Query 036087
Match_columns 344
No_of_seqs 284 out of 1508
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 09:18:42 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036087.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036087hhsearch_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 2.9E-36 6.2E-41 281.1 12.1 125 4-128 16-140 (249)
2 PLN03091 hypothetical protein; 100.0 3.2E-36 6.8E-41 298.8 12.2 132 1-132 1-133 (459)
3 KOG0048 Transcription factor, 100.0 1.8E-33 3.8E-38 263.6 11.5 116 9-124 5-120 (238)
4 KOG0049 Transcription factor, 99.8 9E-20 2E-24 187.3 3.7 144 4-148 291-444 (939)
5 KOG0049 Transcription factor, 99.7 3.4E-18 7.4E-23 175.8 6.0 98 9-107 356-454 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.6 1E-16 2.2E-21 119.3 3.2 60 16-77 1-60 (60)
7 KOG0048 Transcription factor, 99.5 1.7E-15 3.6E-20 142.3 3.1 98 62-159 5-106 (238)
8 PLN03212 Transcription repress 99.5 4.1E-15 9E-20 139.6 4.5 87 62-148 21-109 (249)
9 COG5147 REB1 Myb superfamily p 99.5 1.5E-14 3.3E-19 148.2 6.0 108 8-116 15-122 (512)
10 KOG0050 mRNA splicing protein 99.5 5.9E-15 1.3E-19 149.2 2.5 105 11-117 5-109 (617)
11 KOG0051 RNA polymerase I termi 99.4 9E-14 2E-18 144.0 6.0 106 12-120 383-516 (607)
12 PLN03091 hypothetical protein; 99.4 6.1E-14 1.3E-18 140.5 3.8 87 61-147 9-97 (459)
13 PF00249 Myb_DNA-binding: Myb- 99.4 1.2E-13 2.6E-18 98.9 0.5 48 13-60 1-48 (48)
14 PF13921 Myb_DNA-bind_6: Myb-l 99.4 4.2E-13 9.1E-18 99.8 3.4 58 69-126 1-58 (60)
15 PF00249 Myb_DNA-binding: Myb- 99.3 1.9E-12 4E-17 92.7 5.1 46 66-111 1-48 (48)
16 smart00717 SANT SANT SWI3, AD 99.1 1.2E-10 2.6E-15 80.8 5.7 47 66-112 1-48 (49)
17 smart00717 SANT SANT SWI3, AD 99.0 1.1E-10 2.4E-15 81.0 2.1 48 13-61 1-48 (49)
18 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 9.9E-10 2.1E-14 75.1 5.6 44 68-111 1-45 (45)
19 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 7.3E-10 1.6E-14 75.8 1.7 45 15-60 1-45 (45)
20 KOG0051 RNA polymerase I termi 98.8 2.5E-09 5.5E-14 111.3 4.1 116 12-131 307-450 (607)
21 COG5147 REB1 Myb superfamily p 98.2 6.4E-07 1.4E-11 92.6 3.1 109 1-112 54-168 (512)
22 KOG0050 mRNA splicing protein 98.0 2.9E-06 6.4E-11 87.0 2.8 83 64-146 5-88 (617)
23 TIGR01557 myb_SHAQKYF myb-like 97.8 9.4E-06 2E-10 60.8 2.3 49 12-60 2-54 (57)
24 KOG0457 Histone acetyltransfer 97.7 1.7E-05 3.6E-10 80.1 1.6 50 11-61 70-119 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.4 0.00049 1.1E-08 51.6 5.9 48 65-112 2-55 (57)
26 TIGR02894 DNA_bind_RsfA transc 97.4 0.00022 4.8E-09 63.7 4.7 52 65-117 3-61 (161)
27 KOG0457 Histone acetyltransfer 97.3 0.00036 7.8E-09 70.7 5.9 49 63-111 69-118 (438)
28 PF13325 MCRS_N: N-terminal re 97.0 0.0013 2.8E-08 61.0 6.1 99 15-115 1-130 (199)
29 COG5259 RSC8 RSC chromatin rem 96.9 0.00031 6.7E-09 71.8 1.1 46 12-59 278-323 (531)
30 KOG1279 Chromatin remodeling f 96.9 0.00049 1.1E-08 71.6 2.5 46 12-59 252-297 (506)
31 PF13837 Myb_DNA-bind_4: Myb/S 96.8 0.0012 2.5E-08 52.1 3.4 49 66-114 1-67 (90)
32 COG5259 RSC8 RSC chromatin rem 96.7 0.0017 3.8E-08 66.4 4.3 45 66-110 279-323 (531)
33 KOG1279 Chromatin remodeling f 96.7 0.0022 4.8E-08 66.8 5.2 46 65-110 252-297 (506)
34 PF08914 Myb_DNA-bind_2: Rap1 96.4 0.0058 1.3E-07 47.0 4.5 50 66-115 2-61 (65)
35 PRK13923 putative spore coat p 96.2 0.0058 1.3E-07 55.4 4.1 52 65-117 4-62 (170)
36 PF13837 Myb_DNA-bind_4: Myb/S 96.1 0.0012 2.6E-08 52.1 -0.4 47 13-59 1-63 (90)
37 PF08914 Myb_DNA-bind_2: Rap1 96.0 0.0016 3.6E-08 50.0 -0.1 52 13-64 2-61 (65)
38 TIGR02894 DNA_bind_RsfA transc 95.8 0.003 6.5E-08 56.6 0.8 50 11-62 2-57 (161)
39 COG5114 Histone acetyltransfer 95.5 0.004 8.7E-08 61.3 0.2 48 13-61 63-110 (432)
40 PF13873 Myb_DNA-bind_5: Myb/S 95.3 0.036 7.8E-07 42.9 5.0 48 66-113 2-71 (78)
41 COG5114 Histone acetyltransfer 95.0 0.032 7E-07 55.1 4.8 46 66-111 63-109 (432)
42 PLN03142 Probable chromatin-re 94.5 0.068 1.5E-06 60.4 6.3 100 14-114 825-987 (1033)
43 PF13873 Myb_DNA-bind_5: Myb/S 94.2 0.023 4.9E-07 44.1 1.4 49 12-60 1-69 (78)
44 PRK13923 putative spore coat p 93.8 0.014 3.1E-07 52.8 -0.5 50 10-61 2-57 (170)
45 KOG2656 DNA methyltransferase 91.7 0.2 4.3E-06 50.8 4.1 86 35-121 75-191 (445)
46 PF12776 Myb_DNA-bind_3: Myb/S 91.4 0.48 1E-05 37.6 5.4 46 68-113 1-64 (96)
47 KOG4282 Transcription factor G 91.2 0.39 8.5E-06 47.4 5.7 50 66-115 54-117 (345)
48 PF09111 SLIDE: SLIDE; InterP 90.5 0.47 1E-05 40.6 4.7 51 63-113 46-112 (118)
49 KOG1194 Predicted DNA-binding 89.6 0.93 2E-05 46.9 6.8 49 65-113 186-234 (534)
50 COG5118 BDP1 Transcription ini 87.7 0.86 1.9E-05 46.2 5.0 47 67-113 366-412 (507)
51 PF08281 Sigma70_r4_2: Sigma-7 83.6 3.2 7E-05 29.5 5.1 42 71-113 12-53 (54)
52 COG5118 BDP1 Transcription ini 80.7 1 2.2E-05 45.8 2.1 67 10-78 362-436 (507)
53 KOG4282 Transcription factor G 78.3 0.77 1.7E-05 45.4 0.4 48 13-60 54-113 (345)
54 PF11626 Rap1_C: TRF2-interact 77.7 2.2 4.7E-05 34.2 2.8 30 9-41 43-80 (87)
55 PF09111 SLIDE: SLIDE; InterP 75.0 1.8 3.9E-05 37.0 1.7 35 10-44 46-83 (118)
56 PRK11179 DNA-binding transcrip 71.1 6.7 0.00014 34.3 4.4 46 71-117 8-54 (153)
57 PF12776 Myb_DNA-bind_3: Myb/S 69.3 2.5 5.4E-05 33.5 1.2 44 15-58 1-60 (96)
58 KOG4167 Predicted DNA-binding 68.2 8.7 0.00019 42.2 5.3 46 66-111 619-664 (907)
59 KOG4468 Polycomb-group transcr 67.5 7.9 0.00017 41.6 4.7 50 66-115 88-147 (782)
60 PF13404 HTH_AsnC-type: AsnC-t 67.0 12 0.00026 26.1 4.1 38 72-110 3-41 (42)
61 PF11035 SnAPC_2_like: Small n 67.0 19 0.00041 36.0 6.9 48 66-113 21-72 (344)
62 PRK11169 leucine-responsive tr 65.7 8.6 0.00019 34.0 4.1 46 71-117 13-59 (164)
63 PF04545 Sigma70_r4: Sigma-70, 65.5 17 0.00036 25.5 4.8 41 72-113 7-47 (50)
64 KOG2656 DNA methyltransferase 63.5 9 0.00019 39.2 4.1 47 12-59 129-180 (445)
65 KOG4167 Predicted DNA-binding 60.8 4.1 8.9E-05 44.6 1.2 44 13-58 619-662 (907)
66 smart00595 MADF subfamily of S 58.6 11 0.00023 29.5 3.0 26 87-113 29-54 (89)
67 KOG4329 DNA-binding protein [G 57.6 56 0.0012 33.5 8.4 46 67-112 278-324 (445)
68 TIGR02985 Sig70_bacteroi1 RNA 54.8 28 0.0006 29.1 5.2 35 78-113 122-156 (161)
69 PF13325 MCRS_N: N-terminal re 53.8 26 0.00056 32.8 5.1 47 68-115 1-50 (199)
70 PF13404 HTH_AsnC-type: AsnC-t 53.2 4.5 9.8E-05 28.3 0.0 38 19-58 3-40 (42)
71 PRK11179 DNA-binding transcrip 50.6 5.8 0.00013 34.6 0.3 45 18-64 8-52 (153)
72 PF07750 GcrA: GcrA cell cycle 50.2 20 0.00043 32.2 3.7 40 68-108 2-41 (162)
73 KOG0384 Chromodomain-helicase 48.3 17 0.00037 42.2 3.5 29 12-40 1132-1160(1373)
74 KOG2009 Transcription initiati 47.2 20 0.00044 38.5 3.7 47 64-110 407-453 (584)
75 PF11626 Rap1_C: TRF2-interact 45.9 10 0.00022 30.4 1.0 18 62-79 43-60 (87)
76 KOG1924 RhoA GTPase effector D 45.0 42 0.00092 37.5 5.7 14 254-267 639-652 (1102)
77 PRK11169 leucine-responsive tr 44.9 6.3 0.00014 34.9 -0.4 45 18-64 13-57 (164)
78 PF01388 ARID: ARID/BRIGHT DNA 43.2 53 0.0012 25.8 4.8 38 76-113 40-90 (92)
79 KOG4468 Polycomb-group transcr 43.2 19 0.00041 38.9 2.8 47 12-60 87-143 (782)
80 TIGR02937 sigma70-ECF RNA poly 42.3 52 0.0011 26.6 4.8 33 80-113 121-153 (158)
81 smart00344 HTH_ASNC helix_turn 42.3 49 0.0011 26.5 4.5 45 72-117 3-48 (108)
82 KOG3841 TEF-1 and related tran 42.2 2.1E+02 0.0046 29.5 9.7 72 9-117 72-148 (455)
83 PF07638 Sigma70_ECF: ECF sigm 41.8 51 0.0011 29.5 5.0 40 73-113 139-178 (185)
84 cd08319 Death_RAIDD Death doma 40.7 37 0.00081 27.2 3.5 29 74-103 2-30 (83)
85 PF10545 MADF_DNA_bdg: Alcohol 40.1 28 0.00062 26.2 2.7 27 87-113 28-55 (85)
86 PF11035 SnAPC_2_like: Small n 39.8 68 0.0015 32.2 5.8 86 13-112 21-127 (344)
87 cd06171 Sigma70_r4 Sigma70, re 39.0 86 0.0019 20.6 4.8 41 69-111 11-51 (55)
88 smart00501 BRIGHT BRIGHT, ARID 37.4 73 0.0016 25.3 4.8 38 76-113 36-86 (93)
89 PRK09652 RNA polymerase sigma 37.3 67 0.0015 27.4 4.9 30 83-113 142-171 (182)
90 PRK11924 RNA polymerase sigma 34.8 75 0.0016 27.0 4.8 30 83-113 139-168 (179)
91 PRK09643 RNA polymerase sigma 32.9 86 0.0019 27.9 5.0 30 83-113 148-177 (192)
92 KOG2009 Transcription initiati 31.9 31 0.00068 37.1 2.3 48 9-58 405-452 (584)
93 PRK04217 hypothetical protein; 31.2 1.1E+02 0.0023 25.9 5.0 45 67-113 41-85 (110)
94 COG1522 Lrp Transcriptional re 31.1 85 0.0018 26.6 4.5 46 71-117 7-53 (154)
95 cd08803 Death_ank3 Death domai 31.0 74 0.0016 25.5 3.8 31 74-105 4-34 (84)
96 PRK09641 RNA polymerase sigma 29.4 1E+02 0.0022 26.7 4.8 29 84-113 151-179 (187)
97 PF09420 Nop16: Ribosome bioge 29.2 42 0.00092 29.9 2.4 47 11-58 112-161 (164)
98 KOG1194 Predicted DNA-binding 28.7 31 0.00068 36.1 1.6 48 9-58 183-230 (534)
99 TIGR02939 RpoE_Sigma70 RNA pol 27.7 93 0.002 27.0 4.3 29 84-113 153-181 (190)
100 PF09420 Nop16: Ribosome bioge 27.3 1.5E+02 0.0033 26.3 5.6 47 65-111 113-163 (164)
101 TIGR02954 Sig70_famx3 RNA poly 27.1 1.2E+02 0.0026 26.0 4.9 29 84-113 134-162 (169)
102 PRK12523 RNA polymerase sigma 26.5 1.7E+02 0.0037 25.2 5.7 32 82-114 132-163 (172)
103 cd08317 Death_ank Death domain 26.5 71 0.0015 25.1 3.0 29 74-103 4-32 (84)
104 PF04504 DUF573: Protein of un 26.5 1.1E+02 0.0023 25.2 4.1 48 67-114 5-65 (98)
105 PRK12515 RNA polymerase sigma 26.3 1.4E+02 0.003 26.3 5.1 29 84-113 146-174 (189)
106 PRK12532 RNA polymerase sigma 26.2 1.6E+02 0.0034 26.1 5.5 35 84-119 151-188 (195)
107 COG2963 Transposase and inacti 25.8 1.9E+02 0.0041 23.6 5.6 47 66-113 5-52 (116)
108 PF07750 GcrA: GcrA cell cycle 25.6 46 0.001 29.9 1.9 38 15-55 2-39 (162)
109 PRK09637 RNA polymerase sigma 25.2 1.4E+02 0.003 26.4 5.0 30 83-113 120-149 (181)
110 PRK11923 algU RNA polymerase s 25.1 1.3E+02 0.0028 26.4 4.8 29 84-113 153-181 (193)
111 PRK09047 RNA polymerase factor 25.0 1.6E+02 0.0034 24.8 5.1 29 84-113 121-149 (161)
112 PRK09648 RNA polymerase sigma 24.8 1.5E+02 0.0033 26.0 5.1 30 83-113 153-182 (189)
113 TIGR02948 SigW_bacill RNA poly 24.8 1.3E+02 0.0028 26.1 4.6 29 84-113 151-179 (187)
114 PRK12529 RNA polymerase sigma 24.7 2.1E+02 0.0045 25.0 5.9 34 82-116 140-173 (178)
115 cd08318 Death_NMPP84 Death dom 24.5 97 0.0021 24.6 3.4 24 79-103 12-35 (86)
116 smart00344 HTH_ASNC helix_turn 24.3 32 0.0007 27.6 0.6 44 19-64 3-46 (108)
117 COG2197 CitB Response regulato 23.7 1.3E+02 0.0028 27.6 4.6 44 67-113 147-190 (211)
118 TIGR02943 Sig70_famx1 RNA poly 23.6 1.6E+02 0.0036 26.0 5.1 30 83-113 145-174 (188)
119 PRK09645 RNA polymerase sigma 23.4 1.7E+02 0.0037 25.1 5.1 29 84-113 133-161 (173)
120 PF00046 Homeobox: Homeobox do 23.4 2.2E+02 0.0048 20.0 4.9 45 65-110 3-51 (57)
121 PRK12531 RNA polymerase sigma 23.0 1.7E+02 0.0037 25.9 5.1 29 84-113 156-184 (194)
122 PF02954 HTH_8: Bacterial regu 22.6 1.7E+02 0.0036 19.9 3.9 35 72-107 5-39 (42)
123 PRK09642 RNA polymerase sigma 22.3 1.9E+02 0.0041 24.5 5.1 29 84-113 121-149 (160)
124 smart00005 DEATH DEATH domain, 22.0 1.2E+02 0.0026 23.3 3.5 29 74-103 5-34 (88)
125 cd08311 Death_p75NR Death doma 21.5 1.1E+02 0.0023 24.2 3.1 33 71-105 2-34 (77)
126 PRK12512 RNA polymerase sigma 21.3 2.3E+02 0.005 24.6 5.6 29 84-113 146-174 (184)
127 cd08804 Death_ank2 Death domai 21.3 1.2E+02 0.0026 24.1 3.3 31 74-105 4-34 (84)
128 PRK12530 RNA polymerase sigma 20.9 2E+02 0.0042 25.5 5.0 28 84-112 149-176 (189)
129 KOG1924 RhoA GTPase effector D 20.7 1.1E+02 0.0025 34.4 4.0 12 46-57 414-425 (1102)
130 PF00196 GerE: Bacterial regul 20.5 1.4E+02 0.0029 21.5 3.3 43 68-113 3-45 (58)
131 COG1522 Lrp Transcriptional re 20.5 35 0.00076 29.0 0.1 43 19-63 8-50 (154)
No 1
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=2.9e-36 Score=281.15 Aligned_cols=125 Identities=57% Similarity=1.171 Sum_probs=120.3
Q ss_pred CCCccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCCCCCCCCHHHHHHHHHHHHh
Q 036087 4 RCCSKQKVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQIIIDVHRI 83 (344)
Q Consensus 4 ~c~~Kp~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~~Ll~lv~~ 83 (344)
+||+|++++|++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.++|+|.+++++||+|||++|++++.+
T Consensus 16 pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~ 95 (249)
T PLN03212 16 PCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRL 95 (249)
T ss_pred CCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHh
Confidence 79999999999999999999999999999989999999986689999999999999999999999999999999999999
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCccccccC
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKKKLMSKGLDPKTHILM 128 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~~~~~~~e~~ll 128 (344)
||++|..||+.|||||+++|||||+.++++++.+++..+.++..+
T Consensus 96 ~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~ 140 (249)
T PLN03212 96 LGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPL 140 (249)
T ss_pred ccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCC
Confidence 999999999999999999999999999999999998888876654
No 2
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=3.2e-36 Score=298.84 Aligned_cols=132 Identities=70% Similarity=1.329 Sum_probs=126.0
Q ss_pred CCC-CCCccCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCCCCCCCCHHHHHHHHH
Q 036087 1 MGH-RCCSKQKVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQIIID 79 (344)
Q Consensus 1 mg~-~c~~Kp~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~~Ll~ 79 (344)
||| .||+|++++||+||+|||++|+++|++||.++|..||+.++++|+++|||+||.++|+|.+++++||+|||++|++
T Consensus 1 mgr~~Cc~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLe 80 (459)
T PLN03091 1 MGRHSCCYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIE 80 (459)
T ss_pred CCCCccCcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHH
Confidence 898 6999999999999999999999999999999999999998778999999999999999999999999999999999
Q ss_pred HHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCccccccCchhh
Q 036087 80 VHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKKKLMSKGLDPKTHILMPSHQ 132 (344)
Q Consensus 80 lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~~~~~~~e~~ll~~~q 132 (344)
++++||++|.+||+.|+|||+++||+||+.+++++++..+.++.++.++...+
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~E 133 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEVE 133 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCccccc
Confidence 99999999999999999999999999999999999999899888877776543
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=1.8e-33 Score=263.60 Aligned_cols=116 Identities=59% Similarity=1.107 Sum_probs=109.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCCCCCCCCHHHHHHHHHHHHhcCCch
Q 036087 9 QKVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQIIIDVHRILGNRW 88 (344)
Q Consensus 9 p~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~~Ll~lv~~~G~kW 88 (344)
+.+.||+||+|||++|+++|++||.++|..||+.+|++|++++||.||.|||+|++++|.||+|||++|++++.++|++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 33557999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCccc
Q 036087 89 AQIAKHLPGRTDNEVKNYWNSCIKKKLMSKGLDPKT 124 (344)
Q Consensus 89 ~~IAk~lpgRT~~qcknRW~~~lkkkl~~~~~~~~e 124 (344)
+.||++|||||+++|||+|+..+++++.+.+.++..
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~~~ 120 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDPST 120 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCCCc
Confidence 999999999999999999999999999887744443
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.77 E-value=9e-20 Score=187.26 Aligned_cols=144 Identities=19% Similarity=0.430 Sum_probs=130.7
Q ss_pred CCCcc-----CCCCCCCCCHHHHHHHHHHHHHhCCC---CccccccccccccCcccccchhhcccCCCCCCCCCCHHHHH
Q 036087 4 RCCSK-----QKVKKGLWSPEEDEKLLKHITAHGHG---SWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQ 75 (344)
Q Consensus 4 ~c~~K-----p~~kkg~WT~EEDe~L~~lV~kyG~~---~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~ 75 (344)
||..| +-+++..||.|||.+|+++|.....+ +|++|-..|+ ||+..|...||...|+|.+++|.||.+||.
T Consensus 291 QC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ymp-gr~~~qLI~R~~~~LdPsikhg~wt~~ED~ 369 (939)
T KOG0049|consen 291 QCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMP-GRTRQQLITRFSHTLDPSVKHGRWTDQEDV 369 (939)
T ss_pred HHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcC-CcchhhhhhhheeccCccccCCCCCCHHHH
Confidence 45555 44567889999999999999988543 7999999999 999999999999999999999999999999
Q ss_pred HHHHHHHhcCC-chHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCccc-cccCchhhhhhcccccccccccCC
Q 036087 76 IIIDVHRILGN-RWAQIAKHLPGRTDNEVKNYWNSCIKKKLMSKGLDPKT-HILMPSHQRAAASSKIACNIQLPI 148 (344)
Q Consensus 76 ~Ll~lv~~~G~-kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~~~~~~~e-~~ll~~~q~~~~~~~~~~~~~~p~ 148 (344)
+|+.+|.+||. .|.+|...+|||++.|||.||.+.|...++...|+-++ +.|+.....+..+.|..|+...|.
T Consensus 370 ~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~ 444 (939)
T KOG0049|consen 370 LLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPK 444 (939)
T ss_pred HHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHHccchHHHHHHHccc
Confidence 99999999995 59999999999999999999999999999999998665 677788888999999999988775
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.72 E-value=3.4e-18 Score=175.78 Aligned_cols=98 Identities=26% Similarity=0.505 Sum_probs=92.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCCCCCCCCHHHHHHHHHHHHhcC-Cc
Q 036087 9 QKVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQIIIDVHRILG-NR 87 (344)
Q Consensus 9 p~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~~Ll~lv~~~G-~k 87 (344)
|.+++|.||++||.+|+.+|.+||.++|-+|-+.++ ||+..|||+||.|+|+...|++.||-.||+.|+.+|.+|| ++
T Consensus 356 Psikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~~YG~g~ 434 (939)
T KOG0049|consen 356 PSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVKVYGKGN 434 (939)
T ss_pred ccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHHHHccch
Confidence 899999999999999999999999999999999999 9999999999999999999999999999999999999999 78
Q ss_pred hHHHhhhCCCCCHHHHHHHH
Q 036087 88 WAQIAKHLPGRTDNEVKNYW 107 (344)
Q Consensus 88 W~~IAk~lpgRT~~qcknRW 107 (344)
|.+||..||.||.+|.+.|=
T Consensus 435 WakcA~~Lp~~t~~q~~rrR 454 (939)
T KOG0049|consen 435 WAKCAMLLPKKTSRQLRRRR 454 (939)
T ss_pred HHHHHHHccccchhHHHHHH
Confidence 99999999999996554443
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=99.64 E-value=1e-16 Score=119.25 Aligned_cols=60 Identities=43% Similarity=0.870 Sum_probs=55.4
Q ss_pred CCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCCCCCCCCHHHHHHH
Q 036087 16 WSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQII 77 (344)
Q Consensus 16 WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~~L 77 (344)
||+|||++|+++|.+||. +|..||+.|| .|++.||+.||.++|++.+++++||++||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~-~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLG-NRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHST-TS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHC-cCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999997 9999999998 89999999999999999999999999999987
No 7
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.55 E-value=1.7e-15 Score=142.28 Aligned_cols=98 Identities=15% Similarity=0.220 Sum_probs=86.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcC-CchHHHhhhCC-CCCHHHHHHHHHHHhhhhhhhCCCCccccccCchhhhhhcccc
Q 036087 62 PDLRRGSFTEEEEQIIIDVHRILG-NRWAQIAKHLP-GRTDNEVKNYWNSCIKKKLMSKGLDPKTHILMPSHQRAAASSK 139 (344)
Q Consensus 62 p~lkkg~WT~EED~~Ll~lv~~~G-~kW~~IAk~lp-gRT~~qcknRW~~~lkkkl~~~~~~~~e~~ll~~~q~~~~~~~ 139 (344)
+.+.+|+||.|||++|+++|++|| .+|..||+.++ +|++++||.||.++|++.++++.|+++|+.+|..++...+++|
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 345579999999999999999999 56999999998 9999999999999999999999999999999999999999999
Q ss_pred cccccccCC--CCCCcccCccc
Q 036087 140 IACNIQLPI--SSRAFTVSSSQ 159 (344)
Q Consensus 140 ~~~~~~~p~--S~~~~~~~~~~ 159 (344)
+.++..+|. .+....++++.
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~ 106 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTH 106 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHH
Confidence 999988884 33344455444
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.53 E-value=4.1e-15 Score=139.55 Aligned_cols=87 Identities=18% Similarity=0.345 Sum_probs=80.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcC-CchHHHhhhC-CCCCHHHHHHHHHHHhhhhhhhCCCCccccccCchhhhhhcccc
Q 036087 62 PDLRRGSFTEEEEQIIIDVHRILG-NRWAQIAKHL-PGRTDNEVKNYWNSCIKKKLMSKGLDPKTHILMPSHQRAAASSK 139 (344)
Q Consensus 62 p~lkkg~WT~EED~~Ll~lv~~~G-~kW~~IAk~l-pgRT~~qcknRW~~~lkkkl~~~~~~~~e~~ll~~~q~~~~~~~ 139 (344)
+.+++++||+|||++|+++|++|| .+|..||+.+ ++||++|||.||.++|++.+.++.|+.+|+.+|..++...+++|
T Consensus 21 ~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnKW 100 (249)
T PLN03212 21 MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNRW 100 (249)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhccccH
Confidence 578899999999999999999999 5799999998 69999999999999999999999999999999999998889999
Q ss_pred cccccccCC
Q 036087 140 IACNIQLPI 148 (344)
Q Consensus 140 ~~~~~~~p~ 148 (344)
..++..+|.
T Consensus 101 s~IAk~LpG 109 (249)
T PLN03212 101 SLIAGRIPG 109 (249)
T ss_pred HHHHhhcCC
Confidence 888877654
No 9
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.50 E-value=1.5e-14 Score=148.22 Aligned_cols=108 Identities=31% Similarity=0.543 Sum_probs=102.9
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCCCCCCCCHHHHHHHHHHHHhcCCc
Q 036087 8 KQKVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQIIIDVHRILGNR 87 (344)
Q Consensus 8 Kp~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~~Ll~lv~~~G~k 87 (344)
+.+++.|.|+..||+.|..+|++||..+|..||..+. .|+++||+.||.++++|.++++.|+.+||+.|+.+..++|..
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ 93 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch
Confidence 4567899999999999999999999999999999998 699999999999999999999999999999999999999999
Q ss_pred hHHHhhhCCCCCHHHHHHHHHHHhhhhhh
Q 036087 88 WAQIAKHLPGRTDNEVKNYWNSCIKKKLM 116 (344)
Q Consensus 88 W~~IAk~lpgRT~~qcknRW~~~lkkkl~ 116 (344)
|..||..+++||..+|.+||...+.....
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999988877655
No 10
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.50 E-value=5.9e-15 Score=149.15 Aligned_cols=105 Identities=24% Similarity=0.612 Sum_probs=99.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCCCCCCCCHHHHHHHHHHHHhcCCchHH
Q 036087 11 VKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQIIIDVHRILGNRWAQ 90 (344)
Q Consensus 11 ~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~~Ll~lv~~~G~kW~~ 90 (344)
++.|.|+.-||+.|..+|.+||.+.|.+|++++. ..+++||+.||..+|+|.+++..|+.|||++|+.+.+.....|..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~-~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrt 83 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLN-RKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRT 83 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHh-hcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccch
Confidence 5789999999999999999999999999999998 899999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 036087 91 IAKHLPGRTDNEVKNYWNSCIKKKLMS 117 (344)
Q Consensus 91 IAk~lpgRT~~qcknRW~~~lkkkl~~ 117 (344)
|+..+ ||+.+||-.||+.++......
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~ 109 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSY 109 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhh
Confidence 99999 999999999999998776543
No 11
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.44 E-value=9e-14 Score=144.00 Aligned_cols=106 Identities=28% Similarity=0.590 Sum_probs=95.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCC--CCCCCCCHHHHHHHHHHHH-------
Q 036087 12 KKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPD--LRRGSFTEEEEQIIIDVHR------- 82 (344)
Q Consensus 12 kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~--lkkg~WT~EED~~Ll~lv~------- 82 (344)
++|.||+||++.|..+|.++|. .|..|++.|| |.+..||+||++|..++ .+++.||.||+++|+++|.
T Consensus 383 ~rg~wt~ee~eeL~~l~~~~g~-~W~~Ig~~lg--r~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~ 459 (607)
T KOG0051|consen 383 KRGKWTPEEEEELKKLVVEHGN-DWKEIGKALG--RMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREAL 459 (607)
T ss_pred ccCCCCcchHHHHHHHHHHhcc-cHHHHHHHHc--cCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhh
Confidence 7999999999999999999998 9999999998 99999999999999987 4899999999999999995
Q ss_pred hc-------------------CCchHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCC
Q 036087 83 IL-------------------GNRWAQIAKHLPGRTDNEVKNYWNSCIKKKLMSKGL 120 (344)
Q Consensus 83 ~~-------------------G~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~~~~ 120 (344)
++ +..|..|++.+.+|+..|||.+|+.++......+..
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~~~ 516 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNKRQ 516 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhccc
Confidence 23 135999999999999999999999999887665543
No 12
>PLN03091 hypothetical protein; Provisional
Probab=99.43 E-value=6.1e-14 Score=140.48 Aligned_cols=87 Identities=17% Similarity=0.334 Sum_probs=78.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcC-CchHHHhhhC-CCCCHHHHHHHHHHHhhhhhhhCCCCccccccCchhhhhhccc
Q 036087 61 RPDLRRGSFTEEEEQIIIDVHRILG-NRWAQIAKHL-PGRTDNEVKNYWNSCIKKKLMSKGLDPKTHILMPSHQRAAASS 138 (344)
Q Consensus 61 ~p~lkkg~WT~EED~~Ll~lv~~~G-~kW~~IAk~l-pgRT~~qcknRW~~~lkkkl~~~~~~~~e~~ll~~~q~~~~~~ 138 (344)
+.+++++.||+|||++|+++|.+|| .+|..||+.+ ++|+++|||.||.++|++.++++.|+++|+.+|..+++..+.+
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~GnK 88 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLGNR 88 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhCcc
Confidence 3578899999999999999999999 5799999988 5999999999999999999999999999999998888888888
Q ss_pred ccccccccC
Q 036087 139 KIACNIQLP 147 (344)
Q Consensus 139 ~~~~~~~~p 147 (344)
|..++..+|
T Consensus 89 WskIAk~LP 97 (459)
T PLN03091 89 WSQIAAQLP 97 (459)
T ss_pred hHHHHHhcC
Confidence 877766554
No 13
>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=99.36 E-value=1.2e-13 Score=98.91 Aligned_cols=48 Identities=40% Similarity=0.737 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhccc
Q 036087 13 KGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYL 60 (344)
Q Consensus 13 kg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L 60 (344)
|++||+|||++|+++|++||.++|..||..|+.+||+.||+.||.++|
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 689999999999999999999669999999987999999999999875
No 14
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.36 E-value=4.2e-13 Score=99.76 Aligned_cols=58 Identities=26% Similarity=0.603 Sum_probs=51.0
Q ss_pred CCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCccccc
Q 036087 69 FTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKKKLMSKGLDPKTHI 126 (344)
Q Consensus 69 WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~~~~~~~e~~ 126 (344)
||+|||++|++++.+||++|..||+.|+.||..+|++||+..|++.+.+..|+.+++.
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~ 58 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQ 58 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHh
Confidence 9999999999999999999999999996699999999999988888988899887754
No 15
>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=99.33 E-value=1.9e-12 Score=92.75 Aligned_cols=46 Identities=33% Similarity=0.766 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCc-hHHHhhhCC-CCCHHHHHHHHHHHh
Q 036087 66 RGSFTEEEEQIIIDVHRILGNR-WAQIAKHLP-GRTDNEVKNYWNSCI 111 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G~k-W~~IAk~lp-gRT~~qcknRW~~~l 111 (344)
|++||+|||++|++++.+||.. |..||..|+ +||..||++||+.++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 5799999999999999999988 999999999 999999999999864
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.12 E-value=1.2e-10 Score=80.77 Aligned_cols=47 Identities=43% Similarity=0.941 Sum_probs=44.3
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CchHHHhhhCCCCCHHHHHHHHHHHhh
Q 036087 66 RGSFTEEEEQIIIDVHRILG-NRWAQIAKHLPGRTDNEVKNYWNSCIK 112 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G-~kW~~IAk~lpgRT~~qcknRW~~~lk 112 (344)
++.||++||.+|+.++.+|| .+|..||..+++||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999998764
No 17
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.02 E-value=1.1e-10 Score=80.97 Aligned_cols=48 Identities=38% Similarity=0.774 Sum_probs=44.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccC
Q 036087 13 KGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLR 61 (344)
Q Consensus 13 kg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~ 61 (344)
++.||++||++|+.++..||..+|..||..++ +|++.+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~-~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELP-GRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcC-CCCHHHHHHHHHHHcC
Confidence 47899999999999999999559999999999 9999999999998764
No 18
>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=98.98 E-value=9.9e-10 Score=75.13 Aligned_cols=44 Identities=36% Similarity=0.860 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHhcC-CchHHHhhhCCCCCHHHHHHHHHHHh
Q 036087 68 SFTEEEEQIIIDVHRILG-NRWAQIAKHLPGRTDNEVKNYWNSCI 111 (344)
Q Consensus 68 ~WT~EED~~Ll~lv~~~G-~kW~~IAk~lpgRT~~qcknRW~~~l 111 (344)
+||.+|+.+|+.++.+|| .+|..||+.+++||..+|++||+.++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 89999999999999999999998753
No 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=98.87 E-value=7.3e-10 Score=75.78 Aligned_cols=45 Identities=40% Similarity=0.756 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhccc
Q 036087 15 LWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYL 60 (344)
Q Consensus 15 ~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L 60 (344)
.||++||++|+.++.+||..+|..||+.++ +|++.+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~-~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELP-GRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcC-CCCHHHHHHHHHHhC
Confidence 599999999999999999669999999998 899999999998753
No 20
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.81 E-value=2.5e-09 Score=111.35 Aligned_cols=116 Identities=23% Similarity=0.280 Sum_probs=94.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC---------------CC--------ccccccccccccCcccccc---hhhcccCCCCC
Q 036087 12 KKGLWSPEEDEKLLKHITAHGH---------------GS--------WSSVPKLAGLQRCGKSCRL---RWINYLRPDLR 65 (344)
Q Consensus 12 kkg~WT~EEDe~L~~lV~kyG~---------------~~--------W~~IA~~~~~~Rt~~QCr~---Rw~n~L~p~lk 65 (344)
+-+.|+.+||+.|...|+.|-. .+ |..|...++ -|+.+.+.. |-.+.+.+ +
T Consensus 307 ~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp-~R~~~siy~~~rR~y~~FE~--~ 383 (607)
T KOG0051|consen 307 NLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLP-YRDRKSIYHHLRRAYTPFEN--K 383 (607)
T ss_pred hhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcC-cccchhHHHHHHhcCCcccc--c
Confidence 3488999999999999998811 01 567777888 599988877 33334443 8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhhh--hhhCCCCccccccCchh
Q 036087 66 RGSFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKKK--LMSKGLDPKTHILMPSH 131 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkkk--l~~~~~~~~e~~ll~~~ 131 (344)
+|.||+||++.|..++.++|+.|..|++.| ||.+..|+.||+.+.+.. ..++.|+.++...|..+
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~ 450 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKT 450 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHH
Confidence 999999999999999999999999999999 999999999999998876 47788887776655443
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=98.22 E-value=6.4e-07 Score=92.64 Aligned_cols=109 Identities=20% Similarity=0.253 Sum_probs=93.5
Q ss_pred CCCCCCcc------CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCCCCCCCCHHHH
Q 036087 1 MGHRCCSK------QKVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEE 74 (344)
Q Consensus 1 mg~~c~~K------p~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED 74 (344)
+|.+|..+ +.++++.|+.|||+.|+.+-..+|. .|..||..++ +|+..+|.+||.+.|.+..+ ..|+..++
T Consensus 54 ~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~-~wstia~~~d-~rt~~~~~ery~~~~~~~~s-~~~s~~~~ 130 (512)
T COG5147 54 TGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGT-QWSTIADYKD-RRTAQQCVERYVNTLEDLSS-THDSKLQR 130 (512)
T ss_pred ccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCc-hhhhhccccC-ccchHHHHHHHHHHhhhhhc-cccccccc
Confidence 35667655 7899999999999999999999999 7999999999 99999999999999987666 78999999
Q ss_pred HHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhh
Q 036087 75 QIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIK 112 (344)
Q Consensus 75 ~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lk 112 (344)
...+.-+..|+..|.++....-.+-...+.+++.++..
T Consensus 131 ~~~f~k~d~f~~~~~~~~~~~~~~~~~~~~N~~~~~~~ 168 (512)
T COG5147 131 RNEFDKIDPFNENSARRPDIYEDELLEREVNREASYRL 168 (512)
T ss_pred hhhccccCchhhhhhhhhhhhhcccchhhhhHHHHHHH
Confidence 98888888888888888877666777777887765543
No 22
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.01 E-value=2.9e-06 Score=86.95 Aligned_cols=83 Identities=13% Similarity=0.277 Sum_probs=72.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhcC-CchHHHhhhCCCCCHHHHHHHHHHHhhhhhhhCCCCccccccCchhhhhhccccccc
Q 036087 64 LRRGSFTEEEEQIIIDVHRILG-NRWAQIAKHLPGRTDNEVKNYWNSCIKKKLMSKGLDPKTHILMPSHQRAAASSKIAC 142 (344)
Q Consensus 64 lkkg~WT~EED~~Ll~lv~~~G-~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~~~~~~~e~~ll~~~q~~~~~~~~~~ 142 (344)
++.|.|+.-||+.|-.+|.+|| +.|++|+..++-.|..||++||+..+.+.+++-.|+.+++.-+..+-+..-..|..+
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwrtI 84 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWRTI 84 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccchH
Confidence 4678999999999999999999 679999999999999999999999999999999999888777766666666677665
Q ss_pred cccc
Q 036087 143 NIQL 146 (344)
Q Consensus 143 ~~~~ 146 (344)
+..+
T Consensus 85 a~i~ 88 (617)
T KOG0050|consen 85 ADIM 88 (617)
T ss_pred HHHh
Confidence 5543
No 23
>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=97.84 E-value=9.4e-06 Score=60.85 Aligned_cols=49 Identities=12% Similarity=0.354 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCc---ccccccccccc-Ccccccchhhccc
Q 036087 12 KKGLWSPEEDEKLLKHITAHGHGSW---SSVPKLAGLQR-CGKSCRLRWINYL 60 (344)
Q Consensus 12 kkg~WT~EEDe~L~~lV~kyG~~~W---~~IA~~~~~~R-t~~QCr~Rw~n~L 60 (344)
++-.||+||..+++++|+.+|.++| ..|++.|+..| |..||+.|++.|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3556999999999999999999999 99999887556 9999999988764
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.66 E-value=1.7e-05 Score=80.15 Aligned_cols=50 Identities=18% Similarity=0.538 Sum_probs=46.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccC
Q 036087 11 VKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLR 61 (344)
Q Consensus 11 ~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~ 61 (344)
+-...||.+|+-+|++++..||.|||..||.++| .|+..+|+++|.+++-
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHHh
Confidence 4467899999999999999999999999999999 9999999999998753
No 25
>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=97.37 E-value=0.00049 Score=51.59 Aligned_cols=48 Identities=19% Similarity=0.288 Sum_probs=41.3
Q ss_pred CCCCCCHHHHHHHHHHHHhcCC-ch---HHHhhhCC-CC-CHHHHHHHHHHHhh
Q 036087 65 RRGSFTEEEEQIIIDVHRILGN-RW---AQIAKHLP-GR-TDNEVKNYWNSCIK 112 (344)
Q Consensus 65 kkg~WT~EED~~Ll~lv~~~G~-kW---~~IAk~lp-gR-T~~qcknRW~~~lk 112 (344)
.+-.||+||..++++++..+|. .| ..|++.+. .| |..||+.+.+.+.-
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 3568999999999999999996 99 99999873 45 99999999887643
No 26
>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=97.37 E-value=0.00022 Score=63.74 Aligned_cols=52 Identities=21% Similarity=0.457 Sum_probs=45.6
Q ss_pred CCCCCCHHHHHHHHHHHHhc---CC----chHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 036087 65 RRGSFTEEEEQIIIDVHRIL---GN----RWAQIAKHLPGRTDNEVKNYWNSCIKKKLMS 117 (344)
Q Consensus 65 kkg~WT~EED~~Ll~lv~~~---G~----kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~ 117 (344)
+...||.|||.+|.+.|..| |. -...++..| +||+.+|.-||+.++|+++..
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 45689999999999999887 43 389999999 999999999999999998654
No 27
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.31 E-value=0.00036 Score=70.68 Aligned_cols=49 Identities=24% Similarity=0.495 Sum_probs=44.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcC-CchHHHhhhCCCCCHHHHHHHHHHHh
Q 036087 63 DLRRGSFTEEEEQIIIDVHRILG-NRWAQIAKHLPGRTDNEVKNYWNSCI 111 (344)
Q Consensus 63 ~lkkg~WT~EED~~Ll~lv~~~G-~kW~~IAk~lpgRT~~qcknRW~~~l 111 (344)
.+-...||.+|+-+|++++..|| ++|..||.++..||..+|+.+|.+++
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 45567899999999999999999 89999999999999999999997643
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=97.03 E-value=0.0013 Score=60.97 Aligned_cols=99 Identities=22% Similarity=0.377 Sum_probs=71.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccc--cccCcccccchhhcccC-CCC--------------------CCCCCCH
Q 036087 15 LWSPEEDEKLLKHITAHGHGSWSSVPKLAG--LQRCGKSCRLRWINYLR-PDL--------------------RRGSFTE 71 (344)
Q Consensus 15 ~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~--~~Rt~~QCr~Rw~n~L~-p~l--------------------kkg~WT~ 71 (344)
+|++++|-+|+.+|..-. +-..|+.-+. ..-|-+.+.+||+..|. |.+ .+..||.
T Consensus 1 rW~~~DDl~Li~av~~~~--~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~ 78 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN--DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSK 78 (199)
T ss_pred CCCchhhHHHHHHHHHhc--CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCH
Confidence 599999999999998765 4666665332 24556777889997652 221 3678999
Q ss_pred HHHHHHHHHHHhcCC---chHHHhh----hC-CCCCHHHHHHHHHHHhhhhh
Q 036087 72 EEEQIIIDVHRILGN---RWAQIAK----HL-PGRTDNEVKNYWNSCIKKKL 115 (344)
Q Consensus 72 EED~~Ll~lv~~~G~---kW~~IAk----~l-pgRT~~qcknRW~~~lkkkl 115 (344)
+|+++|......... .+.+|=. .| ++||++++.++|..+.+..+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999997765543 4666633 23 78999999999996655544
No 29
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.92 E-value=0.00031 Score=71.76 Aligned_cols=46 Identities=26% Similarity=0.556 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcc
Q 036087 12 KKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINY 59 (344)
Q Consensus 12 kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~ 59 (344)
....||.+|..+|+++|+.||. +|.+||.++| +|+..||..||.+.
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 5568999999999999999998 9999999999 99999999999864
No 30
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.91 E-value=0.00049 Score=71.59 Aligned_cols=46 Identities=24% Similarity=0.581 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcc
Q 036087 12 KKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINY 59 (344)
Q Consensus 12 kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~ 59 (344)
.++.||.+|+.+|+++|+.||. +|.+||.++| +|+..||..|+.+.
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 4788999999999999999998 9999999999 99999999998763
No 31
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.80 E-value=0.0012 Score=52.13 Aligned_cols=49 Identities=31% Similarity=0.618 Sum_probs=34.7
Q ss_pred CCCCCHHHHHHHHHHHHh------cC--C------chHHHhhhC----CCCCHHHHHHHHHHHhhhh
Q 036087 66 RGSFTEEEEQIIIDVHRI------LG--N------RWAQIAKHL----PGRTDNEVKNYWNSCIKKK 114 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~------~G--~------kW~~IAk~l----pgRT~~qcknRW~~~lkkk 114 (344)
+..||.+|...||+++.. ++ . -|..||..| ..||..||++||.++.+.-
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Y 67 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKY 67 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHH
Confidence 357999999999999877 21 1 399999987 4699999999999966553
No 32
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.68 E-value=0.0017 Score=66.40 Aligned_cols=45 Identities=13% Similarity=0.386 Sum_probs=42.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHH
Q 036087 66 RGSFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSC 110 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~ 110 (344)
...||.+|..+|++.+..||..|.+||+++..||..||--||-++
T Consensus 279 dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 279 DKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred cccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 448999999999999999999999999999999999999999654
No 33
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.68 E-value=0.0022 Score=66.82 Aligned_cols=46 Identities=17% Similarity=0.458 Sum_probs=42.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHH
Q 036087 65 RRGSFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSC 110 (344)
Q Consensus 65 kkg~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~ 110 (344)
.+..||.+|..+|++++..||..|.+||.++.+||..||-.++..+
T Consensus 252 ~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 252 ARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred CCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHHHHhc
Confidence 4678999999999999999999999999999999999999998654
No 34
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.36 E-value=0.0058 Score=47.02 Aligned_cols=50 Identities=20% Similarity=0.427 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHHHHHhcC--------Cc-hHHHhhhCC-CCCHHHHHHHHHHHhhhhh
Q 036087 66 RGSFTEEEEQIIIDVHRILG--------NR-WAQIAKHLP-GRTDNEVKNYWNSCIKKKL 115 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G--------~k-W~~IAk~lp-gRT~~qcknRW~~~lkkkl 115 (344)
+.+||.+||+.|++.|+++. ++ |.++++.-+ .+|-...|+||...|+.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 46899999999999996542 22 999999877 8999999999988877654
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.16 E-value=0.0058 Score=55.37 Aligned_cols=52 Identities=21% Similarity=0.389 Sum_probs=43.7
Q ss_pred CCCCCCHHHHHHHHHHHHhcCC-------chHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 036087 65 RRGSFTEEEEQIIIDVHRILGN-------RWAQIAKHLPGRTDNEVKNYWNSCIKKKLMS 117 (344)
Q Consensus 65 kkg~WT~EED~~Ll~lv~~~G~-------kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~ 117 (344)
+...||.|+|.+|.+.|..|+. -...++..| +||..+|..||+.+++++...
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 4678999999999998888762 266777778 999999999999999987643
No 36
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.14 E-value=0.0012 Score=52.08 Aligned_cols=47 Identities=23% Similarity=0.553 Sum_probs=32.5
Q ss_pred CCCCCHHHHHHHHHHHHH--h----C--CC-----Ccccccccc---ccccCcccccchhhcc
Q 036087 13 KGLWSPEEDEKLLKHITA--H----G--HG-----SWSSVPKLA---GLQRCGKSCRLRWINY 59 (344)
Q Consensus 13 kg~WT~EEDe~L~~lV~k--y----G--~~-----~W~~IA~~~---~~~Rt~~QCr~Rw~n~ 59 (344)
|..||.+|...|+.++.. + + .. -|..||..| |..|++.||+.||.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 357999999999999988 2 1 11 399999876 4679999999999874
No 37
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=96.02 E-value=0.0016 Score=50.05 Aligned_cols=52 Identities=21% Similarity=0.382 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCC------CC--ccccccccccccCcccccchhhcccCCCC
Q 036087 13 KGLWSPEEDEKLLKHITAHGH------GS--WSSVPKLAGLQRCGKSCRLRWINYLRPDL 64 (344)
Q Consensus 13 kg~WT~EEDe~L~~lV~kyG~------~~--W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l 64 (344)
|.+||.|||+.|++.|..+.. |+ |.++++.-++.+|-.+-|+||...|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 567999999999999976632 22 99998876657888999999999987653
No 38
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=95.84 E-value=0.003 Score=56.62 Aligned_cols=50 Identities=28% Similarity=0.622 Sum_probs=42.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC-C-----CccccccccccccCcccccchhhcccCC
Q 036087 11 VKKGLWSPEEDEKLLKHITAHGH-G-----SWSSVPKLAGLQRCGKSCRLRWINYLRP 62 (344)
Q Consensus 11 ~kkg~WT~EEDe~L~~lV~kyG~-~-----~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p 62 (344)
.+...||.|||.+|.+.|-+|-. | ....|++.++ ||+..|.=||..+++.
T Consensus 2 ~RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~--RTsAACGFRWNs~VRk 57 (161)
T TIGR02894 2 TRQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALN--RTAAACGFRWNAYVRK 57 (161)
T ss_pred ccccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHc--ccHHHhcchHHHHHHH
Confidence 56778999999999999999932 1 3788888876 9999999999988763
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.49 E-value=0.004 Score=61.28 Aligned_cols=48 Identities=17% Similarity=0.508 Sum_probs=44.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccC
Q 036087 13 KGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLR 61 (344)
Q Consensus 13 kg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~ 61 (344)
--.|+..|+-+|+++....|-|||..||..+| .|+...|+++|..++.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 44699999999999999999999999999999 9999999999998765
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.27 E-value=0.036 Score=42.92 Aligned_cols=48 Identities=29% Similarity=0.578 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHhcC----C-------------chHHHhhhC-----CCCCHHHHHHHHHHHhhh
Q 036087 66 RGSFTEEEEQIIIDVHRILG----N-------------RWAQIAKHL-----PGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G----~-------------kW~~IAk~l-----pgRT~~qcknRW~~~lkk 113 (344)
+..||.+|...|++++.+|. + .|..|+..| +.||..+++.+|.++...
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 45799999999999998862 1 299999876 369999999999987654
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.02 E-value=0.032 Score=55.09 Aligned_cols=46 Identities=24% Similarity=0.493 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHhcC-CchHHHhhhCCCCCHHHHHHHHHHHh
Q 036087 66 RGSFTEEEEQIIIDVHRILG-NRWAQIAKHLPGRTDNEVKNYWNSCI 111 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G-~kW~~IAk~lpgRT~~qcknRW~~~l 111 (344)
-..|+..|+.+|++...-.| ++|..||.++..|+...||.+|....
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y 109 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMY 109 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHH
Confidence 45699999999999999999 89999999998899999999997543
No 42
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.47 E-value=0.068 Score=60.40 Aligned_cols=100 Identities=14% Similarity=0.292 Sum_probs=78.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccc-------hhhcc---------------------------
Q 036087 14 GLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRL-------RWINY--------------------------- 59 (344)
Q Consensus 14 g~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~-------Rw~n~--------------------------- 59 (344)
+.|+.-+=..++.+..+||..+-..||..|. +++...++. ||..+
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~-~k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~ 903 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEME-GKTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAI 903 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhc-CCCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3599999999999999999989999999987 777776652 22210
Q ss_pred ---------------c-CCCCCCCCCCHHHHHHHHHHHHhcC-CchHHHhhh------------CCCCCHHHHHHHHHHH
Q 036087 60 ---------------L-RPDLRRGSFTEEEEQIIIDVHRILG-NRWAQIAKH------------LPGRTDNEVKNYWNSC 110 (344)
Q Consensus 60 ---------------L-~p~lkkg~WT~EED~~Ll~lv~~~G-~kW~~IAk~------------lpgRT~~qcknRW~~~ 110 (344)
+ .+.-++..+|.+||..|+-.+.+|| .+|..|-.. +..||+..+..|...+
T Consensus 904 ~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l 983 (1033)
T PLN03142 904 GKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTL 983 (1033)
T ss_pred HHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHH
Confidence 0 1223455699999999999999999 679998542 2579999999999998
Q ss_pred hhhh
Q 036087 111 IKKK 114 (344)
Q Consensus 111 lkkk 114 (344)
++--
T Consensus 984 ~~~~ 987 (1033)
T PLN03142 984 IRLI 987 (1033)
T ss_pred HHHH
Confidence 8764
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.21 E-value=0.023 Score=44.08 Aligned_cols=49 Identities=24% Similarity=0.418 Sum_probs=39.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC----------------CCccccccccc----cccCcccccchhhccc
Q 036087 12 KKGLWSPEEDEKLLKHITAHGH----------------GSWSSVPKLAG----LQRCGKSCRLRWINYL 60 (344)
Q Consensus 12 kkg~WT~EEDe~L~~lV~kyG~----------------~~W~~IA~~~~----~~Rt~~QCr~Rw~n~L 60 (344)
++..||.+|.+.|+++|++|.. .-|..|+..+. ..|+..|++.+|.++.
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 3567999999999999999821 13999998762 2699999999998754
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=93.80 E-value=0.014 Score=52.83 Aligned_cols=50 Identities=24% Similarity=0.505 Sum_probs=39.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCC------ccccccccccccCcccccchhhcccC
Q 036087 10 KVKKGLWSPEEDEKLLKHITAHGHGS------WSSVPKLAGLQRCGKSCRLRWINYLR 61 (344)
Q Consensus 10 ~~kkg~WT~EEDe~L~~lV~kyG~~~------W~~IA~~~~~~Rt~~QCr~Rw~n~L~ 61 (344)
+.+...||.|||.+|-+.|-+|+... ...++..+. |++.+|..||..+++
T Consensus 2 k~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 2 KTRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred cchhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 45778999999999999999996533 455555655 999999999976655
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=91.73 E-value=0.2 Score=50.79 Aligned_cols=86 Identities=22% Similarity=0.358 Sum_probs=63.7
Q ss_pred CccccccccccccCcccccchhhcccCCC-------------------------CCCCCCCHHHHHHHHHHHHhcCCchH
Q 036087 35 SWSSVPKLAGLQRCGKSCRLRWINYLRPD-------------------------LRRGSFTEEEEQIIIDVHRILGNRWA 89 (344)
Q Consensus 35 ~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~-------------------------lkkg~WT~EED~~Ll~lv~~~G~kW~ 89 (344)
.|.-+.=..+ -|...--..||.+.-++. +....||.+|-+.|+++.+.|.-+|-
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 PWKWVPFTNS-ARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEYEAHLNDNSWSKEETDYLFDLCKRFDLRFF 153 (445)
T ss_pred CceeeccCCc-cccCCceEEeeeeccCCCCCCchhhhccccCccccchHHHHHhhccccccHHHHHHHHHHHHhcCeeEE
Confidence 4665554333 566666677777663321 22356999999999999999999999
Q ss_pred HHhhh-----CCC-CCHHHHHHHHHHHhhhhhhhCCCC
Q 036087 90 QIAKH-----LPG-RTDNEVKNYWNSCIKKKLMSKGLD 121 (344)
Q Consensus 90 ~IAk~-----lpg-RT~~qcknRW~~~lkkkl~~~~~~ 121 (344)
.||.. ++. ||-..+|.||+..-++-++...-.
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 99976 555 999999999998888776654433
No 46
>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=91.43 E-value=0.48 Score=37.65 Aligned_cols=46 Identities=30% Similarity=0.557 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhc---CC----------chHHHhhhC---C--CCCHHHHHHHHHHHhhh
Q 036087 68 SFTEEEEQIIIDVHRIL---GN----------RWAQIAKHL---P--GRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 68 ~WT~EED~~Ll~lv~~~---G~----------kW~~IAk~l---p--gRT~~qcknRW~~~lkk 113 (344)
.||+++++.|++++.+. |+ .|..|+..| . ..+..||++||..+.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~~ 64 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKKD 64 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHHH
Confidence 59999999999987542 21 299999877 2 35789999999876655
No 47
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=91.19 E-value=0.39 Score=47.42 Aligned_cols=50 Identities=22% Similarity=0.389 Sum_probs=40.4
Q ss_pred CCCCCHHHHHHHHHHHHhc----------CCchHHHhhhC----CCCCHHHHHHHHHHHhhhhh
Q 036087 66 RGSFTEEEEQIIIDVHRIL----------GNRWAQIAKHL----PGRTDNEVKNYWNSCIKKKL 115 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~----------G~kW~~IAk~l----pgRT~~qcknRW~~~lkkkl 115 (344)
...|+.+|-..||++..+. +..|..||+.+ .-||+.+||++|.++.++.-
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk 117 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYK 117 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHH
Confidence 3689999999999987653 23499999965 45999999999999776643
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=90.50 E-value=0.47 Score=40.63 Aligned_cols=51 Identities=24% Similarity=0.479 Sum_probs=40.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCC----chHHHhhhC------------CCCCHHHHHHHHHHHhhh
Q 036087 63 DLRRGSFTEEEEQIIIDVHRILGN----RWAQIAKHL------------PGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 63 ~lkkg~WT~EED~~Ll~lv~~~G~----kW~~IAk~l------------pgRT~~qcknRW~~~lkk 113 (344)
.-++..||++||.-|+-.+.+||- .|..|...+ ..||+..+..|...+++-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~ 112 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKL 112 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHH
Confidence 456779999999999999999995 698887532 469999999999998875
No 49
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=89.65 E-value=0.93 Score=46.92 Aligned_cols=49 Identities=20% Similarity=0.358 Sum_probs=44.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 65 RRGSFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 65 kkg~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
-...||.||--++-.+...||.++.+|.+.||.|+-..+...|+...+.
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~ 234 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKT 234 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHH
Confidence 3558999999999999999999999999999999999999998876554
No 50
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=87.69 E-value=0.86 Score=46.24 Aligned_cols=47 Identities=17% Similarity=0.258 Sum_probs=42.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 67 GSFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 67 g~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.+|+.+|-++...+..++|..+..|+..+|.|..+|||.+|.+--++
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 47999999999999999999999999999999999999999754433
No 51
>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=83.59 E-value=3.2 Score=29.49 Aligned_cols=42 Identities=29% Similarity=0.359 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 71 EEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 71 ~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
++++..++.++...|-.|.+||..+ |.+...|+.+....+++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARKK 53 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHhh
Confidence 4677888888888999999999999 99999999988776553
No 52
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=80.75 E-value=1 Score=45.75 Aligned_cols=67 Identities=25% Similarity=0.364 Sum_probs=52.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhccc--CCC-----C-CCCCCCHHHHHHHH
Q 036087 10 KVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYL--RPD-----L-RRGSFTEEEEQIII 78 (344)
Q Consensus 10 ~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L--~p~-----l-kkg~WT~EED~~Ll 78 (344)
+..--+||.+|-++..++...+|. +...|+.+++ .|..+|++.+|.+-- +|. + .+.++..+|--+|.
T Consensus 362 ~~~~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP-~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~ 436 (507)
T COG5118 362 KKGALRWSKKEIEKFYKALSIWGT-DFSLISSLFP-NRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLR 436 (507)
T ss_pred CCCCCcccHHHHHHHHHHHHHhcc-hHHHHHHhcC-chhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHH
Confidence 445568999999999999999999 9999999999 999999999988642 221 1 24466666665443
No 53
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=78.26 E-value=0.77 Score=45.38 Aligned_cols=48 Identities=25% Similarity=0.410 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHHh----CC-----CCcccccccc---ccccCcccccchhhccc
Q 036087 13 KGLWSPEEDEKLLKHITAH----GH-----GSWSSVPKLA---GLQRCGKSCRLRWINYL 60 (344)
Q Consensus 13 kg~WT~EEDe~L~~lV~ky----G~-----~~W~~IA~~~---~~~Rt~~QCr~Rw~n~L 60 (344)
...|+.+|-..|+++..+. .. .-|..||..+ |..|++.||+.||.++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 3789999999999988654 11 2499999843 45799999999998743
No 54
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=77.70 E-value=2.2 Score=34.24 Aligned_cols=30 Identities=33% Similarity=0.681 Sum_probs=17.1
Q ss_pred CCCCCCCCCHHHHHHH--------HHHHHHhCCCCcccccc
Q 036087 9 QKVKKGLWSPEEDEKL--------LKHITAHGHGSWSSVPK 41 (344)
Q Consensus 9 p~~kkg~WT~EEDe~L--------~~lV~kyG~~~W~~IA~ 41 (344)
|....|.||+|+|+.| .+++++|| +..|+.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG---~~~i~~ 80 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHG---EERIER 80 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH----HHHHHH
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhC---HHHHHH
Confidence 4456899999999999 45667777 444443
No 55
>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=74.96 E-value=1.8 Score=37.04 Aligned_cols=35 Identities=31% Similarity=0.463 Sum_probs=29.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC---CCccccccccc
Q 036087 10 KVKKGLWSPEEDEKLLKHITAHGH---GSWSSVPKLAG 44 (344)
Q Consensus 10 ~~kkg~WT~EEDe~L~~lV~kyG~---~~W~~IA~~~~ 44 (344)
..++..||.+||.-|+-.+.+||- +.|..|-..+-
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir 83 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIR 83 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHH
Confidence 567888999999999999999999 89999987653
No 56
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=71.09 E-value=6.7 Score=34.25 Aligned_cols=46 Identities=11% Similarity=0.207 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHhcC-CchHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 036087 71 EEEEQIIIDVHRILG-NRWAQIAKHLPGRTDNEVKNYWNSCIKKKLMS 117 (344)
Q Consensus 71 ~EED~~Ll~lv~~~G-~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~ 117 (344)
.+-|.+|+++..+-| ..|++||+.+ |-+...|+.|++.+....+.+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI~ 54 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGIIT 54 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 357888999888887 5699999999 999999999998877776544
No 57
>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=69.29 E-value=2.5 Score=33.46 Aligned_cols=44 Identities=23% Similarity=0.540 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------Cccccccccc----cccCcccccchhhc
Q 036087 15 LWSPEEDEKLLKHITAH---GHG---------SWSSVPKLAG----LQRCGKSCRLRWIN 58 (344)
Q Consensus 15 ~WT~EEDe~L~~lV~ky---G~~---------~W~~IA~~~~----~~Rt~~QCr~Rw~n 58 (344)
.||+++++.|++++... |.. .|..|+..+. ...+..||+.||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999988655 221 2888887653 34566788888764
No 58
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=68.18 E-value=8.7 Score=42.22 Aligned_cols=46 Identities=11% Similarity=0.182 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHh
Q 036087 66 RGSFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCI 111 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~l 111 (344)
...||..|-.+.-+++..|...+..|++.++++|-.||-..|+...
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWK 664 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWK 664 (907)
T ss_pred cccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHH
Confidence 3579999999999999999999999999999999999999877543
No 59
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=67.50 E-value=7.9 Score=41.61 Aligned_cols=50 Identities=18% Similarity=0.502 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCchHHHhh----------hCCCCCHHHHHHHHHHHhhhhh
Q 036087 66 RGSFTEEEEQIIIDVHRILGNRWAQIAK----------HLPGRTDNEVKNYWNSCIKKKL 115 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G~kW~~IAk----------~lpgRT~~qcknRW~~~lkkkl 115 (344)
+..||.+|+.-...+++++|..+.+|-+ ...-+|..|+|.+|+..+++.-
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~ 147 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMN 147 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHH
Confidence 6689999999999999999999998822 2344688899999998887743
No 60
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=67.00 E-value=12 Score=26.10 Aligned_cols=38 Identities=21% Similarity=0.357 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHhcCC-chHHHhhhCCCCCHHHHHHHHHHH
Q 036087 72 EEEQIIIDVHRILGN-RWAQIAKHLPGRTDNEVKNYWNSC 110 (344)
Q Consensus 72 EED~~Ll~lv~~~G~-kW~~IAk~lpgRT~~qcknRW~~~ 110 (344)
+=|.+|+.+...-|. .|..||+.+ |=|...|..|+..+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~l-glS~~~v~~Ri~rL 41 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEEL-GLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHH-TS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHH-CcCHHHHHHHHHHh
Confidence 457888888888884 599999999 88999999998764
No 61
>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=66.98 E-value=19 Score=36.03 Aligned_cols=48 Identities=21% Similarity=0.503 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHhc-CC---chHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 66 RGSFTEEEEQIIIDVHRIL-GN---RWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~-G~---kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
-..||.-|.+.|+++.+.. |. .-..|++.++||+..+|++.-+.+..+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~r 72 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGR 72 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHH
Confidence 4579999999999987755 43 356889999999999999976655444
No 62
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=65.67 E-value=8.6 Score=33.99 Aligned_cols=46 Identities=9% Similarity=0.125 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHhcC-CchHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 036087 71 EEEEQIIIDVHRILG-NRWAQIAKHLPGRTDNEVKNYWNSCIKKKLMS 117 (344)
Q Consensus 71 ~EED~~Ll~lv~~~G-~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~ 117 (344)
.+-|.+|+.+..+-| -.|.+||+.+ |-+...|+.|++.+.+..+.+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~GvI~ 59 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGFIQ 59 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCeE
Confidence 567888888888877 4699999999 999999999998887776543
No 63
>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=65.48 E-value=17 Score=25.52 Aligned_cols=41 Identities=24% Similarity=0.375 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 72 EEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 72 EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
+++..++.+.-..|-.+.+||..+ |-+...|+.+-...+++
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~l-g~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERL-GISRSTVRRILKRALKK 47 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHH-TSCHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHH-CCcHHHHHHHHHHHHHH
Confidence 455556666656677899999999 88999999988877765
No 64
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=63.53 E-value=9 Score=39.23 Aligned_cols=47 Identities=15% Similarity=0.210 Sum_probs=41.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccccc-----cccccCcccccchhhcc
Q 036087 12 KKGLWSPEEDEKLLKHITAHGHGSWSSVPKL-----AGLQRCGKSCRLRWINY 59 (344)
Q Consensus 12 kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~-----~~~~Rt~~QCr~Rw~n~ 59 (344)
.-..||.+|-+-|.++.++|.- .|-.||.+ .+..||-...++||..+
T Consensus 129 ~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 129 NDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred ccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 3467999999999999999998 89999987 56459999999999864
No 65
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=60.79 E-value=4.1 Score=44.59 Aligned_cols=44 Identities=16% Similarity=0.290 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhc
Q 036087 13 KGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWIN 58 (344)
Q Consensus 13 kg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n 58 (344)
...||+.|-.+..+++..|.. +...|++.+. +++.+||-+-|+.
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 457999999999999999998 9999999998 9999999987653
No 66
>smart00595 MADF subfamily of SANT domain.
Probab=58.63 E-value=11 Score=29.49 Aligned_cols=26 Identities=31% Similarity=0.670 Sum_probs=22.0
Q ss_pred chHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 87 RWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 87 kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
-|..||..| |.+..+|+.+|.++...
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR~~ 54 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLRDR 54 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 399999999 55999999999987544
No 67
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=57.57 E-value=56 Score=33.47 Aligned_cols=46 Identities=20% Similarity=0.291 Sum_probs=40.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCchHHHhh-hCCCCCHHHHHHHHHHHhh
Q 036087 67 GSFTEEEEQIIIDVHRILGNRWAQIAK-HLPGRTDNEVKNYWNSCIK 112 (344)
Q Consensus 67 g~WT~EED~~Ll~lv~~~G~kW~~IAk-~lpgRT~~qcknRW~~~lk 112 (344)
..|+++|=+..-+.++.||..+..|.+ +++.|+-..|-..|+...+
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWKk 324 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWKK 324 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhhc
Confidence 479999999999999999999999965 5899999999998875443
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=54.80 E-value=28 Score=29.11 Aligned_cols=35 Identities=23% Similarity=0.360 Sum_probs=27.1
Q ss_pred HHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 78 IDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 78 l~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
+.+.-..|-.+.+||+.+ |.+...|+.+....+++
T Consensus 122 l~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 122 FILSRFEGKSYKEIAEEL-GISVKTVEYHISKALKE 156 (161)
T ss_pred HHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 333334567899999999 99999999999886554
No 69
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=53.84 E-value=26 Score=32.76 Aligned_cols=47 Identities=13% Similarity=0.249 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHhcCCchHHHhhhC---CCCCHHHHHHHHHHHhhhhh
Q 036087 68 SFTEEEEQIIIDVHRILGNRWAQIAKHL---PGRTDNEVKNYWNSCIKKKL 115 (344)
Q Consensus 68 ~WT~EED~~Ll~lv~~~G~kW~~IAk~l---pgRT~~qcknRW~~~lkkkl 115 (344)
.|++++|-.|+.+|.. |+.-..|++.+ -.-|-..+..||+.+|....
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~ 50 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYDPV 50 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcChh
Confidence 4999999999998865 55556665543 34589999999999987643
No 70
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=53.19 E-value=4.5 Score=28.25 Aligned_cols=38 Identities=24% Similarity=0.366 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHhCCCCccccccccccccCcccccchhhc
Q 036087 19 EEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWIN 58 (344)
Q Consensus 19 EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n 58 (344)
+=|.+|+.+...-|...|.+||+.+| =+...|..|+.+
T Consensus 3 ~~D~~Il~~Lq~d~r~s~~~la~~lg--lS~~~v~~Ri~r 40 (42)
T PF13404_consen 3 ELDRKILRLLQEDGRRSYAELAEELG--LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHHHH-TTS-HHHHHHHHT--S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHC--cCHHHHHHHHHH
Confidence 45888999999999889999999998 778888888754
No 71
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=50.61 E-value=5.8 Score=34.61 Aligned_cols=45 Identities=11% Similarity=0.199 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCC
Q 036087 18 PEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDL 64 (344)
Q Consensus 18 ~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l 64 (344)
.+-|.+|+++..+.|.-.|.+||+.+| -+...|+.|+.+....++
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 357999999999999989999999997 889999999988765543
No 72
>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=50.16 E-value=20 Score=32.24 Aligned_cols=40 Identities=28% Similarity=0.286 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHH
Q 036087 68 SFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWN 108 (344)
Q Consensus 68 ~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~ 108 (344)
.||+|+.++|.+|..+ |..=.+||+.|.|.|.+.|.-+-+
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~h 41 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAH 41 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhh
Confidence 5999999999998754 777899999997799998876654
No 73
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=48.30 E-value=17 Score=42.18 Aligned_cols=29 Identities=38% Similarity=0.674 Sum_probs=26.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccccc
Q 036087 12 KKGLWSPEEDEKLLKHITAHGHGSWSSVP 40 (344)
Q Consensus 12 kkg~WT~EEDe~L~~lV~kyG~~~W~~IA 40 (344)
.---|..+||..|+-.|-+||.++|..|-
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir 1160 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIR 1160 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhc
Confidence 34569999999999999999999999986
No 74
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=47.22 E-value=20 Score=38.50 Aligned_cols=47 Identities=15% Similarity=0.299 Sum_probs=42.8
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHH
Q 036087 64 LRRGSFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSC 110 (344)
Q Consensus 64 lkkg~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~ 110 (344)
...+.|+.+|-++.-....+.|...+.|+..+|+|..+|+|.++..-
T Consensus 407 ~~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~e 453 (584)
T KOG2009|consen 407 LETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKE 453 (584)
T ss_pred cccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhh
Confidence 34678999999999999999999999999999999999999998643
No 75
>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=45.94 E-value=10 Score=30.36 Aligned_cols=18 Identities=28% Similarity=0.578 Sum_probs=10.5
Q ss_pred CCCCCCCCCHHHHHHHHH
Q 036087 62 PDLRRGSFTEEEEQIIID 79 (344)
Q Consensus 62 p~lkkg~WT~EED~~Ll~ 79 (344)
|.-..|-||+++|+.|..
T Consensus 43 P~n~~GiWT~eDD~~L~~ 60 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRS 60 (87)
T ss_dssp -TT-TT---HHHHHHHTS
T ss_pred CCCCCCCcCHHHHHHHHc
Confidence 555688999999999943
No 76
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=45.02 E-value=42 Score=37.54 Aligned_cols=14 Identities=21% Similarity=0.107 Sum_probs=9.7
Q ss_pred ccccccccccCCCC
Q 036087 254 TDENYCMWGTNTNI 267 (344)
Q Consensus 254 ~d~~~~~~~~~~~~ 267 (344)
|-++|+|..+.|+-
T Consensus 639 ~s~~cFWvkv~Edk 652 (1102)
T KOG1924|consen 639 LSENCFWVKVNEDK 652 (1102)
T ss_pred cCccceeeecchhh
Confidence 34688888777663
No 77
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=44.94 E-value=6.3 Score=34.86 Aligned_cols=45 Identities=20% Similarity=0.233 Sum_probs=38.7
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCC
Q 036087 18 PEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDL 64 (344)
Q Consensus 18 ~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l 64 (344)
.+-|.+|+.+..+.|.-.|.+||+.+| -+...|+.|+.+..+.++
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 567999999999999889999999998 888899999988766554
No 78
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=43.24 E-value=53 Score=25.83 Aligned_cols=38 Identities=13% Similarity=0.315 Sum_probs=27.2
Q ss_pred HHHHHHHhcCC--------chHHHhhhCCC---CC--HHHHHHHHHHHhhh
Q 036087 76 IIIDVHRILGN--------RWAQIAKHLPG---RT--DNEVKNYWNSCIKK 113 (344)
Q Consensus 76 ~Ll~lv~~~G~--------kW~~IAk~lpg---RT--~~qcknRW~~~lkk 113 (344)
+|..+|.+.|+ .|..||+.+.- -+ ..++|..|..+|.+
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 46677777773 59999999821 12 36789999887754
No 79
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=43.16 E-value=19 Score=38.86 Aligned_cols=47 Identities=15% Similarity=0.352 Sum_probs=36.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCCCcccccc----------ccccccCcccccchhhccc
Q 036087 12 KKGLWSPEEDEKLLKHITAHGHGSWSSVPK----------LAGLQRCGKSCRLRWINYL 60 (344)
Q Consensus 12 kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~----------~~~~~Rt~~QCr~Rw~n~L 60 (344)
+|..||..|.+....+++.+|. +...|-+ ... -++..|+|.+|++.+
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~-~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQ-SKTKDQVRHYYYRLV 143 (782)
T ss_pred cccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchh-hhhhHHHHHHHHHHH
Confidence 3668999999999999999998 9988832 222 456678888887654
No 80
>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=42.28 E-value=52 Score=26.57 Aligned_cols=33 Identities=27% Similarity=0.319 Sum_probs=25.7
Q ss_pred HHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 80 VHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 80 lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
+....|..+.+||+.+ |-+...++++....+++
T Consensus 121 ~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 121 LRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred hHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334577899999999 77999999988876554
No 81
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=42.26 E-value=49 Score=26.54 Aligned_cols=45 Identities=18% Similarity=0.204 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHhcC-CchHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 036087 72 EEEQIIIDVHRILG-NRWAQIAKHLPGRTDNEVKNYWNSCIKKKLMS 117 (344)
Q Consensus 72 EED~~Ll~lv~~~G-~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~ 117 (344)
+.|.+|+.+..+.| -.+..||+.+ |-+...|+.+...+.+..+..
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCee
Confidence 56888888888877 4699999999 999999999998887776544
No 82
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=42.16 E-value=2.1e+02 Score=29.55 Aligned_cols=72 Identities=19% Similarity=0.268 Sum_probs=45.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCCCCCCCCHHHHHHHHHHHHhcCCch
Q 036087 9 QKVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQIIIDVHRILGNRW 88 (344)
Q Consensus 9 p~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~~Ll~lv~~~G~kW 88 (344)
.+.--|.|+++=|+...++...|.. .||..--+++-= +.||. =
T Consensus 72 ~~daegvWSpdIEqsFqEALaiypp-----------cGrrKIilsdeg-------------------------kmyGR-N 114 (455)
T KOG3841|consen 72 QRDAEGVWSPDIEQSFQEALAIYPP-----------CGRRKIILSDEG-------------------------KMYGR-N 114 (455)
T ss_pred ccccccccChhHHHHHHHHHhhcCC-----------CCceeEEEccCc-------------------------cccch-H
Confidence 4456789999999999999999876 233322111110 11221 1
Q ss_pred HHHhhhC-----CCCCHHHHHHHHHHHhhhhhhh
Q 036087 89 AQIAKHL-----PGRTDNEVKNYWNSCIKKKLMS 117 (344)
Q Consensus 89 ~~IAk~l-----pgRT~~qcknRW~~~lkkkl~~ 117 (344)
..||+.+ ..||.+||-.+-+.+-|+++++
T Consensus 115 ELIarYIKlrtgktRTrKQVSSHIQVlarrk~re 148 (455)
T KOG3841|consen 115 ELIARYIKLRTGKTRTRKQVSSHIQVLARRKLRE 148 (455)
T ss_pred HHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHH
Confidence 3333332 4699999999998888887664
No 83
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=41.75 E-value=51 Score=29.46 Aligned_cols=40 Identities=15% Similarity=0.243 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 73 EEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 73 ED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
+..+++++....|-.+.+||+.+ |-+...++.+|.....+
T Consensus 139 ~~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR~~ 178 (185)
T PF07638_consen 139 RQRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRARAW 178 (185)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 33444445455678899999999 99999999999876533
No 84
>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=40.73 E-value=37 Score=27.22 Aligned_cols=29 Identities=21% Similarity=0.539 Sum_probs=23.6
Q ss_pred HHHHHHHHHhcCCchHHHhhhCCCCCHHHH
Q 036087 74 EQIIIDVHRILGNRWAQIAKHLPGRTDNEV 103 (344)
Q Consensus 74 D~~Ll~lv~~~G~kW~~IAk~lpgRT~~qc 103 (344)
|+.|..+....|..|..+|.+| |=|..+|
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 5678889999999999999998 6555544
No 85
>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=40.14 E-value=28 Score=26.19 Aligned_cols=27 Identities=22% Similarity=0.539 Sum_probs=21.7
Q ss_pred chHHHhhhCCC-CCHHHHHHHHHHHhhh
Q 036087 87 RWAQIAKHLPG-RTDNEVKNYWNSCIKK 113 (344)
Q Consensus 87 kW~~IAk~lpg-RT~~qcknRW~~~lkk 113 (344)
-|..||..+.. -+..+|+.||.++...
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~ 55 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDR 55 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHH
Confidence 49999999943 5788999999986654
No 86
>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=39.80 E-value=68 Score=32.23 Aligned_cols=86 Identities=16% Similarity=0.332 Sum_probs=59.1
Q ss_pred CCCCCHHHHHHHHHHHHHhCCCCc---cccccccccccCcccccchhhcccCCCCCCCCCCHHHHHHHHHHHHh-c----
Q 036087 13 KGLWSPEEDEKLLKHITAHGHGSW---SSVPKLAGLQRCGKSCRLRWINYLRPDLRRGSFTEEEEQIIIDVHRI-L---- 84 (344)
Q Consensus 13 kg~WT~EEDe~L~~lV~kyG~~~W---~~IA~~~~~~Rt~~QCr~Rw~n~L~p~lkkg~WT~EED~~Ll~lv~~-~---- 84 (344)
-..||.-|...|+++........+ .+|++.+. +|+..++++ |.+.|+ +..+.+++++ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~-~Rs~aEI~~-fl~~LK------------~rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELP-GRSEAEIRD-FLQQLK------------GRVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhcc-CcCHHHHHH-HHHHHH------------HHHHHHHHHHhccccc
Confidence 467999999999998886633344 46677777 899988876 344443 2344444444 2
Q ss_pred -CC------------chHHHhhhCCCCCHHHHHHHHHHHhh
Q 036087 85 -GN------------RWAQIAKHLPGRTDNEVKNYWNSCIK 112 (344)
Q Consensus 85 -G~------------kW~~IAk~lpgRT~~qcknRW~~~lk 112 (344)
|. -|..+|+.+.|.-...+-.-|-..|.
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 11 29999999988888888777766553
No 87
>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=39.03 E-value=86 Score=20.62 Aligned_cols=41 Identities=22% Similarity=0.302 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHh
Q 036087 69 FTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCI 111 (344)
Q Consensus 69 WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~l 111 (344)
++++ +..++.+.-..|..+..||+.+ |-+...|+.+.....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~~ 51 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRAL 51 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 4444 4455555555677899999998 778888877665543
No 88
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=37.38 E-value=73 Score=25.35 Aligned_cols=38 Identities=13% Similarity=0.327 Sum_probs=27.9
Q ss_pred HHHHHHHhcCC--------chHHHhhhCCC-----CCHHHHHHHHHHHhhh
Q 036087 76 IIIDVHRILGN--------RWAQIAKHLPG-----RTDNEVKNYWNSCIKK 113 (344)
Q Consensus 76 ~Ll~lv~~~G~--------kW~~IAk~lpg-----RT~~qcknRW~~~lkk 113 (344)
+|..+|.+.|+ .|..||..+.- ....+++..|..+|.+
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 46677777763 59999999822 2457889989888765
No 89
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.29 E-value=67 Score=27.40 Aligned_cols=30 Identities=20% Similarity=0.209 Sum_probs=24.1
Q ss_pred hcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 83 ILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 83 ~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
..|-.+..||+.+ |.+...|+.+....+++
T Consensus 142 ~~~~s~~eIA~~l-gis~~tV~~~l~ra~~~ 171 (182)
T PRK09652 142 IEGLSYEEIAEIM-GCPIGTVRSRIFRAREA 171 (182)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 4567899999999 88999999887765544
No 90
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=34.81 E-value=75 Score=27.01 Aligned_cols=30 Identities=23% Similarity=0.257 Sum_probs=24.0
Q ss_pred hcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 83 ILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 83 ~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
..|-....||+.+ |-+...|+++....+++
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~~~ 168 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRARQL 168 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467799999999 88999999988765544
No 91
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=32.95 E-value=86 Score=27.90 Aligned_cols=30 Identities=23% Similarity=0.267 Sum_probs=24.4
Q ss_pred hcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 83 ILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 83 ~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
..|....+||..+ |-+...|++|+...+++
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar~~ 177 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGRAR 177 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3567899999999 88999999999665444
No 92
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=31.87 E-value=31 Score=37.09 Aligned_cols=48 Identities=21% Similarity=0.405 Sum_probs=44.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhc
Q 036087 9 QKVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWIN 58 (344)
Q Consensus 9 p~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n 58 (344)
++...++|+.+|-++..++....|. +...|+..++ .|..+|++.+|..
T Consensus 405 k~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p-~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 405 KKLETDKWDASETELFYKALSERGS-DFSLISNLFP-LRDRKQIKAKFKK 452 (584)
T ss_pred CccccCcccchhhHHhhhHHhhhcc-cccccccccc-cccHHHHHHHHhh
Confidence 6677899999999999999999998 9999999998 9999999988764
No 93
>PRK04217 hypothetical protein; Provisional
Probab=31.22 E-value=1.1e+02 Score=25.94 Aligned_cols=45 Identities=22% Similarity=0.099 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 67 GSFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 67 g~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
..-|.+| ..++.+....|-...+||+.+ |.+...|+.+++...++
T Consensus 41 ~~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArkk 85 (110)
T PRK04217 41 IFMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARKK 85 (110)
T ss_pred ccCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 3466666 577777777788999999999 99999999999875544
No 94
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=31.06 E-value=85 Score=26.59 Aligned_cols=46 Identities=11% Similarity=0.137 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHhcC-CchHHHhhhCCCCCHHHHHHHHHHHhhhhhhh
Q 036087 71 EEEEQIIIDVHRILG-NRWAQIAKHLPGRTDNEVKNYWNSCIKKKLMS 117 (344)
Q Consensus 71 ~EED~~Ll~lv~~~G-~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~~ 117 (344)
.+-|.+|+++.++.+ ..+..||+.+ |-+...|++|-+.+.+..+.+
T Consensus 7 D~~D~~IL~~L~~d~r~~~~eia~~l-glS~~~v~~Ri~~L~~~GiI~ 53 (154)
T COG1522 7 DDIDRRILRLLQEDARISNAELAERV-GLSPSTVLRRIKRLEEEGVIK 53 (154)
T ss_pred cHHHHHHHHHHHHhCCCCHHHHHHHH-CCCHHHHHHHHHHHHHCCcee
Confidence 356778888888777 4699999999 899999999998877776544
No 95
>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=31.04 E-value=74 Score=25.50 Aligned_cols=31 Identities=23% Similarity=0.418 Sum_probs=24.6
Q ss_pred HHHHHHHHHhcCCchHHHhhhCCCCCHHHHHH
Q 036087 74 EQIIIDVHRILGNRWAQIAKHLPGRTDNEVKN 105 (344)
Q Consensus 74 D~~Ll~lv~~~G~kW~~IAk~lpgRT~~qckn 105 (344)
|.+|..+....|..|.++|..| |=+...|..
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 5678888899999999999999 656655433
No 96
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=29.37 E-value=1e+02 Score=26.70 Aligned_cols=29 Identities=14% Similarity=-0.008 Sum_probs=23.7
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|..+.+||..+ |-+...++++....+++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456799999999 88999999988766554
No 97
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=29.23 E-value=42 Score=29.87 Aligned_cols=47 Identities=19% Similarity=0.151 Sum_probs=33.5
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCCCccccccccc---cccCcccccchhhc
Q 036087 11 VKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAG---LQRCGKSCRLRWIN 58 (344)
Q Consensus 11 ~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~---~~Rt~~QCr~Rw~n 58 (344)
.+...-|..|.+-|..+|++||. ++...|.-.. ...|+.||+.+...
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~~ 161 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIRK 161 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHHH
Confidence 45667899999999999999997 8888875332 13555555555443
No 98
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=28.68 E-value=31 Score=36.11 Aligned_cols=48 Identities=10% Similarity=0.126 Sum_probs=41.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccchhhc
Q 036087 9 QKVKKGLWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWIN 58 (344)
Q Consensus 9 p~~kkg~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n 58 (344)
.+-....||.||--++-++...||. +..+|-+.|+ +|+-..++.-|..
T Consensus 183 r~~~~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~LP-~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 183 RTEFPDEWTAEDIVLFEQAFQFFGK-DFHKIRQALP-HRSLASLVQYYYS 230 (534)
T ss_pred cCCCcccchHHHHHHHHHHHHHhcc-cHHHHHHHcc-CccHHHHHHHHHH
Confidence 3445678999999999999999998 9999999998 9988888775543
No 99
>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=27.66 E-value=93 Score=27.05 Aligned_cols=29 Identities=14% Similarity=0.114 Sum_probs=23.6
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|-...+||..+ |-+...|+++....+++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~~ 181 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAREA 181 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 356789999999 88899999998776554
No 100
>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=27.35 E-value=1.5e+02 Score=26.28 Aligned_cols=47 Identities=13% Similarity=0.171 Sum_probs=38.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCchHHHhhhCC----CCCHHHHHHHHHHHh
Q 036087 65 RRGSFTEEEEQIIIDVHRILGNRWAQIAKHLP----GRTDNEVKNYWNSCI 111 (344)
Q Consensus 65 kkg~WT~EED~~Ll~lv~~~G~kW~~IAk~lp----gRT~~qcknRW~~~l 111 (344)
....-|..|..-|..|+.+||..+...+.-.. -.|..||+.+...+.
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 45578999999999999999999999987542 379999999887653
No 101
>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=27.14 E-value=1.2e+02 Score=25.99 Aligned_cols=29 Identities=24% Similarity=0.392 Sum_probs=23.8
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|-....||..+ |-|...|+++....+++
T Consensus 134 ~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 134 HDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 88999999998876655
No 102
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=26.51 E-value=1.7e+02 Score=25.22 Aligned_cols=32 Identities=28% Similarity=0.448 Sum_probs=26.0
Q ss_pred HhcCCchHHHhhhCCCCCHHHHHHHHHHHhhhh
Q 036087 82 RILGNRWAQIAKHLPGRTDNEVKNYWNSCIKKK 114 (344)
Q Consensus 82 ~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkkk 114 (344)
...|-...+||..+ |.+...|+.+-...+++-
T Consensus 132 ~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~ 163 (172)
T PRK12523 132 RLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQC 163 (172)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHH
Confidence 34567899999999 999999999987766654
No 103
>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=26.50 E-value=71 Score=25.08 Aligned_cols=29 Identities=28% Similarity=0.769 Sum_probs=22.6
Q ss_pred HHHHHHHHHhcCCchHHHhhhCCCCCHHHH
Q 036087 74 EQIIIDVHRILGNRWAQIAKHLPGRTDNEV 103 (344)
Q Consensus 74 D~~Ll~lv~~~G~kW~~IAk~lpgRT~~qc 103 (344)
|..|..+.+..|..|.++|++| |-+..+|
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHH
Confidence 4567778888999999999999 5555444
No 104
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=26.48 E-value=1.1e+02 Score=25.21 Aligned_cols=48 Identities=19% Similarity=0.160 Sum_probs=32.2
Q ss_pred CCCCHHHHHHHHHHHHhc----C----CchHHH----hhhC-CCCCHHHHHHHHHHHhhhh
Q 036087 67 GSFTEEEEQIIIDVHRIL----G----NRWAQI----AKHL-PGRTDNEVKNYWNSCIKKK 114 (344)
Q Consensus 67 g~WT~EED~~Ll~lv~~~----G----~kW~~I----Ak~l-pgRT~~qcknRW~~~lkkk 114 (344)
.-||++++-.|++.+..| | ..|... ...+ ..=+..|+.++-+.+.++-
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky 65 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKY 65 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHH
Confidence 469999999999988766 5 234443 3333 2237788888887766553
No 105
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=26.28 E-value=1.4e+02 Score=26.29 Aligned_cols=29 Identities=17% Similarity=0.152 Sum_probs=23.8
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|-...+||..+ |-+...++++....+++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~~ 174 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARKK 174 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 88999999998765544
No 106
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=26.16 E-value=1.6e+02 Score=26.08 Aligned_cols=35 Identities=17% Similarity=0.190 Sum_probs=25.2
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHH---hhhhhhhCC
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSC---IKKKLMSKG 119 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~---lkkkl~~~~ 119 (344)
.|-.-.+||..+ |-+...|+.|.... |++.+....
T Consensus 151 ~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~~l~~~~ 188 (195)
T PRK12532 151 LGFSSDEIQQMC-GISTSNYHTIMHRARESLRQCLQIKW 188 (195)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHhh
Confidence 466789999999 88999999887754 444444443
No 107
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.83 E-value=1.9e+02 Score=23.60 Aligned_cols=47 Identities=13% Similarity=0.180 Sum_probs=37.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCchHHHhhhCCCC-CHHHHHHHHHHHhhh
Q 036087 66 RGSFTEEEEQIIIDVHRILGNRWAQIAKHLPGR-TDNEVKNYWNSCIKK 113 (344)
Q Consensus 66 kg~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgR-T~~qcknRW~~~lkk 113 (344)
+..||.|.-..+++++..-|..=..||+.+ |- ..++++.++..+...
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~-gv~~~~~l~~W~~~~~~~ 52 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREF-GIVSATQLYKWRIQLQKG 52 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHh-CCCChHHHHHHHHHHHHc
Confidence 568999999999999999888889999999 75 777776655544443
No 108
>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=25.60 E-value=46 Score=29.89 Aligned_cols=38 Identities=24% Similarity=0.280 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccccccCcccccch
Q 036087 15 LWSPEEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLR 55 (344)
Q Consensus 15 ~WT~EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~R 55 (344)
.||.|+.++|.++... |. .=.+||..|| +.+...+.-+
T Consensus 2 ~Wtde~~~~L~~lw~~-G~-SasqIA~~lg-~vsRnAViGk 39 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GL-SASQIARQLG-GVSRNAVIGK 39 (162)
T ss_pred CCCHHHHHHHHHHHHc-CC-CHHHHHHHhC-Ccchhhhhhh
Confidence 4999999999999854 44 6899999998 5555444443
No 109
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=25.23 E-value=1.4e+02 Score=26.37 Aligned_cols=30 Identities=23% Similarity=0.153 Sum_probs=24.2
Q ss_pred hcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 83 ILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 83 ~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
..|-...+||..+ |-+...|+++....+++
T Consensus 120 ~~g~~~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 120 LEGLSQKEIAEKL-GLSLSGAKSRVQRGRVK 149 (181)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3467799999999 88999999998765544
No 110
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=25.12 E-value=1.3e+02 Score=26.42 Aligned_cols=29 Identities=14% Similarity=0.060 Sum_probs=23.1
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|-...+||..+ |-+...|+++....+++
T Consensus 153 ~g~s~~eIA~~l-gis~~tv~~~l~Rar~~ 181 (193)
T PRK11923 153 DGLSYEDIASVM-QCPVGTVRSRIFRAREA 181 (193)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 355689999999 88999999998765544
No 111
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=25.01 E-value=1.6e+02 Score=24.82 Aligned_cols=29 Identities=17% Similarity=0.158 Sum_probs=23.4
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|-.-.+||..+ |-+...|+.|....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 149 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATHA 149 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 456789999999 88999999988765544
No 112
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=24.83 E-value=1.5e+02 Score=25.95 Aligned_cols=30 Identities=17% Similarity=0.275 Sum_probs=24.3
Q ss_pred hcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 83 ILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 83 ~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
..|....+||..+ |-+...|+.+....+++
T Consensus 153 ~~g~s~~EIA~~l-gis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 153 VVGLSAEETAEAV-GSTPGAVRVAQHRALAR 182 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3467799999999 88999999988766554
No 113
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.81 E-value=1.3e+02 Score=26.06 Aligned_cols=29 Identities=14% Similarity=-0.008 Sum_probs=23.2
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|..-.+||..+ |.+...|+++....+++
T Consensus 151 ~g~s~~eIA~~l-gis~~~v~~~l~Rar~~ 179 (187)
T TIGR02948 151 EDLSLKEISEIL-DLPVGTVKTRIHRGREA 179 (187)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 356789999999 88999999998765554
No 114
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.75 E-value=2.1e+02 Score=25.04 Aligned_cols=34 Identities=24% Similarity=0.205 Sum_probs=27.2
Q ss_pred HhcCCchHHHhhhCCCCCHHHHHHHHHHHhhhhhh
Q 036087 82 RILGNRWAQIAKHLPGRTDNEVKNYWNSCIKKKLM 116 (344)
Q Consensus 82 ~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkkkl~ 116 (344)
...|-...+||..+ |-+...++.|....+..-+.
T Consensus 140 ~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 140 TLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 33467899999999 89999999998877766443
No 115
>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=24.52 E-value=97 Score=24.63 Aligned_cols=24 Identities=33% Similarity=0.612 Sum_probs=18.9
Q ss_pred HHHHhcCCchHHHhhhCCCCCHHHH
Q 036087 79 DVHRILGNRWAQIAKHLPGRTDNEV 103 (344)
Q Consensus 79 ~lv~~~G~kW~~IAk~lpgRT~~qc 103 (344)
.+....|..|.++|++| |-+..+|
T Consensus 12 ~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 12 VFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 35577899999999999 7666655
No 116
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=24.27 E-value=32 Score=27.59 Aligned_cols=44 Identities=18% Similarity=0.188 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCCC
Q 036087 19 EEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPDL 64 (344)
Q Consensus 19 EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~l 64 (344)
+.|.+++.++.+.+.-.+..||+.++ -+...|+.|..+..+.++
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 57889999999988889999999987 788888888877655443
No 117
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=23.75 E-value=1.3e+02 Score=27.62 Aligned_cols=44 Identities=20% Similarity=0.250 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 67 GSFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 67 g~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
...|+.|-+.|.-+.+ |-.=++||..| +.+.+.||++..++++|
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHH
Confidence 3688888887766554 44447999999 99999999999998887
No 118
>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=23.59 E-value=1.6e+02 Score=26.02 Aligned_cols=30 Identities=13% Similarity=0.133 Sum_probs=24.0
Q ss_pred hcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 83 ILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 83 ~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
..|....+||..+ |-+...|+.|....+++
T Consensus 145 ~~g~s~~EIA~~l-gis~~tvk~rl~Rar~~ 174 (188)
T TIGR02943 145 VLGFESDEICQEL-EISTSNCHVLLYRARLS 174 (188)
T ss_pred HhCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 88999999997765544
No 119
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=23.41 E-value=1.7e+02 Score=25.13 Aligned_cols=29 Identities=31% Similarity=0.344 Sum_probs=23.4
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|-.-.+||..+ |.+...|+.|....+++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~~ 161 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALRA 161 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHH
Confidence 466789999999 88999999998765544
No 120
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=23.35 E-value=2.2e+02 Score=19.97 Aligned_cols=45 Identities=27% Similarity=0.451 Sum_probs=35.9
Q ss_pred CCCCCCHHHHHHHHHHHHhcCC----chHHHhhhCCCCCHHHHHHHHHHH
Q 036087 65 RRGSFTEEEEQIIIDVHRILGN----RWAQIAKHLPGRTDNEVKNYWNSC 110 (344)
Q Consensus 65 kkg~WT~EED~~Ll~lv~~~G~----kW~~IAk~lpgRT~~qcknRW~~~ 110 (344)
++..+|.++-..|.+....... .-..||..+ |-+..+|++.|.+-
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF~nr 51 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWFQNR 51 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCHHHh
Confidence 4568999999999998887441 367888888 88999999988753
No 121
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=23.04 E-value=1.7e+02 Score=25.90 Aligned_cols=29 Identities=17% Similarity=0.082 Sum_probs=23.6
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|-...+||..+ |-+...|+.|....+++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~~ 184 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVEK 184 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHH
Confidence 466789999999 89999999998766554
No 122
>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=22.65 E-value=1.7e+02 Score=19.94 Aligned_cols=35 Identities=20% Similarity=0.193 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHH
Q 036087 72 EEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYW 107 (344)
Q Consensus 72 EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW 107 (344)
-|...|.++...++++..+.|+.+ |=+...+..+-
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~kl 39 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYRKL 39 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHH
Confidence 477888899999999999999998 65666555543
No 123
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.26 E-value=1.9e+02 Score=24.50 Aligned_cols=29 Identities=14% Similarity=-0.051 Sum_probs=23.2
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|-.-.+||+.+ |-+...|++|....+++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~ 149 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARKW 149 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 466789999999 89999999987765443
No 124
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=21.99 E-value=1.2e+02 Score=23.25 Aligned_cols=29 Identities=21% Similarity=0.565 Sum_probs=20.8
Q ss_pred HHHHHHHHHh-cCCchHHHhhhCCCCCHHHH
Q 036087 74 EQIIIDVHRI-LGNRWAQIAKHLPGRTDNEV 103 (344)
Q Consensus 74 D~~Ll~lv~~-~G~kW~~IAk~lpgRT~~qc 103 (344)
++.|..++.. .|..|..+|+++ |-+..++
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 4556666666 789999999999 4444443
No 125
>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=21.55 E-value=1.1e+02 Score=24.20 Aligned_cols=33 Identities=24% Similarity=0.521 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHH
Q 036087 71 EEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKN 105 (344)
Q Consensus 71 ~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qckn 105 (344)
+||-++|+.. -..|..|..+|.+| |=+...|++
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5788888742 24578899999999 777777665
No 126
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.27 E-value=2.3e+02 Score=24.59 Aligned_cols=29 Identities=14% Similarity=0.164 Sum_probs=23.8
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
.|....+||..| |-+...|+.+....+++
T Consensus 146 ~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 146 EGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred cCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 466789999999 88999999998766554
No 127
>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=21.26 E-value=1.2e+02 Score=24.12 Aligned_cols=31 Identities=23% Similarity=0.506 Sum_probs=24.4
Q ss_pred HHHHHHHHHhcCCchHHHhhhCCCCCHHHHHH
Q 036087 74 EQIIIDVHRILGNRWAQIAKHLPGRTDNEVKN 105 (344)
Q Consensus 74 D~~Ll~lv~~~G~kW~~IAk~lpgRT~~qckn 105 (344)
|..|-.+....|..|..+|+.+ |=+...|.+
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 4567777888999999999999 667666654
No 128
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=20.86 E-value=2e+02 Score=25.51 Aligned_cols=28 Identities=11% Similarity=-0.007 Sum_probs=22.9
Q ss_pred cCCchHHHhhhCCCCCHHHHHHHHHHHhh
Q 036087 84 LGNRWAQIAKHLPGRTDNEVKNYWNSCIK 112 (344)
Q Consensus 84 ~G~kW~~IAk~lpgRT~~qcknRW~~~lk 112 (344)
.|-...+||..+ |-+...|+.|....++
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr~ 176 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRARL 176 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466799999999 9999999998765543
No 129
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=20.70 E-value=1.1e+02 Score=34.38 Aligned_cols=12 Identities=17% Similarity=0.094 Sum_probs=5.2
Q ss_pred ccCcccccchhh
Q 036087 46 QRCGKSCRLRWI 57 (344)
Q Consensus 46 ~Rt~~QCr~Rw~ 57 (344)
.|.....|..|.
T Consensus 414 irnDy~~rpqYy 425 (1102)
T KOG1924|consen 414 IRNDYYIRPQYY 425 (1102)
T ss_pred HhhhhhhhHHHH
Confidence 444444444443
No 130
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=20.54 E-value=1.4e+02 Score=21.45 Aligned_cols=43 Identities=30% Similarity=0.387 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHHhcCCchHHHhhhCCCCCHHHHHHHHHHHhhh
Q 036087 68 SFTEEEEQIIIDVHRILGNRWAQIAKHLPGRTDNEVKNYWNSCIKK 113 (344)
Q Consensus 68 ~WT~EED~~Ll~lv~~~G~kW~~IAk~lpgRT~~qcknRW~~~lkk 113 (344)
..|+.|-+.|.-+.. |..=.+||..+ +.+...|+.+...++++
T Consensus 3 ~LT~~E~~vl~~l~~--G~~~~eIA~~l-~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ--GMSNKEIAEEL-GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHT--TS-HHHHHHHH-TSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh--cCCcchhHHhc-CcchhhHHHHHHHHHHH
Confidence 356667665554443 44558999999 89999999988887766
No 131
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=20.48 E-value=35 Score=29.00 Aligned_cols=43 Identities=12% Similarity=0.116 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHhCCCCccccccccccccCcccccchhhcccCCC
Q 036087 19 EEDEKLLKHITAHGHGSWSSVPKLAGLQRCGKSCRLRWINYLRPD 63 (344)
Q Consensus 19 EEDe~L~~lV~kyG~~~W~~IA~~~~~~Rt~~QCr~Rw~n~L~p~ 63 (344)
+-|.+++++.++.+...+..||+.+| -+...|+.|-++..+.+
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~G 50 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEG 50 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCC
Confidence 56889999999999889999999998 88888988877665544
Done!