Query 047101
Match_columns 344
No_of_seqs 310 out of 1564
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 07:36:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047101.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047101hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03091 hypothetical protein; 100.0 5.8E-40 1.3E-44 325.7 14.8 170 1-174 1-170 (459)
2 PLN03212 Transcription repress 100.0 6E-38 1.3E-42 292.7 11.3 129 2-130 13-141 (249)
3 KOG0048 Transcription factor, 100.0 3.1E-36 6.7E-41 282.1 11.7 118 11-128 6-123 (238)
4 KOG0049 Transcription factor, 99.8 5.6E-20 1.2E-24 189.0 5.2 140 7-146 246-441 (939)
5 KOG0049 Transcription factor, 99.8 4E-19 8.7E-24 182.8 5.9 111 1-112 347-458 (939)
6 PLN03212 Transcription repress 99.6 2.5E-16 5.4E-21 147.9 4.6 98 62-159 20-126 (249)
7 PF13921 Myb_DNA-bind_6: Myb-l 99.6 3.8E-16 8.2E-21 116.2 2.7 60 17-78 1-60 (60)
8 KOG0050 mRNA splicing protein 99.6 4.2E-15 9E-20 150.4 6.4 108 12-121 5-112 (617)
9 COG5147 REB1 Myb superfamily p 99.5 6.1E-15 1.3E-19 151.2 7.3 107 10-117 16-122 (512)
10 KOG0048 Transcription factor, 99.5 2.4E-15 5.2E-20 141.2 -0.7 92 63-154 5-105 (238)
11 PLN03091 hypothetical protein; 99.5 5.9E-15 1.3E-19 147.8 2.0 96 60-155 7-111 (459)
12 KOG0051 RNA polymerase I termi 99.4 1.4E-13 3.1E-18 142.7 5.3 103 13-118 383-513 (607)
13 PF13921 Myb_DNA-bind_6: Myb-l 99.4 1.9E-13 4.1E-18 101.7 1.6 57 70-126 1-57 (60)
14 PF00249 Myb_DNA-binding: Myb- 99.4 9.3E-13 2E-17 94.4 4.9 46 67-112 1-48 (48)
15 PF00249 Myb_DNA-binding: Myb- 99.3 2.1E-13 4.6E-18 97.7 -0.1 48 14-61 1-48 (48)
16 smart00717 SANT SANT SWI3, AD 99.2 4.6E-11 1E-15 82.9 5.5 47 67-113 1-48 (49)
17 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 3.8E-10 8.2E-15 77.2 5.6 44 69-112 1-45 (45)
18 smart00717 SANT SANT SWI3, AD 99.0 2.3E-10 4.9E-15 79.4 1.5 48 14-62 1-48 (49)
19 KOG0051 RNA polymerase I termi 98.8 1.3E-09 2.8E-14 113.6 2.1 120 12-133 306-451 (607)
20 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 1.6E-09 3.5E-14 74.1 1.2 45 16-61 1-45 (45)
21 KOG0050 mRNA splicing protein 98.2 3.8E-07 8.2E-12 93.4 1.3 82 65-146 5-87 (617)
22 COG5147 REB1 Myb superfamily p 98.2 1.2E-07 2.6E-12 98.0 -2.5 97 13-112 290-396 (512)
23 TIGR01557 myb_SHAQKYF myb-like 97.6 2.4E-05 5.1E-10 58.8 1.6 48 14-61 3-54 (57)
24 KOG0457 Histone acetyltransfer 97.5 0.00017 3.6E-09 73.1 6.2 49 64-112 69-118 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.3 0.00065 1.4E-08 51.0 6.0 46 67-112 3-54 (57)
26 KOG0457 Histone acetyltransfer 97.3 8.1E-05 1.7E-09 75.4 0.9 50 11-61 69-118 (438)
27 TIGR02894 DNA_bind_RsfA transc 97.2 0.00058 1.3E-08 61.2 4.9 52 66-118 3-61 (161)
28 PF13325 MCRS_N: N-terminal re 97.0 0.00089 1.9E-08 62.1 4.6 100 16-117 1-131 (199)
29 PF13837 Myb_DNA-bind_4: Myb/S 96.8 0.0011 2.3E-08 52.4 3.2 52 67-119 1-70 (90)
30 COG5259 RSC8 RSC chromatin rem 96.6 0.0022 4.8E-08 65.8 4.3 54 68-121 280-335 (531)
31 PF08914 Myb_DNA-bind_2: Rap1 96.6 0.0031 6.7E-08 48.6 4.1 51 67-117 2-62 (65)
32 KOG1279 Chromatin remodeling f 96.5 0.0032 7E-08 65.7 5.2 46 66-111 252-297 (506)
33 COG5259 RSC8 RSC chromatin rem 96.4 0.001 2.2E-08 68.2 0.7 46 13-60 278-323 (531)
34 KOG1279 Chromatin remodeling f 96.2 0.0018 3.9E-08 67.6 1.3 49 10-60 249-297 (506)
35 PRK13923 putative spore coat p 95.9 0.011 2.3E-07 53.7 4.5 51 66-117 4-61 (170)
36 PF08914 Myb_DNA-bind_2: Rap1 95.7 0.0021 4.7E-08 49.5 -0.7 51 14-64 2-60 (65)
37 PF13873 Myb_DNA-bind_5: Myb/S 95.7 0.039 8.4E-07 42.8 6.3 47 68-114 3-71 (78)
38 COG5114 Histone acetyltransfer 95.5 0.014 3.1E-07 57.6 4.0 46 67-112 63-109 (432)
39 PF13837 Myb_DNA-bind_4: Myb/S 95.0 0.0045 9.8E-08 48.8 -0.9 46 15-60 2-63 (90)
40 TIGR02894 DNA_bind_RsfA transc 94.8 0.0067 1.4E-07 54.5 -0.5 50 12-63 2-57 (161)
41 COG5114 Histone acetyltransfer 94.0 0.013 2.9E-07 57.9 -0.4 49 13-62 62-110 (432)
42 PF13873 Myb_DNA-bind_5: Myb/S 93.5 0.014 3.1E-07 45.3 -1.0 49 13-61 1-69 (78)
43 PLN03142 Probable chromatin-re 93.3 0.16 3.5E-06 57.5 6.4 100 15-115 825-987 (1033)
44 PF09111 SLIDE: SLIDE; InterP 91.5 0.31 6.8E-06 41.8 4.7 51 64-114 46-112 (118)
45 PF12776 Myb_DNA-bind_3: Myb/S 91.2 0.56 1.2E-05 37.2 5.6 45 69-113 1-63 (96)
46 PRK13923 putative spore coat p 91.1 0.037 8.1E-07 50.3 -1.5 49 12-62 3-57 (170)
47 KOG2656 DNA methyltransferase 90.4 0.29 6.3E-06 49.7 3.9 84 36-120 75-189 (445)
48 COG5118 BDP1 Transcription ini 90.0 0.45 9.7E-06 48.3 4.8 46 69-114 367-412 (507)
49 KOG1194 Predicted DNA-binding 90.0 0.79 1.7E-05 47.5 6.6 48 67-114 187-234 (534)
50 KOG4282 Transcription factor G 89.9 0.56 1.2E-05 46.3 5.5 51 67-118 54-118 (345)
51 KOG4167 Predicted DNA-binding 88.1 1.6 3.5E-05 47.6 7.6 46 68-113 620-665 (907)
52 PF08281 Sigma70_r4_2: Sigma-7 82.8 3 6.5E-05 29.7 4.7 41 72-113 12-52 (54)
53 PF09111 SLIDE: SLIDE; InterP 78.0 1.5 3.4E-05 37.5 2.1 34 11-44 46-82 (118)
54 smart00595 MADF subfamily of S 73.6 4.8 0.0001 31.5 3.8 23 89-112 30-52 (89)
55 COG5118 BDP1 Transcription ini 71.4 1.8 3.9E-05 44.1 1.0 44 14-59 365-408 (507)
56 PF11035 SnAPC_2_like: Small n 69.2 17 0.00037 36.3 7.2 54 68-122 22-79 (344)
57 PF11626 Rap1_C: TRF2-interact 68.2 4.9 0.00011 32.2 2.7 24 11-34 44-75 (87)
58 KOG4282 Transcription factor G 65.4 2.4 5.1E-05 41.9 0.4 47 15-61 55-113 (345)
59 KOG4468 Polycomb-group transcr 64.4 14 0.00031 39.9 5.9 57 67-124 88-154 (782)
60 PF04545 Sigma70_r4: Sigma-70, 62.7 17 0.00037 25.5 4.4 41 73-114 7-47 (50)
61 PF13404 HTH_AsnC-type: AsnC-t 56.7 22 0.00048 24.8 4.0 38 73-111 3-41 (42)
62 PRK11179 DNA-binding transcrip 55.9 16 0.00034 31.9 3.9 45 72-117 8-53 (153)
63 PF13325 MCRS_N: N-terminal re 53.5 27 0.00058 32.7 5.1 44 69-113 1-47 (199)
64 TIGR02985 Sig70_bacteroi1 RNA 53.4 29 0.00064 28.9 5.1 40 76-117 119-158 (161)
65 PF11626 Rap1_C: TRF2-interact 52.9 14 0.0003 29.6 2.8 17 63-79 43-59 (87)
66 PF01388 ARID: ARID/BRIGHT DNA 50.8 35 0.00077 26.9 4.9 38 77-114 40-90 (92)
67 PF12776 Myb_DNA-bind_3: Myb/S 50.6 8.7 0.00019 30.3 1.3 44 16-59 1-60 (96)
68 KOG4468 Polycomb-group transcr 49.0 12 0.00027 40.3 2.4 48 14-62 88-144 (782)
69 PF13404 HTH_AsnC-type: AsnC-t 48.8 4 8.8E-05 28.6 -0.8 38 20-59 3-40 (42)
70 KOG4329 DNA-binding protein [G 48.1 31 0.00067 35.4 4.9 45 68-112 278-323 (445)
71 PF07750 GcrA: GcrA cell cycle 47.9 20 0.00043 32.3 3.3 40 69-109 2-41 (162)
72 smart00501 BRIGHT BRIGHT, ARID 46.7 43 0.00093 26.7 4.8 38 77-114 36-86 (93)
73 KOG0384 Chromodomain-helicase 45.9 18 0.00039 42.1 3.2 74 13-93 1132-1206(1373)
74 PRK11169 leucine-responsive tr 45.7 34 0.00073 30.2 4.4 44 72-116 13-57 (164)
75 KOG2009 Transcription initiati 43.9 27 0.00058 37.6 4.0 47 65-111 407-453 (584)
76 PRK11179 DNA-binding transcrip 41.2 7.9 0.00017 33.8 -0.3 46 19-66 8-53 (153)
77 PRK09645 RNA polymerase sigma 40.9 71 0.0015 27.5 5.7 28 85-113 133-160 (173)
78 PRK12532 RNA polymerase sigma 40.7 74 0.0016 28.2 5.9 39 84-123 150-191 (195)
79 PRK11169 leucine-responsive tr 40.5 6.7 0.00014 34.7 -0.9 46 19-66 13-58 (164)
80 TIGR02937 sigma70-ECF RNA poly 40.3 56 0.0012 26.4 4.7 36 78-114 118-153 (158)
81 cd08319 Death_RAIDD Death doma 39.0 42 0.0009 27.0 3.5 29 75-104 2-30 (83)
82 PF09420 Nop16: Ribosome bioge 37.9 64 0.0014 28.8 5.0 46 67-112 114-163 (164)
83 PF10545 MADF_DNA_bdg: Alcohol 37.1 34 0.00073 25.8 2.7 25 89-113 29-54 (85)
84 PRK09047 RNA polymerase factor 36.7 1.1E+02 0.0024 25.8 6.1 28 85-113 121-148 (161)
85 PRK09643 RNA polymerase sigma 35.5 96 0.0021 27.6 5.8 28 84-112 148-175 (192)
86 PF04504 DUF573: Protein of un 34.2 71 0.0015 26.3 4.3 46 68-113 5-63 (98)
87 KOG4167 Predicted DNA-binding 34.0 17 0.00036 40.2 0.6 43 15-59 620-662 (907)
88 PRK09652 RNA polymerase sigma 33.5 82 0.0018 26.9 4.8 29 83-112 141-169 (182)
89 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 32.6 72 0.0016 23.5 3.6 35 72-107 6-40 (50)
90 cd06171 Sigma70_r4 Sigma70, re 32.3 1.2E+02 0.0026 19.9 4.7 36 74-110 14-49 (55)
91 smart00344 HTH_ASNC helix_turn 32.3 77 0.0017 25.4 4.2 44 73-117 3-47 (108)
92 PRK12529 RNA polymerase sigma 32.1 1.4E+02 0.0029 26.2 6.1 35 84-119 141-175 (178)
93 PRK11924 RNA polymerase sigma 32.0 87 0.0019 26.6 4.7 28 84-112 139-166 (179)
94 PRK04217 hypothetical protein; 31.8 1E+02 0.0022 26.2 4.9 43 69-113 42-84 (110)
95 PRK09642 RNA polymerase sigma 31.6 1.2E+02 0.0027 25.6 5.6 28 85-113 121-148 (160)
96 cd08803 Death_ank3 Death domai 31.2 72 0.0016 25.6 3.8 29 75-104 4-32 (84)
97 PRK05602 RNA polymerase sigma 31.0 1.3E+02 0.0028 26.3 5.8 37 85-122 143-182 (186)
98 PF07638 Sigma70_ECF: ECF sigm 29.8 1E+02 0.0022 27.6 4.9 36 76-112 141-176 (185)
99 PRK09641 RNA polymerase sigma 28.6 1.1E+02 0.0023 26.6 4.8 28 85-113 151-178 (187)
100 PRK12530 RNA polymerase sigma 28.6 1.2E+02 0.0027 26.8 5.3 27 85-112 149-175 (189)
101 cd08317 Death_ank Death domain 28.4 62 0.0013 25.5 3.0 29 75-104 4-32 (84)
102 TIGR02939 RpoE_Sigma70 RNA pol 28.3 85 0.0018 27.3 4.1 28 85-113 153-180 (190)
103 PRK12523 RNA polymerase sigma 28.1 1.7E+02 0.0036 25.3 5.9 37 80-117 129-165 (172)
104 TIGR02954 Sig70_famx3 RNA poly 26.8 1.2E+02 0.0026 26.0 4.8 29 85-114 134-162 (169)
105 PRK12512 RNA polymerase sigma 26.1 1.8E+02 0.0039 25.3 5.8 29 85-114 146-174 (184)
106 PF09420 Nop16: Ribosome bioge 25.4 35 0.00075 30.5 1.1 47 12-59 112-161 (164)
107 KOG2656 DNA methyltransferase 25.3 38 0.00083 34.9 1.5 49 11-60 127-180 (445)
108 PRK09648 RNA polymerase sigma 25.0 1.5E+02 0.0032 26.1 5.0 30 84-114 153-182 (189)
109 cd08318 Death_NMPP84 Death dom 25.0 93 0.002 24.8 3.4 26 78-104 10-35 (86)
110 PRK12515 RNA polymerase sigma 24.8 1.5E+02 0.0032 26.1 5.1 28 85-113 146-173 (189)
111 PRK11923 algU RNA polymerase s 24.7 1.3E+02 0.0028 26.4 4.7 27 86-113 154-180 (193)
112 TIGR02948 SigW_bacill RNA poly 24.6 1.3E+02 0.0028 26.1 4.5 27 86-113 152-178 (187)
113 PF00046 Homeobox: Homeobox do 24.4 2E+02 0.0044 20.2 4.9 49 66-116 3-55 (57)
114 PRK09637 RNA polymerase sigma 23.9 1.5E+02 0.0032 26.2 4.9 29 84-113 120-148 (181)
115 PRK12531 RNA polymerase sigma 23.5 1.6E+02 0.0035 26.1 5.1 28 85-113 156-183 (194)
116 PRK12545 RNA polymerase sigma 23.4 1.8E+02 0.004 26.0 5.5 36 85-121 154-192 (201)
117 cd08779 Death_PIDD Death Domai 23.1 51 0.0011 26.4 1.6 21 76-96 3-23 (86)
118 cd08777 Death_RIP1 Death Domai 23.0 93 0.002 25.0 3.0 30 76-106 3-32 (86)
119 TIGR02943 Sig70_famx1 RNA poly 22.7 1.8E+02 0.0038 25.9 5.1 30 83-113 144-173 (188)
120 smart00005 DEATH DEATH domain, 22.5 95 0.0021 23.9 3.0 30 74-104 4-34 (88)
121 PF02954 HTH_8: Bacterial regu 22.5 1.6E+02 0.0035 20.0 3.8 33 73-106 5-37 (42)
122 cd08804 Death_ank2 Death domai 22.2 1.1E+02 0.0024 24.3 3.3 31 75-106 4-34 (84)
123 PF10440 WIYLD: Ubiquitin-bind 21.6 68 0.0015 24.9 1.9 19 76-94 30-48 (65)
124 PRK12514 RNA polymerase sigma 21.6 1.8E+02 0.0039 25.2 4.9 27 86-113 145-171 (179)
125 smart00351 PAX Paired Box doma 21.0 1.5E+02 0.0033 25.1 4.2 72 13-86 14-92 (125)
126 KOG1194 Predicted DNA-binding 20.0 40 0.00088 35.4 0.5 45 13-59 186-230 (534)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=5.8e-40 Score=325.71 Aligned_cols=170 Identities=52% Similarity=0.921 Sum_probs=155.0
Q ss_pred CCCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHH
Q 047101 1 MGRSPCSDTNGLKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIKRGKFSLHEEQTIIQ 80 (344)
Q Consensus 1 mgR~pc~~k~~lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ikrg~WT~EED~~Ll~ 80 (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 99999999999999999999999999999999999999999999889999999999999999999999999999999999
Q ss_pred HHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCcccccCCCCCcccccccchhhhhhhHHHHH
Q 047101 81 LHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKKRLARMGIDPMTHRPKIPSLASADGDPKKASNLSHMAQWENARLEAE 160 (344)
Q Consensus 81 lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~k~~~~p~e~kp~~~~~~~~~~~~k~~s~l~h~~qwesarlEae 160 (344)
+|++||++|.+||++|||||+++||+||+.+|+++++..++++.+++++.+.....+ ..+....+.+++++++++|
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~E~~~d----~~p~~~~~~~~~s~~~~~e 156 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEVENGED----KNPPTDDKSDKASSVVSNE 156 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCccccccccc----cCCccccccccchhhhhhh
Confidence 999999999999999999999999999999999999999999999999976543322 2245567888999999999
Q ss_pred HhhhhhcCCCCCCC
Q 047101 161 ARLVRESKPKQNDQ 174 (344)
Q Consensus 161 arl~r~~~~~~~~~ 174 (344)
..|.....++....
T Consensus 157 l~~~~~~~~~~~~~ 170 (459)
T PLN03091 157 LNLLKADNSKPLAA 170 (459)
T ss_pred hhhhhhhccCcccc
Confidence 98887776655443
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=6e-38 Score=292.73 Aligned_cols=129 Identities=63% Similarity=1.191 Sum_probs=124.8
Q ss_pred CCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHH
Q 047101 2 GRSPCSDTNGLKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIKRGKFSLHEEQTIIQL 81 (344)
Q Consensus 2 gR~pc~~k~~lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ikrg~WT~EED~~Ll~l 81 (344)
.|+|||+|++++|++||+|||++|+++|++||..+|..||+.++++|+++|||+||.+||+|.+++++||.|||++|+++
T Consensus 13 ~~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel 92 (249)
T PLN03212 13 KTTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRL 92 (249)
T ss_pred CCCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHH
Confidence 37899999999999999999999999999999999999999997799999999999999999999999999999999999
Q ss_pred HHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCCCCCC
Q 047101 82 HALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKKRLARMGIDPMTHRPKI 130 (344)
Q Consensus 82 v~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~k~~~~p~e~kp~~ 130 (344)
|.+||++|..||++|||||+++||+||+.+|++++.+.++++.+++++.
T Consensus 93 ~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~~ 141 (249)
T PLN03212 93 HRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPLD 141 (249)
T ss_pred HHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCCC
Confidence 9999999999999999999999999999999999999999999988764
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=3.1e-36 Score=282.11 Aligned_cols=118 Identities=66% Similarity=1.136 Sum_probs=111.6
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCChh
Q 047101 11 GLKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIKRGKFSLHEEQTIIQLHALLGNRWS 90 (344)
Q Consensus 11 ~lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ikrg~WT~EED~~Ll~lv~~~G~kWs 90 (344)
.+.||+||+|||++|++||++||.++|..||+.++++||+|+||+||.|||+|++++|.||+|||.+|++||+.+|++|+
T Consensus 6 ~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrWs 85 (238)
T KOG0048|consen 6 ELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRWS 85 (238)
T ss_pred cccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHHH
Confidence 34579999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCCCC
Q 047101 91 AIAAHLPKRTDNEIKNYWNTHIKKRLARMGIDPMTHRP 128 (344)
Q Consensus 91 ~IA~~LpgRT~~qcKnRW~~~Lkk~l~k~~~~p~e~kp 128 (344)
.||++|||||+++|||+|+++|++|+.+.+.++.+..+
T Consensus 86 ~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~~~~~~ 123 (238)
T KOG0048|consen 86 LIAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDPSTHRP 123 (238)
T ss_pred HHHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCCCcccc
Confidence 99999999999999999999999999998865555443
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.79 E-value=5.6e-20 Score=189.03 Aligned_cols=140 Identities=16% Similarity=0.331 Sum_probs=127.2
Q ss_pred CCCCCCccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccc--------------------------------
Q 047101 7 SDTNGLKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCR-------------------------------- 54 (344)
Q Consensus 7 ~~k~~lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr-------------------------------- 54 (344)
...|.++|..|++|||++|+.+...+++.+|..||..++..|+..||.
T Consensus 246 ~l~P~~nk~~WS~EE~E~L~AiA~A~~~~~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ekeWsEEed~kL~alV~~~~~ 325 (939)
T KOG0049|consen 246 ELNPKWNKEHWSNEEVEKLKALAEAPKFVSWPMIALNLGTNRSSYQCMEKFKTEVSQLSEKEWSEEEDTKLIALVKITSI 325 (939)
T ss_pred hcCCccchhccChHHHHHHHHHHhccccccHHHHHHHhCCCcchHHHHHHHHHHHHHHHhhhcchhhhHHHHHHHHHhhc
Confidence 467889999999999999999999998888888888888778888886
Q ss_pred ----------------------cccccccCCCCCCCCCCHHHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHH
Q 047101 55 ----------------------LRWTNYLRPDIKRGKFSLHEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTH 111 (344)
Q Consensus 55 ----------------------~Rw~n~L~P~ikrg~WT~EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~ 111 (344)
.||...|+|.+++|+||.+||.+|+++|.+|| ..|.+|-..+|||++.|||.||.+.
T Consensus 326 nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nv 405 (939)
T KOG0049|consen 326 NSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNV 405 (939)
T ss_pred cCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHH
Confidence 68999999999999999999999999999999 5599999999999999999999999
Q ss_pred HHHHHHhCCCCCCCCCCCCcccccCC-CCCcccccc
Q 047101 112 IKKRLARMGIDPMTHRPKIPSLASAD-GDPKKASNL 146 (344)
Q Consensus 112 Lkk~l~k~~~~p~e~kp~~~~~~~~~-~~~k~~s~l 146 (344)
|..+.+++.|+-.++..+..++..+| ++|.+++.+
T Consensus 406 L~~s~K~~rW~l~edeqL~~~V~~YG~g~WakcA~~ 441 (939)
T KOG0049|consen 406 LNRSAKVERWTLVEDEQLLYAVKVYGKGNWAKCAML 441 (939)
T ss_pred HHHhhccCceeecchHHHHHHHHHHccchHHHHHHH
Confidence 99999999999999999999998876 578887665
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.76 E-value=4e-19 Score=182.77 Aligned_cols=111 Identities=25% Similarity=0.479 Sum_probs=102.5
Q ss_pred CCCCCCCCCCCCccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHH
Q 047101 1 MGRSPCSDTNGLKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIKRGKFSLHEEQTIIQ 80 (344)
Q Consensus 1 mgR~pc~~k~~lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ikrg~WT~EED~~Ll~ 80 (344)
+||......|++++|+||++||.+|+.+|.+||.++|.+|-+.++ +|+..|||+||.|.|....|.+.||..||+.||.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vP-nRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVP-NRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcC-CccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 478888899999999999999999999999999999999999998 9999999999999999999999999999999999
Q ss_pred HHHHhC-CChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 81 LHALLG-NRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 81 lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (344)
+|++|| ++|.+||..||+||..|...|=...+
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~ 458 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLI 458 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHHHHH
Confidence 999999 89999999999999966654443333
No 6
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.62 E-value=2.5e-16 Score=147.91 Aligned_cols=98 Identities=13% Similarity=0.238 Sum_probs=88.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHHhC-CChhHHhhhC-CCCCHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCcccccCCCC
Q 047101 62 RPDIKRGKFSLHEEQTIIQLHALLG-NRWSAIAAHL-PKRTDNEIKNYWNTHIKKRLARMGIDPMTHRPKIPSLASADGD 139 (344)
Q Consensus 62 ~P~ikrg~WT~EED~~Ll~lv~~~G-~kWs~IA~~L-pgRT~~qcKnRW~~~Lkk~l~k~~~~p~e~kp~~~~~~~~~~~ 139 (344)
++.+++++||+|||++|+++|++|| .+|..||+.+ ++||++|||.||.++|++.+++.+|+++|++.+...+...|.+
T Consensus 20 K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~~~~GnK 99 (249)
T PLN03212 20 KMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLHRLLGNR 99 (249)
T ss_pred cCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHHHhcccc
Confidence 4678999999999999999999999 6899999998 6999999999999999999999999999999999999999999
Q ss_pred Cccccccc-------chhhhhhhHHHH
Q 047101 140 PKKASNLS-------HMAQWENARLEA 159 (344)
Q Consensus 140 ~k~~s~l~-------h~~qwesarlEa 159 (344)
|..|+... .+.+|.+.....
T Consensus 100 Ws~IAk~LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 100 WSLIAGRIPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred HHHHHhhcCCCCHHHHHHHHHHHHhHH
Confidence 99998753 557888765443
No 7
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.60 E-value=3.8e-16 Score=116.22 Aligned_cols=60 Identities=45% Similarity=0.910 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCCCCCCCHHHHHHH
Q 047101 17 WTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIKRGKFSLHEEQTI 78 (344)
Q Consensus 17 WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ikrg~WT~EED~~L 78 (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 999999999999999996 9999999997 89999999999999999999999999999987
No 8
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.55 E-value=4.2e-15 Score=150.44 Aligned_cols=108 Identities=24% Similarity=0.529 Sum_probs=102.0
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCChhH
Q 047101 12 LKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIKRGKFSLHEEQTIIQLHALLGNRWSA 91 (344)
Q Consensus 12 lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ikrg~WT~EED~~Ll~lv~~~G~kWs~ 91 (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 5679999999999999999999999999999998 889999999999999999999999999999999999999999999
Q ss_pred HhhhCCCCCHHHHHHHHHHHHHHHHHhCCC
Q 047101 92 IAAHLPKRTDNEIKNYWNTHIKKRLARMGI 121 (344)
Q Consensus 92 IA~~LpgRT~~qcKnRW~~~Lkk~l~k~~~ 121 (344)
|+..| ||+.+||-.||+++|........-
T Consensus 84 Ia~i~-gr~~~qc~eRy~~ll~~~~s~~~~ 112 (617)
T KOG0050|consen 84 IADIM-GRTSQQCLERYNNLLDVYVSYHYH 112 (617)
T ss_pred HHHHh-hhhHHHHHHHHHHHHHHHHhhhcc
Confidence 99999 999999999999999877766443
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=99.55 E-value=6.1e-15 Score=151.16 Aligned_cols=107 Identities=28% Similarity=0.520 Sum_probs=102.7
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhCCCh
Q 047101 10 NGLKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIKRGKFSLHEEQTIIQLHALLGNRW 89 (344)
Q Consensus 10 ~~lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ikrg~WT~EED~~Ll~lv~~~G~kW 89 (344)
..++.|.|+..||+.|+.+|+++|..+|..||..+. .|+++||+.||.++++|.+++..|+.+||..|+.+..++|.+|
T Consensus 16 ~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~-~~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~w 94 (512)
T COG5147 16 TKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLI-SSTGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQW 94 (512)
T ss_pred ceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhc-ccccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCchh
Confidence 357789999999999999999999999999999999 5999999999999999999999999999999999999999999
Q ss_pred hHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q 047101 90 SAIAAHLPKRTDNEIKNYWNTHIKKRLA 117 (344)
Q Consensus 90 s~IA~~LpgRT~~qcKnRW~~~Lkk~l~ 117 (344)
..||..+++||..+|.+||...+.....
T Consensus 95 stia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 95 STIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhccccCccchHHHHHHHHHHhhhhhc
Confidence 9999999999999999999999987776
No 10
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.49 E-value=2.4e-15 Score=141.18 Aligned_cols=92 Identities=15% Similarity=0.225 Sum_probs=84.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CChhHHhhhCC-CCCHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCcccccCCCCC
Q 047101 63 PDIKRGKFSLHEEQTIIQLHALLG-NRWSAIAAHLP-KRTDNEIKNYWNTHIKKRLARMGIDPMTHRPKIPSLASADGDP 140 (344)
Q Consensus 63 P~ikrg~WT~EED~~Ll~lv~~~G-~kWs~IA~~Lp-gRT~~qcKnRW~~~Lkk~l~k~~~~p~e~kp~~~~~~~~~~~~ 140 (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 445689999999999999999999 66999999999 9999999999999999999999999999999999999999999
Q ss_pred cccccc-------cchhhhhh
Q 047101 141 KKASNL-------SHMAQWEN 154 (344)
Q Consensus 141 k~~s~l-------~h~~qwes 154 (344)
..||.. ..+.+|.+
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt 105 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNT 105 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHH
Confidence 999876 44568844
No 11
>PLN03091 hypothetical protein; Provisional
Probab=99.49 E-value=5.9e-15 Score=147.84 Aligned_cols=96 Identities=14% Similarity=0.265 Sum_probs=86.3
Q ss_pred ccCCCCCCCCCCHHHHHHHHHHHHHhC-CChhHHhhhC-CCCCHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCcccccCC
Q 047101 60 YLRPDIKRGKFSLHEEQTIIQLHALLG-NRWSAIAAHL-PKRTDNEIKNYWNTHIKKRLARMGIDPMTHRPKIPSLASAD 137 (344)
Q Consensus 60 ~L~P~ikrg~WT~EED~~Ll~lv~~~G-~kWs~IA~~L-pgRT~~qcKnRW~~~Lkk~l~k~~~~p~e~kp~~~~~~~~~ 137 (344)
..++.+++++||+|||++|+++|++|| .+|..||+.+ ++|+++|||.||+++|++.+++.+|+++|++.++..+...|
T Consensus 7 c~KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k~~G 86 (459)
T PLN03091 7 CYKQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHAVLG 86 (459)
T ss_pred CcCCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHHHhC
Confidence 334678999999999999999999999 5799999988 49999999999999999999999999999999999999999
Q ss_pred CCCcccccc-------cchhhhhhh
Q 047101 138 GDPKKASNL-------SHMAQWENA 155 (344)
Q Consensus 138 ~~~k~~s~l-------~h~~qwesa 155 (344)
.+|..|+.. ..+.+|...
T Consensus 87 nKWskIAk~LPGRTDnqIKNRWnsl 111 (459)
T PLN03091 87 NRWSQIAAQLPGRTDNEIKNLWNSC 111 (459)
T ss_pred cchHHHHHhcCCCCHHHHHHHHHHH
Confidence 999999875 345677764
No 12
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.41 E-value=1.4e-13 Score=142.66 Aligned_cols=103 Identities=26% Similarity=0.594 Sum_probs=93.7
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCC--CCCCCCCHHHHHHHHHHHH-------
Q 047101 13 KRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPD--IKRGKFSLHEEQTIIQLHA------- 83 (344)
Q Consensus 13 kKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~--ikrg~WT~EED~~Ll~lv~------- 83 (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 7999999999999999999996 9999999998 99999999999999987 4899999999999999995
Q ss_pred Hh-------------------CCChhHHhhhCCCCCHHHHHHHHHHHHHHHHHh
Q 047101 84 LL-------------------GNRWSAIAAHLPKRTDNEIKNYWNTHIKKRLAR 118 (344)
Q Consensus 84 ~~-------------------G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~k 118 (344)
++ +..|+.|++.+..|+..||+.+|+.++......
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n 513 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFN 513 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhh
Confidence 23 235999999999999999999999999776554
No 13
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.36 E-value=1.9e-13 Score=101.66 Aligned_cols=57 Identities=26% Similarity=0.569 Sum_probs=49.2
Q ss_pred CCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCC
Q 047101 70 FSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKKRLARMGIDPMTH 126 (344)
Q Consensus 70 WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~k~~~~p~e~ 126 (344)
||.|||++|+++|.+||++|..||++|+.||..+|++||+.+|++.+.+.+|+++++
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd 57 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEED 57 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHH
Confidence 999999999999999999999999999779999999999998888888888876543
No 14
>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=99.35 E-value=9.3e-13 Score=94.38 Aligned_cols=46 Identities=22% Similarity=0.554 Sum_probs=41.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCC-hhHHhhhCC-CCCHHHHHHHHHHHH
Q 047101 67 RGKFSLHEEQTIIQLHALLGNR-WSAIAAHLP-KRTDNEIKNYWNTHI 112 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~~G~k-Ws~IA~~Lp-gRT~~qcKnRW~~~L 112 (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 999999999999875
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=99.32 E-value=2.1e-13 Score=97.73 Aligned_cols=48 Identities=46% Similarity=0.915 Sum_probs=43.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCcccccccccccccccccccccccc
Q 047101 14 RGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYL 61 (344)
Q Consensus 14 Kg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L 61 (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 689999999999999999999679999999998999999999999875
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.17 E-value=4.6e-11 Score=82.87 Aligned_cols=47 Identities=34% Similarity=0.726 Sum_probs=44.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 67 RGKFSLHEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (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
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.05 E-value=3.8e-10 Score=77.20 Aligned_cols=44 Identities=25% Similarity=0.588 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 69 KFSLHEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (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 99999999999999999999998753
No 18
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.95 E-value=2.3e-10 Score=79.37 Aligned_cols=48 Identities=38% Similarity=0.892 Sum_probs=44.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccC
Q 047101 14 RGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLR 62 (344)
Q Consensus 14 Kg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~ 62 (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 47899999999999999999669999999999 9999999999998764
No 19
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=98.82 E-value=1.3e-09 Score=113.60 Aligned_cols=120 Identities=21% Similarity=0.279 Sum_probs=95.4
Q ss_pred CccCCCCHHHHHHHHHHHHHhCC----C-------------------CCccccccccccccccccccccccccCCCC-CC
Q 047101 12 LKRGPWTPEEDQKLLDYIKKHGH----G-------------------SWRSLPEKADLQRCGKSCRLRWTNYLRPDI-KR 67 (344)
Q Consensus 12 lkKg~WT~EEDekL~~lV~k~G~----~-------------------~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~i-kr 67 (344)
++-+.|+.+||+.|-..|+.|-. . -|..|...++. |+.+.++.+-++...|-- ++
T Consensus 306 ~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~-R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 306 INLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPY-RDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCc-ccchhHHHHHHhcCCcccccc
Confidence 34489999999999999998821 0 15667777884 999998873333333322 89
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHHH--HHhCCCCCCCCCCCCccc
Q 047101 68 GKFSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKKR--LARMGIDPMTHRPKIPSL 133 (344)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~--l~k~~~~p~e~kp~~~~~ 133 (344)
|.||++|++.|..+|.++|+.|..|++.| ||.+..|++||..+.+.. .++..|+-++...++..+
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V 451 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTV 451 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHH
Confidence 99999999999999999999999999999 999999999999999877 477778766666555444
No 20
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.79 E-value=1.6e-09 Score=74.06 Aligned_cols=45 Identities=44% Similarity=0.909 Sum_probs=41.7
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCcccccccccccccccccccccccc
Q 047101 16 PWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYL 61 (344)
Q Consensus 16 ~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L 61 (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 599999999999999999779999999998 899999999998653
No 21
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=98.22 E-value=3.8e-07 Score=93.44 Aligned_cols=82 Identities=17% Similarity=0.291 Sum_probs=75.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCcccccCCCCCccc
Q 047101 65 IKRGKFSLHEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTHIKKRLARMGIDPMTHRPKIPSLASADGDPKKA 143 (344)
Q Consensus 65 ikrg~WT~EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~k~~~~p~e~kp~~~~~~~~~~~~k~~ 143 (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 5678899999999999999999 789999999999999999999999999999999999999988888777778888888
Q ss_pred ccc
Q 047101 144 SNL 146 (344)
Q Consensus 144 s~l 146 (344)
+.+
T Consensus 85 a~i 87 (617)
T KOG0050|consen 85 ADI 87 (617)
T ss_pred HHH
Confidence 765
No 22
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.21 E-value=1.2e-07 Score=97.99 Aligned_cols=97 Identities=29% Similarity=0.620 Sum_probs=84.4
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCC--CCCCCCCCHHHHHHHHHHHHHhC----
Q 047101 13 KRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRP--DIKRGKFSLHEEQTIIQLHALLG---- 86 (344)
Q Consensus 13 kKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P--~ikrg~WT~EED~~Ll~lv~~~G---- 86 (344)
.+|.||+||++.|...+.++|. .|..|...++ |-+..||+||.+|..+ .+++++|+.||+.+|...+...-
T Consensus 290 ~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~~ 366 (512)
T COG5147 290 QRGKWTKEEEQELAKLVVEHGG-SWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEAQ 366 (512)
T ss_pred hhccCccccccccccccccccc-hhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHHh
Confidence 4689999999999999999995 9999987776 9999999999999998 68889999999999998886431
Q ss_pred ----CChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 87 ----NRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 87 ----~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (344)
..|..|+.++++|...+|+.++..+.
T Consensus 367 ~~~~~~~~li~~~~~~~~~~~~~~~~~~~~ 396 (512)
T COG5147 367 QSSRILWLLIAQNIRNRLQHHCRDKYGVLI 396 (512)
T ss_pred hhhhhhHHHHHHhhhccccCCCCCcccccc
Confidence 45999999999999888887765544
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=97.63 E-value=2.4e-05 Score=58.79 Aligned_cols=48 Identities=19% Similarity=0.376 Sum_probs=42.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCC---ccccccccccc-ccccccccccccc
Q 047101 14 RGPWTPEEDQKLLDYIKKHGHGSW---RSLPEKADLQR-CGKSCRLRWTNYL 61 (344)
Q Consensus 14 Kg~WT~EEDekL~~lV~k~G~~~W---~~IA~~~~~~R-t~kQCr~Rw~n~L 61 (344)
+-.||+||.++++++|+.+|.++| ..|++.|...| +..||+.+++.|.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 567999999999999999999899 99999988666 9999999887764
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.50 E-value=0.00017 Score=73.12 Aligned_cols=49 Identities=24% Similarity=0.448 Sum_probs=44.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 64 DIKRGKFSLHEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 64 ~ikrg~WT~EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (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 34456799999999999999999 99999999999999999999997654
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=97.32 E-value=0.00065 Score=51.04 Aligned_cols=46 Identities=15% Similarity=0.223 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-Ch---hHHhhhCC-CC-CHHHHHHHHHHHH
Q 047101 67 RGKFSLHEEQTIIQLHALLGN-RW---SAIAAHLP-KR-TDNEIKNYWNTHI 112 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~~G~-kW---s~IA~~Lp-gR-T~~qcKnRW~~~L 112 (344)
+-.||+||..+.+++++.+|. +| ..|++.|. .| |..||+.+...+.
T Consensus 3 r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 457999999999999999995 99 99999885 45 9999999987654
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.28 E-value=8.1e-05 Score=75.39 Aligned_cols=50 Identities=18% Similarity=0.535 Sum_probs=46.3
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCCcccccccccccccccccccccccc
Q 047101 11 GLKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYL 61 (344)
Q Consensus 11 ~lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L 61 (344)
.+-...||.+|+-+|+++++.||-|||..||.++| .|++.+|+++|.+++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIG-tKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIG-TKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHc-ccchHHHHHHHHHHH
Confidence 45567899999999999999999999999999999 999999999998864
No 27
>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=97.16 E-value=0.00058 Score=61.23 Aligned_cols=52 Identities=15% Similarity=0.325 Sum_probs=45.2
Q ss_pred CCCCCCHHHHHHHHHHHHHh---CC----ChhHHhhhCCCCCHHHHHHHHHHHHHHHHHh
Q 047101 66 KRGKFSLHEEQTIIQLHALL---GN----RWSAIAAHLPKRTDNEIKNYWNTHIKKRLAR 118 (344)
Q Consensus 66 krg~WT~EED~~Ll~lv~~~---G~----kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~k 118 (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 45689999999999999888 42 289999999 999999999999999977654
No 28
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.99 E-value=0.00089 Score=62.10 Aligned_cols=100 Identities=21% Similarity=0.370 Sum_probs=71.3
Q ss_pred CCCHHHHHHHHHHHHHhCCCCCccccccccc--ccccccccccccccc-CCCC--------------------CCCCCCH
Q 047101 16 PWTPEEDQKLLDYIKKHGHGSWRSLPEKADL--QRCGKSCRLRWTNYL-RPDI--------------------KRGKFSL 72 (344)
Q Consensus 16 ~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~--~Rt~kQCr~Rw~n~L-~P~i--------------------krg~WT~ 72 (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 45555544332 346677789998875 3433 2358999
Q ss_pred HHHHHHHHHHHHhCC---ChhHHhh-----hCCCCCHHHHHHHHHHHHHHHHH
Q 047101 73 HEEQTIIQLHALLGN---RWSAIAA-----HLPKRTDNEIKNYWNTHIKKRLA 117 (344)
Q Consensus 73 EED~~Ll~lv~~~G~---kWs~IA~-----~LpgRT~~qcKnRW~~~Lkk~l~ 117 (344)
+||++|......... .+.+|=. +-++||+.++.++|..+.+..+-
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~LL 131 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHLL 131 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhchh
Confidence 999999997665542 3666632 23789999999999866555543
No 29
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.81 E-value=0.0011 Score=52.36 Aligned_cols=52 Identities=27% Similarity=0.553 Sum_probs=36.0
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--C------ChhHHhhhC----CCCCHHHHHHHHHHHHHHHHHhC
Q 047101 67 RGKFSLHEEQTIIQLHAL------LG--N------RWSAIAAHL----PKRTDNEIKNYWNTHIKKRLARM 119 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~------~G--~------kWs~IA~~L----pgRT~~qcKnRW~~~Lkk~l~k~ 119 (344)
|..||.+|...||+++.. ++ . -|..||..| ..||..||+++|.+ |+++.++.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~-L~~~Yk~~ 70 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKN-LKKKYKKI 70 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHH-HHHHHHCS
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHH-HHHHHHHH
Confidence 347999999999999877 21 1 399999987 36999999999988 55566553
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.58 E-value=0.0022 Score=65.75 Aligned_cols=54 Identities=15% Similarity=0.220 Sum_probs=45.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHH--HHHHHhCCC
Q 047101 68 GKFSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHI--KKRLARMGI 121 (344)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~L--kk~l~k~~~ 121 (344)
..||.+|..+|++.++.||..|.+||.|+..||..||--||-++- .+-+.++..
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~LPieD~~l~k~~~ 335 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQLPIEDNYLSKGDG 335 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcCCcchhhhhcccC
Confidence 389999999999999999999999999999999999999997542 344444433
No 31
>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=96.57 E-value=0.0031 Score=48.63 Aligned_cols=51 Identities=16% Similarity=0.384 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------CC-hhHHhhhCC-CCCHHHHHHHHHHHHHHHHH
Q 047101 67 RGKFSLHEEQTIIQLHALLG--------NR-WSAIAAHLP-KRTDNEIKNYWNTHIKKRLA 117 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~~G--------~k-Ws~IA~~Lp-gRT~~qcKnRW~~~Lkk~l~ 117 (344)
|.+||.+||+.|++.|.++. ++ |.++++.-+ .+|-...|+||...|+.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~~ 62 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRPR 62 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT-----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcccc
Confidence 45899999999999997652 22 999999888 89999999999998877654
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.53 E-value=0.0032 Score=65.69 Aligned_cols=46 Identities=13% Similarity=0.341 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHH
Q 047101 66 KRGKFSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTH 111 (344)
Q Consensus 66 krg~WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~ 111 (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 3567999999999999999999999999999999999999988643
No 33
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.41 E-value=0.001 Score=68.16 Aligned_cols=46 Identities=20% Similarity=0.473 Sum_probs=43.3
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccc
Q 047101 13 KRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNY 60 (344)
Q Consensus 13 kKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~ 60 (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 5679999999999999999997 9999999999 99999999999874
No 34
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.23 E-value=0.0018 Score=67.55 Aligned_cols=49 Identities=22% Similarity=0.521 Sum_probs=44.5
Q ss_pred CCCccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccc
Q 047101 10 NGLKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNY 60 (344)
Q Consensus 10 ~~lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~ 60 (344)
...-++.||.+|+-+|+++|+.||. +|.+||.+++ .|+..||..++.+.
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg-~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYGD-DWNKVADHVG-TKSQEQCILKFLRL 297 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccC-CCCHHHHHHHHHhc
Confidence 3455789999999999999999997 9999999999 99999999998764
No 35
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.89 E-value=0.011 Score=53.74 Aligned_cols=51 Identities=14% Similarity=0.288 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCC-------hhHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q 047101 66 KRGKFSLHEEQTIIQLHALLGNR-------WSAIAAHLPKRTDNEIKNYWNTHIKKRLA 117 (344)
Q Consensus 66 krg~WT~EED~~Ll~lv~~~G~k-------Ws~IA~~LpgRT~~qcKnRW~~~Lkk~l~ 117 (344)
++..||.|||.+|-+.|..|+.. ...++..| +||..+|..||+.+++++..
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Ye 61 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQ 61 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHH
Confidence 46789999999999998888622 66677777 99999999999999986543
No 36
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=95.68 E-value=0.0021 Score=49.49 Aligned_cols=51 Identities=39% Similarity=0.651 Sum_probs=32.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCC------C--CCccccccccccccccccccccccccCCC
Q 047101 14 RGPWTPEEDQKLLDYIKKHGH------G--SWRSLPEKADLQRCGKSCRLRWTNYLRPD 64 (344)
Q Consensus 14 Kg~WT~EEDekL~~lV~k~G~------~--~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ 64 (344)
+-+||.|||+.|+++|..+.. | =|..+++..+..++-.+-|+||...|.+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~ 60 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGR 60 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT---
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcc
Confidence 457999999999999976632 1 28888888766788888899999988764
No 37
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.66 E-value=0.039 Score=42.79 Aligned_cols=47 Identities=30% Similarity=0.493 Sum_probs=39.2
Q ss_pred CCCCHHHHHHHHHHHHHhC----C-------------ChhHHhhhC-----CCCCHHHHHHHHHHHHHH
Q 047101 68 GKFSLHEEQTIIQLHALLG----N-------------RWSAIAAHL-----PKRTDNEIKNYWNTHIKK 114 (344)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G----~-------------kWs~IA~~L-----pgRT~~qcKnRW~~~Lkk 114 (344)
..||.+|...|++++.+|. + -|..|+..| +.||..+++.+|.++...
T Consensus 3 ~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~ 71 (78)
T PF13873_consen 3 PNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSK 71 (78)
T ss_pred CCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHH
Confidence 4699999999999998872 1 299999887 359999999999887654
No 38
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.50 E-value=0.014 Score=57.64 Aligned_cols=46 Identities=26% Similarity=0.403 Sum_probs=42.2
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 67 RGKFSLHEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (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 34699999999999999999 99999999999999999999997654
No 39
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=95.01 E-value=0.0045 Score=48.77 Aligned_cols=46 Identities=30% Similarity=0.732 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHHHHHHH--h----CC-C------CCccccccc---cccccccccccccccc
Q 047101 15 GPWTPEEDQKLLDYIKK--H----GH-G------SWRSLPEKA---DLQRCGKSCRLRWTNY 60 (344)
Q Consensus 15 g~WT~EEDekL~~lV~k--~----G~-~------~W~~IA~~~---~~~Rt~kQCr~Rw~n~ 60 (344)
-.||.+|...|++++.. + +. + -|..||..| |..|++.||+.+|.++
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 47999999999999887 1 11 1 399999886 4579999999999875
No 40
>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=94.78 E-value=0.0067 Score=54.51 Aligned_cols=50 Identities=28% Similarity=0.669 Sum_probs=41.9
Q ss_pred CccCCCCHHHHHHHHHHHHHhCC-C-----CCccccccccccccccccccccccccCC
Q 047101 12 LKRGPWTPEEDQKLLDYIKKHGH-G-----SWRSLPEKADLQRCGKSCRLRWTNYLRP 63 (344)
Q Consensus 12 lkKg~WT~EEDekL~~lV~k~G~-~-----~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P 63 (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 35678999999999999999922 1 4788888887 9999999999988863
No 41
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=94.01 E-value=0.013 Score=57.87 Aligned_cols=49 Identities=14% Similarity=0.445 Sum_probs=45.1
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccC
Q 047101 13 KRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLR 62 (344)
Q Consensus 13 kKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~ 62 (344)
---.|+.+|+-+|++..+..|-|+|..||..+| .|....|+.+|..++.
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~dIadyiG-sr~kee~k~HylK~y~ 110 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWEDIADYIG-SRAKEEIKSHYLKMYD 110 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHh-hhhhHHHHHHHHHHHh
Confidence 345699999999999999999999999999999 9999999999988765
No 42
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=93.48 E-value=0.014 Score=45.26 Aligned_cols=49 Identities=22% Similarity=0.518 Sum_probs=39.1
Q ss_pred ccCCCCHHHHHHHHHHHHHhCC----------------CCCccccccc----ccccccccccccccccc
Q 047101 13 KRGPWTPEEDQKLLDYIKKHGH----------------GSWRSLPEKA----DLQRCGKSCRLRWTNYL 61 (344)
Q Consensus 13 kKg~WT~EEDekL~~lV~k~G~----------------~~W~~IA~~~----~~~Rt~kQCr~Rw~n~L 61 (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 3578999999999999999822 1499999875 22699999999998753
No 43
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=93.29 E-value=0.16 Score=57.52 Aligned_cols=100 Identities=15% Similarity=0.316 Sum_probs=74.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccc----------------------------------------
Q 047101 15 GPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCR---------------------------------------- 54 (344)
Q Consensus 15 g~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr---------------------------------------- 54 (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 4588888888888999999888888888886 56666554
Q ss_pred --------cccccc-c-CCCCCCCCCCHHHHHHHHHHHHHhC-CChhHHhhh------------CCCCCHHHHHHHHHHH
Q 047101 55 --------LRWTNY-L-RPDIKRGKFSLHEEQTIIQLHALLG-NRWSAIAAH------------LPKRTDNEIKNYWNTH 111 (344)
Q Consensus 55 --------~Rw~n~-L-~P~ikrg~WT~EED~~Ll~lv~~~G-~kWs~IA~~------------LpgRT~~qcKnRW~~~ 111 (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 111110 0 1233344699999999999999999 789999432 2579999999999998
Q ss_pred HHHH
Q 047101 112 IKKR 115 (344)
Q Consensus 112 Lkk~ 115 (344)
|+--
T Consensus 984 ~~~~ 987 (1033)
T PLN03142 984 IRLI 987 (1033)
T ss_pred HHHH
Confidence 8654
No 44
>PF09111 SLIDE: SLIDE; InterPro: IPR015195 The SLIDE domain adopts a secondary structure comprising a main core of three alpha-helices. It has a role in DNA binding, contacting DNA target sites similar to c-Myb (IPR014778 from INTERPRO) repeats or homeodomains []. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006338 chromatin remodeling, 0005634 nucleus; PDB: 2NOG_A 2Y9Y_A 2Y9Z_A 1OFC_X.
Probab=91.55 E-value=0.31 Score=41.76 Aligned_cols=51 Identities=25% Similarity=0.397 Sum_probs=40.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----ChhHHhhhC------------CCCCHHHHHHHHHHHHHH
Q 047101 64 DIKRGKFSLHEEQTIIQLHALLGN----RWSAIAAHL------------PKRTDNEIKNYWNTHIKK 114 (344)
Q Consensus 64 ~ikrg~WT~EED~~Ll~lv~~~G~----kWs~IA~~L------------pgRT~~qcKnRW~~~Lkk 114 (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 455678999999999999999995 798886543 479999999999998854
No 45
>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=91.22 E-value=0.56 Score=37.23 Aligned_cols=45 Identities=27% Similarity=0.482 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------ChhHHhhhCC-----CCCHHHHHHHHHHHHH
Q 047101 69 KFSLHEEQTIIQLHALL---GN----------RWSAIAAHLP-----KRTDNEIKNYWNTHIK 113 (344)
Q Consensus 69 ~WT~EED~~Ll~lv~~~---G~----------kWs~IA~~Lp-----gRT~~qcKnRW~~~Lk 113 (344)
.||+++++.|++++.+. |+ .|..|+..|. ..|..||++||..+.+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~lk~ 63 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTLKK 63 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHHHH
Confidence 49999999999988553 32 2999998872 3688999999976554
No 46
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=91.14 E-value=0.037 Score=50.28 Aligned_cols=49 Identities=22% Similarity=0.578 Sum_probs=37.9
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCC------CccccccccccccccccccccccccC
Q 047101 12 LKRGPWTPEEDQKLLDYIKKHGHGS------WRSLPEKADLQRCGKSCRLRWTNYLR 62 (344)
Q Consensus 12 lkKg~WT~EEDekL~~lV~k~G~~~------W~~IA~~~~~~Rt~kQCr~Rw~n~L~ 62 (344)
.++..||.|||.+|.+.|-.|+... ...++..+. |+..+|..||..+++
T Consensus 3 ~rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~--rt~aac~fRwNs~vr 57 (170)
T PRK13923 3 TRQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALK--RTAAACGFRWNSVVR 57 (170)
T ss_pred chhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHh--hhHHHHHhHHHHHHH
Confidence 4678899999999999999886532 444444554 999999999966665
No 47
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=90.36 E-value=0.29 Score=49.69 Aligned_cols=84 Identities=19% Similarity=0.304 Sum_probs=62.5
Q ss_pred CCccccccccccccccccccccccccCCC-------------------------CCCCCCCHHHHHHHHHHHHHhCCChh
Q 047101 36 SWRSLPEKADLQRCGKSCRLRWTNYLRPD-------------------------IKRGKFSLHEEQTIIQLHALLGNRWS 90 (344)
Q Consensus 36 ~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~-------------------------ikrg~WT~EED~~Ll~lv~~~G~kWs 90 (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 4665543333 566666677787763321 11246999999999999999999999
Q ss_pred HHhhh-----CCC-CCHHHHHHHHHHHHHHHHHhCC
Q 047101 91 AIAAH-----LPK-RTDNEIKNYWNTHIKKRLARMG 120 (344)
Q Consensus 91 ~IA~~-----Lpg-RT~~qcKnRW~~~Lkk~l~k~~ 120 (344)
.||.. ++. ||-.++|+||+..-++-++...
T Consensus 154 VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~ 189 (445)
T KOG2656|consen 154 VIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARA 189 (445)
T ss_pred EEeeccchhhccccccHHHHHHHHHHHHHHHHHccC
Confidence 99987 565 9999999999988877665543
No 48
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=90.00 E-value=0.45 Score=48.31 Aligned_cols=46 Identities=22% Similarity=0.359 Sum_probs=42.7
Q ss_pred CCCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHH
Q 047101 69 KFSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKK 114 (344)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk 114 (344)
+|+.+|-++...+...+|..+..|+..+|.|...|||-+|.+--+.
T Consensus 367 ~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~ 412 (507)
T COG5118 367 RWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKV 412 (507)
T ss_pred cccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhh
Confidence 7999999999999999999999999999999999999999865543
No 49
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=89.99 E-value=0.79 Score=47.47 Aligned_cols=48 Identities=17% Similarity=0.324 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHH
Q 047101 67 RGKFSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKK 114 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk 114 (344)
...||.||-.++-+++..||.++.+|-+.||.|+-..+..+|+...+.
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~KK~ 234 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWKKT 234 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHHHH
Confidence 347999999999999999999999999999999999999998876653
No 50
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=89.95 E-value=0.56 Score=46.35 Aligned_cols=51 Identities=20% Similarity=0.365 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCChhHHhhhC----CCCCHHHHHHHHHHHHHHHHHh
Q 047101 67 RGKFSLHEEQTIIQLHALL----------GNRWSAIAAHL----PKRTDNEIKNYWNTHIKKRLAR 118 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~~----------G~kWs~IA~~L----pgRT~~qcKnRW~~~Lkk~l~k 118 (344)
...|+.+|-..||++..+. +.-|..||+.+ --||+.|||++|.++. +++++
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~-k~Yk~ 118 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK-KKYKK 118 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH-HHHHH
Confidence 3679999999999988653 23499999965 2499999999998866 44544
No 51
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=88.07 E-value=1.6 Score=47.64 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=42.4
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 68 GKFSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
..||+.|..+.-+++..|-..+-.|++.++++|-.||-.+|++..|
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtWKK 665 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTWKK 665 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHHHH
Confidence 4799999999999999999999999999999999999999877654
No 52
>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=82.80 E-value=3 Score=29.71 Aligned_cols=41 Identities=20% Similarity=0.255 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 72 LHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 72 ~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
++++..++.++-..|-.+.+||+.+ |.+...|+.+....++
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l-~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEIL-GISESTVKRRLRRARK 52 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHC-TS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHH-CcCHHHHHHHHHHHHh
Confidence 4677888888888999999999999 9999999998876554
No 53
>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=77.97 E-value=1.5 Score=37.52 Aligned_cols=34 Identities=29% Similarity=0.518 Sum_probs=28.4
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCC---CCCccccccc
Q 047101 11 GLKRGPWTPEEDQKLLDYIKKHGH---GSWRSLPEKA 44 (344)
Q Consensus 11 ~lkKg~WT~EEDekL~~lV~k~G~---~~W~~IA~~~ 44 (344)
+-++..||.+||.-|+-++.+||. +.|..|-..+
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~I 82 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEI 82 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHH
Confidence 567899999999999999999999 8999986654
No 54
>smart00595 MADF subfamily of SANT domain.
Probab=73.61 E-value=4.8 Score=31.49 Aligned_cols=23 Identities=30% Similarity=0.534 Sum_probs=20.3
Q ss_pred hhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 89 WSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 89 Ws~IA~~LpgRT~~qcKnRW~~~L 112 (344)
|..||..|. -|..+|+.+|+++-
T Consensus 30 W~~Ia~~l~-~~~~~~~~kw~~LR 52 (89)
T smart00595 30 WEEIAEELG-LSVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHHC-cCHHHHHHHHHHHH
Confidence 999999994 49999999998764
No 55
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=71.45 E-value=1.8 Score=44.08 Aligned_cols=44 Identities=14% Similarity=0.256 Sum_probs=40.7
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCcccccccccccccccccccccc
Q 047101 14 RGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTN 59 (344)
Q Consensus 14 Kg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n 59 (344)
--+||.+|-++..++....|. ++..|+..++ .|..+|++..|.+
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP-~R~RkqIKaKfi~ 408 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGT-DFSLISSLFP-NRERKQIKAKFIK 408 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcc-hHHHHHHhcC-chhHHHHHHHHHH
Confidence 357999999999999999998 9999999999 9999999998865
No 56
>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=69.21 E-value=17 Score=36.35 Aligned_cols=54 Identities=28% Similarity=0.508 Sum_probs=41.7
Q ss_pred CCCCHHHHHHHHHHHHHh-CC---ChhHHhhhCCCCCHHHHHHHHHHHHHHHHHhCCCC
Q 047101 68 GKFSLHEEQTIIQLHALL-GN---RWSAIAAHLPKRTDNEIKNYWNTHIKKRLARMGID 122 (344)
Q Consensus 68 g~WT~EED~~Ll~lv~~~-G~---kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~k~~~~ 122 (344)
..||.-|...|+.+.+.. |. .-..|++.++||+..+|++ |...||.|+.+..+.
T Consensus 22 ~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~-fl~~LK~rvareaiq 79 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRD-FLQQLKGRVAREAIQ 79 (344)
T ss_pred ccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHH-HHHHHHHHHHHHHHH
Confidence 469999999999887665 43 3568899999999999998 556777776655443
No 57
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=68.20 E-value=4.9 Score=32.21 Aligned_cols=24 Identities=50% Similarity=0.815 Sum_probs=14.4
Q ss_pred CCccCCCCHHHHHHH--------HHHHHHhCC
Q 047101 11 GLKRGPWTPEEDQKL--------LDYIKKHGH 34 (344)
Q Consensus 11 ~lkKg~WT~EEDekL--------~~lV~k~G~ 34 (344)
.-..|-||+|+|+.| .+++++||.
T Consensus 44 ~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 44 DNMPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp TT-TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 344789999999999 356778874
No 58
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=65.40 E-value=2.4 Score=41.92 Aligned_cols=47 Identities=21% Similarity=0.436 Sum_probs=36.8
Q ss_pred CCCCHHHHHHHHHHHHHh----CC-----CCCccccccc---ccccccccccccccccc
Q 047101 15 GPWTPEEDQKLLDYIKKH----GH-----GSWRSLPEKA---DLQRCGKSCRLRWTNYL 61 (344)
Q Consensus 15 g~WT~EEDekL~~lV~k~----G~-----~~W~~IA~~~---~~~Rt~kQCr~Rw~n~L 61 (344)
..|+.+|-..|+++..+. .. .-|..||.++ +..|++.||+.+|.++.
T Consensus 55 ~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 55 PRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 789999999999886643 11 2499999853 45799999999998743
No 59
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=64.44 E-value=14 Score=39.85 Aligned_cols=57 Identities=11% Similarity=0.373 Sum_probs=43.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhHHhhh----------CCCCCHHHHHHHHHHHHHHHHHhCCCCCC
Q 047101 67 RGKFSLHEEQTIIQLHALLGNRWSAIAAH----------LPKRTDNEIKNYWNTHIKKRLARMGIDPM 124 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~~G~kWs~IA~~----------LpgRT~~qcKnRW~~~Lkk~l~k~~~~p~ 124 (344)
+..||.+|+.-...+..++|.++.+|-.+ ..-+|..|++.+|+..+++.-+-. |.++
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~-F~~~ 154 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLL-FGPD 154 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhh-cccc
Confidence 56899999999999999999999998322 234688999999998886544333 5443
No 60
>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=62.74 E-value=17 Score=25.53 Aligned_cols=41 Identities=22% Similarity=0.332 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHH
Q 047101 73 HEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKK 114 (344)
Q Consensus 73 EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk 114 (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 456666766666677899999999 88999999988777653
No 61
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=56.72 E-value=22 Score=24.79 Aligned_cols=38 Identities=13% Similarity=0.258 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHH
Q 047101 73 HEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTH 111 (344)
Q Consensus 73 EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~ 111 (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 45788888888888 5599999999 99999999998653
No 62
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=55.91 E-value=16 Score=31.90 Aligned_cols=45 Identities=7% Similarity=0.042 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q 047101 72 LHEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTHIKKRLA 117 (344)
Q Consensus 72 ~EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~ 117 (344)
.+-|.+|+++.++-| ..|+.||+.+ |-+...|+.|+..+....+-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 357888888888888 5699999999 99999999999776665543
No 63
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=53.47 E-value=27 Score=32.74 Aligned_cols=44 Identities=16% Similarity=0.232 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHhCCChhHHhhhC---CCCCHHHHHHHHHHHHH
Q 047101 69 KFSLHEEQTIIQLHALLGNRWSAIAAHL---PKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWs~IA~~L---pgRT~~qcKnRW~~~Lk 113 (344)
.|++++|-+||.+|.. |+.-..|+.-+ -.-|-.+|..||+.+|.
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~lly 47 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLY 47 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHc
Confidence 4999999999998865 55566666544 24689999999999985
No 64
>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=53.42 E-value=29 Score=28.93 Aligned_cols=40 Identities=20% Similarity=0.285 Sum_probs=29.0
Q ss_pred HHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q 047101 76 QTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKKRLA 117 (344)
Q Consensus 76 ~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~ 117 (344)
..++.+.-..|-.+.+||+.| |.+...|+.+.+..+ ++++
T Consensus 119 r~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~-~~Lr 158 (161)
T TIGR02985 119 RKIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKAL-KELR 158 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH-HHHH
Confidence 334444334577899999998 899999999998755 3443
No 65
>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=52.88 E-value=14 Score=29.65 Aligned_cols=17 Identities=18% Similarity=0.429 Sum_probs=10.3
Q ss_pred CCCCCCCCCHHHHHHHH
Q 047101 63 PDIKRGKFSLHEEQTII 79 (344)
Q Consensus 63 P~ikrg~WT~EED~~Ll 79 (344)
|....|-||+++|+.|.
T Consensus 43 P~n~~GiWT~eDD~~L~ 59 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLR 59 (87)
T ss_dssp -TT-TT---HHHHHHHT
T ss_pred CCCCCCCcCHHHHHHHH
Confidence 66778999999999984
No 66
>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=50.80 E-value=35 Score=26.89 Aligned_cols=38 Identities=13% Similarity=0.314 Sum_probs=28.1
Q ss_pred HHHHHHHHhC--------CChhHHhhhCCC---CC--HHHHHHHHHHHHHH
Q 047101 77 TIIQLHALLG--------NRWSAIAAHLPK---RT--DNEIKNYWNTHIKK 114 (344)
Q Consensus 77 ~Ll~lv~~~G--------~kWs~IA~~Lpg---RT--~~qcKnRW~~~Lkk 114 (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 4777788877 369999999832 22 36899999888754
No 67
>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=50.60 E-value=8.7 Score=30.33 Aligned_cols=44 Identities=30% Similarity=0.690 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHHh---CCC---------CCcccccccc----cccccccccccccc
Q 047101 16 PWTPEEDQKLLDYIKKH---GHG---------SWRSLPEKAD----LQRCGKSCRLRWTN 59 (344)
Q Consensus 16 ~WT~EEDekL~~lV~k~---G~~---------~W~~IA~~~~----~~Rt~kQCr~Rw~n 59 (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 59999999999987655 211 2777776654 23455566666543
No 68
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=48.98 E-value=12 Score=40.32 Aligned_cols=48 Identities=15% Similarity=0.389 Sum_probs=36.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCCccccccccc---------cccccccccccccccC
Q 047101 14 RGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADL---------QRCGKSCRLRWTNYLR 62 (344)
Q Consensus 14 Kg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~---------~Rt~kQCr~Rw~n~L~ 62 (344)
|..||-.|.+....+++++|. ++..|-..+-. -++..|+|++|++.+.
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 668999999999999999996 99888222211 3566788888877543
No 69
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=48.80 E-value=4 Score=28.55 Aligned_cols=38 Identities=26% Similarity=0.413 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHhCCCCCcccccccccccccccccccccc
Q 047101 20 EEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTN 59 (344)
Q Consensus 20 EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n 59 (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 45899999999999999999999998 567778877653
No 70
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=48.10 E-value=31 Score=35.36 Aligned_cols=45 Identities=18% Similarity=0.243 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHHHHHHHhCCChhHHh-hhCCCCCHHHHHHHHHHHH
Q 047101 68 GKFSLHEEQTIIQLHALLGNRWSAIA-AHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 68 g~WT~EED~~Ll~lv~~~G~kWs~IA-~~LpgRT~~qcKnRW~~~L 112 (344)
..|+++|=...-+-.+.||+.+..|. ..++.|+-.+|-.+|+...
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYlWK 323 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYLWK 323 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHHhh
Confidence 36999999999999999999999995 5789999999999886544
No 71
>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=47.86 E-value=20 Score=32.28 Aligned_cols=40 Identities=20% Similarity=0.138 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHH
Q 047101 69 KFSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWN 109 (344)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~ 109 (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 5999999999988744 888899999998899999876543
No 72
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=46.71 E-value=43 Score=26.73 Aligned_cols=38 Identities=16% Similarity=0.341 Sum_probs=28.5
Q ss_pred HHHHHHHHhCC--------ChhHHhhhCCC-----CCHHHHHHHHHHHHHH
Q 047101 77 TIIQLHALLGN--------RWSAIAAHLPK-----RTDNEIKNYWNTHIKK 114 (344)
Q Consensus 77 ~Ll~lv~~~G~--------kWs~IA~~Lpg-----RT~~qcKnRW~~~Lkk 114 (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 46677777773 69999999833 2467889999888865
No 73
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=45.87 E-value=18 Score=42.07 Aligned_cols=74 Identities=24% Similarity=0.307 Sum_probs=44.4
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHh-CCChhH
Q 047101 13 KRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIKRGKFSLHEEQTIIQLHALL-GNRWSA 91 (344)
Q Consensus 13 kKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ikrg~WT~EED~~Ll~lv~~~-G~kWs~ 91 (344)
.---|..+||..|+-.|-+||.|+|..|-.--.++-+.+ ..+.-...++++=..+-..|+.+...+ +.+|..
T Consensus 1132 ~~~~W~~e~Ds~LLiGI~khGygswe~Ir~Dp~L~l~dK-------i~~~e~~P~a~~L~~R~~yLls~~~~~~~~~~~~ 1204 (1373)
T KOG0384|consen 1132 WDCDWGSEDDSMLLIGIFKHGYGSWEAIRLDPDLGLTDK-------IFLVETVPQAKHLQRRADYLLSLLRKHDKGNTPK 1204 (1373)
T ss_pred cccCCCchhhhhHhhhhhhcccccHHHhccCccccchhh-------hcccccCCchHHHHHHHHHHHHHHhhcccCCCch
Confidence 345699999999999999999999999832211111111 111111334455555666666666555 444554
Q ss_pred Hh
Q 047101 92 IA 93 (344)
Q Consensus 92 IA 93 (344)
..
T Consensus 1205 ~~ 1206 (1373)
T KOG0384|consen 1205 KL 1206 (1373)
T ss_pred hh
Confidence 43
No 74
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=45.73 E-value=34 Score=30.22 Aligned_cols=44 Identities=5% Similarity=-0.062 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 047101 72 LHEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTHIKKRL 116 (344)
Q Consensus 72 ~EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l 116 (344)
.+-|.+|+.+.++-| -.|+.||+.+ |-+...|+.|++.+.+..+
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~l-glS~~tv~~Ri~rL~~~Gv 57 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRV-GLSPTPCLERVRRLERQGF 57 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 456888888888877 5699999999 9999999999976665554
No 75
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=43.86 E-value=27 Score=37.64 Aligned_cols=47 Identities=19% Similarity=0.337 Sum_probs=42.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHH
Q 047101 65 IKRGKFSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTH 111 (344)
Q Consensus 65 ikrg~WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~ 111 (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 34468999999999999999999999999999999999999988643
No 76
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=41.25 E-value=7.9 Score=33.79 Aligned_cols=46 Identities=11% Similarity=0.183 Sum_probs=39.1
Q ss_pred HHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCC
Q 047101 19 PEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIK 66 (344)
Q Consensus 19 ~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ik 66 (344)
.+-|.+|+++.++.|.-.|.+||+.++ -+...|+.|+.+...-++-
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~lg--lS~~tV~~Ri~rL~~~GvI 53 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQFG--VSPGTIHVRVEKMKQAGII 53 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 467999999999999999999999998 7888899998887655443
No 77
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=40.95 E-value=71 Score=27.55 Aligned_cols=28 Identities=21% Similarity=0.234 Sum_probs=22.8
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
.|-.-.+||+.| |.+...|+.|.+..++
T Consensus 133 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~ 160 (173)
T PRK09645 133 RGWSTAQIAADL-GIPEGTVKSRLHYALR 160 (173)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 466789999999 9999999999875553
No 78
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=40.71 E-value=74 Score=28.16 Aligned_cols=39 Identities=10% Similarity=0.098 Sum_probs=28.5
Q ss_pred HhCCChhHHhhhCCCCCHHHHHHHHHH---HHHHHHHhCCCCC
Q 047101 84 LLGNRWSAIAAHLPKRTDNEIKNYWNT---HIKKRLARMGIDP 123 (344)
Q Consensus 84 ~~G~kWs~IA~~LpgRT~~qcKnRW~~---~Lkk~l~k~~~~p 123 (344)
..|-.-.+||+.| |-+...|+.+.+. .|++.+.+..+..
T Consensus 150 ~~g~s~~EIA~~l-gis~~tVk~~l~Rar~~Lr~~l~~~~~~~ 191 (195)
T PRK12532 150 ILGFSSDEIQQMC-GISTSNYHTIMHRARESLRQCLQIKWFNQ 191 (195)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 3467789999999 9999999988775 5556665554443
No 79
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=40.45 E-value=6.7 Score=34.71 Aligned_cols=46 Identities=20% Similarity=0.237 Sum_probs=39.0
Q ss_pred HHHHHHHHHHHHHhCCCCCccccccccccccccccccccccccCCCCC
Q 047101 19 PEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTNYLRPDIK 66 (344)
Q Consensus 19 ~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n~L~P~ik 66 (344)
.+-|.+|+.+.++.|.-.|.+||+.++ -+...|+.|+.+..+-.+-
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lg--lS~~tv~~Ri~rL~~~GvI 58 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVG--LSPTPCLERVRRLERQGFI 58 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCCe
Confidence 567999999999999999999999998 6777899998887665543
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=40.27 E-value=56 Score=26.35 Aligned_cols=36 Identities=25% Similarity=0.253 Sum_probs=26.5
Q ss_pred HHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHH
Q 047101 78 IIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKK 114 (344)
Q Consensus 78 Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk 114 (344)
++.++-..|..+..||+.+ |-+...|+.+....+++
T Consensus 118 ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~k 153 (158)
T TIGR02937 118 VLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARKK 153 (158)
T ss_pred HHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3334444578899999999 67999999988775543
No 81
>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=38.97 E-value=42 Score=27.00 Aligned_cols=29 Identities=24% Similarity=0.499 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhCCChhHHhhhCCCCCHHHH
Q 047101 75 EQTIIQLHALLGNRWSAIAAHLPKRTDNEI 104 (344)
Q Consensus 75 D~~Ll~lv~~~G~kWs~IA~~LpgRT~~qc 104 (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 5678889999999999999999 5555444
No 82
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=37.86 E-value=64 Score=28.76 Aligned_cols=46 Identities=17% Similarity=0.161 Sum_probs=37.9
Q ss_pred CCCCCHHHHHHHHHHHHHhCCChhHHhhhCC----CCCHHHHHHHHHHHH
Q 047101 67 RGKFSLHEEQTIIQLHALLGNRWSAIAAHLP----KRTDNEIKNYWNTHI 112 (344)
Q Consensus 67 rg~WT~EED~~Ll~lv~~~G~kWs~IA~~Lp----gRT~~qcKnRW~~~L 112 (344)
...-|..|..-|..|+++||.++...+.-.. -.|..||+.+...+.
T Consensus 114 ~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~k 163 (164)
T PF09420_consen 114 PRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKYK 163 (164)
T ss_pred CCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHhc
Confidence 4467899999999999999999999987653 389999998876543
No 83
>PF10545 MADF_DNA_bdg: Alcohol dehydrogenase transcription factor Myb/SANT-like; InterPro: IPR006578 The MADF (myb/SANT-like domain in Adf-1) domain is an approximately 80-amino-acid module that directs sequence specific DNA binding to a site consisting of multiple tri-nucleotide repeats. The MADF domain is found in one or more copies in eukaryotic and viral proteins and is often associated with the BESS domain []. MADF is related to the Myb DNA-binding domain (IPR001005 from INTERPRO). The retroviral oncogene v-myb, and its cellular counterpart c-myb, are nuclear DNA-binding proteins that specifically recognise the sequence YAAC(G/T)G. It is likely that the MADF domain is more closely related to the myb/SANT domain than it is to other HTH domains. Some proteins known to contain a MADF domain are listed below: Drosophila Adf-1, a transcription factor first identified on the basis of its interaction with the alcohol dehydrogenase promoter but that binds the promoters of a diverse group of genes []. Drosophila Dorsal-interacting protein 3 (Dip3), which functions both as an activator to bind DNA in a sequence specific manner and a coactivator to stimulate synergistic activation by Dorsal and Twist []. Drosophila Stonewall (Stwl), a putative transcription factor required for maintenance of female germline stem cells as well as oocyte differentiation.
Probab=37.06 E-value=34 Score=25.78 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=20.5
Q ss_pred hhHHhhhCCC-CCHHHHHHHHHHHHH
Q 047101 89 WSAIAAHLPK-RTDNEIKNYWNTHIK 113 (344)
Q Consensus 89 Ws~IA~~Lpg-RT~~qcKnRW~~~Lk 113 (344)
|..||..|.. -+..+|+.+|.++..
T Consensus 29 w~~Ia~~l~~~~~~~~~~~~w~~Lr~ 54 (85)
T PF10545_consen 29 WQEIARELGKEFSVDDCKKRWKNLRD 54 (85)
T ss_pred HHHHHHHHccchhHHHHHHHHHHHHH
Confidence 9999999953 578899999987654
No 84
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=36.69 E-value=1.1e+02 Score=25.82 Aligned_cols=28 Identities=11% Similarity=0.056 Sum_probs=23.0
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
.|-.-.+||..| |-+...|+.+....++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~ra~~ 148 (161)
T PRK09047 121 EDMDVAETAAAM-GCSEGSVKTHCSRATH 148 (161)
T ss_pred hcCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466789999999 8899999998875553
No 85
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=35.50 E-value=96 Score=27.59 Aligned_cols=28 Identities=14% Similarity=0.106 Sum_probs=23.1
Q ss_pred HhCCChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 84 LLGNRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 84 ~~G~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (344)
..|-...+||..| |-+...|+.|....+
T Consensus 148 ~~g~s~~EIA~~l-g~s~~tV~~rl~rar 175 (192)
T PRK09643 148 MQGYSVADAARML-GVAEGTVKSRCARGR 175 (192)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3467899999999 999999999995444
No 86
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=34.17 E-value=71 Score=26.29 Aligned_cols=46 Identities=17% Similarity=0.123 Sum_probs=30.9
Q ss_pred CCCCHHHHHHHHHHHHHh----C----CChhHHhhhCC-----CCCHHHHHHHHHHHHH
Q 047101 68 GKFSLHEEQTIIQLHALL----G----NRWSAIAAHLP-----KRTDNEIKNYWNTHIK 113 (344)
Q Consensus 68 g~WT~EED~~Ll~lv~~~----G----~kWs~IA~~Lp-----gRT~~qcKnRW~~~Lk 113 (344)
..||+++|..||+.+..| | ..|...-..+. .=+..|+.++-..+-+
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~ 63 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKK 63 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHH
Confidence 369999999999998777 6 24544444332 2377888877765443
No 87
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=34.04 E-value=17 Score=40.22 Aligned_cols=43 Identities=12% Similarity=0.219 Sum_probs=38.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCCcccccccccccccccccccccc
Q 047101 15 GPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTN 59 (344)
Q Consensus 15 g~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n 59 (344)
-.||+.|-.++.+++-.|.. ++-.|++.+. +++.+||-+-|+.
T Consensus 620 d~WTp~E~~lF~kA~y~~~K-DF~~v~km~~-~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSK-DFIFVQKMVK-SKTVAQCVEYYYT 662 (907)
T ss_pred ccccHHHHHHHHHHHHHhcc-cHHHHHHHhc-cccHHHHHHHHHH
Confidence 46999999999999999996 9999998888 9999999887754
No 88
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=33.54 E-value=82 Score=26.86 Aligned_cols=29 Identities=10% Similarity=0.055 Sum_probs=23.3
Q ss_pred HHhCCChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 83 ALLGNRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 83 ~~~G~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (344)
...|-.+..||+.| |.+...|+.+....+
T Consensus 141 ~~~~~s~~eIA~~l-gis~~tV~~~l~ra~ 169 (182)
T PRK09652 141 EIEGLSYEEIAEIM-GCPIGTVRSRIFRAR 169 (182)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 34577899999999 889999988876544
No 89
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=32.60 E-value=72 Score=23.46 Aligned_cols=35 Identities=26% Similarity=0.377 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHH
Q 047101 72 LHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNY 107 (344)
Q Consensus 72 ~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnR 107 (344)
.++|+-.+.+..+.|-.-.+||+.+ ||+.+.|+++
T Consensus 6 t~~Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~y 40 (50)
T PF11427_consen 6 TDAEQAQIDVMHQLGMSLREISRRI-GRSRTCIRRY 40 (50)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHH-T--HHHHHHH
T ss_pred CHHHHHHHHHHHHhchhHHHHHHHh-CccHHHHHHH
Confidence 3455666777888999999999999 9999888765
No 90
>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=32.27 E-value=1.2e+02 Score=19.88 Aligned_cols=36 Identities=19% Similarity=0.237 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHH
Q 047101 74 EEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNT 110 (344)
Q Consensus 74 ED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~ 110 (344)
++..++.++-..|..+..||+.+ |-+...|+.+...
T Consensus 14 ~~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~ 49 (55)
T cd06171 14 REREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHR 49 (55)
T ss_pred HHHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHH
Confidence 34555666656778899999998 7777777665544
No 91
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=32.26 E-value=77 Score=25.38 Aligned_cols=44 Identities=7% Similarity=0.036 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHhC-CChhHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q 047101 73 HEEQTIIQLHALLG-NRWSAIAAHLPKRTDNEIKNYWNTHIKKRLA 117 (344)
Q Consensus 73 EED~~Ll~lv~~~G-~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~ 117 (344)
+.|..|+.+..+.| -.+..||+.+ |-+...|+.+...+.+..+-
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~i 47 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGVI 47 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCCe
Confidence 56788888888877 5799999999 99999999999777665543
No 92
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=32.05 E-value=1.4e+02 Score=26.23 Aligned_cols=35 Identities=26% Similarity=0.226 Sum_probs=28.5
Q ss_pred HhCCChhHHhhhCCCCCHHHHHHHHHHHHHHHHHhC
Q 047101 84 LLGNRWSAIAAHLPKRTDNEIKNYWNTHIKKRLARM 119 (344)
Q Consensus 84 ~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~k~ 119 (344)
..|-...+||..| |-+...||.|...-+..-+...
T Consensus 141 ~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 141 LDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHhC
Confidence 3467899999999 9999999999988776655543
No 93
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.96 E-value=87 Score=26.62 Aligned_cols=28 Identities=18% Similarity=0.127 Sum_probs=22.7
Q ss_pred HhCCChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 84 LLGNRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 84 ~~G~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (344)
..|-....||+.| |-+...|+.+....+
T Consensus 139 ~~~~~~~eIA~~l-gis~~tv~~~~~ra~ 166 (179)
T PRK11924 139 VEGLSYREIAEIL-GVPVGTVKSRLRRAR 166 (179)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3467899999999 888999998877644
No 94
>PRK04217 hypothetical protein; Provisional
Probab=31.78 E-value=1e+02 Score=26.17 Aligned_cols=43 Identities=9% Similarity=0.037 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 69 KFSLHEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 69 ~WT~EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
.-|.+| ..++.+....|-...+||+.+ |-+...|+.+++...+
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RArk 84 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSARK 84 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 355555 677777777888999999999 9999999999886553
No 95
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.57 E-value=1.2e+02 Score=25.65 Aligned_cols=28 Identities=14% Similarity=0.016 Sum_probs=22.5
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
.|-.-.+||+.| |-+...|+.|....++
T Consensus 121 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~ 148 (160)
T PRK09642 121 EEKSYQEIALQE-KIEVKTVEMKLYRARK 148 (160)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 466789999999 9999999998765443
No 96
>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=31.21 E-value=72 Score=25.62 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhCCChhHHhhhCCCCCHHHH
Q 047101 75 EQTIIQLHALLGNRWSAIAAHLPKRTDNEI 104 (344)
Q Consensus 75 D~~Ll~lv~~~G~kWs~IA~~LpgRT~~qc 104 (344)
|..|..+....|..|..+|..| |=+..+|
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI 32 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEI 32 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHH
Confidence 5678888899999999999999 6555554
No 97
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=30.96 E-value=1.3e+02 Score=26.35 Aligned_cols=37 Identities=14% Similarity=0.113 Sum_probs=25.9
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHH---HHHHHHhCCCC
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTH---IKKRLARMGID 122 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~---Lkk~l~k~~~~ 122 (344)
.|-...+||+.| |-+...|+.+.+.. |++.+.+.+.+
T Consensus 143 ~g~s~~EIA~~l-gis~~tV~~~l~Rar~~Lr~~l~~~~~~ 182 (186)
T PRK05602 143 QGLSNIEAAAVM-DISVDALESLLARGRRALRAQLADLPGS 182 (186)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHHHHHHHHHhcccc
Confidence 466789999998 88888888887644 44445544443
No 98
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=29.84 E-value=1e+02 Score=27.56 Aligned_cols=36 Identities=14% Similarity=0.225 Sum_probs=27.8
Q ss_pred HHHHHHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 76 QTIIQLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 76 ~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (344)
..++.+....|-.+.+||+.| |-+...|+.+|....
T Consensus 141 ~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~aR 176 (185)
T PF07638_consen 141 RRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRAR 176 (185)
T ss_pred HHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 334444444578899999999 999999999997654
No 99
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=28.65 E-value=1.1e+02 Score=26.58 Aligned_cols=28 Identities=11% Similarity=-0.024 Sum_probs=22.8
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
.|..+.+||..| |-+...++++.+..++
T Consensus 151 ~~~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T PRK09641 151 EDLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred hCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 467799999999 9999999998765543
No 100
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=28.59 E-value=1.2e+02 Score=26.82 Aligned_cols=27 Identities=7% Similarity=-0.034 Sum_probs=22.6
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHI 112 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~L 112 (344)
.|-...+||..| |-+...||.|....+
T Consensus 149 ~g~s~~EIA~~l-gis~~tVk~~l~RAr 175 (189)
T PRK12530 149 LELSSEQICQEC-DISTSNLHVLLYRAR 175 (189)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 467799999999 999999999876544
No 101
>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=28.44 E-value=62 Score=25.47 Aligned_cols=29 Identities=24% Similarity=0.606 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhCCChhHHhhhCCCCCHHHH
Q 047101 75 EQTIIQLHALLGNRWSAIAAHLPKRTDNEI 104 (344)
Q Consensus 75 D~~Ll~lv~~~G~kWs~IA~~LpgRT~~qc 104 (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 4567788889999999999999 5555544
No 102
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=28.27 E-value=85 Score=27.28 Aligned_cols=28 Identities=11% Similarity=0.057 Sum_probs=22.8
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
.|-...+||..| |-+...|+.+.+..++
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar~ 180 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRARE 180 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 356789999999 8889999999876554
No 103
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=28.07 E-value=1.7e+02 Score=25.30 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=27.7
Q ss_pred HHHHHhCCChhHHhhhCCCCCHHHHHHHHHHHHHHHHH
Q 047101 80 QLHALLGNRWSAIAAHLPKRTDNEIKNYWNTHIKKRLA 117 (344)
Q Consensus 80 ~lv~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l~ 117 (344)
.|....|-...+||+.| |-+...|+.+-..-+++=..
T Consensus 129 ~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 129 LYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred HHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHH
Confidence 33334577899999999 99999999998776654433
No 104
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=26.85 E-value=1.2e+02 Score=26.00 Aligned_cols=29 Identities=21% Similarity=0.351 Sum_probs=23.4
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHIKK 114 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk 114 (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 466789999999 78999999998766643
No 105
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=26.07 E-value=1.8e+02 Score=25.31 Aligned_cols=29 Identities=14% Similarity=0.182 Sum_probs=23.8
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHIKK 114 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk 114 (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 467789999999 99999999998766543
No 106
>PF09420 Nop16: Ribosome biogenesis protein Nop16; InterPro: IPR019002 Nucleolar protein 16 (Nop16) is a protein involved in the biogenesis of the 60S ribosomal subunit.
Probab=25.39 E-value=35 Score=30.46 Aligned_cols=47 Identities=19% Similarity=0.258 Sum_probs=33.0
Q ss_pred CccCCCCHHHHHHHHHHHHHhCCCCCccccccccc---ccccccccccccc
Q 047101 12 LKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADL---QRCGKSCRLRWTN 59 (344)
Q Consensus 12 lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~---~Rt~kQCr~Rw~n 59 (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 44567788999999999999996 88777643321 4566666655443
No 107
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=25.33 E-value=38 Score=34.91 Aligned_cols=49 Identities=18% Similarity=0.344 Sum_probs=41.8
Q ss_pred CCccCCCCHHHHHHHHHHHHHhCCCCCcccccc-----ccccccccccccccccc
Q 047101 11 GLKRGPWTPEEDQKLLDYIKKHGHGSWRSLPEK-----ADLQRCGKSCRLRWTNY 60 (344)
Q Consensus 11 ~lkKg~WT~EEDekL~~lV~k~G~~~W~~IA~~-----~~~~Rt~kQCr~Rw~n~ 60 (344)
.++-..||.||-+-|.++.+.|-- .|-.||.. ++..|+--..++||+.+
T Consensus 127 ~l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 127 HLNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hhccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 345577999999999999999986 89999988 66559999999999765
No 108
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=25.04 E-value=1.5e+02 Score=26.07 Aligned_cols=30 Identities=10% Similarity=0.128 Sum_probs=24.0
Q ss_pred HhCCChhHHhhhCCCCCHHHHHHHHHHHHHH
Q 047101 84 LLGNRWSAIAAHLPKRTDNEIKNYWNTHIKK 114 (344)
Q Consensus 84 ~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lkk 114 (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 88899999988766543
No 109
>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=25.01 E-value=93 Score=24.77 Aligned_cols=26 Identities=38% Similarity=0.705 Sum_probs=20.2
Q ss_pred HHHHHHHhCCChhHHhhhCCCCCHHHH
Q 047101 78 IIQLHALLGNRWSAIAAHLPKRTDNEI 104 (344)
Q Consensus 78 Ll~lv~~~G~kWs~IA~~LpgRT~~qc 104 (344)
|..+....|..|..+|.+| |=+..+|
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI 35 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEI 35 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHH
Confidence 3346678899999999999 6666665
No 110
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.81 E-value=1.5e+02 Score=26.08 Aligned_cols=28 Identities=7% Similarity=-0.023 Sum_probs=23.0
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
.|-....||..| |-+...|+.+....++
T Consensus 146 ~~~s~~eIA~~l-gis~~tV~~~l~Rar~ 173 (189)
T PRK12515 146 HEKSVEEVGEIV-GIPESTVKTRMFYARK 173 (189)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 467799999999 8899999999876543
No 111
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=24.70 E-value=1.3e+02 Score=26.42 Aligned_cols=27 Identities=11% Similarity=0.129 Sum_probs=21.8
Q ss_pred CCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 86 GNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 86 G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
|-...+||..| |-+...|+.+....++
T Consensus 154 g~s~~eIA~~l-gis~~tv~~~l~Rar~ 180 (193)
T PRK11923 154 GLSYEDIASVM-QCPVGTVRSRIFRARE 180 (193)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56689999999 8889999998875543
No 112
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.57 E-value=1.3e+02 Score=26.08 Aligned_cols=27 Identities=11% Similarity=0.010 Sum_probs=22.1
Q ss_pred CCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 86 GNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 86 G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
|....+||..| |.+...|+.+.+..++
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar~ 178 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGRE 178 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 56789999999 8899999998866553
No 113
>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=24.37 E-value=2e+02 Score=20.18 Aligned_cols=49 Identities=16% Similarity=0.312 Sum_probs=35.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhC----CChhHHhhhCCCCCHHHHHHHHHHHHHHHH
Q 047101 66 KRGKFSLHEEQTIIQLHALLG----NRWSAIAAHLPKRTDNEIKNYWNTHIKKRL 116 (344)
Q Consensus 66 krg~WT~EED~~Ll~lv~~~G----~kWs~IA~~LpgRT~~qcKnRW~~~Lkk~l 116 (344)
++..||.+.-..|.+.+.... ..-..||..+ |=+..+|++-| ..-+.+.
T Consensus 3 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l-~l~~~~V~~WF-~nrR~k~ 55 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQENPYPSKEEREELAKEL-GLTERQVKNWF-QNRRRKE 55 (57)
T ss_dssp SSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHH-TSSHHHHHHHH-HHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHhccccccccccccccc-cccccccccCH-HHhHHHh
Confidence 356789999999988888743 2367788888 89999998744 4444443
No 114
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.91 E-value=1.5e+02 Score=26.21 Aligned_cols=29 Identities=21% Similarity=0.016 Sum_probs=23.5
Q ss_pred HhCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 84 LLGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 84 ~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
..|-...+||..| |-+...|+.+....++
T Consensus 120 ~~g~~~~EIA~~l-gis~~tV~~~l~Rar~ 148 (181)
T PRK09637 120 LEGLSQKEIAEKL-GLSLSGAKSRVQRGRV 148 (181)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 3477899999999 8999999999875543
No 115
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=23.50 E-value=1.6e+02 Score=26.07 Aligned_cols=28 Identities=7% Similarity=-0.002 Sum_probs=23.0
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
.|-...+||..| |-+...|+.|.+..++
T Consensus 156 eg~s~~EIA~~l-gis~~tVk~rl~ra~~ 183 (194)
T PRK12531 156 EELPHQQVAEMF-DIPLGTVKSRLRLAVE 183 (194)
T ss_pred cCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 467789999999 9999999998776554
No 116
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=23.36 E-value=1.8e+02 Score=26.01 Aligned_cols=36 Identities=19% Similarity=0.226 Sum_probs=25.8
Q ss_pred hCCChhHHhhhCCCCCHHHHHHHHHHH---HHHHHHhCCC
Q 047101 85 LGNRWSAIAAHLPKRTDNEIKNYWNTH---IKKRLARMGI 121 (344)
Q Consensus 85 ~G~kWs~IA~~LpgRT~~qcKnRW~~~---Lkk~l~k~~~ 121 (344)
.|-.-.+||..| |.+...||.|.... |++.+...+.
T Consensus 154 eg~s~~EIA~~l-gis~~tVk~~l~RAr~~Lr~~l~~~~~ 192 (201)
T PRK12545 154 LDFEIDDICTEL-TLTANHCSVLLYRARTRLRTCLSEKGL 192 (201)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 356789999999 99999999887643 4444544443
No 117
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members
Probab=23.08 E-value=51 Score=26.36 Aligned_cols=21 Identities=33% Similarity=0.702 Sum_probs=18.9
Q ss_pred HHHHHHHHHhCCChhHHhhhC
Q 047101 76 QTIIQLHALLGNRWSAIAAHL 96 (344)
Q Consensus 76 ~~Ll~lv~~~G~kWs~IA~~L 96 (344)
..|..+....|..|..+|.+|
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L 23 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL 23 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc
Confidence 457888999999999999998
No 118
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=22.96 E-value=93 Score=24.97 Aligned_cols=30 Identities=30% Similarity=0.499 Sum_probs=23.0
Q ss_pred HHHHHHHHHhCCChhHHhhhCCCCCHHHHHH
Q 047101 76 QTIIQLHALLGNRWSAIAAHLPKRTDNEIKN 106 (344)
Q Consensus 76 ~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKn 106 (344)
+.|-.+....|.+|..+|+.| |=++.+|..
T Consensus 3 ~~l~~l~~~lG~~Wk~lar~L-G~s~~eI~~ 32 (86)
T cd08777 3 KHLDLLRENLGKKWKRCARKL-GFTESEIEE 32 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHc-CCCHHHHHH
Confidence 345556678899999999999 777776654
No 119
>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=22.74 E-value=1.8e+02 Score=25.86 Aligned_cols=30 Identities=13% Similarity=0.084 Sum_probs=23.9
Q ss_pred HHhCCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 83 ALLGNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 83 ~~~G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
-..|.....||..| |-+.+.|+.|....++
T Consensus 144 ~~~g~s~~EIA~~l-gis~~tvk~rl~Rar~ 173 (188)
T TIGR02943 144 EVLGFESDEICQEL-EISTSNCHVLLYRARL 173 (188)
T ss_pred HHhCCCHHHHHHHh-CCCHHHHHHHHHHHHH
Confidence 33467799999999 9999999998776543
No 120
>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=22.45 E-value=95 Score=23.89 Aligned_cols=30 Identities=23% Similarity=0.482 Sum_probs=21.5
Q ss_pred HHHHHHHHHHH-hCCChhHHhhhCCCCCHHHH
Q 047101 74 EEQTIIQLHAL-LGNRWSAIAAHLPKRTDNEI 104 (344)
Q Consensus 74 ED~~Ll~lv~~-~G~kWs~IA~~LpgRT~~qc 104 (344)
-++.|..+... .|..|..+|++| |=+..+|
T Consensus 4 ~~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i 34 (88)
T smart00005 4 TREKLAKLLDHPLGLDWRELARKL-GLSEADI 34 (88)
T ss_pred HHHHHHHHHcCccchHHHHHHHHc-CCCHHHH
Confidence 34556666666 899999999999 4445544
No 121
>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=22.45 E-value=1.6e+02 Score=20.05 Aligned_cols=33 Identities=24% Similarity=0.124 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhCCChhHHhhhCCCCCHHHHHH
Q 047101 73 HEEQTIIQLHALLGNRWSAIAAHLPKRTDNEIKN 106 (344)
Q Consensus 73 EED~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKn 106 (344)
-|.+.|.++...++++-...|+.| |=+...+..
T Consensus 5 ~E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~ 37 (42)
T PF02954_consen 5 FEKQLIRQALERCGGNVSKAARLL-GISRRTLYR 37 (42)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHH
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHH
Confidence 367788899999999999999998 655555443
No 122
>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=22.23 E-value=1.1e+02 Score=24.35 Aligned_cols=31 Identities=26% Similarity=0.515 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhCCChhHHhhhCCCCCHHHHHH
Q 047101 75 EQTIIQLHALLGNRWSAIAAHLPKRTDNEIKN 106 (344)
Q Consensus 75 D~~Ll~lv~~~G~kWs~IA~~LpgRT~~qcKn 106 (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 4567777889999999999999 666666543
No 123
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=21.62 E-value=68 Score=24.94 Aligned_cols=19 Identities=21% Similarity=0.438 Sum_probs=15.5
Q ss_pred HHHHHHHHHhCCChhHHhh
Q 047101 76 QTIIQLHALLGNRWSAIAA 94 (344)
Q Consensus 76 ~~Ll~lv~~~G~kWs~IA~ 94 (344)
..|.+|.+.||++|..|-.
T Consensus 30 ~vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 30 PVLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHHcCCchhhhc
Confidence 3567888999999999964
No 124
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=21.60 E-value=1.8e+02 Score=25.16 Aligned_cols=27 Identities=11% Similarity=0.243 Sum_probs=22.7
Q ss_pred CCChhHHhhhCCCCCHHHHHHHHHHHHH
Q 047101 86 GNRWSAIAAHLPKRTDNEIKNYWNTHIK 113 (344)
Q Consensus 86 G~kWs~IA~~LpgRT~~qcKnRW~~~Lk 113 (344)
|-.-..||+.| |.+...|+.+.+..++
T Consensus 145 g~s~~eIA~~l-gis~~tV~~~l~Rar~ 171 (179)
T PRK12514 145 GLSYKELAERH-DVPLNTMRTWLRRSLL 171 (179)
T ss_pred CCCHHHHHHHH-CCChHHHHHHHHHHHH
Confidence 66789999999 9999999998876554
No 125
>smart00351 PAX Paired Box domain.
Probab=21.03 E-value=1.5e+02 Score=25.06 Aligned_cols=72 Identities=14% Similarity=0.164 Sum_probs=47.1
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCccccccccccc-ccccccccccc--ccCCCCCC----CCCCHHHHHHHHHHHHHh
Q 047101 13 KRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQR-CGKSCRLRWTN--YLRPDIKR----GKFSLHEEQTIIQLHALL 85 (344)
Q Consensus 13 kKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~R-t~kQCr~Rw~n--~L~P~ikr----g~WT~EED~~Ll~lv~~~ 85 (344)
...+.+.++-++++.++. -|. .-..||+.++..| +...+..||.. .+.|.... ..-+.+++..|++++.+.
T Consensus 14 ~~~~~s~~~R~riv~~~~-~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~ 91 (125)
T smart00351 14 NGRPLPDEERQRIVELAQ-NGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQEN 91 (125)
T ss_pred CCCCCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHC
Confidence 345689999999998886 453 7799999998654 45556666653 35553222 235566666777676664
Q ss_pred C
Q 047101 86 G 86 (344)
Q Consensus 86 G 86 (344)
+
T Consensus 92 p 92 (125)
T smart00351 92 P 92 (125)
T ss_pred C
Confidence 3
No 126
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=20.00 E-value=40 Score=35.38 Aligned_cols=45 Identities=13% Similarity=0.159 Sum_probs=38.5
Q ss_pred ccCCCCHHHHHHHHHHHHHhCCCCCcccccccccccccccccccccc
Q 047101 13 KRGPWTPEEDQKLLDYIKKHGHGSWRSLPEKADLQRCGKSCRLRWTN 59 (344)
Q Consensus 13 kKg~WT~EEDekL~~lV~k~G~~~W~~IA~~~~~~Rt~kQCr~Rw~n 59 (344)
....||.||--++-+++..||. ++.+|-+.++ .|+-.++++-|+.
T Consensus 186 ~~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~LP-~rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 186 FPDEWTAEDIVLFEQAFQFFGK-DFHKIRQALP-HRSLASLVQYYYS 230 (534)
T ss_pred CcccchHHHHHHHHHHHHHhcc-cHHHHHHHcc-CccHHHHHHHHHH
Confidence 3567999999999999999996 9999988888 8988888776654
Done!