~IA~~LPGRTDNeIK 100 (238)
T KOG0048|consen 73 IIKLHALLGNRWSLIAGRLPGRTDNEVK 100 (238)
T ss_pred HHHHHHHHCcHHHHHHhhCCCcCHHHHH
Confidence 7777788888899999888888884444
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=99.14 E-value=5e-11 Score=72.44 Aligned_cols=42 Identities=36% Similarity=0.608 Sum_probs=40.1
Q ss_pred CCCHHHHHHHHHHhh-cC-CccccccccCCCCCHHHHHHHHHHh
Q 037352 81 DFTLEEDELIINLCR-AG-SKWTNIGLLLPGRTHKDVMNYCKTS 122 (189)
Q Consensus 81 ~WT~eEd~~L~~~v~-~g-~~W~~Ia~~l~gRt~~q~k~rw~~~ 122 (189)
+||.+||..|+.++. +| .+|..||..|++||..+|++||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999 99 8999999999999999999999875
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.13 E-value=1.4e-11 Score=76.11 Aligned_cols=48 Identities=38% Similarity=0.750 Sum_probs=43.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCC
Q 037352 23 RGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLN 74 (189)
Q Consensus 23 kg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~ 74 (189)
+++||++||+.|..++..||. . +|..||..|+ +|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~-~--~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGK-N--NWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCc-C--CHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 468999999999999999993 2 9999999996 8999999999988654
No 19
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.97 E-value=1.3e-10 Score=70.60 Aligned_cols=44 Identities=39% Similarity=0.678 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCccccccccc
Q 037352 25 FWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNH 72 (189)
Q Consensus 25 ~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~ 72 (189)
+||++||+.|..++..||. . +|..||..|+ +|++.+|+.+|.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~-~--~w~~Ia~~~~-~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGK-N--NWEKIAKELP-GRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCc-C--CHHHHHhHcC-CCCHHHHHHHHHHh
Confidence 5999999999999999994 3 9999999996 79999999999765
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.76 E-value=4.8e-09 Score=95.67 Aligned_cols=101 Identities=27% Similarity=0.380 Sum_probs=80.0
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCC--------------------CccccccccCCccCCCcccccccccCCCCc-cC
Q 037352 21 IRRGFWTGEEDERLKSFILLNGEEGGW--------------------NWEDVPRGAGLLRCGKSCHDRWFNHLNPNI-RR 79 (189)
Q Consensus 21 lkkg~WT~eED~~L~~~v~~~g~~~~~--------------------~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~-~~ 79 (189)
++-+.|+++||+.|-+.|+.|-...++ -|..|...|+ -|+...+..+-++...|-- ++
T Consensus 306 ~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 306 INLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCcccccc
Confidence 445899999999999999977221111 2466666775 4888888763333333322 89
Q ss_pred CCCCHHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 80 GDFTLEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 80 ~~WT~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
|.||+||++.|..+|. +|+.|..|++.| ||.+.+|+.||..+.
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~ 428 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYV 428 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhh
Confidence 9999999999999999 999999999999 999999999998887
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=98.43 E-value=9.6e-09 Score=92.70 Aligned_cols=99 Identities=23% Similarity=0.510 Sum_probs=87.2
Q ss_pred CCcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCC--CccCCCCCHHHHHHHHHHhh-
Q 037352 19 HMIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNP--NIRRGDFTLEEDELIINLCR- 95 (189)
Q Consensus 19 ~~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p--~~~~~~WT~eEd~~L~~~v~- 95 (189)
+.-.+|.||++|++.|..++..+|. .|..|...++ |-+..|++||.++... .+++++|+.||+.+|...|.
T Consensus 287 ~f~~~~~wt~e~~~eL~~~~~~~~~----~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e 360 (512)
T COG5147 287 IFEQRGKWTKEEEQELAKLVVEHGG----SWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNE 360 (512)
T ss_pred HHhhhccCccccccccccccccccc----hhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHH
Confidence 4456899999999999999999998 9999999885 9999999999999988 68888999999999988875
Q ss_pred c--------CCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 A--------GSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~--------g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
. --.|..|+..++.|...+|+..+..+.
T Consensus 361 ~~~~~~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 361 MRLEAQQSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred HHHHHhhhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 2 235999999999999988888887655
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.98 E-value=2.5e-06 Score=55.43 Aligned_cols=49 Identities=12% Similarity=0.152 Sum_probs=42.7
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCCCc---cccccccCCcc-CCCcccccccccC
Q 037352 22 RRGFWTGEEDERLKSFILLNGEEGGWNW---EDVPRGAGLLR-CGKSCHDRWFNHL 73 (189)
Q Consensus 22 kkg~WT~eED~~L~~~v~~~g~~~~~~W---~~Ia~~~~~~R-t~~qc~~Rw~~~L 73 (189)
++-.||+||.+.++++|+.+|. + +| ..|++.|+..+ |..||+.+.+.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~-g--~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGG-P--DWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCC-C--cccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3557999999999999999998 7 99 99999987666 9999999887653
No 23
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.81 E-value=5.1e-06 Score=73.15 Aligned_cols=50 Identities=26% Similarity=0.549 Sum_probs=46.4
Q ss_pred CcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccC
Q 037352 20 MIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHL 73 (189)
Q Consensus 20 ~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L 73 (189)
++-...||.+|+-+|++++..||- | ||..||.++| .|++.+|.++|.+++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~-G--NW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGF-G--NWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCC-C--cHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 466788999999999999999999 8 9999999999 799999999998864
No 24
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=97.76 E-value=1.4e-05 Score=62.02 Aligned_cols=50 Identities=26% Similarity=0.319 Sum_probs=42.9
Q ss_pred cCCCCCHHHHHHHHHHhh-c---CCc----cccccccCCCCCHHHHHHHHHHhhhhhhhh
Q 037352 78 RRGDFTLEEDELIINLCR-A---GSK----WTNIGLLLPGRTHKDVMNYCKTSYMRNKMS 129 (189)
Q Consensus 78 ~~~~WT~eEd~~L~~~v~-~---g~~----W~~Ia~~l~gRt~~q~k~rw~~~l~k~~~~ 129 (189)
....||.|||.+|.+.|- | |+. ..++++.| +||...|.-|||+.+ ++.+.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~V-RkqY~ 60 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYV-RKQYE 60 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHH-HHHHH
Confidence 467899999999999997 5 654 88999999 999999999999999 65553
No 25
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.65 E-value=2.9e-06 Score=76.07 Aligned_cols=63 Identities=29% Similarity=0.549 Sum_probs=55.1
Q ss_pred ccccCCCcccccCC----CCcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccC
Q 037352 5 IMEKMCPSCVSKDH----HMIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHL 73 (189)
Q Consensus 5 ~~~~~~~~~~~~~~----~~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L 73 (189)
+..+++++|..++. |.|++.-|+.|||++|+-+...... .|..||..|| |++.||.+||.+.|
T Consensus 37 l~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~----qwrtIa~i~g--r~~~qc~eRy~~ll 103 (617)
T KOG0050|consen 37 LNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPT----QWRTIADIMG--RTSQQCLERYNNLL 103 (617)
T ss_pred HhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCC----ccchHHHHhh--hhHHHHHHHHHHHH
Confidence 45677888875543 7799999999999999999999998 9999999996 99999999997664
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.56 E-value=8.1e-05 Score=65.73 Aligned_cols=48 Identities=17% Similarity=0.356 Sum_probs=43.0
Q ss_pred CccCCCCCHHHHHHHHHHhh-cC-CccccccccCCCCCHHHHHHHHHHhh
Q 037352 76 NIRRGDFTLEEDELIINLCR-AG-SKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 76 ~~~~~~WT~eEd~~L~~~v~-~g-~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.+-...||.+|+..|++++. || ++|..||.+++.||..+|+.+|..++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHH
Confidence 34556899999999999999 87 67999999999999999999998766
No 27
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.55 E-value=0.00016 Score=47.00 Aligned_cols=45 Identities=18% Similarity=0.235 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHhh-cCC-cc---ccccccCC-CC-CHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-AGS-KW---TNIGLLLP-GR-THKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~g~-~W---~~Ia~~l~-gR-t~~q~k~rw~~~l 123 (189)
+-.||+||...+++++. +|. +| ..|+..|. .+ |..||+.+.+.+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 45799999999999999 886 99 99999874 45 9999999987665
No 28
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.42 E-value=3.6e-05 Score=68.43 Aligned_cols=46 Identities=24% Similarity=0.471 Sum_probs=43.2
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCccccccccc
Q 037352 22 RRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNH 72 (189)
Q Consensus 22 kkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~ 72 (189)
....||.+|..+|++.|+.||. +|.+||.++| +++..||..+|.+.
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 6679999999999999999999 9999999998 79999999999864
No 29
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.37 E-value=5.8e-05 Score=68.57 Aligned_cols=47 Identities=23% Similarity=0.468 Sum_probs=43.3
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCccccccccc
Q 037352 21 IRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNH 72 (189)
Q Consensus 21 lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~ 72 (189)
.-++.||.+|+-+|+++|+.||. +|.+||.++| +||..||..++.+.
T Consensus 251 ~~~~~WT~qE~lLLLE~ie~y~d----dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIEMYGD----DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHHHhcc----cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 45788999999999999999999 9999999998 79999999998764
No 30
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.30 E-value=0.00044 Score=55.74 Aligned_cols=94 Identities=21% Similarity=0.355 Sum_probs=67.4
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCCccccccccCCc--cCCCcccccccccC-CCCc--------------------cCCC
Q 037352 25 FWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLL--RCGKSCHDRWFNHL-NPNI--------------------RRGD 81 (189)
Q Consensus 25 ~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~--Rt~~qc~~Rw~~~L-~p~~--------------------~~~~ 81 (189)
+|++++|-.|+.+|.. |. +-..|+..+.+. -|-..+.+||...| +|.+ .+.+
T Consensus 1 rW~~~DDl~Li~av~~-~~----~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kal 75 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TN----DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKAL 75 (199)
T ss_pred CCCchhhHHHHHHHHH-hc----CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCC
Confidence 5999999999999964 44 667777654332 36667788998765 3322 2468
Q ss_pred CCHHHHHHHHHHhh-cCC---ccccccc----cC-CCCCHHHHHHHHHHhh
Q 037352 82 FTLEEDELIINLCR-AGS---KWTNIGL----LL-PGRTHKDVMNYCKTSY 123 (189)
Q Consensus 82 WT~eEd~~L~~~v~-~g~---~W~~Ia~----~l-~gRt~~q~k~rw~~~l 123 (189)
||.+|+++|..... ... .+.+|-. .| ++||..++.++|..+.
T Consensus 76 fS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmk 126 (199)
T PF13325_consen 76 FSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMK 126 (199)
T ss_pred CCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHH
Confidence 99999999999765 432 3555532 34 7899999999998654
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.02 E-value=0.00062 Score=62.00 Aligned_cols=46 Identities=13% Similarity=0.244 Sum_probs=42.6
Q ss_pred cCCCCCHHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 78 RRGDFTLEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 78 ~~~~WT~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
....||.+|..+|++++. ||..|.+||.++.+||..||--+|..+=
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~LP 298 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRLP 298 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhcC
Confidence 456899999999999999 9999999999999999999999997654
No 32
>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=97.00 E-value=0.00053 Score=45.71 Aligned_cols=45 Identities=22% Similarity=0.409 Sum_probs=31.6
Q ss_pred CCCCCHHHHHHHHHHhh-c--------CCc-cccccccCC-CCCHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-A--------GSK-WTNIGLLLP-GRTHKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~--------g~~-W~~Ia~~l~-gRt~~q~k~rw~~~l 123 (189)
+.+||.+||.+|++.|. + |+. |.+++..-+ .+|-...++||...|
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L 57 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHL 57 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 45899999999999994 3 222 999999877 999999999998777
No 33
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.92 E-value=0.00058 Score=60.97 Aligned_cols=44 Identities=11% Similarity=0.184 Sum_probs=41.4
Q ss_pred CCCCHHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 80 GDFTLEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 80 ~~WT~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.+||.+|..+|++.++ ||..|.+||.+++.+|..||--||-.+=
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LP 324 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLP 324 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCC
Confidence 4899999999999999 9999999999999999999999997653
No 34
>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=96.84 E-value=0.00026 Score=55.00 Aligned_cols=52 Identities=33% Similarity=0.504 Sum_probs=42.1
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCC---CccccccccCCccCCCcccccccccCC
Q 037352 21 IRRGFWTGEEDERLKSFILLNGEEGGW---NWEDVPRGAGLLRCGKSCHDRWFNHLN 74 (189)
Q Consensus 21 lkkg~WT~eED~~L~~~v~~~g~~~~~---~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~ 74 (189)
.+.-.||.|||.+|.+.|-.|-..|+. .+..|+..++ ||+..|.-||..++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VR 56 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVR 56 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHH
Confidence 466789999999999999999443321 4677888885 999999999998876
No 35
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.49 E-value=0.0023 Score=44.44 Aligned_cols=49 Identities=29% Similarity=0.371 Sum_probs=33.9
Q ss_pred CCCCHHHHHHHHHHhh-c------C--C------ccccccccC----CCCCHHHHHHHHHHhhhhhhhhh
Q 037352 80 GDFTLEEDELIINLCR-A------G--S------KWTNIGLLL----PGRTHKDVMNYCKTSYMRNKMSN 130 (189)
Q Consensus 80 ~~WT~eEd~~L~~~v~-~------g--~------~W~~Ia~~l----~gRt~~q~k~rw~~~l~k~~~~~ 130 (189)
..||.+|...||+++. . + + .|..||..| ..||..||+++|.++. +.+..
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~--~~Yk~ 69 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK--KKYKK 69 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH--HHHHC
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH--HHHHH
Confidence 4799999999998875 2 1 1 399999977 3699999999999877 55543
No 36
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.41 E-value=0.0016 Score=51.21 Aligned_cols=47 Identities=21% Similarity=0.266 Sum_probs=37.7
Q ss_pred ccCCCCCHHHHHHHHHHhh-c---CCc----cccccccCCCCCHHHHHHHHHHhhh
Q 037352 77 IRRGDFTLEEDELIINLCR-A---GSK----WTNIGLLLPGRTHKDVMNYCKTSYM 124 (189)
Q Consensus 77 ~~~~~WT~eEd~~L~~~v~-~---g~~----W~~Ia~~l~gRt~~q~k~rw~~~l~ 124 (189)
..++.||.|+|.+|-+.|- + |+. ...++..| +||..+|..|||+.++
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 3467899999999987776 5 332 56667777 9999999999999993
No 37
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.38 E-value=0.00042 Score=48.20 Aligned_cols=49 Identities=22% Similarity=0.455 Sum_probs=32.9
Q ss_pred CCCCHHHHHHHHHHHHH------hC---CCCC-CCcccccccc---CCccCCCccccccccc
Q 037352 24 GFWTGEEDERLKSFILL------NG---EEGG-WNWEDVPRGA---GLLRCGKSCHDRWFNH 72 (189)
Q Consensus 24 g~WT~eED~~L~~~v~~------~g---~~~~-~~W~~Ia~~~---~~~Rt~~qc~~Rw~~~ 72 (189)
..||.+|...|+.++.. ++ .... .-|..||..| |..||+.||+.+|.+.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 46999999999999987 11 1111 1599999985 6679999999999864
No 38
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.02 E-value=0.0011 Score=44.25 Aligned_cols=54 Identities=24% Similarity=0.399 Sum_probs=33.1
Q ss_pred cCCCCHHHHHHHHHHHHHhCCC-----CCCCccccccccCCccCCCcccccccccCCCC
Q 037352 23 RGFWTGEEDERLKSFILLNGEE-----GGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPN 76 (189)
Q Consensus 23 kg~WT~eED~~L~~~v~~~g~~-----~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~ 76 (189)
+.+||.+||+.|...|..+... |+--|..++..-...+|-.+-++||...|.+.
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 4579999999999999765221 22248888888644789999999999988764
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.88 E-value=0.0016 Score=55.75 Aligned_cols=51 Identities=24% Similarity=0.405 Sum_probs=45.8
Q ss_pred CcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCC
Q 037352 20 MIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLN 74 (189)
Q Consensus 20 ~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~ 74 (189)
+|---.|+..|+-+|++.....|- | ||..||..+| .|+...|+++|..++.
T Consensus 60 pI~~e~WgadEEllli~~~~TlGl-G--NW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 60 PIGEEGWGADEELLLIECLDTLGL-G--NWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred cccCCCcCchHHHHHHHHHHhcCC-C--cHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 345556999999999999999999 8 9999999999 7999999999988765
No 40
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.77 E-value=0.0012 Score=51.89 Aligned_cols=53 Identities=30% Similarity=0.501 Sum_probs=40.9
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCC---CccccccccCCccCCCcccccccccCCC
Q 037352 21 IRRGFWTGEEDERLKSFILLNGEEGGW---NWEDVPRGAGLLRCGKSCHDRWFNHLNP 75 (189)
Q Consensus 21 lkkg~WT~eED~~L~~~v~~~g~~~~~---~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p 75 (189)
.++..||.|||.+|-+.|..|+..++. -...++..+ +|++.+|..||..++..
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L--~rt~aac~fRwNs~vrk 58 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL--KRTAAACGFRWNSVVRK 58 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH--hhhHHHHHhHHHHHHHH
Confidence 577889999999999999999775533 234445556 49999999999766653
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.56 E-value=0.023 Score=48.91 Aligned_cols=45 Identities=18% Similarity=0.406 Sum_probs=40.4
Q ss_pred CCCCCHHHHHHHHHHhh-cC-CccccccccCCCCCHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-AG-SKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~g-~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
...|+.+|+.+|++... .| ++|..||.+++.|+...||.+|....
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 45799999999999999 76 67999999999999999999997665
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.16 E-value=0.029 Score=38.02 Aligned_cols=45 Identities=24% Similarity=0.415 Sum_probs=37.2
Q ss_pred CCCCCHHHHHHHHHHhh-c-----CC------------ccccccccC-----CCCCHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-A-----GS------------KWTNIGLLL-----PGRTHKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~-----g~------------~W~~Ia~~l-----~gRt~~q~k~rw~~~l 123 (189)
...||.+|...|++++. + |. -|..|+..| +.||..+++.+|.++.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 35799999999999987 5 31 299999865 3599999999999876
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.02 E-value=0.0041 Score=42.29 Aligned_cols=51 Identities=20% Similarity=0.252 Sum_probs=38.6
Q ss_pred cCCCCHHHHHHHHHHHHHh-----CCC--------CCCCcccccccc----CCccCCCcccccccccC
Q 037352 23 RGFWTGEEDERLKSFILLN-----GEE--------GGWNWEDVPRGA----GLLRCGKSCHDRWFNHL 73 (189)
Q Consensus 23 kg~WT~eED~~L~~~v~~~-----g~~--------~~~~W~~Ia~~~----~~~Rt~~qc~~Rw~~~L 73 (189)
+..||.+|.+.|+++|.+| |.. ..--|..|+..| |..|+..|++..|.++.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 5679999999999999987 310 011799999875 22589999999998753
No 44
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=94.69 E-value=0.054 Score=47.67 Aligned_cols=75 Identities=17% Similarity=0.300 Sum_probs=57.0
Q ss_pred CccccccccCCccCCCcccccccccCCCC-------------------------ccCCCCCHHHHHHHHHHhh-cCCccc
Q 037352 48 NWEDVPRGAGLLRCGKSCHDRWFNHLNPN-------------------------IRRGDFTLEEDELIINLCR-AGSKWT 101 (189)
Q Consensus 48 ~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~-------------------------~~~~~WT~eEd~~L~~~v~-~g~~W~ 101 (189)
.|.-+.-.. +.|...--..+|....++. ++...||.+|-..|+++.+ |.-+|-
T Consensus 75 ~W~w~pFtn-~aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEYe~~l~dn~WskeETD~LF~lck~fDLRf~ 153 (445)
T KOG2656|consen 75 PWKWVPFTN-SARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCC-ccccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 566555444 3566666666776653221 1235699999999999999 999999
Q ss_pred ccccc-----CCC-CCHHHHHHHHHHhh
Q 037352 102 NIGLL-----LPG-RTHKDVMNYCKTSY 123 (189)
Q Consensus 102 ~Ia~~-----l~g-Rt~~q~k~rw~~~l 123 (189)
.||.. ++. ||-.++|.||+...
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHH
Confidence 99997 655 99999999999988
No 45
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=92.41 E-value=0.13 Score=44.75 Aligned_cols=54 Identities=15% Similarity=0.191 Sum_probs=40.6
Q ss_pred CCCCCHHHHHHHHHHhh-c----------CCccccccccC----CCCCHHHHHHHHHHhhhhhhhhhcC
Q 037352 79 RGDFTLEEDELIINLCR-A----------GSKWTNIGLLL----PGRTHKDVMNYCKTSYMRNKMSNRG 132 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~----------g~~W~~Ia~~l----~gRt~~q~k~rw~~~l~k~~~~~~~ 132 (189)
...|+.+|-..||++.. . +..|..||..+ .-||+.||+++|.++.++-+-.+.+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~ 122 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAK 122 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 36899999999999875 2 34599999955 2499999999999988333333333
No 46
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=92.20 E-value=0.23 Score=49.29 Aligned_cols=95 Identities=12% Similarity=0.295 Sum_probs=68.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccc-------------------------------------
Q 037352 25 FWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHD------------------------------------- 67 (189)
Q Consensus 25 ~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~------------------------------------- 67 (189)
.||.-+=..++.+..+||. . +-..||..|+ +++...++.
T Consensus 826 ~w~~~~f~~f~~~~~~~gr-~--~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~ 901 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGR-N--DIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMK 901 (1033)
T ss_pred cccHHHHHHHHHHHHHhCH-h--HHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3777777888888889998 5 7889999885 566666542
Q ss_pred -----------ccccc-C-CCCccCCCCCHHHHHHHHHHhh-cC-Cccccccc------------cCCCCCHHHHHHHHH
Q 037352 68 -----------RWFNH-L-NPNIRRGDFTLEEDELIINLCR-AG-SKWTNIGL------------LLPGRTHKDVMNYCK 120 (189)
Q Consensus 68 -----------Rw~~~-L-~p~~~~~~WT~eEd~~L~~~v~-~g-~~W~~Ia~------------~l~gRt~~q~k~rw~ 120 (189)
-|... + .+..++..+|++||..|+-++. || .+|..|-. .|..||...+..|.+
T Consensus 902 ~~~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~ 981 (1033)
T PLN03142 902 AIGKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCD 981 (1033)
T ss_pred HHHHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHH
Confidence 11110 0 1233455799999999998887 76 45988832 235799999999999
Q ss_pred Hhh
Q 037352 121 TSY 123 (189)
Q Consensus 121 ~~l 123 (189)
.++
T Consensus 982 ~l~ 984 (1033)
T PLN03142 982 TLI 984 (1033)
T ss_pred HHH
Confidence 988
No 47
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.57 E-value=0.25 Score=43.52 Aligned_cols=44 Identities=18% Similarity=0.197 Sum_probs=41.0
Q ss_pred CCCCHHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 80 GDFTLEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 80 ~~WT~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.+||..|-++...+.. .|..+..|+..||.|...||+-+|..--
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Ee 410 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEE 410 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHh
Confidence 3899999999999999 9999999999999999999999997755
No 48
>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=90.04 E-value=0.18 Score=37.50 Aligned_cols=48 Identities=23% Similarity=0.450 Sum_probs=36.7
Q ss_pred CccCCCCCHHHHHHHHHHhh-cCC----ccccccccC------------CCCCHHHHHHHHHHhh
Q 037352 76 NIRRGDFTLEEDELIINLCR-AGS----KWTNIGLLL------------PGRTHKDVMNYCKTSY 123 (189)
Q Consensus 76 ~~~~~~WT~eEd~~L~~~v~-~g~----~W~~Ia~~l------------~gRt~~q~k~rw~~~l 123 (189)
..++..+|++||..|+-++. +|- .|..|-..+ ..||+..+..|.+.++
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi 110 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLI 110 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHH
Confidence 45567899999999999988 876 687775532 3699999999999988
No 49
>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=88.76 E-value=0.48 Score=32.95 Aligned_cols=43 Identities=30% Similarity=0.431 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHhh-c---CC----------ccccccccCC---C--CCHHHHHHHHHHhh
Q 037352 81 DFTLEEDELIINLCR-A---GS----------KWTNIGLLLP---G--RTHKDVMNYCKTSY 123 (189)
Q Consensus 81 ~WT~eEd~~L~~~v~-~---g~----------~W~~Ia~~l~---g--Rt~~q~k~rw~~~l 123 (189)
.||++++..|++++. . |+ .|..|+..|. | .+..||++||..+-
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk 62 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLK 62 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHH
Confidence 499999999998874 2 32 2888988762 2 57789999997655
No 50
>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=86.70 E-value=0.69 Score=32.25 Aligned_cols=23 Identities=43% Similarity=0.702 Sum_probs=14.3
Q ss_pred cccCCCCHHHHHHH--------HHHHHHhCC
Q 037352 21 IRRGFWTGEEDERL--------KSFILLNGE 43 (189)
Q Consensus 21 lkkg~WT~eED~~L--------~~~v~~~g~ 43 (189)
-..|-||+++|+.| .+++++||.
T Consensus 45 n~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 45 NMPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp T-TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 45889999999999 456678875
No 51
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=85.70 E-value=0.34 Score=42.73 Aligned_cols=63 Identities=16% Similarity=0.230 Sum_probs=49.2
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCccccccccc--CCCC-----c-cCCCCCHHHHHH
Q 037352 22 RRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNH--LNPN-----I-RRGDFTLEEDEL 89 (189)
Q Consensus 22 kkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~--L~p~-----~-~~~~WT~eEd~~ 89 (189)
.--+||.+|-++...+....|. ++..||+.+ |+|..+|+...|.+- .+|. + .+-|+..+|-..
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGt----dF~LIs~lf-P~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k 434 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGT----DFSLISSLF-PNRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNK 434 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcc----hHHHHHHhc-CchhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhh
Confidence 3457999999999999999999 999999999 589999999988763 2331 1 234677777543
No 52
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=85.32 E-value=0.27 Score=42.71 Aligned_cols=50 Identities=30% Similarity=0.363 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHHh------CCCCCCCccccccc---cCCccCCCcccccccccC
Q 037352 24 GFWTGEEDERLKSFILLN------GEEGGWNWEDVPRG---AGLLRCGKSCHDRWFNHL 73 (189)
Q Consensus 24 g~WT~eED~~L~~~v~~~------g~~~~~~W~~Ia~~---~~~~Rt~~qc~~Rw~~~L 73 (189)
..|+.+|-..|+.+.... |..+..-|..||.. .|..|++.||+.+|.++.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 789999999999987633 22122279999995 356699999999998753
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=85.26 E-value=1.2 Score=27.61 Aligned_cols=39 Identities=21% Similarity=0.244 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 84 LEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 84 ~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
++++..++.++. .|-.+.+||..+ |.|...|+.+....+
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRAR 51 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 456677788877 899999999999 999999999887665
No 54
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=83.54 E-value=1.5 Score=35.50 Aligned_cols=43 Identities=16% Similarity=0.152 Sum_probs=36.4
Q ss_pred CCCHHHHHHHHHHhhcCCccccccccC---CCCCHHHHHHHHHHhh
Q 037352 81 DFTLEEDELIINLCRAGSKWTNIGLLL---PGRTHKDVMNYCKTSY 123 (189)
Q Consensus 81 ~WT~eEd~~L~~~v~~g~~W~~Ia~~l---~gRt~~q~k~rw~~~l 123 (189)
.|++.+|-.|+.+|..|+.-..|+..+ -.-|-..|..||+.+|
T Consensus 1 rW~~~DDl~Li~av~~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~ll 46 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTNDLESVHLGVKFSCKFTLQEIEERWYALL 46 (199)
T ss_pred CCCchhhHHHHHHHHHhcCHHHHHccCCcCCcCcHHHHHHHHHHHH
Confidence 499999999999999888877777743 3468899999999988
No 55
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=82.66 E-value=1.6 Score=39.45 Aligned_cols=45 Identities=20% Similarity=0.291 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
...||.||-.++-+++. ||.++.+|-+.||.|+-..+...|.+.-
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~K 232 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWK 232 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHH
Confidence 45799999999999999 9999999999999999999999887754
No 56
>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=81.47 E-value=1.2 Score=32.99 Aligned_cols=37 Identities=22% Similarity=0.389 Sum_probs=29.1
Q ss_pred CcccCCCCHHHHHHHHHHHHHhCCCCCCCcccccccc
Q 037352 20 MIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGA 56 (189)
Q Consensus 20 ~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~ 56 (189)
.-++..||.+||.-|+-++.+||-...-.|..|-..+
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 4678899999999999999999984333899998875
No 57
>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=77.43 E-value=3.2 Score=25.32 Aligned_cols=38 Identities=21% Similarity=0.231 Sum_probs=30.5
Q ss_pred HHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 85 EEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 85 eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
+++..++.++- .|-.+.+||..| |-|...|+.+....+
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al 45 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRAL 45 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHH
Confidence 45566666666 788899999999 889999999988877
No 58
>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=75.83 E-value=1.9 Score=33.67 Aligned_cols=40 Identities=23% Similarity=0.231 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHH
Q 037352 81 DFTLEEDELIINLCRAGSKWTNIGLLLPGRTHKDVMNYCK 120 (189)
Q Consensus 81 ~WT~eEd~~L~~~v~~g~~W~~Ia~~l~gRt~~q~k~rw~ 120 (189)
.||+|+.+.|.+|..-|-.=++||..|+|.|.+.|--+-+
T Consensus 2 ~Wtde~~~~L~~lw~~G~SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEGLSASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCHHHHHHHHHHHHcCCCHHHHHHHhCCcchhhhhhhhh
Confidence 5999999999999998999999999998788888776554
No 59
>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=72.59 E-value=9.6 Score=33.04 Aligned_cols=49 Identities=14% Similarity=0.413 Sum_probs=37.7
Q ss_pred CCCCCHHHHHHHHHHhh--cCCcc---ccccccCCCCCHHHHHHHHHHhhhhhhhh
Q 037352 79 RGDFTLEEDELIINLCR--AGSKW---TNIGLLLPGRTHKDVMNYCKTSYMRNKMS 129 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~--~g~~W---~~Ia~~l~gRt~~q~k~rw~~~l~k~~~~ 129 (189)
-..||..|...|+.+.+ .|... .+|++.++||+..+|++-- ..| |.++.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl-~~L-K~rva 74 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFL-QQL-KGRVA 74 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHH-HHH-HHHHH
Confidence 35899999999999988 46554 5788899999999999854 445 44443
No 60
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=68.40 E-value=1.8 Score=41.33 Aligned_cols=44 Identities=11% Similarity=0.231 Sum_probs=39.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccc
Q 037352 23 RGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFN 71 (189)
Q Consensus 23 kg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~ 71 (189)
--.||+.|-.+..+++-.|.. ++..|+.++. ++|..||-+.|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K----DF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK----DFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc----cHHHHHHHhc-cccHHHHHHHHHH
Confidence 456999999999999999998 9999999995 8999999887653
No 61
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=66.74 E-value=5.8 Score=38.07 Aligned_cols=44 Identities=14% Similarity=0.139 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHh
Q 037352 79 RGDFTLEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTS 122 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~ 122 (189)
...||+.|-.+.-+++. |..++-.|++.++++|-.||-..|+.-
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 35899999999999988 999999999999999999999988753
No 62
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=64.75 E-value=9.9 Score=35.57 Aligned_cols=46 Identities=24% Similarity=0.312 Sum_probs=41.3
Q ss_pred cCCCCCHHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 78 RRGDFTLEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 78 ~~~~WT~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
..+.||.+|-++.-.+.. .|.+.+.|+..+|+|+..|||.+|..--
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~eE 454 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKEE 454 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhhh
Confidence 346899999999999999 9999999999999999999999996533
No 63
>smart00595 MADF subfamily of SANT domain.
Probab=63.87 E-value=3.4 Score=28.24 Aligned_cols=23 Identities=22% Similarity=0.322 Sum_probs=20.1
Q ss_pred cccccccCCCCCHHHHHHHHHHhh
Q 037352 100 WTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 100 W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
|..||..| |-+..+|+.+|+++-
T Consensus 30 W~~Ia~~l-~~~~~~~~~kw~~LR 52 (89)
T smart00595 30 WEEIAEEL-GLSVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHH-CcCHHHHHHHHHHHH
Confidence 99999999 449999999998764
No 64
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=62.71 E-value=4.2 Score=24.48 Aligned_cols=36 Identities=31% Similarity=0.341 Sum_probs=19.3
Q ss_pred CCCHHHHHHHHHHhhcCCccccccccCCCCCHHHHHH
Q 037352 81 DFTLEEDELIINLCRAGSKWTNIGLLLPGRTHKDVMN 117 (189)
Q Consensus 81 ~WT~eEd~~L~~~v~~g~~W~~Ia~~l~gRt~~q~k~ 117 (189)
.+|.+|-..|..++..|..=.+||+.| ||+...|.+
T Consensus 4 ~Lt~~eR~~I~~l~~~G~s~~~IA~~l-g~s~sTV~r 39 (44)
T PF13936_consen 4 HLTPEERNQIEALLEQGMSIREIAKRL-GRSRSTVSR 39 (44)
T ss_dssp --------HHHHHHCS---HHHHHHHT-T--HHHHHH
T ss_pred chhhhHHHHHHHHHHcCCCHHHHHHHH-CcCcHHHHH
Confidence 577888888877776888889999999 999988765
No 65
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=61.73 E-value=10 Score=35.67 Aligned_cols=45 Identities=18% Similarity=0.330 Sum_probs=38.0
Q ss_pred CCCCCHHHHHHHHHHhh-cCCccccc----------cccCCCCCHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-AGSKWTNI----------GLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~g~~W~~I----------a~~l~gRt~~q~k~rw~~~l 123 (189)
+..||-.|+.-...++. +|.++..| -..+.-+|..|++.+|+.++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 56899999999999999 99999888 22344578889999998888
No 66
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=61.15 E-value=3.8 Score=36.41 Aligned_cols=48 Identities=13% Similarity=0.169 Sum_probs=41.5
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCCCccccccc-----cCCccCCCccccccccc
Q 037352 21 IRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRG-----AGLLRCGKSCHDRWFNH 72 (189)
Q Consensus 21 lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~-----~~~~Rt~~qc~~Rw~~~ 72 (189)
+....||.+|.+.|-++...|-- .|--||.. ++..||-....+||..+
T Consensus 128 l~dn~WskeETD~LF~lck~fDL----Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFDL----RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hccccccHHHHHHHHHHHHhcCe----eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 55678999999999999999988 99999987 66559999999998654
No 67
>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=59.12 E-value=6.7 Score=30.62 Aligned_cols=33 Identities=30% Similarity=0.485 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCCCccccccccC-CccCC
Q 037352 25 FWTGEEDERLKSFILLNGEEGGWNWEDVPRGAG-LLRCG 62 (189)
Q Consensus 25 ~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~-~~Rt~ 62 (189)
.||.|+.+.|.+|. .-|. .=.+||..|| ..|++
T Consensus 2 ~Wtde~~~~L~~lw-~~G~----SasqIA~~lg~vsRnA 35 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGL----SASQIARQLGGVSRNA 35 (162)
T ss_pred CCCHHHHHHHHHHH-HcCC----CHHHHHHHhCCcchhh
Confidence 59999999999988 3455 6699999998 44444
No 68
>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=59.05 E-value=13 Score=27.48 Aligned_cols=35 Identities=26% Similarity=0.278 Sum_probs=27.6
Q ss_pred HHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 88 ELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 88 ~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
..++.+.- .|-.+.+||..+ |.|...|+++.+...
T Consensus 119 r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~ 154 (161)
T TIGR02985 119 RKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKAL 154 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 34444444 577899999999 999999999998766
No 69
>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=56.59 E-value=11 Score=22.53 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=27.2
Q ss_pred HHHHHHHHHhh-cC-CccccccccCCCCCHHHHHHHHHH
Q 037352 85 EEDELIINLCR-AG-SKWTNIGLLLPGRTHKDVMNYCKT 121 (189)
Q Consensus 85 eEd~~L~~~v~-~g-~~W~~Ia~~l~gRt~~q~k~rw~~ 121 (189)
+=|..|+.+.+ -| -.+.+||..+ |=|...|..|...
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHH
Confidence 44778888887 44 4599999999 9999999999864
No 70
>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=50.33 E-value=12 Score=25.49 Aligned_cols=33 Identities=24% Similarity=0.406 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhhcCCccccccccCCCCCHHHHHH
Q 037352 84 LEEDELIINLCRAGSKWTNIGLLLPGRTHKDVMN 117 (189)
Q Consensus 84 ~eEd~~L~~~v~~g~~W~~Ia~~l~gRt~~q~k~ 117 (189)
.||-++|+..=..|.+|..+|..| |=+...|.+
T Consensus 2 ~~~v~~ll~~~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLESGRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhCCCCccCHHHHHHHc-CCCHHHHHH
Confidence 578888884333799999999999 777777655
No 71
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=45.44 E-value=23 Score=26.91 Aligned_cols=38 Identities=8% Similarity=0.089 Sum_probs=32.1
Q ss_pred HHHHHHHHHhh-cC-CccccccccCCCCCHHHHHHHHHHhh
Q 037352 85 EEDELIINLCR-AG-SKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 85 eEd~~L~~~v~-~g-~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
+-|..|+.+.+ -| ..|++||+.+ |-|...|+.|+..+.
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~ 48 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMK 48 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 56788888887 43 4599999999 999999999998777
No 72
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=45.43 E-value=17 Score=22.80 Aligned_cols=38 Identities=21% Similarity=0.261 Sum_probs=24.2
Q ss_pred CCCHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHH
Q 037352 81 DFTLEEDELIINLCRAGSKWTNIGLLLPGRTHKDVMNYC 119 (189)
Q Consensus 81 ~WT~eEd~~L~~~v~~g~~W~~Ia~~l~gRt~~q~k~rw 119 (189)
.-|..|-..|.-+++.|-.-.+||+.+ ||+..-|++.-
T Consensus 4 ~Lt~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 4 TLTDAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp ---HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred cCCHHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 356667666666666999999999999 99998877653
No 73
>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=42.30 E-value=11 Score=22.20 Aligned_cols=29 Identities=21% Similarity=0.187 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHhCCCCCCCccccccccCCccC
Q 037352 29 EEDERLKSFILLNGEEGGWNWEDVPRGAGLLRC 61 (189)
Q Consensus 29 eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt 61 (189)
=|.+.|.+++..+|- +-...|..+|.+|+
T Consensus 5 ~E~~~i~~aL~~~~g----n~~~aA~~Lgisr~ 33 (42)
T PF02954_consen 5 FEKQLIRQALERCGG----NVSKAARLLGISRR 33 (42)
T ss_dssp HHHHHHHHHHHHTTT-----HHHHHHHHTS-HH
T ss_pred HHHHHHHHHHHHhCC----CHHHHHHHHCCCHH
Confidence 377889999999986 88999999986554
No 74
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=42.00 E-value=32 Score=30.61 Aligned_cols=43 Identities=14% Similarity=0.106 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHhh-cCCccccccc-cCCCCCHHHHHHHHHHh
Q 037352 80 GDFTLEEDELIINLCR-AGSKWTNIGL-LLPGRTHKDVMNYCKTS 122 (189)
Q Consensus 80 ~~WT~eEd~~L~~~v~-~g~~W~~Ia~-~l~gRt~~q~k~rw~~~ 122 (189)
..|+++|-...-+-++ ||.++..|.+ .++.|+--.|-..|+.-
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlW 322 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLW 322 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHh
Confidence 4799999999999999 9999999977 78999999999887653
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=39.33 E-value=20 Score=24.84 Aligned_cols=28 Identities=29% Similarity=0.578 Sum_probs=21.7
Q ss_pred HHHHHHHhh-cCCccccccccCCCCCHHHH
Q 037352 87 DELIINLCR-AGSKWTNIGLLLPGRTHKDV 115 (189)
Q Consensus 87 d~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~ 115 (189)
|+.|..+.. .|..|..+|..| |=|..+|
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 456777778 899999999999 6665544
No 76
>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=38.94 E-value=35 Score=24.36 Aligned_cols=27 Identities=22% Similarity=0.274 Sum_probs=23.1
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|..+.+||+.+ |=+...|+++....+
T Consensus 125 ~g~s~~eIA~~l-~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 125 EGLSYKEIAEIL-GISVGTVKRRLKRAR 151 (158)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 578899999999 779999999887766
No 77
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=38.28 E-value=26 Score=24.21 Aligned_cols=30 Identities=17% Similarity=0.285 Sum_probs=22.5
Q ss_pred HHHHHHHhh-cCCccccccccCCCCCHHHHHH
Q 037352 87 DELIINLCR-AGSKWTNIGLLLPGRTHKDVMN 117 (189)
Q Consensus 87 d~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~ 117 (189)
|..|..+.. .|..|..+|..| |=+..+|.+
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 455666667 899999999999 767665443
No 78
>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=37.63 E-value=14 Score=24.36 Aligned_cols=24 Identities=21% Similarity=0.193 Sum_probs=19.6
Q ss_pred cccccccCCC-CCHHHHHHHHHHhh
Q 037352 100 WTNIGLLLPG-RTHKDVMNYCKTSY 123 (189)
Q Consensus 100 W~~Ia~~l~g-Rt~~q~k~rw~~~l 123 (189)
|..||..|++ -+..+|+.+|.++.
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr 53 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLR 53 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHH
Confidence 9999998853 57788999998765
No 79
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=37.55 E-value=36 Score=26.18 Aligned_cols=39 Identities=10% Similarity=0.023 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhh-c-CCccccccccCCCCCHHHHHHHHHHhh
Q 037352 84 LEEDELIINLCR-A-GSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 84 ~eEd~~L~~~v~-~-g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.+-|.+|+.+.+ - .-.|++||+.+ |=|...|+.|++.+.
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~ 53 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLE 53 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 455777887777 3 45699999999 999999999998777
No 80
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=36.71 E-value=35 Score=26.67 Aligned_cols=35 Identities=17% Similarity=0.188 Sum_probs=27.5
Q ss_pred HHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 88 ELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 88 ~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
..++.+.. .|-.+.+||..+ |-|...++.+|...-
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 34444444 588999999999 999999999997643
No 81
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=36.31 E-value=9.5 Score=29.04 Aligned_cols=42 Identities=12% Similarity=0.135 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCC
Q 037352 29 EEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNP 75 (189)
Q Consensus 29 eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p 75 (189)
+-|.+|+.+.+..|. - .|..||+.+| -+...|+.|+....+.
T Consensus 9 ~~D~~Il~~Lq~d~R-~--s~~eiA~~lg--lS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 9 NLDRGILEALMENAR-T--PYAELAKQFG--VSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHHHcCC-C--CHHHHHHHHC--cCHHHHHHHHHHHHHC
Confidence 578899999988877 5 9999999997 6888898888765443
No 82
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=35.74 E-value=42 Score=25.21 Aligned_cols=27 Identities=15% Similarity=0.169 Sum_probs=23.2
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-+...|+.+....+
T Consensus 143 ~~~s~~eIA~~l-gis~~tV~~~l~ra~ 169 (182)
T PRK09652 143 EGLSYEEIAEIM-GCPIGTVRSRIFRAR 169 (182)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 577899999999 889999998887655
No 83
>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=35.68 E-value=16 Score=28.36 Aligned_cols=31 Identities=16% Similarity=0.288 Sum_probs=25.7
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCCCcccccccc
Q 037352 22 RRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGA 56 (189)
Q Consensus 22 kkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~ 56 (189)
+...=|..|.+-|..||++||. |+...|.-.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGd----Dy~aMarD~ 143 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGD----DYKAMARDR 143 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCc----cHHHHhccC
Confidence 4566899999999999999998 887777653
No 84
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=34.63 E-value=46 Score=25.95 Aligned_cols=27 Identities=19% Similarity=0.300 Sum_probs=23.4
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-+...|++|.....
T Consensus 149 ~g~s~~EIA~~l-g~s~~tV~~rl~rar 175 (192)
T PRK09643 149 QGYSVADAARML-GVAEGTVKSRCARGR 175 (192)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 577899999999 999999999996655
No 85
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=33.33 E-value=15 Score=33.35 Aligned_cols=43 Identities=14% Similarity=0.244 Sum_probs=36.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCccccccc
Q 037352 23 RGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWF 70 (189)
Q Consensus 23 kg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~ 70 (189)
...||.||--++-++...||. ++.+|-+.|+ .|+-..+.+.|.
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK----~F~kIrq~LP-~rsLaSlvqyYy 229 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGK----DFHKIRQALP-HRSLASLVQYYY 229 (534)
T ss_pred cccchHHHHHHHHHHHHHhcc----cHHHHHHHcc-CccHHHHHHHHH
Confidence 456999999999999999999 9999999994 688777766554
No 86
>PRK04217 hypothetical protein; Provisional
Probab=33.24 E-value=55 Score=23.89 Aligned_cols=41 Identities=20% Similarity=0.153 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 81 DFTLEEDELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 81 ~WT~eEd~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.-|.+| ..++.+.. .|-...+||+.+ |-|...|+.+++...
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RAr 83 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSAR 83 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 455666 56667776 788999999999 999999999998765
No 87
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.67 E-value=29 Score=26.65 Aligned_cols=37 Identities=24% Similarity=0.297 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHhhcCCccccccccCCCCCHHHHHH
Q 037352 81 DFTLEEDELIINLCRAGSKWTNIGLLLPGRTHKDVMN 117 (189)
Q Consensus 81 ~WT~eEd~~L~~~v~~g~~W~~Ia~~l~gRt~~q~k~ 117 (189)
.||.|.-+.|.+|-..|-.=++||..|+|=|.+.+--
T Consensus 2 nWtdERve~LkKLWseGLSASQIAaQLGGVsRnAVIG 38 (169)
T COG5352 2 NWTDERVETLKKLWSEGLSASQIAAQLGGVSRNAVIG 38 (169)
T ss_pred CchHHHHHHHHHHHHcccCHHHHHHHhcCcchhhhhe
Confidence 5999999999999887777799999999988776544
No 88
>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=31.65 E-value=46 Score=22.73 Aligned_cols=35 Identities=14% Similarity=0.195 Sum_probs=24.0
Q ss_pred HHHHHhh-cCC--------ccccccccCCC---CC--HHHHHHHHHHhh
Q 037352 89 LIINLCR-AGS--------KWTNIGLLLPG---RT--HKDVMNYCKTSY 123 (189)
Q Consensus 89 ~L~~~v~-~g~--------~W~~Ia~~l~g---Rt--~~q~k~rw~~~l 123 (189)
.|..+|. .|+ .|..||..|+- -+ ..+++..|..+|
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L 88 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYL 88 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHT
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHh
Confidence 3566666 553 59999998822 12 367888888776
No 89
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.63 E-value=51 Score=24.63 Aligned_cols=27 Identities=19% Similarity=0.260 Sum_probs=22.9
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-|...|+++.....
T Consensus 140 ~~~~~~eIA~~l-gis~~tv~~~~~ra~ 166 (179)
T PRK11924 140 EGLSYREIAEIL-GVPVGTVKSRLRRAR 166 (179)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 477799999999 889999999887755
No 90
>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=31.56 E-value=81 Score=24.38 Aligned_cols=45 Identities=13% Similarity=0.041 Sum_probs=36.9
Q ss_pred CCCCCHHHHHHHHHHhh-cCCccccccccC----CCCCHHHHHHHHHHhh
Q 037352 79 RGDFTLEEDELIINLCR-AGSKWTNIGLLL----PGRTHKDVMNYCKTSY 123 (189)
Q Consensus 79 ~~~WT~eEd~~L~~~v~-~g~~W~~Ia~~l----~gRt~~q~k~rw~~~l 123 (189)
...-|..|...|..|+. ||.++..++... --.|..||+.+...+.
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 44678999999999999 999999998844 2589999999876543
No 91
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=30.79 E-value=53 Score=25.00 Aligned_cols=27 Identities=11% Similarity=0.006 Sum_probs=22.7
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|....+||..| |-|...++++.+...
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar 177 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGR 177 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 467799999999 899999999887655
No 92
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=30.22 E-value=29 Score=32.56 Aligned_cols=48 Identities=15% Similarity=0.205 Sum_probs=42.6
Q ss_pred CCcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccc
Q 037352 19 HMIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFN 71 (189)
Q Consensus 19 ~~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~ 71 (189)
.....++||.+|-++...+....|. +...|+..+ ++|+..|++..|..
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~gs----~~slis~l~-p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERGS----DFSLISNLF-PLRDRKQIKAKFKK 452 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhcc----ccccccccc-ccccHHHHHHHHhh
Confidence 4467889999999999999999998 999999999 48999999887754
No 93
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=30.01 E-value=11 Score=29.01 Aligned_cols=44 Identities=11% Similarity=0.135 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCC
Q 037352 28 GEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPN 76 (189)
Q Consensus 28 ~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~ 76 (189)
.+-|.+|+.+.+..|. - .|..||+.+| =+...|+.|+....+.+
T Consensus 13 D~~D~~IL~~Lq~d~R-~--s~~eiA~~lg--lS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 13 DRIDRNILNELQKDGR-I--SNVELSKRVG--LSPTPCLERVRRLERQG 56 (164)
T ss_pred HHHHHHHHHHhccCCC-C--CHHHHHHHHC--cCHHHHHHHHHHHHHCC
Confidence 4568888888887776 4 8999999997 58888888877664443
No 94
>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=29.03 E-value=28 Score=23.71 Aligned_cols=29 Identities=24% Similarity=0.507 Sum_probs=20.9
Q ss_pred HHHHHHHhh-cCCccccccccCCCCCHHHHH
Q 037352 87 DELIINLCR-AGSKWTNIGLLLPGRTHKDVM 116 (189)
Q Consensus 87 d~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k 116 (189)
|..|..+.. .|..|.++|..| |=+..+|.
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 345566666 899999999999 66655443
No 95
>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=28.79 E-value=50 Score=25.22 Aligned_cols=26 Identities=12% Similarity=0.119 Sum_probs=22.0
Q ss_pred CCccccccccCCCCCHHHHHHHHHHhh
Q 037352 97 GSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 97 g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
|-...+||..| |=|...|+++.+...
T Consensus 154 ~~s~~EIA~~l-gis~~tv~~~l~rar 179 (190)
T TIGR02939 154 GLSYEDIARIM-DCPVGTVRSRIFRAR 179 (190)
T ss_pred CCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 66789999999 888999999887766
No 96
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=28.00 E-value=71 Score=24.55 Aligned_cols=27 Identities=15% Similarity=0.032 Sum_probs=23.2
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|....+||..| |-+...|+.+.+..+
T Consensus 154 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~ 180 (189)
T PRK09648 154 VGLSAEETAEAV-GSTPGAVRVAQHRAL 180 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 477899999999 889999999887766
No 97
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=27.80 E-value=18 Score=34.04 Aligned_cols=46 Identities=15% Similarity=0.285 Sum_probs=34.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCCCccccccccC---------CccCCCccccccccc
Q 037352 23 RGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAG---------LLRCGKSCHDRWFNH 72 (189)
Q Consensus 23 kg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~---------~~Rt~~qc~~Rw~~~ 72 (189)
|..||-.|.+..-.++.+||. ++..|-..+- .-+|..|.+.+|.+.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK----dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~ 142 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK----DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRL 142 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc----cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHH
Confidence 678999999999999999999 9999933321 125666777777554
No 98
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=27.70 E-value=46 Score=33.58 Aligned_cols=33 Identities=18% Similarity=0.378 Sum_probs=28.6
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCCCcccccccc
Q 037352 21 IRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGA 56 (189)
Q Consensus 21 lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~ 56 (189)
-++..+|.|||..|+-.+.+||- + +|..|-..+
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~-~--~~~~~~~~i 956 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGY-G--NWDELKAAF 956 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhcc-c--hHHHHHHHH
Confidence 34556999999999999999998 7 899998766
No 99
>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=27.60 E-value=36 Score=23.37 Aligned_cols=30 Identities=20% Similarity=0.378 Sum_probs=22.6
Q ss_pred HHHHHHHhh-cCCccccccccCCCCCHHHHHH
Q 037352 87 DELIINLCR-AGSKWTNIGLLLPGRTHKDVMN 117 (189)
Q Consensus 87 d~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~ 117 (189)
|..|-.+.. .|.+|..+|..| |=+..+|.+
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 345555566 899999999999 777776655
No 100
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=27.51 E-value=68 Score=22.10 Aligned_cols=35 Identities=17% Similarity=0.244 Sum_probs=24.3
Q ss_pred HHHHHhh-cCC--------ccccccccCCC-----CCHHHHHHHHHHhh
Q 037352 89 LIINLCR-AGS--------KWTNIGLLLPG-----RTHKDVMNYCKTSY 123 (189)
Q Consensus 89 ~L~~~v~-~g~--------~W~~Ia~~l~g-----Rt~~q~k~rw~~~l 123 (189)
.|..+|. .|+ .|..||..|.- ....+++..|...|
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L 84 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYL 84 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHh
Confidence 3566666 543 69999998732 23567888888777
No 101
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=27.38 E-value=30 Score=35.33 Aligned_cols=75 Identities=19% Similarity=0.213 Sum_probs=50.1
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccCCCCccCCCCCHHHHHHHHHHhh-c-CCc
Q 037352 22 RRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHLNPNIRRGDFTLEEDELIINLCR-A-GSK 99 (189)
Q Consensus 22 kkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L~p~~~~~~WT~eEd~~L~~~v~-~-g~~ 99 (189)
.-.-|..++|..|+-.|-+||- + +|..|-.---.+=+.+ ..+......+.+=..+-..|+.+.. . +.+
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGy-g--swe~Ir~Dp~L~l~dK-------i~~~e~~P~a~~L~~R~~yLls~~~~~~~~~ 1201 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGY-G--SWEAIRLDPDLGLTDK-------IFLVETVPQAKHLQRRADYLLSLLRKHDKGN 1201 (1373)
T ss_pred cccCCCchhhhhHhhhhhhccc-c--cHHHhccCccccchhh-------hcccccCCchHHHHHHHHHHHHHHhhcccCC
Confidence 4456999999999999999999 8 9998865411111111 1122224456677777788888887 5 666
Q ss_pred ccccccc
Q 037352 100 WTNIGLL 106 (189)
Q Consensus 100 W~~Ia~~ 106 (189)
|......
T Consensus 1202 ~~~~~~~ 1208 (1373)
T KOG0384|consen 1202 TPKKLKR 1208 (1373)
T ss_pred Cchhhhc
Confidence 7665543
No 102
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=27.29 E-value=94 Score=23.50 Aligned_cols=33 Identities=21% Similarity=0.211 Sum_probs=26.6
Q ss_pred HHHHhh-cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 90 IINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 90 L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
++.+.. .|-...+||..| |-+...|+.+-...+
T Consensus 127 v~~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~ 160 (172)
T PRK12523 127 AFLYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGL 160 (172)
T ss_pred HHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 334444 577899999999 999999999988877
No 103
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.20 E-value=72 Score=24.63 Aligned_cols=27 Identities=15% Similarity=0.106 Sum_probs=23.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-|...|+++.....
T Consensus 121 ~g~~~~EIA~~l-gis~~tV~~~l~Rar 147 (181)
T PRK09637 121 EGLSQKEIAEKL-GLSLSGAKSRVQRGR 147 (181)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 477899999999 899999999987665
No 104
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=27.19 E-value=69 Score=23.29 Aligned_cols=46 Identities=17% Similarity=0.131 Sum_probs=32.0
Q ss_pred cccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCccCCCcccccccccC
Q 037352 21 IRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLRCGKSCHDRWFNHL 73 (189)
Q Consensus 21 lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~Rt~~qc~~Rw~~~L 73 (189)
.++..||.|+-..++..+...|. .=..||..+|. +..++ .+|.+.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gI--s~~tl-~~W~r~y 53 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGV--AASQL-FLWRKQY 53 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCc--CHHHH-HHHHHHH
Confidence 34678999998888777777776 66889998875 33333 3465543
No 105
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=27.15 E-value=69 Score=25.65 Aligned_cols=42 Identities=21% Similarity=0.089 Sum_probs=33.3
Q ss_pred CCCCHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 80 GDFTLEEDELIINLCRAGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 80 ~~WT~eEd~~L~~~v~~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
...|+.|-+.|.-+ ..|-.=++||..| +.|...|+++..+++
T Consensus 147 ~~LT~RE~eVL~ll-a~G~snkeIA~~L-~iS~~TVk~h~~~i~ 188 (211)
T COG2197 147 ELLTPRELEVLRLL-AEGLSNKEIAEEL-NLSEKTVKTHVSNIL 188 (211)
T ss_pred CCCCHHHHHHHHHH-HCCCCHHHHHHHH-CCCHhHHHHHHHHHH
Confidence 36788887665544 4455558999999 999999999999988
No 106
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=27.15 E-value=76 Score=23.45 Aligned_cols=27 Identities=11% Similarity=0.187 Sum_probs=23.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-.-.+||..| |-+...|+++....+
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~ 147 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRAT 147 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 467789999999 899999999987766
No 107
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=27.11 E-value=76 Score=23.92 Aligned_cols=27 Identities=19% Similarity=0.087 Sum_probs=23.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-.-.+||..| |-+...|+.+....+
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~ 159 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYAL 159 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 477789999999 999999999987766
No 108
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=27.08 E-value=75 Score=24.27 Aligned_cols=27 Identities=11% Similarity=0.044 Sum_probs=23.5
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-+...|+.+....+
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~ 172 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGL 172 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 477899999999 999999999988766
No 109
>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=26.72 E-value=71 Score=24.01 Aligned_cols=27 Identities=11% Similarity=0.194 Sum_probs=22.7
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-|...|+++....+
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~ 160 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRAL 160 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 467789999999 789999999987766
No 110
>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=26.48 E-value=61 Score=23.55 Aligned_cols=23 Identities=9% Similarity=0.063 Sum_probs=16.6
Q ss_pred ccccccCCCCCHHHHHHHHHHhh
Q 037352 101 TNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 101 ~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
...+...|..|...=|.||+..+
T Consensus 53 ~~~~~~~p~HT~~sWRDR~RKfv 75 (105)
T PF09197_consen 53 KDLARKNPRHTENSWRDRYRKFV 75 (105)
T ss_dssp HHHHHHTTTS-HHHHHHHHHHTH
T ss_pred HHHHHcCCccchhHHHHHHHHHH
Confidence 44467778889988888887655
No 111
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=25.50 E-value=84 Score=24.38 Aligned_cols=27 Identities=4% Similarity=-0.025 Sum_probs=23.2
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-+...|+.|.+..+
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~ 182 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAV 182 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHH
Confidence 477789999999 999999999987766
No 112
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.36 E-value=85 Score=23.29 Aligned_cols=27 Identities=15% Similarity=-0.013 Sum_probs=22.9
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-.-.+||..| |-+...|+++.....
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar 147 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRAR 147 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 467789999999 999999999987655
No 113
>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=25.12 E-value=86 Score=24.30 Aligned_cols=27 Identities=11% Similarity=-0.055 Sum_probs=23.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-|...|+.|....+
T Consensus 146 ~g~s~~EIA~~l-gis~~tvk~rl~Rar 172 (188)
T TIGR02943 146 LGFESDEICQEL-EISTSNCHVLLYRAR 172 (188)
T ss_pred hCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 477899999999 999999999887765
No 114
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=24.85 E-value=94 Score=22.80 Aligned_cols=27 Identities=19% Similarity=0.094 Sum_probs=22.7
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-.-.+||..+ |-+...|+++-...+
T Consensus 121 ~~~s~~EIA~~l-~is~~tV~~~~~ra~ 147 (154)
T PRK06759 121 VGKTMGEIALET-EMTYYQVRWIYRQAL 147 (154)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 466789999999 999999999887666
No 115
>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=24.60 E-value=88 Score=23.28 Aligned_cols=27 Identities=15% Similarity=0.124 Sum_probs=22.2
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-+-.+||..| |-+...|+.+-...+
T Consensus 137 ~g~s~~eIA~~l-~is~~tv~~~l~ra~ 163 (170)
T TIGR02952 137 QNLPIAEVARIL-GKTEGAVKILQFRAI 163 (170)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 367789999999 888999998877655
No 116
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=24.58 E-value=79 Score=24.36 Aligned_cols=26 Identities=12% Similarity=0.093 Sum_probs=21.8
Q ss_pred CCccccccccCCCCCHHHHHHHHHHhh
Q 037352 97 GSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 97 g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
|-...+||..+ |-|...|+++....+
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar 179 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRAR 179 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 66789999999 888999999887665
No 117
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=24.54 E-value=87 Score=24.27 Aligned_cols=27 Identities=4% Similarity=-0.190 Sum_probs=23.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-+...|+.|.....
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr 175 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRAR 175 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 477899999999 999999999987655
No 118
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.42 E-value=75 Score=24.14 Aligned_cols=27 Identities=11% Similarity=0.006 Sum_probs=22.2
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|..-.+||..| |-+...|+++.+...
T Consensus 151 ~g~s~~eIA~~l-gis~~~v~~~l~Rar 177 (187)
T TIGR02948 151 EDLSLKEISEIL-DLPVGTVKTRIHRGR 177 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 366789999999 889999999887655
No 119
>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=23.80 E-value=49 Score=22.74 Aligned_cols=22 Identities=18% Similarity=0.513 Sum_probs=17.6
Q ss_pred Hhh-cCCccccccccCCCCCHHHH
Q 037352 93 LCR-AGSKWTNIGLLLPGRTHKDV 115 (189)
Q Consensus 93 ~v~-~g~~W~~Ia~~l~gRt~~q~ 115 (189)
+.. .|..|..+|..| |=+..+|
T Consensus 13 ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 13 FANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHhhhHHHHHHHc-CCCHHHH
Confidence 335 799999999999 7777665
No 120
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=23.49 E-value=1.1e+02 Score=23.52 Aligned_cols=35 Identities=23% Similarity=0.262 Sum_probs=26.2
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhhhhhhhhhcCC
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSYMRNKMSNRGV 133 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l~k~~~~~~~~ 133 (189)
.|-.-.+||..| |-|...|+++-.... +++.+...
T Consensus 146 ~g~s~~EIAe~l-gis~~~V~~~l~Ra~--~~Lr~~~~ 180 (189)
T PRK06811 146 LGEKIEEIAKKL-GLTRSAIDNRLSRGR--KKLQKNKL 180 (189)
T ss_pred ccCCHHHHHHHH-CCCHHHHHHHHHHHH--HHHHHccc
Confidence 366678999999 999999999877665 55555443
No 121
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=22.94 E-value=1.2e+02 Score=15.21 Aligned_cols=34 Identities=26% Similarity=0.239 Sum_probs=19.6
Q ss_pred CCHHHHHHHHHHhhcCCccccccccCCCCCHHHHH
Q 037352 82 FTLEEDELIINLCRAGSKWTNIGLLLPGRTHKDVM 116 (189)
Q Consensus 82 WT~eEd~~L~~~v~~g~~W~~Ia~~l~gRt~~q~k 116 (189)
.+.++-..++.++..|.....|+..+ |.+...+.
T Consensus 6 ~~~~~~~~i~~~~~~~~s~~~ia~~~-~is~~tv~ 39 (42)
T cd00569 6 LTPEQIEEARRLLAAGESVAEIARRL-GVSRSTLY 39 (42)
T ss_pred CCHHHHHHHHHHHHcCCCHHHHHHHH-CCCHHHHH
Confidence 44444444444444455678888877 66655544
No 122
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=22.93 E-value=99 Score=24.02 Aligned_cols=27 Identities=11% Similarity=0.032 Sum_probs=22.9
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-.+.+||..| |=+...|+++....+
T Consensus 151 ~g~s~~eIA~~l-gis~~tV~~~l~Ra~ 177 (196)
T PRK12524 151 EGLSNPEIAEVM-EIGVEAVESLTARGK 177 (196)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 477899999999 888899999887765
No 123
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.81 E-value=98 Score=23.48 Aligned_cols=27 Identities=7% Similarity=0.137 Sum_probs=23.0
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-.-.+||..| |.|...|+.+....+
T Consensus 144 ~g~s~~eIA~~l-gis~~tV~~~l~Rar 170 (179)
T PRK12514 144 EGLSYKELAERH-DVPLNTMRTWLRRSL 170 (179)
T ss_pred cCCCHHHHHHHH-CCChHHHHHHHHHHH
Confidence 367789999999 999999999887665
No 124
>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=22.36 E-value=46 Score=23.00 Aligned_cols=27 Identities=26% Similarity=0.393 Sum_probs=20.2
Q ss_pred HHHHhh-cCCccccccccCCCCCHHHHHH
Q 037352 90 IINLCR-AGSKWTNIGLLLPGRTHKDVMN 117 (189)
Q Consensus 90 L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~ 117 (189)
|-.+.. .|..|..+|..| |=+..+|..
T Consensus 5 l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 5 LDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 333445 799999999999 777777655
No 125
>smart00351 PAX Paired Box domain.
Probab=22.12 E-value=1.2e+02 Score=22.25 Aligned_cols=72 Identities=17% Similarity=0.193 Sum_probs=46.4
Q ss_pred CCcccCCCCHHHHHHHHHHHHHhCCCCCCCccccccccCCcc-CCCcccccccc--cCCCCcc----CCCCCHHHHHHHH
Q 037352 19 HMIRRGFWTGEEDERLKSFILLNGEEGGWNWEDVPRGAGLLR-CGKSCHDRWFN--HLNPNIR----RGDFTLEEDELII 91 (189)
Q Consensus 19 ~~lkkg~WT~eED~~L~~~v~~~g~~~~~~W~~Ia~~~~~~R-t~~qc~~Rw~~--~L~p~~~----~~~WT~eEd~~L~ 91 (189)
.+....+.+.++-+.++.++. -|. .-..||..+|..+ |...+..||.. .+.|... ...-+.+++..|+
T Consensus 11 ~~~~~~~~s~~~R~riv~~~~-~G~----s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~ 85 (125)
T smart00351 11 VFVNGRPLPDEERQRIVELAQ-NGV----RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIA 85 (125)
T ss_pred eecCCCCCCHHHHHHHHHHHH-cCC----CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHH
Confidence 456667899999999998886 565 6799999998654 34445555543 3444221 1234555666666
Q ss_pred HHhh
Q 037352 92 NLCR 95 (189)
Q Consensus 92 ~~v~ 95 (189)
+++.
T Consensus 86 ~~~~ 89 (125)
T smart00351 86 DYKQ 89 (125)
T ss_pred HHHH
Confidence 6665
No 126
>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=22.07 E-value=1.2e+02 Score=17.28 Aligned_cols=35 Identities=20% Similarity=0.268 Sum_probs=24.7
Q ss_pred HHHHHHHhh-cCCccccccccCCCCCHHHHHHHHHHh
Q 037352 87 DELIINLCR-AGSKWTNIGLLLPGRTHKDVMNYCKTS 122 (189)
Q Consensus 87 d~~L~~~v~-~g~~W~~Ia~~l~gRt~~q~k~rw~~~ 122 (189)
+..++.++- .|-....||..+ |-+...|+.+....
T Consensus 15 ~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 15 EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 445555555 788899999998 77777777665543
No 127
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.71 E-value=1.1e+02 Score=23.39 Aligned_cols=27 Identities=15% Similarity=0.078 Sum_probs=23.6
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-+...|+++-+..+
T Consensus 144 ~g~s~~EIA~~l-~is~~tV~~~l~rar 170 (181)
T PRK12536 144 EGLSVAETAQLT-GLSESAVKVGIHRGL 170 (181)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 477899999999 999999999987766
No 128
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=21.70 E-value=1.1e+02 Score=23.49 Aligned_cols=27 Identities=11% Similarity=0.089 Sum_probs=23.1
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-|...|+++....+
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar 172 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYAR 172 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 467799999999 889999999987765
No 129
>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=21.63 E-value=1.1e+02 Score=23.12 Aligned_cols=27 Identities=26% Similarity=0.241 Sum_probs=23.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-+...|+.|.+...
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~Rar 175 (183)
T TIGR02999 149 AGLTVEEIAELL-GVSVRTVERDWRFAR 175 (183)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 477899999999 999999999987765
No 130
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=21.53 E-value=1.1e+02 Score=24.25 Aligned_cols=41 Identities=15% Similarity=0.101 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHhhcCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 81 DFTLEEDELIINLCRAGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 81 ~WT~eEd~~L~~~v~~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
..|+.|-+.| .++..|..-++||+.| +-|...++++-..++
T Consensus 137 ~LT~RE~eVL-~lla~G~snkeIA~~L-~iS~~TVk~h~~~I~ 177 (207)
T PRK15411 137 SLSRTESSML-RMWMAGQGTIQISDQM-NIKAKTVSSHKGNIK 177 (207)
T ss_pred cCCHHHHHHH-HHHHcCCCHHHHHHHc-CCCHHHHHHHHHHHH
Confidence 4788887655 4555566679999999 899999999988877
No 131
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=21.49 E-value=1.2e+02 Score=22.48 Aligned_cols=27 Identities=19% Similarity=0.117 Sum_probs=22.5
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-.-.+||..| |-+...++.|....+
T Consensus 120 ~~~s~~eIA~~l-gis~~tv~~~l~ra~ 146 (159)
T PRK12527 120 EGLSHQQIAEHL-GISRSLVEKHIVNAM 146 (159)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 466778999999 999999999987665
No 132
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=21.45 E-value=72 Score=24.23 Aligned_cols=27 Identities=22% Similarity=0.365 Sum_probs=23.3
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..+ |-+...|+++....+
T Consensus 134 ~g~s~~EIA~~l-gis~~tV~~~l~Ra~ 160 (172)
T PRK09651 134 DGLTYSEIAHKL-GVSVSSVKKYVAKAT 160 (172)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 366789999999 999999999987766
No 133
>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=21.02 E-value=60 Score=22.45 Aligned_cols=26 Identities=12% Similarity=0.220 Sum_probs=18.7
Q ss_pred HHHHHHHhh-cCCccccccccCCCCCHH
Q 037352 87 DELIINLCR-AGSKWTNIGLLLPGRTHK 113 (189)
Q Consensus 87 d~~L~~~v~-~g~~W~~Ia~~l~gRt~~ 113 (189)
|..|..+.. .|..|.++|..| |=+..
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~ 30 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVE 30 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHH
Confidence 445556666 899999999988 54443
No 134
>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=20.63 E-value=71 Score=20.91 Aligned_cols=27 Identities=22% Similarity=0.516 Sum_probs=18.7
Q ss_pred HHHHHhh--cCCccccccccCCCCCHHHHH
Q 037352 89 LIINLCR--AGSKWTNIGLLLPGRTHKDVM 116 (189)
Q Consensus 89 ~L~~~v~--~g~~W~~Ia~~l~gRt~~q~k 116 (189)
.|..++. .|..|..+|..| |=+..++.
T Consensus 2 ~l~~~l~~~~~~~Wk~La~~L-g~~~~~i~ 30 (83)
T PF00531_consen 2 KLFDLLAEDLGSDWKRLARKL-GLSESEIE 30 (83)
T ss_dssp HHHHHHHHSHSTCHHHHHHHT-TS-HHHHH
T ss_pred hHHHHHhhcchhhHHHHHHHh-CcCHHHHH
Confidence 4556665 699999999998 66555443
No 135
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=20.15 E-value=1.1e+02 Score=23.52 Aligned_cols=27 Identities=7% Similarity=0.122 Sum_probs=23.5
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-.-.+||..| |-|...|+.+....+
T Consensus 145 ~g~s~~EIA~~l-gis~~tVk~~l~Rar 171 (185)
T PRK09649 145 LGLSYADAAAVC-GCPVGTIRSRVARAR 171 (185)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 466789999999 999999999997766
No 136
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.06 E-value=1.6e+02 Score=22.50 Aligned_cols=27 Identities=26% Similarity=0.350 Sum_probs=24.2
Q ss_pred cCCccccccccCCCCCHHHHHHHHHHhh
Q 037352 96 AGSKWTNIGLLLPGRTHKDVMNYCKTSY 123 (189)
Q Consensus 96 ~g~~W~~Ia~~l~gRt~~q~k~rw~~~l 123 (189)
.|-...+||..| |-+...|+.|....+
T Consensus 142 ~g~s~~EIA~~l-gis~~tVk~~l~rAl 168 (178)
T PRK12529 142 DGMKQKDIAQAL-DIALPTVKKYIHQAY 168 (178)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 477899999999 999999999998877
Done!