Query 040841
Match_columns 280
No_of_seqs 233 out of 1388
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 12:20:38 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040841.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040841hhsearch_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 3.6E-39 7.8E-44 308.2 12.5 137 1-137 1-137 (459)
2 PLN03212 Transcription repress 100.0 2.9E-38 6.3E-43 283.6 10.9 129 3-131 14-142 (249)
3 KOG0048 Transcription factor, 100.0 3.5E-35 7.6E-40 266.0 10.9 114 10-123 5-118 (238)
4 KOG0049 Transcription factor, 99.8 2.8E-20 6E-25 184.2 6.1 114 1-115 347-461 (939)
5 KOG0049 Transcription factor, 99.7 1.3E-18 2.7E-23 172.5 5.9 119 12-131 303-425 (939)
6 PF13921 Myb_DNA-bind_6: Myb-l 99.7 3.3E-17 7.2E-22 117.7 4.6 60 17-78 1-60 (60)
7 COG5147 REB1 Myb superfamily p 99.6 1.7E-15 3.7E-20 149.6 5.9 108 9-117 15-122 (512)
8 KOG0050 mRNA splicing protein 99.6 2.3E-15 4.9E-20 146.6 4.4 107 11-119 4-110 (617)
9 PLN03212 Transcription repress 99.5 3E-14 6.4E-19 128.8 8.8 68 63-130 21-90 (249)
10 KOG0051 RNA polymerase I termi 99.5 1.2E-14 2.7E-19 144.9 6.1 104 13-119 383-514 (607)
11 PF00249 Myb_DNA-binding: Myb- 99.4 2.6E-14 5.6E-19 98.7 1.8 48 14-61 1-48 (48)
12 PF13921 Myb_DNA-bind_6: Myb-l 99.4 3.3E-14 7.2E-19 102.1 2.2 59 70-128 1-59 (60)
13 PF00249 Myb_DNA-binding: Myb- 99.4 2.4E-13 5.1E-18 93.9 3.7 46 67-112 1-48 (48)
14 KOG0048 Transcription factor, 99.3 1.5E-12 3.2E-17 118.3 3.4 88 63-150 5-101 (238)
15 PLN03091 hypothetical protein; 99.3 1.5E-12 3.2E-17 125.8 2.9 68 63-130 10-79 (459)
16 smart00717 SANT SANT SWI3, AD 99.2 2.4E-11 5.2E-16 81.7 4.5 47 67-113 1-48 (49)
17 smart00717 SANT SANT SWI3, AD 99.1 4.6E-11 9.9E-16 80.3 3.3 48 14-62 1-48 (49)
18 cd00167 SANT 'SWI3, ADA2, N-Co 99.1 1.7E-10 3.6E-15 76.4 4.4 43 69-111 1-44 (45)
19 KOG0051 RNA polymerase I termi 99.0 1.4E-10 3E-15 116.3 2.9 114 13-130 307-448 (607)
20 cd00167 SANT 'SWI3, ADA2, N-Co 99.0 2.8E-10 6E-15 75.3 2.9 45 16-61 1-45 (45)
21 COG5147 REB1 Myb superfamily p 98.5 9.2E-09 2E-13 102.2 -3.9 99 12-113 289-397 (512)
22 TIGR01557 myb_SHAQKYF myb-like 98.0 6E-06 1.3E-10 59.4 3.3 49 13-61 2-54 (57)
23 KOG0050 mRNA splicing protein 97.9 4.1E-06 8.9E-11 82.7 1.4 67 65-131 5-72 (617)
24 KOG0457 Histone acetyltransfer 97.9 6.6E-06 1.4E-10 79.8 2.6 111 12-123 70-232 (438)
25 TIGR01557 myb_SHAQKYF myb-like 97.7 7.6E-05 1.6E-09 53.7 4.7 46 67-112 3-54 (57)
26 KOG0457 Histone acetyltransfer 97.5 7.7E-05 1.7E-09 72.6 4.3 48 64-111 69-117 (438)
27 TIGR02894 DNA_bind_RsfA transc 97.4 0.00014 3E-09 62.5 3.1 52 66-118 3-61 (161)
28 COG5259 RSC8 RSC chromatin rem 97.2 0.00015 3.3E-09 71.1 2.3 46 13-60 278-323 (531)
29 KOG1279 Chromatin remodeling f 97.1 0.00028 6E-09 70.7 3.0 48 11-60 250-297 (506)
30 PF08914 Myb_DNA-bind_2: Rap1 96.9 0.00035 7.5E-09 51.5 1.3 52 14-65 2-61 (65)
31 PF13325 MCRS_N: N-terminal re 96.9 0.0026 5.5E-08 56.7 6.3 99 16-116 1-130 (199)
32 KOG1279 Chromatin remodeling f 96.9 0.0011 2.3E-08 66.6 4.2 46 66-111 252-297 (506)
33 PF13837 Myb_DNA-bind_4: Myb/S 96.7 0.00074 1.6E-08 51.4 1.7 50 67-116 1-68 (90)
34 COG5259 RSC8 RSC chromatin rem 96.7 0.0012 2.5E-08 65.1 3.0 44 68-111 280-323 (531)
35 PF08914 Myb_DNA-bind_2: Rap1 96.3 0.0041 8.9E-08 45.9 3.3 50 67-116 2-61 (65)
36 PRK13923 putative spore coat p 96.3 0.0028 6E-08 55.1 2.5 52 66-118 4-62 (170)
37 TIGR02894 DNA_bind_RsfA transc 96.3 0.0017 3.6E-08 55.9 1.1 50 12-63 2-57 (161)
38 PF13837 Myb_DNA-bind_4: Myb/S 96.3 0.0018 3.9E-08 49.3 1.2 47 14-60 1-63 (90)
39 COG5114 Histone acetyltransfer 95.9 0.0029 6.2E-08 59.9 1.1 47 15-62 64-110 (432)
40 COG5114 Histone acetyltransfer 95.1 0.014 3E-07 55.3 2.6 45 67-111 63-108 (432)
41 PF13873 Myb_DNA-bind_5: Myb/S 95.1 0.0093 2E-07 44.5 1.0 49 13-61 1-69 (78)
42 PLN03142 Probable chromatin-re 94.9 0.056 1.2E-06 58.8 6.8 100 16-116 826-988 (1033)
43 PF13873 Myb_DNA-bind_5: Myb/S 94.5 0.072 1.6E-06 39.7 4.5 47 67-113 2-70 (78)
44 PRK13923 putative spore coat p 94.3 0.014 3E-07 50.8 0.4 49 12-62 3-57 (170)
45 KOG2656 DNA methyltransferase 93.1 0.2 4.3E-06 48.8 5.9 55 68-122 131-191 (445)
46 PF09111 SLIDE: SLIDE; InterP 92.9 0.11 2.3E-06 42.8 3.3 52 64-115 46-113 (118)
47 COG5118 BDP1 Transcription ini 92.6 0.12 2.6E-06 50.2 3.6 45 68-112 366-410 (507)
48 KOG4282 Transcription factor G 90.0 0.38 8.2E-06 45.9 4.2 51 67-117 54-118 (345)
49 PF09111 SLIDE: SLIDE; InterP 88.7 0.21 4.5E-06 41.0 1.2 49 10-58 45-107 (118)
50 PF12776 Myb_DNA-bind_3: Myb/S 86.7 1 2.2E-05 34.4 3.9 45 69-113 1-63 (96)
51 PF08281 Sigma70_r4_2: Sigma-7 84.8 1.2 2.6E-05 30.5 3.2 41 72-113 12-52 (54)
52 KOG1194 Predicted DNA-binding 83.5 1.4 3.1E-05 43.8 4.1 45 67-111 187-231 (534)
53 COG5118 BDP1 Transcription ini 81.6 1 2.3E-05 43.9 2.4 45 14-60 365-409 (507)
54 KOG4282 Transcription factor G 81.3 0.78 1.7E-05 43.7 1.5 47 14-60 54-112 (345)
55 PF11626 Rap1_C: TRF2-interact 79.7 1.8 3.9E-05 33.3 2.7 25 10-34 43-75 (87)
56 KOG4468 Polycomb-group transcr 73.8 4.4 9.6E-05 41.8 4.3 54 66-119 87-150 (782)
57 PF11626 Rap1_C: TRF2-interact 68.4 5 0.00011 30.8 2.7 17 63-79 43-59 (87)
58 PF04545 Sigma70_r4: Sigma-70, 67.0 7 0.00015 26.3 3.0 41 73-114 7-47 (50)
59 PF07750 GcrA: GcrA cell cycle 66.8 4 8.7E-05 35.2 2.1 41 69-110 2-42 (162)
60 PF13404 HTH_AsnC-type: AsnC-t 66.0 3.7 8.1E-05 27.4 1.4 38 20-59 3-40 (42)
61 KOG0384 Chromodomain-helicase 65.9 6.2 0.00014 43.9 3.7 27 14-40 1133-1159(1373)
62 KOG4167 Predicted DNA-binding 65.4 7.1 0.00015 41.2 3.8 43 68-110 620-662 (907)
63 KOG4167 Predicted DNA-binding 64.1 4.6 0.0001 42.5 2.2 44 14-59 619-662 (907)
64 KOG2009 Transcription initiati 63.7 9.6 0.00021 39.3 4.4 45 66-110 408-452 (584)
65 PF13404 HTH_AsnC-type: AsnC-t 58.7 12 0.00027 24.8 2.9 38 73-111 3-41 (42)
66 PRK11179 DNA-binding transcrip 58.6 11 0.00024 31.6 3.3 44 72-116 8-52 (153)
67 KOG4468 Polycomb-group transcr 58.2 9.7 0.00021 39.4 3.3 47 14-61 88-143 (782)
68 KOG2656 DNA methyltransferase 57.9 9.2 0.0002 37.6 2.9 48 12-60 128-180 (445)
69 PF12776 Myb_DNA-bind_3: Myb/S 56.7 13 0.00029 28.1 3.2 44 16-59 1-60 (96)
70 PF13325 MCRS_N: N-terminal re 56.1 17 0.00037 32.6 4.2 45 69-114 1-48 (199)
71 PRK11179 DNA-binding transcrip 55.6 6.6 0.00014 32.9 1.4 46 19-66 8-53 (153)
72 TIGR02985 Sig70_bacteroi1 RNA 55.3 15 0.00033 29.6 3.5 35 77-112 120-154 (161)
73 smart00595 MADF subfamily of S 54.1 8.6 0.00019 28.8 1.7 24 88-112 29-52 (89)
74 PRK11169 leucine-responsive tr 52.4 14 0.0003 31.4 2.9 44 72-116 13-57 (164)
75 PLN03142 Probable chromatin-re 50.9 9.9 0.00021 41.9 2.2 34 11-44 923-956 (1033)
76 KOG4329 DNA-binding protein [G 50.4 21 0.00045 35.0 4.0 43 68-110 278-321 (445)
77 PRK11169 leucine-responsive tr 50.4 6.7 0.00014 33.4 0.6 46 19-66 13-58 (164)
78 cd08319 Death_RAIDD Death doma 50.1 12 0.00027 28.7 2.0 30 75-105 2-31 (83)
79 PF09420 Nop16: Ribosome bioge 48.9 18 0.00038 31.1 3.0 48 12-60 112-162 (164)
80 PF11035 SnAPC_2_like: Small n 47.9 45 0.00099 32.0 5.8 48 67-115 21-72 (344)
81 PF01388 ARID: ARID/BRIGHT DNA 47.3 24 0.00052 26.7 3.3 38 77-114 40-90 (92)
82 PRK09413 IS2 repressor TnpA; R 46.6 47 0.001 26.8 5.1 45 13-61 9-53 (121)
83 smart00501 BRIGHT BRIGHT, ARID 45.0 27 0.00059 26.7 3.3 39 77-115 36-87 (93)
84 cd08803 Death_ank3 Death domai 42.6 22 0.00047 27.3 2.4 31 75-106 4-34 (84)
85 KOG1194 Predicted DNA-binding 41.9 18 0.00039 36.3 2.2 46 12-59 185-230 (534)
86 PF11035 SnAPC_2_like: Small n 40.8 31 0.00068 33.1 3.5 85 14-112 21-126 (344)
87 KOG2009 Transcription initiati 38.6 33 0.00071 35.5 3.6 50 8-59 403-452 (584)
88 TIGR02937 sigma70-ECF RNA poly 37.3 37 0.00079 26.5 3.1 35 78-113 118-152 (158)
89 cd08317 Death_ank Death domain 35.7 23 0.00049 26.8 1.5 30 75-105 4-33 (84)
90 PRK11924 RNA polymerase sigma 35.7 39 0.00085 27.7 3.1 29 83-112 138-166 (179)
91 PRK09652 RNA polymerase sigma 35.6 41 0.0009 27.7 3.2 31 81-112 139-169 (182)
92 smart00351 PAX Paired Box doma 35.4 1.1E+02 0.0023 24.9 5.6 71 14-86 15-92 (125)
93 cd00131 PAX Paired Box domain 34.9 1.3E+02 0.0029 24.6 6.1 70 15-86 16-92 (128)
94 PF07638 Sigma70_ECF: ECF sigm 33.8 42 0.0009 28.9 3.0 36 75-111 140-175 (185)
95 cd06171 Sigma70_r4 Sigma70, re 33.8 57 0.0012 20.7 3.1 40 70-111 11-50 (55)
96 PF10545 MADF_DNA_bdg: Alcohol 33.2 26 0.00056 25.4 1.4 27 88-114 28-55 (85)
97 PRK09643 RNA polymerase sigma 32.6 50 0.0011 28.3 3.3 28 83-111 147-174 (192)
98 PRK04217 hypothetical protein; 32.3 56 0.0012 26.5 3.3 42 69-112 42-83 (110)
99 cd08804 Death_ank2 Death domai 32.2 32 0.0007 26.2 1.8 31 75-106 4-34 (84)
100 KOG4329 DNA-binding protein [G 32.0 40 0.00087 33.1 2.8 42 16-59 279-321 (445)
101 PF02954 HTH_8: Bacterial regu 31.7 49 0.0011 21.6 2.4 35 74-109 6-40 (42)
102 smart00344 HTH_ASNC helix_turn 31.3 50 0.0011 25.4 2.9 43 73-116 3-46 (108)
103 cd08318 Death_NMPP84 Death dom 31.3 35 0.00076 26.0 1.9 27 78-105 10-36 (86)
104 PF09420 Nop16: Ribosome bioge 30.4 88 0.0019 26.7 4.5 46 66-111 113-162 (164)
105 PF04504 DUF573: Protein of un 30.0 51 0.0011 25.9 2.7 46 68-113 5-63 (98)
106 cd08311 Death_p75NR Death doma 29.6 32 0.00069 26.0 1.4 33 72-106 2-34 (77)
107 PRK12529 RNA polymerase sigma 29.4 90 0.0019 26.3 4.3 36 82-118 139-174 (178)
108 PRK12523 RNA polymerase sigma 29.3 83 0.0018 26.2 4.1 36 80-116 129-164 (172)
109 PF10440 WIYLD: Ubiquitin-bind 29.3 34 0.00074 25.3 1.4 18 77-94 31-48 (65)
110 PRK09641 RNA polymerase sigma 28.9 59 0.0013 27.2 3.2 28 85-113 151-178 (187)
111 PF13936 HTH_38: Helix-turn-he 28.8 23 0.00049 23.6 0.4 37 69-107 4-40 (44)
112 TIGR02954 Sig70_famx3 RNA poly 28.3 63 0.0014 26.8 3.2 30 84-114 133-162 (169)
113 cd08777 Death_RIP1 Death Domai 28.3 37 0.0008 26.1 1.6 30 76-106 3-32 (86)
114 TIGR02939 RpoE_Sigma70 RNA pol 27.7 51 0.0011 27.6 2.5 27 85-112 153-179 (190)
115 smart00005 DEATH DEATH domain, 26.7 43 0.00093 24.8 1.7 30 75-105 5-35 (88)
116 PRK09047 RNA polymerase factor 26.7 80 0.0017 25.6 3.5 29 84-113 120-148 (161)
117 PLN00032 DNA-directed RNA poly 26.5 65 0.0014 24.2 2.5 27 247-273 10-37 (71)
118 PRK09648 RNA polymerase sigma 26.1 78 0.0017 26.7 3.4 30 84-114 153-182 (189)
119 PF02216 B: B domain; InterPr 26.1 57 0.0012 23.2 2.0 21 258-278 13-34 (54)
120 PF11427 HTH_Tnp_Tc3_1: Tc3 tr 26.0 61 0.0013 22.6 2.2 36 71-108 6-41 (50)
121 PF01710 HTH_Tnp_IS630: Transp 25.6 1.2E+02 0.0026 24.3 4.2 57 19-78 56-112 (119)
122 PRK09637 RNA polymerase sigma 25.4 77 0.0017 26.9 3.3 28 84-112 120-147 (181)
123 COG2197 CitB Response regulato 24.5 70 0.0015 28.2 2.9 45 68-115 147-191 (211)
124 PRK09645 RNA polymerase sigma 24.3 89 0.0019 25.9 3.4 28 84-112 132-159 (173)
125 COG1522 Lrp Transcriptional re 24.2 40 0.00086 27.6 1.2 44 20-65 8-51 (154)
126 PRK11923 algU RNA polymerase s 24.2 78 0.0017 26.8 3.1 27 85-112 153-179 (193)
127 PRK12512 RNA polymerase sigma 24.2 1.1E+02 0.0024 25.6 4.0 30 84-114 145-174 (184)
128 PRK12515 RNA polymerase sigma 24.1 90 0.002 26.4 3.4 28 84-112 145-172 (189)
129 smart00344 HTH_ASNC helix_turn 23.8 53 0.0011 25.3 1.8 44 20-65 3-46 (108)
130 cd08779 Death_PIDD Death Domai 23.5 54 0.0012 25.0 1.7 27 76-103 3-29 (86)
131 PRK12530 RNA polymerase sigma 23.2 93 0.002 26.5 3.4 28 84-112 148-175 (189)
132 PRK12532 RNA polymerase sigma 23.1 1.1E+02 0.0024 25.9 3.8 28 83-111 149-176 (195)
133 TIGR02948 SigW_bacill RNA poly 23.1 81 0.0018 26.3 2.9 26 86-112 152-177 (187)
134 TIGR02943 Sig70_famx1 RNA poly 22.9 99 0.0022 26.4 3.5 31 81-112 142-172 (188)
135 PRK12531 RNA polymerase sigma 22.8 99 0.0021 26.4 3.4 29 84-113 155-183 (194)
136 PRK09642 RNA polymerase sigma 22.6 1E+02 0.0022 25.1 3.4 28 84-112 120-147 (160)
137 PRK12524 RNA polymerase sigma 22.0 1E+02 0.0022 26.4 3.4 30 83-113 149-178 (196)
138 PRK00118 putative DNA-binding 21.4 1.2E+02 0.0025 24.3 3.3 39 72-111 19-57 (104)
139 cd08805 Death_ank1 Death domai 21.2 67 0.0015 24.7 1.8 28 75-103 4-31 (84)
140 PF01133 ER: Enhancer of rudim 20.5 99 0.0021 24.9 2.7 31 249-279 30-65 (102)
141 PRK12528 RNA polymerase sigma 20.1 1.3E+02 0.0028 24.6 3.5 31 82-113 125-155 (161)
No 1
>PLN03091 hypothetical protein; Provisional
Probab=100.00 E-value=3.6e-39 Score=308.20 Aligned_cols=137 Identities=61% Similarity=1.119 Sum_probs=130.4
Q ss_pred CCCCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHHHH
Q 040841 1 MGRAPCCSKVGLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLIIR 80 (280)
Q Consensus 1 mgr~~~~~k~~lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L~~ 80 (280)
|||++||+|+.++||+||+|||++|+++|.+||.++|..||+.++.+|+++|||+||.++|+|.+++++||+|||++|++
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 99999999999999999999999999999999999999999998755999999999999999999999999999999999
Q ss_pred HHHHhCCccccccccCCCCCHHHHHHHHHHhhhhHHhhCCCCccccccCCCCccccc
Q 040841 81 LHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRLRVQGTDPNTHKKLSEPSLVQD 137 (280)
Q Consensus 81 lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~~~~~~~~~e~~~l~~~~~~~~ 137 (280)
++++||++|..||+.|||||+++||+||+.+++++++..+..+.+++.+.+.....+
T Consensus 81 L~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr~~~I~p~t~kpl~e~E~~~d 137 (459)
T PLN03091 81 LHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLRQRGIDPNTHKPLSEVENGED 137 (459)
T ss_pred HHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHHHcCCCCCCCCCccccccccc
Confidence 999999999999999999999999999999999999999999999998887654433
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=100.00 E-value=2.9e-38 Score=283.61 Aligned_cols=129 Identities=73% Similarity=1.381 Sum_probs=122.4
Q ss_pred CCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHHHHHH
Q 040841 3 RAPCCSKVGLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLIIRLH 82 (280)
Q Consensus 3 r~~~~~k~~lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L~~lv 82 (280)
+.|||.|++++|++||+|||++|+++|++||..+|..||+.++.+|+++|||+||.++|+|.+++++||+|||++|++++
T Consensus 14 ~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLlel~ 93 (249)
T PLN03212 14 TTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLILRLH 93 (249)
T ss_pred CCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHHHHH
Confidence 67999999999999999999999999999999999999999964599999999999999999999999999999999999
Q ss_pred HHhCCccccccccCCCCCHHHHHHHHHHhhhhHHhhCCCCccccccCCC
Q 040841 83 SLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRLRVQGTDPNTHKKLSE 131 (280)
Q Consensus 83 ~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~~~~~~~~~e~~~l~~ 131 (280)
.+||++|..||+.|||||+++||+||+.++++++...+..+.+.+++..
T Consensus 94 ~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~l~r~~i~p~~~kp~~~ 142 (249)
T PLN03212 94 RLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKKLLRQGIDPQTHKPLDA 142 (249)
T ss_pred HhccccHHHHHhhcCCCCHHHHHHHHHHHHhHHHHhcCCCCCCCCCCCc
Confidence 9999999999999999999999999999999999998888877766543
No 3
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=100.00 E-value=3.5e-35 Score=266.03 Aligned_cols=114 Identities=65% Similarity=1.140 Sum_probs=107.5
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCcc
Q 040841 10 VGLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLIIRLHSLLGNRW 89 (280)
Q Consensus 10 ~~lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L~~lv~~~G~~W 89 (280)
+.+.||+||+|||++|+++|++||.++|..||+.+|.+|++++||+||.|||+|++++|.||+|||++|++||..||++|
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 33558999999999999999999999999999999955999999999999999999999999999999999999999999
Q ss_pred ccccccCCCCCHHHHHHHHHHhhhhHHhhCCCCc
Q 040841 90 SLIAGRLPGRTDNEIKNYWNTHLSKRLRVQGTDP 123 (280)
Q Consensus 90 ~~IA~~lpgRt~~qck~Rw~~~l~~~~~~~~~~~ 123 (280)
+.||++|||||++.|||+|+..|++++...+.++
T Consensus 85 s~IA~~LPGRTDNeIKN~Wnt~lkkkl~~~~~~~ 118 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKNHWNTHLKKKLLKMGIDP 118 (238)
T ss_pred HHHHhhCCCcCHHHHHHHHHHHHHHHHHHcCCCC
Confidence 9999999999999999999999999998776443
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.80 E-value=2.8e-20 Score=184.17 Aligned_cols=114 Identities=23% Similarity=0.388 Sum_probs=104.0
Q ss_pred CCCCCCCCCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHHHH
Q 040841 1 MGRAPCCSKVGLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLIIR 80 (280)
Q Consensus 1 mgr~~~~~k~~lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L~~ 80 (280)
+||......|++++|+||++||.+|+.+|.+||.++|.+|-+.+++ |+..|||+||+|.|+...|.+.||-.||+.|+.
T Consensus 347 I~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPn-RSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 347 ITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPN-RSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred hhhheeccCccccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCC-ccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 5889999999999999999999999999999999999999999998 999999999999999999999999999999999
Q ss_pred HHHHhC-CccccccccCCCCCHHHHHHHHHHhhhhH
Q 040841 81 LHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLSKR 115 (280)
Q Consensus 81 lv~~~G-~~W~~IA~~lpgRt~~qck~Rw~~~l~~~ 115 (280)
+|.+|| ++|.+||..||.||..|...|-...+.-+
T Consensus 426 ~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~~~~k 461 (939)
T KOG0049|consen 426 AVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRLIAAK 461 (939)
T ss_pred HHHHHccchHHHHHHHccccchhHHHHHHHHHHHHH
Confidence 999999 79999999999999966544443333333
No 5
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.74 E-value=1.3e-18 Score=172.52 Aligned_cols=119 Identities=22% Similarity=0.399 Sum_probs=111.4
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCC---CccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHHHHHHHHhC-C
Q 040841 12 LQRGPWTPREDTLLTEYIQVHGEG---HWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLIIRLHSLLG-N 87 (280)
Q Consensus 12 lkkg~WT~EED~~L~~lV~~~G~~---~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L~~lv~~~G-~ 87 (280)
+.+..||.|||.+|+++|+....+ +|++|-..|++ |+..|...||.+.|+|.+++|.||.+||.+|+.+|.+|| .
T Consensus 303 L~ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympg-r~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~~Yg~k 381 (939)
T KOG0049|consen 303 LSEKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPG-RTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVSRYGAK 381 (939)
T ss_pred HHhhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCC-cchhhhhhhheeccCccccCCCCCCHHHHHHHHHHHHhCcc
Confidence 566889999999999999988654 79999999999 999999999999999999999999999999999999999 5
Q ss_pred ccccccccCCCCCHHHHHHHHHHhhhhHHhhCCCCccccccCCC
Q 040841 88 RWSLIAGRLPGRTDNEIKNYWNTHLSKRLRVQGTDPNTHKKLSE 131 (280)
Q Consensus 88 ~W~~IA~~lpgRt~~qck~Rw~~~l~~~~~~~~~~~~e~~~l~~ 131 (280)
.|.+|-..+|||++.|||.||.+.|...++.+.|+..++..+..
T Consensus 382 dw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~ 425 (939)
T KOG0049|consen 382 DWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLY 425 (939)
T ss_pred chhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHH
Confidence 69999999999999999999999999999999999988776653
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.68 E-value=3.3e-17 Score=117.75 Aligned_cols=60 Identities=43% Similarity=0.832 Sum_probs=55.0
Q ss_pred CCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHH
Q 040841 17 WTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLI 78 (280)
Q Consensus 17 WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L 78 (280)
||+|||++|+++|..||. +|..||+.|+. |+..||+.||.++|.|.+++++||.+||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~-~W~~Ia~~l~~-Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-DWKKIAEHLGN-RTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS--HHHHHHHSTT-S-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-CHHHHHHHHCc-CCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 999999999999999996 99999999975 9999999999999999999999999999987
No 7
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.57 E-value=1.7e-15 Score=149.59 Aligned_cols=108 Identities=27% Similarity=0.455 Sum_probs=102.8
Q ss_pred CCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCc
Q 040841 9 KVGLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLIIRLHSLLGNR 88 (280)
Q Consensus 9 k~~lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L~~lv~~~G~~ 88 (280)
...++.|.|+..||+.|..+|+.+|..+|..||..+.. |+++||+.||.++++|.++++.|+.|||..|+.+..++|+.
T Consensus 15 ~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~-~~~kq~~~rw~~~lnp~lk~~~~~~eed~~li~l~~~~~~~ 93 (512)
T COG5147 15 QTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLIS-STGKQSSNRWNNHLNPQLKKKNWSEEEDEQLIDLDKELGTQ 93 (512)
T ss_pred cceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcc-cccccccchhhhhhchhcccccccHHHHHHHHHHHHhcCch
Confidence 45678899999999999999999999999999999998 99999999999999999999999999999999999999999
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhhHHh
Q 040841 89 WSLIAGRLPGRTDNEIKNYWNTHLSKRLR 117 (280)
Q Consensus 89 W~~IA~~lpgRt~~qck~Rw~~~l~~~~~ 117 (280)
|+.||..++||+..+|.+||...+.....
T Consensus 94 wstia~~~d~rt~~~~~ery~~~~~~~~s 122 (512)
T COG5147 94 WSTIADYKDRRTAQQCVERYVNTLEDLSS 122 (512)
T ss_pred hhhhccccCccchHHHHHHHHHHhhhhhc
Confidence 99999999999999999999988776655
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=2.3e-15 Score=146.59 Aligned_cols=107 Identities=24% Similarity=0.548 Sum_probs=101.1
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHHHHHHHHhCCccc
Q 040841 11 GLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLIIRLHSLLGNRWS 90 (280)
Q Consensus 11 ~lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L~~lv~~~G~~W~ 90 (280)
-++.|-|+.-||+.|..+|.+||...|++|++.+.- .+++||+.||..+|+|.|++..|+.|||++|+.+...+.+.|.
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~nqws~i~sll~~-kt~rqC~~rw~e~ldp~i~~tews~eederlLhlakl~p~qwr 82 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNR-KTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAKLEPTQWR 82 (617)
T ss_pred EEecceecccHHHHHHHHHHHcchHHHHHHHHHHhh-cchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHHhcCCccc
Confidence 357789999999999999999999999999999987 9999999999999999999999999999999999999999999
Q ss_pred cccccCCCCCHHHHHHHHHHhhhhHHhhC
Q 040841 91 LIAGRLPGRTDNEIKNYWNTHLSKRLRVQ 119 (280)
Q Consensus 91 ~IA~~lpgRt~~qck~Rw~~~l~~~~~~~ 119 (280)
.|+..| ||+.+||-.||..++.......
T Consensus 83 tIa~i~-gr~~~qc~eRy~~ll~~~~s~~ 110 (617)
T KOG0050|consen 83 TIADIM-GRTSQQCLERYNNLLDVYVSYH 110 (617)
T ss_pred hHHHHh-hhhHHHHHHHHHHHHHHHHhhh
Confidence 999999 9999999999999988776544
No 9
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.52 E-value=3e-14 Score=128.81 Aligned_cols=68 Identities=21% Similarity=0.380 Sum_probs=63.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CccccccccC-CCCCHHHHHHHHHHhhhhHHhhCCCCccccccCC
Q 040841 63 PDIKRGNITPDEDDLIIRLHSLLG-NRWSLIAGRL-PGRTDNEIKNYWNTHLSKRLRVQGTDPNTHKKLS 130 (280)
Q Consensus 63 p~ikkg~WT~EED~~L~~lv~~~G-~~W~~IA~~l-pgRt~~qck~Rw~~~l~~~~~~~~~~~~e~~~l~ 130 (280)
+.+++++||+|||++|+++|++|| .+|..||+.+ +|||..||+.||.++|++.+++..|+.+|+..+.
T Consensus 21 ~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~EED~lLl 90 (249)
T PLN03212 21 MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITSDEEDLIL 90 (249)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCChHHHHHHH
Confidence 578999999999999999999999 5899999998 6999999999999999999999999999988654
No 10
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.51 E-value=1.2e-14 Score=144.94 Aligned_cols=104 Identities=25% Similarity=0.554 Sum_probs=94.5
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCC--CCCCCCHHHHHHHHHHHH-------
Q 040841 13 QRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDI--KRGNITPDEDDLIIRLHS------- 83 (280)
Q Consensus 13 kkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~i--kkg~WT~EED~~L~~lv~------- 83 (280)
.||.||+||++.|..+|..||. .|..|+..|+ |.+..|++||+++..++- +++.||.||+++|+++|.
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 8999999999999999999997 9999999998 999999999999998884 899999999999999995
Q ss_pred Hh-------------------CCccccccccCCCCCHHHHHHHHHHhhhhHHhhC
Q 040841 84 LL-------------------GNRWSLIAGRLPGRTDNEIKNYWNTHLSKRLRVQ 119 (280)
Q Consensus 84 ~~-------------------G~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~~~~ 119 (280)
++ +.+|..|++.+.+|+..||+.+|+.++......+
T Consensus 460 q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s~n~ 514 (607)
T KOG0051|consen 460 QPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPSFNK 514 (607)
T ss_pred cccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHHhhc
Confidence 33 2469999999999999999999999887776544
No 11
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.44 E-value=2.6e-14 Score=98.67 Aligned_cols=48 Identities=40% Similarity=0.751 Sum_probs=42.8
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhcc
Q 040841 14 RGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYL 61 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L 61 (280)
|++||+|||++|+++|.+||.++|..||..|+++||..||+.||.++|
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 689999999999999999999779999999994499999999999875
No 12
>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=99.44 E-value=3.3e-14 Score=102.08 Aligned_cols=59 Identities=29% Similarity=0.531 Sum_probs=51.5
Q ss_pred CCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHhhhhHHhhCCCCcccccc
Q 040841 70 ITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRLRVQGTDPNTHKK 128 (280)
Q Consensus 70 WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~~~~~~~~~e~~~ 128 (280)
||+|||++|+++|.+||++|..||+.|+.||..+|++||+..|++.+....|++.++..
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~ 59 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQR 59 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhc
Confidence 99999999999999999999999999966999999999999888888888898877643
No 13
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.39 E-value=2.4e-13 Score=93.86 Aligned_cols=46 Identities=33% Similarity=0.629 Sum_probs=41.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCCc-cccccccCC-CCCHHHHHHHHHHhh
Q 040841 67 RGNITPDEDDLIIRLHSLLGNR-WSLIAGRLP-GRTDNEIKNYWNTHL 112 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~G~~-W~~IA~~lp-gRt~~qck~Rw~~~l 112 (280)
+++||+|||++|++++.+||.+ |..||..|| |||..||++||++++
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 999999999998864
No 14
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.29 E-value=1.5e-12 Score=118.26 Aligned_cols=88 Identities=16% Similarity=0.190 Sum_probs=72.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CccccccccCC-CCCHHHHHHHHHHhhhhHHhhCCCCccccccCC-------CCc
Q 040841 63 PDIKRGNITPDEDDLIIRLHSLLG-NRWSLIAGRLP-GRTDNEIKNYWNTHLSKRLRVQGTDPNTHKKLS-------EPS 133 (280)
Q Consensus 63 p~ikkg~WT~EED~~L~~lv~~~G-~~W~~IA~~lp-gRt~~qck~Rw~~~l~~~~~~~~~~~~e~~~l~-------~~~ 133 (280)
+.+.+|+||+|||++|+++|++|| .+|..|++.++ ||+..+||-||.++|++.++++.|+++|+..+. ...
T Consensus 5 ~~~~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~~~GNrW 84 (238)
T KOG0048|consen 5 PELVKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHALLGNRW 84 (238)
T ss_pred ccccCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHHHHCcHH
Confidence 345579999999999999999999 57999999998 999999999999999999999999998866554 444
Q ss_pred cccchhhhhhhcchhhH
Q 040841 134 LVQDGIIKKRRRISKTE 150 (280)
Q Consensus 134 ~~~~~~~~~~~~~~~~~ 150 (280)
...+..++.+..+..++
T Consensus 85 s~IA~~LPGRTDNeIKN 101 (238)
T KOG0048|consen 85 SLIAGRLPGRTDNEVKN 101 (238)
T ss_pred HHHHhhCCCcCHHHHHH
Confidence 45555566665555543
No 15
>PLN03091 hypothetical protein; Provisional
Probab=99.27 E-value=1.5e-12 Score=125.80 Aligned_cols=68 Identities=18% Similarity=0.350 Sum_probs=63.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhC-CccccccccC-CCCCHHHHHHHHHHhhhhHHhhCCCCccccccCC
Q 040841 63 PDIKRGNITPDEDDLIIRLHSLLG-NRWSLIAGRL-PGRTDNEIKNYWNTHLSKRLRVQGTDPNTHKKLS 130 (280)
Q Consensus 63 p~ikkg~WT~EED~~L~~lv~~~G-~~W~~IA~~l-pgRt~~qck~Rw~~~l~~~~~~~~~~~~e~~~l~ 130 (280)
+.++++.||+|||++|+++|.+|| .+|..||+.+ +||+++|||.||.++|++.++++.|+++|+..|.
T Consensus 10 qklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLL 79 (459)
T PLN03091 10 QKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLII 79 (459)
T ss_pred CCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHH
Confidence 578999999999999999999999 5799999988 5999999999999999999999999999997654
No 16
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.19 E-value=2.4e-11 Score=81.71 Aligned_cols=47 Identities=43% Similarity=0.802 Sum_probs=44.0
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CccccccccCCCCCHHHHHHHHHHhhh
Q 040841 67 RGNITPDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~G-~~W~~IA~~lpgRt~~qck~Rw~~~l~ 113 (280)
++.||++||.+|+.++..|| .+|..||..|++||..+|++||+.+++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999999999 999999999999999999999988653
No 17
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=99.12 E-value=4.6e-11 Score=80.31 Aligned_cols=48 Identities=38% Similarity=0.808 Sum_probs=44.3
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccC
Q 040841 14 RGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLR 62 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~ 62 (280)
++.||++||++|+.++..||..+|..||..+++ |+..+|+.||.+++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~-rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPG-RTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCC-CCHHHHHHHHHHHcC
Confidence 478999999999999999996699999999997 999999999998764
No 18
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=99.07 E-value=1.7e-10 Score=76.43 Aligned_cols=43 Identities=35% Similarity=0.679 Sum_probs=41.2
Q ss_pred CCCHHHHHHHHHHHHHhC-CccccccccCCCCCHHHHHHHHHHh
Q 040841 69 NITPDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 69 ~WT~EED~~L~~lv~~~G-~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
+||.+|+..|+.++..|| .+|..||..|++||..+|++||..+
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 8999999999999999999999865
No 19
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.01 E-value=1.4e-10 Score=116.28 Aligned_cols=114 Identities=23% Similarity=0.293 Sum_probs=93.7
Q ss_pred CcCCCCHHHHHHHHHHHHHhCC-----------------------CCccccccccCccccchhhhh---hhhhccCCCCC
Q 040841 13 QRGPWTPREDTLLTEYIQVHGE-----------------------GHWRSLPKKAGLLRCGKSCRL---RWMNYLRPDIK 66 (280)
Q Consensus 13 kkg~WT~EED~~L~~lV~~~G~-----------------------~~W~~IA~~~~~~Rt~~qCr~---Rw~~~L~p~ik 66 (280)
+-+.|+.+||+.|.+.|..|-. +-|..|...++. |+.+.++. |-.+.+.+ +
T Consensus 307 ~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~-R~~~siy~~~rR~y~~FE~--~ 383 (607)
T KOG0051|consen 307 NLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPY-RDRKSIYHHLRRAYTPFEN--K 383 (607)
T ss_pred hhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCc-ccchhHHHHHHhcCCcccc--c
Confidence 3489999999999999988711 126778888898 99999888 43344443 8
Q ss_pred CCCCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHhhhhH--HhhCCCCccccccCC
Q 040841 67 RGNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKR--LRVQGTDPNTHKKLS 130 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~~--~~~~~~~~~e~~~l~ 130 (280)
+|.||+||++.|..+|.++|+.|..|++.| ||.+.+|+.||++++... .+++.|+-++..+|.
T Consensus 384 rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~l-gr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Ll 448 (607)
T KOG0051|consen 384 RGKWTPEEEEELKKLVVEHGNDWKEIGKAL-GRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLL 448 (607)
T ss_pred cCCCCcchHHHHHHHHHHhcccHHHHHHHH-ccCcHHHHHHHHHhhccccccccCcchHHHHHHHH
Confidence 999999999999999999999999999999 999999999999987766 466678766655544
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=98.99 E-value=2.8e-10 Score=75.35 Aligned_cols=45 Identities=42% Similarity=0.815 Sum_probs=41.9
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhcc
Q 040841 16 PWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYL 61 (280)
Q Consensus 16 ~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L 61 (280)
+||++||+.|+.++..||.++|..||..+++ |+..+|+.||.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~-rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPG-RTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCC-CCHHHHHHHHHHhC
Confidence 5999999999999999996699999999998 99999999998753
No 21
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=98.45 E-value=9.2e-09 Score=102.22 Aligned_cols=99 Identities=28% Similarity=0.586 Sum_probs=87.1
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCC--CCCCCCCCHHHHHHHHHHHHHhC---
Q 040841 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRP--DIKRGNITPDEDDLIIRLHSLLG--- 86 (280)
Q Consensus 12 lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p--~ikkg~WT~EED~~L~~lv~~~G--- 86 (280)
-.+|.||+||+..|..++..+|. .|..|...++ |-+..||+||++|..+ .+++++|+.||+.+|...+.+.-
T Consensus 289 ~~~~~wt~e~~~eL~~~~~~~~~-~w~~ig~~~~--rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~ 365 (512)
T COG5147 289 EQRGKWTKEEEQELAKLVVEHGG-SWTEIGKLLG--RMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEA 365 (512)
T ss_pred hhhccCccccccccccccccccc-hhhHhhhhhc--cCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHH
Confidence 35799999999999999999997 9999998777 9999999999999988 67888999999999998886432
Q ss_pred -----CccccccccCCCCCHHHHHHHHHHhhh
Q 040841 87 -----NRWSLIAGRLPGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 87 -----~~W~~IA~~lpgRt~~qck~Rw~~~l~ 113 (280)
..|..|+..+++|...+|+.++..+..
T Consensus 366 ~~~~~~~~~li~~~~~~~~~~~~~~~~~~~~~ 397 (512)
T COG5147 366 QQSSRILWLLIAQNIRNRLQHHCRDKYGVLIS 397 (512)
T ss_pred hhhhhhhHHHHHHhhhccccCCCCCccccccc
Confidence 459999999999999999988866543
No 22
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=97.99 E-value=6e-06 Score=59.38 Aligned_cols=49 Identities=14% Similarity=0.197 Sum_probs=43.5
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCc---cccccccCccc-cchhhhhhhhhcc
Q 040841 13 QRGPWTPREDTLLTEYIQVHGEGHW---RSLPKKAGLLR-CGKSCRLRWMNYL 61 (280)
Q Consensus 13 kkg~WT~EED~~L~~lV~~~G~~~W---~~IA~~~~~~R-t~~qCr~Rw~~~L 61 (280)
.|-.||+||..+++++|..+|.|+| +.|++.|+..| |..||+.++..|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 3567999999999999999999999 99999987657 9999999988764
No 23
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=97.89 E-value=4.1e-06 Score=82.70 Aligned_cols=67 Identities=25% Similarity=0.387 Sum_probs=61.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhC-CccccccccCCCCCHHHHHHHHHHhhhhHHhhCCCCccccccCCC
Q 040841 65 IKRGNITPDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLSKRLRVQGTDPNTHKKLSE 131 (280)
Q Consensus 65 ikkg~WT~EED~~L~~lv~~~G-~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~~~~~~~~~e~~~l~~ 131 (280)
++.|.|+.-||+.|-.+|.+|| +.|++|++.++-.+..||++||...+.+.++.-.|+..++.++..
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLh 72 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLH 72 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHH
Confidence 5678999999999999999999 679999999999999999999999999999999999988776543
No 24
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.88 E-value=6.6e-06 Score=79.85 Aligned_cols=111 Identities=23% Similarity=0.390 Sum_probs=77.2
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhcc-CCCCCCCCC-------CHHHHHHHHHH-H
Q 040841 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYL-RPDIKRGNI-------TPDEDDLIIRL-H 82 (280)
Q Consensus 12 lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L-~p~ikkg~W-------T~EED~~L~~l-v 82 (280)
+-...||++|+-+|++++..||.|||..||.++|. |++.+|+++|.+++ +..+-.-+| ...|+.....- +
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGt-Ktkeeck~hy~k~fv~s~~~~~~~i~~~~~~~q~e~~~~~k~~~ 148 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGT-KTKEECKEHYLKHFVNSPIFPLPDISLGIGVNQDEDAAMAKNRA 148 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcc-cchHHHHHHHHHHHhcCccccccccccccCcchHHHhhhccccc
Confidence 44678999999999999999999999999999997 99999999999864 322222223 23344433322 2
Q ss_pred HHhCC-------------ccccccccCCCCCH------------------------------HHHHHHHHHhhhhHHhhC
Q 040841 83 SLLGN-------------RWSLIAGRLPGRTD------------------------------NEIKNYWNTHLSKRLRVQ 119 (280)
Q Consensus 83 ~~~G~-------------~W~~IA~~lpgRt~------------------------------~qck~Rw~~~l~~~~~~~ 119 (280)
..++. .=.+|+..||+|.+ .++.+-|.+.|+.+.+++
T Consensus 149 ~~~~~~~~~pr~p~~~~p~~~e~~gyMp~R~dFd~Eydn~AE~li~dm~f~e~D~~~d~elKla~ldiY~srl~eR~RRK 228 (438)
T KOG0457|consen 149 EPFQPTDLVPRKPGVSNPLRREISGYMPGRLDFDEEYDNEAEQLIRDMEFEEDDTEEDHELKLAVLDIYNSRLKERKRRK 228 (438)
T ss_pred ccCCCCCCCCCCCCCCCchHHHHhhhCccchhhhhhhcchhhhhHhhcccCCCCcHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 22221 13478888999843 255667877777777666
Q ss_pred CCCc
Q 040841 120 GTDP 123 (280)
Q Consensus 120 ~~~~ 123 (280)
.|-.
T Consensus 229 ~~I~ 232 (438)
T KOG0457|consen 229 RFIR 232 (438)
T ss_pred HHHh
Confidence 5543
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=97.67 E-value=7.6e-05 Score=53.65 Aligned_cols=46 Identities=20% Similarity=0.221 Sum_probs=40.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-cc---ccccccCC-CC-CHHHHHHHHHHhh
Q 040841 67 RGNITPDEDDLIIRLHSLLGN-RW---SLIAGRLP-GR-TDNEIKNYWNTHL 112 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~G~-~W---~~IA~~lp-gR-t~~qck~Rw~~~l 112 (280)
+-.||+||..+.++++..||. +| ..|++.|. .| |..||+.|.+.+.
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 557999999999999999996 99 99999884 45 9999999987664
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.55 E-value=7.7e-05 Score=72.58 Aligned_cols=48 Identities=27% Similarity=0.407 Sum_probs=43.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhC-CccccccccCCCCCHHHHHHHHHHh
Q 040841 64 DIKRGNITPDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 64 ~ikkg~WT~EED~~L~~lv~~~G-~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
.+-...||.+|+.+|++++..|| ++|..||.++..|+..+|+.+|.++
T Consensus 69 ~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~ 117 (438)
T KOG0457|consen 69 PILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKH 117 (438)
T ss_pred CCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHH
Confidence 44567899999999999999999 8999999999999999999999754
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=97.37 E-value=0.00014 Score=62.48 Aligned_cols=52 Identities=21% Similarity=0.274 Sum_probs=46.1
Q ss_pred CCCCCCHHHHHHHHHHHHHh---CC----ccccccccCCCCCHHHHHHHHHHhhhhHHhh
Q 040841 66 KRGNITPDEDDLIIRLHSLL---GN----RWSLIAGRLPGRTDNEIKNYWNTHLSKRLRV 118 (280)
Q Consensus 66 kkg~WT~EED~~L~~lv~~~---G~----~W~~IA~~lpgRt~~qck~Rw~~~l~~~~~~ 118 (280)
+...||.|||.+|.+.|-.| |. -+..|++.| +||+.+|.-||++.+++.+..
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~ 61 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEE 61 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHH
Confidence 45689999999999999887 42 499999999 999999999999999998864
No 28
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=97.24 E-value=0.00015 Score=71.13 Aligned_cols=46 Identities=24% Similarity=0.602 Sum_probs=43.1
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhc
Q 040841 13 QRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNY 60 (280)
Q Consensus 13 kkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~ 60 (280)
....||.+|-.+|++.|+.||. +|.+||.++|+ |+..||..||.+.
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygD-dW~kVA~HVgt-Kt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGD-DWDKVARHVGT-KTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhh-hHHHHHHHhCC-CCHHHHHHHHHcC
Confidence 5669999999999999999998 99999999997 9999999999864
No 29
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=97.13 E-value=0.00028 Score=70.71 Aligned_cols=48 Identities=27% Similarity=0.632 Sum_probs=44.1
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhc
Q 040841 11 GLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNY 60 (280)
Q Consensus 11 ~lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~ 60 (280)
.-.++.||.+|+-+|+++|+.||. +|.+||.++++ |+..||..++.+.
T Consensus 250 ~~~~~~WT~qE~lLLLE~ie~y~d-dW~kVa~hVg~-ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 250 ESARPNWTEQETLLLLEAIEMYGD-DWNKVADHVGT-KSQEQCILKFLRL 297 (506)
T ss_pred ccCCCCccHHHHHHHHHHHHHhcc-cHHHHHhccCC-CCHHHHHHHHHhc
Confidence 345788999999999999999998 99999999998 9999999998763
No 30
>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=96.95 E-value=0.00035 Score=51.55 Aligned_cols=52 Identities=29% Similarity=0.501 Sum_probs=33.5
Q ss_pred cCCCCHHHHHHHHHHHHHhCC------C--CccccccccCccccchhhhhhhhhccCCCC
Q 040841 14 RGPWTPREDTLLTEYIQVHGE------G--HWRSLPKKAGLLRCGKSCRLRWMNYLRPDI 65 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~G~------~--~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~i 65 (280)
|.+||.|||+.|+..|..+.. | =|..+++..++.+|..+-|+||...|.+..
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 568999999999999976521 2 399999998855999999999999987643
No 31
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.86 E-value=0.0026 Score=56.71 Aligned_cols=99 Identities=19% Similarity=0.350 Sum_probs=68.8
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCc--cccchhhhhhhhhcc-CCCCC--------------------CCCCCH
Q 040841 16 PWTPREDTLLTEYIQVHGEGHWRSLPKKAGL--LRCGKSCRLRWMNYL-RPDIK--------------------RGNITP 72 (280)
Q Consensus 16 ~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~--~Rt~~qCr~Rw~~~L-~p~ik--------------------kg~WT~ 72 (280)
+|++++|-.|+.+|..-. +-..|+.-+.- .-|-..+.+||+..| +|.+. +..||.
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 599999999999998643 34444443322 245678889999876 44332 458999
Q ss_pred HHHHHHHHHHHHhCC---cccccc----ccC-CCCCHHHHHHHHHHhhhhHH
Q 040841 73 DEDDLIIRLHSLLGN---RWSLIA----GRL-PGRTDNEIKNYWNTHLSKRL 116 (280)
Q Consensus 73 EED~~L~~lv~~~G~---~W~~IA----~~l-pgRt~~qck~Rw~~~l~~~~ 116 (280)
+|+++|......... .+.+|- ..| ++||+.++.++|..+.+..+
T Consensus 79 ~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmkqy~L 130 (199)
T PF13325_consen 79 EEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMKQYHL 130 (199)
T ss_pred HHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHHHhch
Confidence 999999987665542 355552 234 79999999999986544333
No 32
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=96.85 E-value=0.0011 Score=66.61 Aligned_cols=46 Identities=17% Similarity=0.302 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHh
Q 040841 66 KRGNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 66 kkg~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
.++.||.+|..+|++.+..||.+|.+||.++.+||..||-.||.++
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 3568999999999999999999999999999999999999999765
No 33
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.73 E-value=0.00074 Score=51.42 Aligned_cols=50 Identities=32% Similarity=0.458 Sum_probs=34.6
Q ss_pred CCCCCHHHHHHHHHHHHH------hC--C------ccccccccC----CCCCHHHHHHHHHHhhhhHH
Q 040841 67 RGNITPDEDDLIIRLHSL------LG--N------RWSLIAGRL----PGRTDNEIKNYWNTHLSKRL 116 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~------~G--~------~W~~IA~~l----pgRt~~qck~Rw~~~l~~~~ 116 (280)
+..||.+|...||.++.. ++ . -|..||..| ..||+.||+++|.++.+...
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~~Yk 68 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKKKYK 68 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHH
Confidence 347999999999999877 21 1 399999987 36999999999998544433
No 34
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.69 E-value=0.0012 Score=65.09 Aligned_cols=44 Identities=16% Similarity=0.216 Sum_probs=42.0
Q ss_pred CCCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHh
Q 040841 68 GNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 68 g~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
..||.+|..+|++.+..||..|.+||+++.+||..||--||-++
T Consensus 280 k~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 280 KNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 48999999999999999999999999999999999999999765
No 35
>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=96.33 E-value=0.0041 Score=45.86 Aligned_cols=50 Identities=20% Similarity=0.341 Sum_probs=32.5
Q ss_pred CCCCCHHHHHHHHHHHHHhC--------Cc-cccccccCC-CCCHHHHHHHHHHhhhhHH
Q 040841 67 RGNITPDEDDLIIRLHSLLG--------NR-WSLIAGRLP-GRTDNEIKNYWNTHLSKRL 116 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~G--------~~-W~~IA~~lp-gRt~~qck~Rw~~~l~~~~ 116 (280)
+.+||.+||..|+..|.++. |. |..+++.-+ .+|-.+.|+||...|..+.
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~~~ 61 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRGRP 61 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT----
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhccc
Confidence 45799999999999997652 22 999999887 9999999999988776654
No 36
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=96.27 E-value=0.0028 Score=55.14 Aligned_cols=52 Identities=17% Similarity=0.242 Sum_probs=44.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-------ccccccccCCCCCHHHHHHHHHHhhhhHHhh
Q 040841 66 KRGNITPDEDDLIIRLHSLLGN-------RWSLIAGRLPGRTDNEIKNYWNTHLSKRLRV 118 (280)
Q Consensus 66 kkg~WT~EED~~L~~lv~~~G~-------~W~~IA~~lpgRt~~qck~Rw~~~l~~~~~~ 118 (280)
+...||.|||.+|.+.|-.|+. -...++..| +||..+|..||+..+++++..
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L-~rt~aac~fRwNs~vrk~Yee 62 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDAL-KRTAAACGFRWNSVVRKQYQE 62 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHH-hhhHHHHHhHHHHHHHHHHHH
Confidence 5678999999999999888863 277778888 999999999999999988754
No 37
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.27 E-value=0.0017 Score=55.89 Aligned_cols=50 Identities=30% Similarity=0.644 Sum_probs=42.1
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCC-C-----CccccccccCccccchhhhhhhhhccCC
Q 040841 12 LQRGPWTPREDTLLTEYIQVHGE-G-----HWRSLPKKAGLLRCGKSCRLRWMNYLRP 63 (280)
Q Consensus 12 lkkg~WT~EED~~L~~lV~~~G~-~-----~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p 63 (280)
.+.-.||.|||.+|.+.|-+|-. | .+..|+..++ ||+.-|.-||..+++.
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 2 4788888887 9999999999988763
No 38
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.25 E-value=0.0018 Score=49.26 Aligned_cols=47 Identities=30% Similarity=0.643 Sum_probs=32.4
Q ss_pred cCCCCHHHHHHHHHHHHHh------C--CC-----Ccccccccc---Cccccchhhhhhhhhc
Q 040841 14 RGPWTPREDTLLTEYIQVH------G--EG-----HWRSLPKKA---GLLRCGKSCRLRWMNY 60 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~------G--~~-----~W~~IA~~~---~~~Rt~~qCr~Rw~~~ 60 (280)
|..||.+|...|++++... + .. -|..||..| |-.|++.||+.||.+.
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L 63 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNL 63 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 4579999999999999872 1 11 399999987 3459999999999873
No 39
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.95 E-value=0.0029 Score=59.86 Aligned_cols=47 Identities=21% Similarity=0.516 Sum_probs=44.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccC
Q 040841 15 GPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLR 62 (280)
Q Consensus 15 g~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~ 62 (280)
--|+..|+-+|++.....|-|||.-||..+|. |+...|+.+|..++.
T Consensus 64 e~WgadEEllli~~~~TlGlGNW~dIadyiGs-r~kee~k~HylK~y~ 110 (432)
T COG5114 64 EGWGADEELLLIECLDTLGLGNWEDIADYIGS-RAKEEIKSHYLKMYD 110 (432)
T ss_pred CCcCchHHHHHHHHHHhcCCCcHHHHHHHHhh-hhhHHHHHHHHHHHh
Confidence 35999999999999999999999999999997 999999999998765
No 40
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=95.14 E-value=0.014 Score=55.30 Aligned_cols=45 Identities=29% Similarity=0.412 Sum_probs=41.5
Q ss_pred CCCCCHHHHHHHHHHHHHhC-CccccccccCCCCCHHHHHHHHHHh
Q 040841 67 RGNITPDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~G-~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
-..|+.+|+.+|++...-+| ++|..||.++..|+...||.+|..+
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~ 108 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKM 108 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHH
Confidence 45799999999999999999 8999999999999999999999654
No 41
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=95.05 E-value=0.0093 Score=44.53 Aligned_cols=49 Identities=18% Similarity=0.419 Sum_probs=39.4
Q ss_pred CcCCCCHHHHHHHHHHHHHhCC----------------CCcccccccc----Cccccchhhhhhhhhcc
Q 040841 13 QRGPWTPREDTLLTEYIQVHGE----------------GHWRSLPKKA----GLLRCGKSCRLRWMNYL 61 (280)
Q Consensus 13 kkg~WT~EED~~L~~lV~~~G~----------------~~W~~IA~~~----~~~Rt~~qCr~Rw~~~L 61 (280)
++..||.+|.+.|+++|.+|.. .-|..|+..+ ++.|+..|++.+|.+..
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 3578999999999999998822 1499998876 22499999999998853
No 42
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=94.93 E-value=0.056 Score=58.80 Aligned_cols=100 Identities=14% Similarity=0.228 Sum_probs=75.5
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhh-------hhhh-----------------------------
Q 040841 16 PWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRL-------RWMN----------------------------- 59 (280)
Q Consensus 16 ~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~-------Rw~~----------------------------- 59 (280)
.||..+=..++.+..+||..+-..||..|.+ ++...++. ||..
T Consensus 826 ~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~-k~~~ev~~y~~~f~~~~~~~~~~~~~~~~ie~~e~~~~~~~~~~~~~~ 904 (1033)
T PLN03142 826 TWSRRDFNAFIRACEKYGRNDIKSIASEMEG-KTEEEVERYAKVFWERYKELNDYDRIIKNIERGEARISRKDEIMKAIG 904 (1033)
T ss_pred cccHHHHHHHHHHHHHhCHhHHHHHHHHhcC-CCHHHHHHHHHHHHHhhhhhccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4888888888889999998888999998876 66655442 1111
Q ss_pred ------------c-c-CCCCCCCCCCHHHHHHHHHHHHHhC-Cccccccc------------cCCCCCHHHHHHHHHHhh
Q 040841 60 ------------Y-L-RPDIKRGNITPDEDDLIIRLHSLLG-NRWSLIAG------------RLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 60 ------------~-L-~p~ikkg~WT~EED~~L~~lv~~~G-~~W~~IA~------------~lpgRt~~qck~Rw~~~l 112 (280)
. + .+..++..||+|||..|+-++.+|| .+|..|-. ++..||+..+..|...++
T Consensus 905 ~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 905 KKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred HHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 0 0 1233445699999999999999999 67999843 346899999999999887
Q ss_pred hhHH
Q 040841 113 SKRL 116 (280)
Q Consensus 113 ~~~~ 116 (280)
+-..
T Consensus 985 ~~~~ 988 (1033)
T PLN03142 985 RLIE 988 (1033)
T ss_pred HHHH
Confidence 6653
No 43
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.45 E-value=0.072 Score=39.68 Aligned_cols=47 Identities=26% Similarity=0.473 Sum_probs=38.5
Q ss_pred CCCCCHHHHHHHHHHHHHhC----C-------------ccccccccC-----CCCCHHHHHHHHHHhhh
Q 040841 67 RGNITPDEDDLIIRLHSLLG----N-------------RWSLIAGRL-----PGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~G----~-------------~W~~IA~~l-----pgRt~~qck~Rw~~~l~ 113 (280)
...||.+|...|++++.+|. + .|..|+..| +.||..+++.+|.++..
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~ 70 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKS 70 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHH
Confidence 45799999999999998872 1 299999866 36999999999998643
No 44
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=94.30 E-value=0.014 Score=50.84 Aligned_cols=49 Identities=24% Similarity=0.521 Sum_probs=38.8
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCC------ccccccccCccccchhhhhhhhhccC
Q 040841 12 LQRGPWTPREDTLLTEYIQVHGEGH------WRSLPKKAGLLRCGKSCRLRWMNYLR 62 (280)
Q Consensus 12 lkkg~WT~EED~~L~~lV~~~G~~~------W~~IA~~~~~~Rt~~qCr~Rw~~~L~ 62 (280)
.++..||.|||.+|.+.|-.|+... ...++..+. |++.+|..||.-+++
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 4678899999999999999996532 455556665 999999999966654
No 45
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=93.09 E-value=0.2 Score=48.77 Aligned_cols=55 Identities=22% Similarity=0.337 Sum_probs=47.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCcccccccc-----CCC-CCHHHHHHHHHHhhhhHHhhCCCC
Q 040841 68 GNITPDEDDLIIRLHSLLGNRWSLIAGR-----LPG-RTDNEIKNYWNTHLSKRLRVQGTD 122 (280)
Q Consensus 68 g~WT~EED~~L~~lv~~~G~~W~~IA~~-----lpg-Rt~~qck~Rw~~~l~~~~~~~~~~ 122 (280)
..||.+|-+.|+.|++.|.-+|-.||.+ ++. ||-..+|.||+...++-++...-+
T Consensus 131 n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~r~l~kAr~~s 191 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVCRKLLKARAPS 191 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHHHHHHHccCCC
Confidence 4699999999999999999999999987 655 999999999998887776655433
No 46
>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=92.94 E-value=0.11 Score=42.79 Aligned_cols=52 Identities=21% Similarity=0.320 Sum_probs=41.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC----ccccccc------------cCCCCCHHHHHHHHHHhhhhH
Q 040841 64 DIKRGNITPDEDDLIIRLHSLLGN----RWSLIAG------------RLPGRTDNEIKNYWNTHLSKR 115 (280)
Q Consensus 64 ~ikkg~WT~EED~~L~~lv~~~G~----~W~~IA~------------~lpgRt~~qck~Rw~~~l~~~ 115 (280)
..++..||++||.-|+-++.+||- .|..|-. .+..||+..+..|...+++-.
T Consensus 46 ~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi~~i 113 (118)
T PF09111_consen 46 NNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLIKLI 113 (118)
T ss_dssp TSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHHHHH
T ss_pred CCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHHHHH
Confidence 556778999999999999999995 7988865 335899999999999887543
No 47
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=92.59 E-value=0.12 Score=50.17 Aligned_cols=45 Identities=22% Similarity=0.299 Sum_probs=42.1
Q ss_pred CCCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 68 GNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 68 g~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
-+||.+|-++...+...+|..+..|+..+|.|...|||.+|.+--
T Consensus 366 ~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Ee 410 (507)
T COG5118 366 LRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEE 410 (507)
T ss_pred CcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHh
Confidence 379999999999999999999999999999999999999998643
No 48
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=90.01 E-value=0.38 Score=45.87 Aligned_cols=51 Identities=16% Similarity=0.238 Sum_probs=40.2
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CCccccccccC----CCCCHHHHHHHHHHhhhhHHh
Q 040841 67 RGNITPDEDDLIIRLHSLL----------GNRWSLIAGRL----PGRTDNEIKNYWNTHLSKRLR 117 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~----------G~~W~~IA~~l----pgRt~~qck~Rw~~~l~~~~~ 117 (280)
...|+.+|-..||++..+. +..|..||+.| .-||+.+|+++|.++.++..+
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~ 118 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKK 118 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHH
Confidence 3689999999999997653 24599999955 359999999999987655443
No 49
>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=88.73 E-value=0.21 Score=41.05 Aligned_cols=49 Identities=16% Similarity=0.256 Sum_probs=36.3
Q ss_pred CCCCcCCCCHHHHHHHHHHHHHhCC---CCccccccccCc-----------cccchhhhhhhh
Q 040841 10 VGLQRGPWTPREDTLLTEYIQVHGE---GHWRSLPKKAGL-----------LRCGKSCRLRWM 58 (280)
Q Consensus 10 ~~lkkg~WT~EED~~L~~lV~~~G~---~~W~~IA~~~~~-----------~Rt~~qCr~Rw~ 58 (280)
|+.++..||.+||.-|+-.+.+||. +.|..|-..+-. .||+..+..|-.
T Consensus 45 ~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~ 107 (118)
T PF09111_consen 45 PNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCN 107 (118)
T ss_dssp STSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHH
T ss_pred CCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHH
Confidence 4778899999999999999999999 899988765422 266666666643
No 50
>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=86.68 E-value=1 Score=34.41 Aligned_cols=45 Identities=29% Similarity=0.496 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHHh---CC----------ccccccccCC-----CCCHHHHHHHHHHhhh
Q 040841 69 NITPDEDDLIIRLHSLL---GN----------RWSLIAGRLP-----GRTDNEIKNYWNTHLS 113 (280)
Q Consensus 69 ~WT~EED~~L~~lv~~~---G~----------~W~~IA~~lp-----gRt~~qck~Rw~~~l~ 113 (280)
.||++++..|++++.+. |+ .|..|+..|. ..+..||++||..+-+
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 49999999999998553 21 2999988772 2478899999986533
No 51
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=84.81 E-value=1.2 Score=30.53 Aligned_cols=41 Identities=22% Similarity=0.316 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHhhh
Q 040841 72 PDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 72 ~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~ 113 (280)
++++..++.++...|-.|.+||..+ |.|...|+.+....++
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 4677888889999999999999999 9999999998876543
No 52
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=83.47 E-value=1.4 Score=43.82 Aligned_cols=45 Identities=18% Similarity=0.313 Sum_probs=41.4
Q ss_pred CCCCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHh
Q 040841 67 RGNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
...||.||-.++-+++..||.++.+|-+.||.|+-..+...|...
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~ 231 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSW 231 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHH
Confidence 457999999999999999999999999999999999999887653
No 53
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=81.60 E-value=1 Score=43.86 Aligned_cols=45 Identities=11% Similarity=0.208 Sum_probs=41.6
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhc
Q 040841 14 RGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNY 60 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~ 60 (280)
--+||.+|-++..++....|. ++..|+..+|. |..+|+...|.+-
T Consensus 365 ~~~Ws~~e~ekFYKALs~wGt-dF~LIs~lfP~-R~RkqIKaKfi~E 409 (507)
T COG5118 365 ALRWSKKEIEKFYKALSIWGT-DFSLISSLFPN-RERKQIKAKFIKE 409 (507)
T ss_pred CCcccHHHHHHHHHHHHHhcc-hHHHHHHhcCc-hhHHHHHHHHHHH
Confidence 357999999999999999998 99999999998 9999999998763
No 54
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=81.29 E-value=0.78 Score=43.71 Aligned_cols=47 Identities=26% Similarity=0.476 Sum_probs=36.9
Q ss_pred cCCCCHHHHHHHHHHHHHh----CCC-----Ccccccccc---Cccccchhhhhhhhhc
Q 040841 14 RGPWTPREDTLLTEYIQVH----GEG-----HWRSLPKKA---GLLRCGKSCRLRWMNY 60 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~----G~~-----~W~~IA~~~---~~~Rt~~qCr~Rw~~~ 60 (280)
...|+.+|-..|+++.... ..+ .|..||..+ +..|++.||+.+|.+.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl 112 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENL 112 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHH
Confidence 3789999999999988643 222 499999854 3459999999999884
No 55
>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=79.66 E-value=1.8 Score=33.32 Aligned_cols=25 Identities=40% Similarity=0.753 Sum_probs=14.3
Q ss_pred CCCCcCCCCHHHHHHH--------HHHHHHhCC
Q 040841 10 VGLQRGPWTPREDTLL--------TEYIQVHGE 34 (280)
Q Consensus 10 ~~lkkg~WT~EED~~L--------~~lV~~~G~ 34 (280)
|.-..|-||+|+|+.| .+++++||.
T Consensus 43 P~n~~GiWT~eDD~~L~~~~~~~~~~L~~khG~ 75 (87)
T PF11626_consen 43 PDNMPGIWTPEDDEMLRSGDKDDIERLIKKHGE 75 (87)
T ss_dssp -TT-TT---HHHHHHHTS--HHHHHHHHHHH-H
T ss_pred CCCCCCCcCHHHHHHHHcCCHHHHHHHHHHhCH
Confidence 4456788999999999 456667764
No 56
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=73.76 E-value=4.4 Score=41.77 Aligned_cols=54 Identities=11% Similarity=0.335 Sum_probs=44.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCccccc----------cccCCCCCHHHHHHHHHHhhhhHHhhC
Q 040841 66 KRGNITPDEDDLIIRLHSLLGNRWSLI----------AGRLPGRTDNEIKNYWNTHLSKRLRVQ 119 (280)
Q Consensus 66 kkg~WT~EED~~L~~lv~~~G~~W~~I----------A~~lpgRt~~qck~Rw~~~l~~~~~~~ 119 (280)
++..||..|+.-...+.+++|.++..| -....-+|..|++.+|+..+.+..+..
T Consensus 87 ~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k~~ 150 (782)
T KOG4468|consen 87 AKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNKLL 150 (782)
T ss_pred cccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHhhh
Confidence 367899999999999999999999998 334445788899999998877765544
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=68.44 E-value=5 Score=30.82 Aligned_cols=17 Identities=35% Similarity=0.692 Sum_probs=10.1
Q ss_pred CCCCCCCCCHHHHHHHH
Q 040841 63 PDIKRGNITPDEDDLII 79 (280)
Q Consensus 63 p~ikkg~WT~EED~~L~ 79 (280)
|....|-||+++|..|.
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 55678899999999983
No 58
>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=67.04 E-value=7 Score=26.31 Aligned_cols=41 Identities=27% Similarity=0.370 Sum_probs=31.5
Q ss_pred HHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHhhhh
Q 040841 73 DEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSK 114 (280)
Q Consensus 73 EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~ 114 (280)
+++..++.++-..|-.+..||..| |-|...|+.+....+++
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 455666666666677899999999 99999999988776643
No 59
>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=66.79 E-value=4 Score=35.23 Aligned_cols=41 Identities=22% Similarity=0.182 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHH
Q 040841 69 NITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNT 110 (280)
Q Consensus 69 ~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~ 110 (280)
.||+|+.++|.+|..+ |-.=+.||..|.|.|.+.|.-+-+.
T Consensus 2 ~Wtde~~~~L~~lw~~-G~SasqIA~~lg~vsRnAViGk~hR 42 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-GLSASQIARQLGGVSRNAVIGKAHR 42 (162)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHhCCcchhhhhhhhhc
Confidence 5999999999999865 8788999999977999999877654
No 60
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=66.04 E-value=3.7 Score=27.37 Aligned_cols=38 Identities=18% Similarity=0.267 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhh
Q 040841 20 REDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMN 59 (280)
Q Consensus 20 EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~ 59 (280)
+=|.+|+.+.+..|...|.+||+.+| =+...|..|+..
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 44889999999999989999999998 588889988764
No 61
>KOG0384 consensus Chromodomain-helicase DNA-binding protein [Transcription]
Probab=65.91 E-value=6.2 Score=43.86 Aligned_cols=27 Identities=30% Similarity=0.656 Sum_probs=25.2
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCcccc
Q 040841 14 RGPWTPREDTLLTEYIQVHGEGHWRSL 40 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~G~~~W~~I 40 (280)
---|..++|..|+-.|-+||.|+|..|
T Consensus 1133 ~~~W~~e~Ds~LLiGI~khGygswe~I 1159 (1373)
T KOG0384|consen 1133 DCDWGSEDDSMLLIGIFKHGYGSWEAI 1159 (1373)
T ss_pred ccCCCchhhhhHhhhhhhcccccHHHh
Confidence 356999999999999999999999998
No 62
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=65.40 E-value=7.1 Score=41.21 Aligned_cols=43 Identities=16% Similarity=0.225 Sum_probs=39.6
Q ss_pred CCCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHH
Q 040841 68 GNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNT 110 (280)
Q Consensus 68 g~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~ 110 (280)
..||+.|-.+.-+++..|..++-.|++.++++|-.+|-..|+.
T Consensus 620 d~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYt 662 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYT 662 (907)
T ss_pred ccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHH
Confidence 4799999999999999999999999999999999999877653
No 63
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=64.13 E-value=4.6 Score=42.54 Aligned_cols=44 Identities=16% Similarity=0.289 Sum_probs=39.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhh
Q 040841 14 RGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMN 59 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~ 59 (280)
...||+.|-.++.+++..|.. ++-.|++.+.+ +|.+||-+-|..
T Consensus 619 Sd~WTp~E~~lF~kA~y~~~K-DF~~v~km~~~-KtVaqCVeyYYt 662 (907)
T KOG4167|consen 619 SDKWTPLERKLFNKALYTYSK-DFIFVQKMVKS-KTVAQCVEYYYT 662 (907)
T ss_pred cccccHHHHHHHHHHHHHhcc-cHHHHHHHhcc-ccHHHHHHHHHH
Confidence 357999999999999999997 99999999998 999999887754
No 64
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=63.65 E-value=9.6 Score=39.28 Aligned_cols=45 Identities=24% Similarity=0.372 Sum_probs=42.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHH
Q 040841 66 KRGNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNT 110 (280)
Q Consensus 66 kkg~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~ 110 (280)
..+.|+.+|-++-.......|.+.+.|+..+|+|...|||.+|..
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKK 452 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhh
Confidence 456899999999999999999999999999999999999999974
No 65
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=58.69 E-value=12 Score=24.83 Aligned_cols=38 Identities=21% Similarity=0.328 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhCC-ccccccccCCCCCHHHHHHHHHHh
Q 040841 73 DEDDLIIRLHSLLGN-RWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 73 EED~~L~~lv~~~G~-~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
+=|.+|+.+...-|. .|..||+.+ |=|...|..|++.+
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 457889988888884 699999999 99999999998753
No 66
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=58.59 E-value=11 Score=31.61 Aligned_cols=44 Identities=11% Similarity=0.067 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHhC-CccccccccCCCCCHHHHHHHHHHhhhhHH
Q 040841 72 PDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116 (280)
Q Consensus 72 ~EED~~L~~lv~~~G-~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~ 116 (280)
.+-|.+|+.+.++-| ..|+.||+.+ |-+...|+.|++.+....+
T Consensus 8 D~~D~~Il~~Lq~d~R~s~~eiA~~l-glS~~tV~~Ri~rL~~~Gv 52 (153)
T PRK11179 8 DNLDRGILEALMENARTPYAELAKQF-GVSPGTIHVRVEKMKQAGI 52 (153)
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 357888999988888 5799999999 9999999999987654443
No 67
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=58.21 E-value=9.7 Score=39.39 Aligned_cols=47 Identities=11% Similarity=0.256 Sum_probs=35.4
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCc---------cccchhhhhhhhhcc
Q 040841 14 RGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGL---------LRCGKSCRLRWMNYL 61 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~---------~Rt~~qCr~Rw~~~L 61 (280)
|..||..|.+....++..+|. ++.+|-..+.- -++..|.|.+|++.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GK-dFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~ 143 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGK-DFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLV 143 (782)
T ss_pred ccccchhhHHHHHHHHHHhcc-cHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHH
Confidence 668999999999999999997 88888322221 155667888877643
No 68
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=57.89 E-value=9.2 Score=37.59 Aligned_cols=48 Identities=13% Similarity=0.228 Sum_probs=41.9
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccc-----cCccccchhhhhhhhhc
Q 040841 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKK-----AGLLRCGKSCRLRWMNY 60 (280)
Q Consensus 12 lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~-----~~~~Rt~~qCr~Rw~~~ 60 (280)
++-..||.+|.+.|.++.++|.- .|-.||.. .+..||-....+||..+
T Consensus 128 l~dn~WskeETD~LF~lck~fDL-Rf~VIaDRyd~qq~~~sRTvEdLKeRyY~v 180 (445)
T KOG2656|consen 128 LNDNSWSKEETDYLFDLCKRFDL-RFFVIADRYDNQQYKKSRTVEDLKERYYSV 180 (445)
T ss_pred hccccccHHHHHHHHHHHHhcCe-eEEEEeeccchhhccccccHHHHHHHHHHH
Confidence 44567999999999999999998 99999987 66669999999999764
No 69
>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=56.66 E-value=13 Score=28.10 Aligned_cols=44 Identities=20% Similarity=0.536 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHHHHh---CC----C-----CccccccccCc----cccchhhhhhhhh
Q 040841 16 PWTPREDTLLTEYIQVH---GE----G-----HWRSLPKKAGL----LRCGKSCRLRWMN 59 (280)
Q Consensus 16 ~WT~EED~~L~~lV~~~---G~----~-----~W~~IA~~~~~----~Rt~~qCr~Rw~~ 59 (280)
.||+++++.|++++... |. + .|..|+..+.. ..+..||..||..
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999988655 22 1 27777766532 3566788888765
No 70
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=56.11 E-value=17 Score=32.57 Aligned_cols=45 Identities=22% Similarity=0.232 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHHhCCccccccccC---CCCCHHHHHHHHHHhhhh
Q 040841 69 NITPDEDDLIIRLHSLLGNRWSLIAGRL---PGRTDNEIKNYWNTHLSK 114 (280)
Q Consensus 69 ~WT~EED~~L~~lv~~~G~~W~~IA~~l---pgRt~~qck~Rw~~~l~~ 114 (280)
.|++++|-+|+.+|.. |+.-..|+..+ -.-|-..+..||+.+|.-
T Consensus 1 rW~~~DDl~Li~av~~-~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd 48 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQ-TNDLESVHLGVKFSCKFTLQEIEERWYALLYD 48 (199)
T ss_pred CCCchhhHHHHHHHHH-hcCHHHHHccCCcCCcCcHHHHHHHHHHHHcC
Confidence 4999999999998865 55555555543 245889999999988754
No 71
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=55.62 E-value=6.6 Score=32.95 Aligned_cols=46 Identities=15% Similarity=0.127 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCC
Q 040841 19 PREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIK 66 (280)
Q Consensus 19 ~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ik 66 (280)
.+-|.+|+++.++.|.-.|.+||+.++ -+...|+.|+.+...-++-
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 357999999999999989999999998 7999999999887665543
No 72
>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=55.26 E-value=15 Score=29.62 Aligned_cols=35 Identities=23% Similarity=0.273 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 77 LIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 77 ~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
.++.+.-..|-.+.+||+.+ |.+...|+.++...+
T Consensus 120 ~il~l~~~~~~~~~eIA~~l-gis~~tv~~~~~ra~ 154 (161)
T TIGR02985 120 KIFILSRFEGKSYKEIAEEL-GISVKTVEYHISKAL 154 (161)
T ss_pred HHHHHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 33344344577899999999 999999999998754
No 73
>smart00595 MADF subfamily of SANT domain.
Probab=54.12 E-value=8.6 Score=28.83 Aligned_cols=24 Identities=33% Similarity=0.570 Sum_probs=20.7
Q ss_pred ccccccccCCCCCHHHHHHHHHHhh
Q 040841 88 RWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 88 ~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
-|..||..| |-+..+|+.+|+++-
T Consensus 29 aW~~Ia~~l-~~~~~~~~~kw~~LR 52 (89)
T smart00595 29 AWEEIAEEL-GLSVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 399999999 559999999998764
No 74
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=52.44 E-value=14 Score=31.42 Aligned_cols=44 Identities=11% Similarity=-0.028 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHHHhC-CccccccccCCCCCHHHHHHHHHHhhhhHH
Q 040841 72 PDEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116 (280)
Q Consensus 72 ~EED~~L~~lv~~~G-~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~ 116 (280)
.+-|.+|+.+.++-| -.|+.||+.+ |-+...|+.|++.+....+
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 567888998888888 5799999999 9999999999987655544
No 75
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=50.95 E-value=9.9 Score=41.90 Aligned_cols=34 Identities=15% Similarity=0.258 Sum_probs=28.6
Q ss_pred CCCcCCCCHHHHHHHHHHHHHhCCCCcccccccc
Q 040841 11 GLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKA 44 (280)
Q Consensus 11 ~lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~ 44 (280)
.-++..||.|||..|+-.+.+||.++|..|-..+
T Consensus 923 ~~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i 956 (1033)
T PLN03142 923 QNKGKLYNEECDRFMLCMVHKLGYGNWDELKAAF 956 (1033)
T ss_pred CCCCCcCCHHHHHHHHHHHHHhccchHHHHHHHH
Confidence 3455669999999999999999999999985544
No 76
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=50.43 E-value=21 Score=35.02 Aligned_cols=43 Identities=19% Similarity=0.278 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHHHHhCCcccccc-ccCCCCCHHHHHHHHHH
Q 040841 68 GNITPDEDDLIIRLHSLLGNRWSLIA-GRLPGRTDNEIKNYWNT 110 (280)
Q Consensus 68 g~WT~EED~~L~~lv~~~G~~W~~IA-~~lpgRt~~qck~Rw~~ 110 (280)
..|+++|-...-+-.+.||.++..|. -.++.|+--.|-..|+.
T Consensus 278 ~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVeyYYl 321 (445)
T KOG4329|consen 278 SGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEYYYL 321 (445)
T ss_pred ccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHHHHH
Confidence 36999999999999999999999995 47899999999887754
No 77
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=50.38 E-value=6.7 Score=33.37 Aligned_cols=46 Identities=22% Similarity=0.185 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCC
Q 040841 19 PREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIK 66 (280)
Q Consensus 19 ~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ik 66 (280)
.+-|.+|+.+.++.|.-.|.+||+.++ =+...|+.|+.+..+-++-
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 467999999999999999999999998 6888999999887665543
No 78
>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=50.12 E-value=12 Score=28.68 Aligned_cols=30 Identities=27% Similarity=0.449 Sum_probs=25.2
Q ss_pred HHHHHHHHHHhCCccccccccCCCCCHHHHH
Q 040841 75 DDLIIRLHSLLGNRWSLIAGRLPGRTDNEIK 105 (280)
Q Consensus 75 D~~L~~lv~~~G~~W~~IA~~lpgRt~~qck 105 (280)
|+.|..+....|..|..+|.+| |=|..+|.
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~L-gls~~~I~ 31 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDL-GLSQTDIY 31 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 5668889999999999999999 77776654
No 79
>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=48.91 E-value=18 Score=31.05 Aligned_cols=48 Identities=17% Similarity=0.295 Sum_probs=34.6
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccCc---cccchhhhhhhhhc
Q 040841 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGL---LRCGKSCRLRWMNY 60 (280)
Q Consensus 12 lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~---~Rt~~qCr~Rw~~~ 60 (280)
-+...-|..|.+-+..||++||+ ++..++.-.-. ..|..||+.+...+
T Consensus 112 ~~~~~ls~~e~~~i~~Li~KhGd-Dy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 112 KKPRRLSEREIEYIEYLIEKHGD-DYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred cCCCCCCHHHHHHHHHHHHHHCc-cHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 45667789999999999999997 88888754431 15666666655443
No 80
>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=47.87 E-value=45 Score=32.03 Aligned_cols=48 Identities=27% Similarity=0.474 Sum_probs=36.8
Q ss_pred CCCCCHHHHHHHHHHHHHh-CCc---cccccccCCCCCHHHHHHHHHHhhhhH
Q 040841 67 RGNITPDEDDLIIRLHSLL-GNR---WSLIAGRLPGRTDNEIKNYWNTHLSKR 115 (280)
Q Consensus 67 kg~WT~EED~~L~~lv~~~-G~~---W~~IA~~lpgRt~~qck~Rw~~~l~~~ 115 (280)
...||.-|...|+++.+.. |.. -.+|++.++||+..+|++.-+. |+.+
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~-LK~r 72 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQ-LKGR 72 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHH-HHHH
Confidence 4579999999999888765 543 4578899999999999986554 4444
No 81
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=47.29 E-value=24 Score=26.72 Aligned_cols=38 Identities=16% Similarity=0.277 Sum_probs=27.0
Q ss_pred HHHHHHHHhC--------CccccccccCCCC---C--HHHHHHHHHHhhhh
Q 040841 77 LIIRLHSLLG--------NRWSLIAGRLPGR---T--DNEIKNYWNTHLSK 114 (280)
Q Consensus 77 ~L~~lv~~~G--------~~W~~IA~~lpgR---t--~~qck~Rw~~~l~~ 114 (280)
+|..+|...| ..|..||+.|.-- + ..+++..|..+|.+
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 3777777777 3599999988221 2 36789999887753
No 82
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=46.62 E-value=47 Score=26.76 Aligned_cols=45 Identities=16% Similarity=0.201 Sum_probs=33.4
Q ss_pred CcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhcc
Q 040841 13 QRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYL 61 (280)
Q Consensus 13 kkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L 61 (280)
++..||.|+-...+..+...|. .-..||..++- ..+-..+|.+.+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~-sv~evA~e~gI---s~~tl~~W~r~y 53 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM-TVSLVARQHGV---AASQLFLWRKQY 53 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC-CHHHHHHHHCc---CHHHHHHHHHHH
Confidence 3578999998888877777665 67788888875 445566787754
No 83
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=45.01 E-value=27 Score=26.70 Aligned_cols=39 Identities=21% Similarity=0.284 Sum_probs=28.1
Q ss_pred HHHHHHHHhC--------CccccccccCCC-----CCHHHHHHHHHHhhhhH
Q 040841 77 LIIRLHSLLG--------NRWSLIAGRLPG-----RTDNEIKNYWNTHLSKR 115 (280)
Q Consensus 77 ~L~~lv~~~G--------~~W~~IA~~lpg-----Rt~~qck~Rw~~~l~~~ 115 (280)
+|..+|.+.| +.|..||+.|.- ....+++..|..+|.+-
T Consensus 36 ~Ly~~V~~~GG~~~v~~~~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~y 87 (93)
T smart00501 36 RLYRLVQERGGYDQVTKDKKWKEIARELGIPDTSTSAASSLRKHYERYLLPF 87 (93)
T ss_pred HHHHHHHHccCHHHHcCCCCHHHHHHHhCCCcccchHHHHHHHHHHHHhHHH
Confidence 3677777777 369999998832 23578899898887653
No 84
>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=42.63 E-value=22 Score=27.31 Aligned_cols=31 Identities=26% Similarity=0.363 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhCCccccccccCCCCCHHHHHH
Q 040841 75 DDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKN 106 (280)
Q Consensus 75 D~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~ 106 (280)
|..|..+....|..|..+|..| |=+...|..
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eL-g~s~~dI~~ 34 (84)
T cd08803 4 DIRMAIVADHLGLSWTELAREL-NFSVDEINQ 34 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHc-CCCHHHHHH
Confidence 5678888999999999999999 777766554
No 85
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=41.95 E-value=18 Score=36.30 Aligned_cols=46 Identities=15% Similarity=0.216 Sum_probs=39.9
Q ss_pred CCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhh
Q 040841 12 LQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMN 59 (280)
Q Consensus 12 lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~ 59 (280)
-..-.||.||--++-++...||. ++.+|-+.|+- |+-.+++.-|..
T Consensus 185 ~~~d~WT~Ed~vlFe~aF~~~GK-~F~kIrq~LP~-rsLaSlvqyYy~ 230 (534)
T KOG1194|consen 185 EFPDEWTAEDIVLFEQAFQFFGK-DFHKIRQALPH-RSLASLVQYYYS 230 (534)
T ss_pred CCcccchHHHHHHHHHHHHHhcc-cHHHHHHHccC-ccHHHHHHHHHH
Confidence 34567999999999999999998 99999999997 999888876654
No 86
>PF11035 SnAPC_2_like: Small nuclear RNA activating complex subunit 2-like; InterPro: IPR021281 This family of proteins is SnAPC subunit 2-like. SnAPC allows the transcription of human small nuclear RNA genes to occur by recognition of the proximal sequence element [].
Probab=40.83 E-value=31 Score=33.10 Aligned_cols=85 Identities=19% Similarity=0.293 Sum_probs=60.1
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCC---ccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHHHHHHHH-h----
Q 040841 14 RGPWTPREDTLLTEYIQVHGEGH---WRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLIIRLHSL-L---- 85 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~G~~~---W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L~~lv~~-~---- 85 (280)
-..||..|...|+++.+...... -.+|++.+.+ |+..++++ |.+.|+- ..+.+++++ |
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~-Rs~aEI~~-fl~~LK~------------rvareaiqkv~~~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPG-RSEAEIRD-FLQQLKG------------RVAREAIQKVHPGGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccC-cCHHHHHH-HHHHHHH------------HHHHHHHHHhccccc
Confidence 45799999999999998764333 4577888888 99988876 3444432 234444444 2
Q ss_pred -CCc------------cccccccCCCCCHHHHHHHHHHhh
Q 040841 86 -GNR------------WSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 86 -G~~------------W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
|.+ |..+|+.+.|.-...+-.-|-+.|
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l 126 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVL 126 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHH
Confidence 211 999999999998888888776654
No 87
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=38.65 E-value=33 Score=35.49 Aligned_cols=50 Identities=16% Similarity=0.292 Sum_probs=45.1
Q ss_pred CCCCCCcCCCCHHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhh
Q 040841 8 SKVGLQRGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMN 59 (280)
Q Consensus 8 ~k~~lkkg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~ 59 (280)
+.+....++|+.+|-++...+....|. +...|+..+++ |..+|++..|..
T Consensus 403 ~sk~~~~~~w~~se~e~fyka~~~~gs-~~slis~l~p~-R~rk~iK~K~~~ 452 (584)
T KOG2009|consen 403 YSKKLETDKWDASETELFYKALSERGS-DFSLISNLFPL-RDRKQIKAKFKK 452 (584)
T ss_pred ccCccccCcccchhhHHhhhHHhhhcc-ccccccccccc-ccHHHHHHHHhh
Confidence 455677899999999999999999998 99999999998 999999998764
No 88
>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=37.32 E-value=37 Score=26.51 Aligned_cols=35 Identities=23% Similarity=0.237 Sum_probs=26.4
Q ss_pred HHHHHHHhCCccccccccCCCCCHHHHHHHHHHhhh
Q 040841 78 IIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 78 L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~ 113 (280)
++.++...|..+..||+.+ |-+...|+++.+..++
T Consensus 118 ii~~~~~~g~s~~eIA~~l-~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 118 VLVLRYLEGLSYKEIAEIL-GISVGTVKRRLKRARK 152 (158)
T ss_pred HHhhHHhcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3344444578899999999 7899999998877543
No 89
>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=35.72 E-value=23 Score=26.78 Aligned_cols=30 Identities=30% Similarity=0.636 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhCCccccccccCCCCCHHHHH
Q 040841 75 DDLIIRLHSLLGNRWSLIAGRLPGRTDNEIK 105 (280)
Q Consensus 75 D~~L~~lv~~~G~~W~~IA~~lpgRt~~qck 105 (280)
|..|..+....|..|..+|+.| |=+..+|.
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~L-g~~~~dI~ 33 (84)
T cd08317 4 DIRLADISNLLGSDWPQLAREL-GVSETDID 33 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHc-CCCHHHHH
Confidence 4567788899999999999999 66665554
No 90
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=35.72 E-value=39 Score=27.74 Aligned_cols=29 Identities=21% Similarity=0.148 Sum_probs=23.8
Q ss_pred HHhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 83 SLLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 83 ~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
...|-.+..||..| |-+...|++++...+
T Consensus 138 ~~~~~~~~eIA~~l-gis~~tv~~~~~ra~ 166 (179)
T PRK11924 138 YVEGLSYREIAEIL-GVPVGTVKSRLRRAR 166 (179)
T ss_pred HHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 34577899999999 999999999887643
No 91
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=35.57 E-value=41 Score=27.69 Aligned_cols=31 Identities=16% Similarity=0.147 Sum_probs=24.5
Q ss_pred HHHHhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 81 LHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 81 lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
+....|-.+..||+.| |.+...|+.+....+
T Consensus 139 l~~~~~~s~~eIA~~l-gis~~tV~~~l~ra~ 169 (182)
T PRK09652 139 LREIEGLSYEEIAEIM-GCPIGTVRSRIFRAR 169 (182)
T ss_pred HHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3344577899999999 999999998877543
No 92
>smart00351 PAX Paired Box domain.
Probab=35.38 E-value=1.1e+02 Score=24.88 Aligned_cols=71 Identities=17% Similarity=0.164 Sum_probs=45.9
Q ss_pred cCCCCHHHHHHHHHHHHHhCCCCccccccccCccc-cchhhhhhhhh--ccCCCCC----CCCCCHHHHHHHHHHHHHhC
Q 040841 14 RGPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLR-CGKSCRLRWMN--YLRPDIK----RGNITPDEDDLIIRLHSLLG 86 (280)
Q Consensus 14 kg~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~R-t~~qCr~Rw~~--~L~p~ik----kg~WT~EED~~L~~lv~~~G 86 (280)
..+++.++=++++.++. -|. .-..||+.++-.| |...+..||.. .+.|.-. ...-+.+++..|++++.+.+
T Consensus 15 ~~~~s~~~R~riv~~~~-~G~-s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p 92 (125)
T smart00351 15 GRPLPDEERQRIVELAQ-NGV-RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENP 92 (125)
T ss_pred CCCCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCC
Confidence 34588888888888886 454 7799999998643 34456666654 3455322 22346666667776766654
No 93
>cd00131 PAX Paired Box domain
Probab=34.93 E-value=1.3e+02 Score=24.55 Aligned_cols=70 Identities=17% Similarity=0.167 Sum_probs=44.8
Q ss_pred CCCCHHHHHHHHHHHHHhCCCCccccccccCccc-cchhhhhhhhh--ccCCCCCCC----CCCHHHHHHHHHHHHHhC
Q 040841 15 GPWTPREDTLLTEYIQVHGEGHWRSLPKKAGLLR-CGKSCRLRWMN--YLRPDIKRG----NITPDEDDLIIRLHSLLG 86 (280)
Q Consensus 15 g~WT~EED~~L~~lV~~~G~~~W~~IA~~~~~~R-t~~qCr~Rw~~--~L~p~ikkg----~WT~EED~~L~~lv~~~G 86 (280)
.+.|.++=++++.+++ .|. ....||+.++-.+ +..-+..||.. .+.|....| .-+++.+..|+.++.+.+
T Consensus 16 ~~lS~d~R~rIv~~~~-~G~-s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p 92 (128)
T cd00131 16 RPLPDSIRQRIVELAQ-SGI-RPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENP 92 (128)
T ss_pred CcCCHHHHHHHHHHHH-cCC-CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCC
Confidence 4588888888888875 565 7899999987643 23345555554 245543222 236666777777776654
No 94
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=33.82 E-value=42 Score=28.86 Aligned_cols=36 Identities=19% Similarity=0.279 Sum_probs=28.4
Q ss_pred HHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHh
Q 040841 75 DDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 75 D~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
..+++.+....|-.+.+||..| |-+...++.+|...
T Consensus 140 ~~~~v~l~~~~Gls~~EIA~~l-giS~~tV~r~l~~a 175 (185)
T PF07638_consen 140 QRRVVELRFFEGLSVEEIAERL-GISERTVRRRLRRA 175 (185)
T ss_pred HHHHHHHHHHCCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 3444445455678899999999 99999999999865
No 95
>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=33.77 E-value=57 Score=20.69 Aligned_cols=40 Identities=18% Similarity=0.199 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHh
Q 040841 70 ITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 70 WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
++++ +..++.++..-|-.+..||..+ |-+...|+.+....
T Consensus 11 l~~~-~~~~~~~~~~~~~~~~~ia~~~-~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPER-EREVILLRFGEGLSYEEIAEIL-GISRSTVRQRLHRA 50 (55)
T ss_pred CCHH-HHHHHHHHHhcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 4444 4455555556678899999999 88888887766543
No 96
>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=33.23 E-value=26 Score=25.39 Aligned_cols=27 Identities=22% Similarity=0.426 Sum_probs=20.8
Q ss_pred ccccccccCC-CCCHHHHHHHHHHhhhh
Q 040841 88 RWSLIAGRLP-GRTDNEIKNYWNTHLSK 114 (280)
Q Consensus 88 ~W~~IA~~lp-gRt~~qck~Rw~~~l~~ 114 (280)
-|..||..|. .-+...|+.+|+++...
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr~~ 55 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLRDR 55 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHHHH
Confidence 3899999984 25788999999885443
No 97
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=32.58 E-value=50 Score=28.32 Aligned_cols=28 Identities=18% Similarity=0.178 Sum_probs=23.6
Q ss_pred HHhCCccccccccCCCCCHHHHHHHHHHh
Q 040841 83 SLLGNRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 83 ~~~G~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
...|-...+||..| |-+...|++|+...
T Consensus 147 ~~~g~s~~EIA~~l-g~s~~tV~~rl~ra 174 (192)
T PRK09643 147 DMQGYSVADAARML-GVAEGTVKSRCARG 174 (192)
T ss_pred HHcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 34577899999999 99999999998654
No 98
>PRK04217 hypothetical protein; Provisional
Probab=32.25 E-value=56 Score=26.48 Aligned_cols=42 Identities=17% Similarity=0.086 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 69 NITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 69 ~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
.-|.+| ..++.+....|-....||+.+ |-+...|+.+++...
T Consensus 42 ~Lt~ee-reai~l~~~eGlS~~EIAk~L-GIS~sTV~r~L~RAr 83 (110)
T PRK04217 42 FMTYEE-FEALRLVDYEGLTQEEAGKRM-GVSRGTVWRALTSAR 83 (110)
T ss_pred cCCHHH-HHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 456666 577777777788999999999 999999999998654
No 99
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=32.20 E-value=32 Score=26.22 Aligned_cols=31 Identities=23% Similarity=0.459 Sum_probs=25.8
Q ss_pred HHHHHHHHHHhCCccccccccCCCCCHHHHHH
Q 040841 75 DDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKN 106 (280)
Q Consensus 75 D~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~ 106 (280)
|..|-.+....|.+|..+|+.| |=+...|.+
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 4567778899999999999999 788777765
No 100
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=31.97 E-value=40 Score=33.10 Aligned_cols=42 Identities=14% Similarity=0.194 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHHhCCCCccccc-cccCccccchhhhhhhhh
Q 040841 16 PWTPREDTLLTEYIQVHGEGHWRSLP-KKAGLLRCGKSCRLRWMN 59 (280)
Q Consensus 16 ~WT~EED~~L~~lV~~~G~~~W~~IA-~~~~~~Rt~~qCr~Rw~~ 59 (280)
-|+.+|-...-+.++.||. ++..|- .++.+ |+...|.+-|..
T Consensus 279 ~wsEeEcr~FEegl~~yGK-DF~lIr~nkvrt-RsvgElVeyYYl 321 (445)
T KOG4329|consen 279 GWSEEECRNFEEGLELYGK-DFHLIRANKVRT-RSVGELVEYYYL 321 (445)
T ss_pred cCCHHHHHHHHHHHHHhcc-cHHHHHhccccc-chHHHHHHHHHH
Confidence 5999999999999999997 888884 45666 888999887653
No 101
>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=31.70 E-value=49 Score=21.61 Aligned_cols=35 Identities=23% Similarity=0.167 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHH
Q 040841 74 EDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWN 109 (280)
Q Consensus 74 ED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~ 109 (280)
|-..|.++...+|++....|+.| |=+...+..+-+
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~L-gisr~tL~~klk 40 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLL-GISRRTLYRKLK 40 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHH-TS-HHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHH-CCCHHHHHHHHH
Confidence 67788899999999999999999 777777666543
No 102
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=31.35 E-value=50 Score=25.40 Aligned_cols=43 Identities=12% Similarity=0.078 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHHhC-CccccccccCCCCCHHHHHHHHHHhhhhHH
Q 040841 73 DEDDLIIRLHSLLG-NRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116 (280)
Q Consensus 73 EED~~L~~lv~~~G-~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~ 116 (280)
+.|.+|+.+....| -.++.||+.+ |-+...|+.+...+....+
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l-~~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV-GLSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH-CcCHHHHHHHHHHHHHCCC
Confidence 56888888888877 4799999999 9999999999988766554
No 103
>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=31.31 E-value=35 Score=26.03 Aligned_cols=27 Identities=33% Similarity=0.583 Sum_probs=21.5
Q ss_pred HHHHHHHhCCccccccccCCCCCHHHHH
Q 040841 78 IIRLHSLLGNRWSLIAGRLPGRTDNEIK 105 (280)
Q Consensus 78 L~~lv~~~G~~W~~IA~~lpgRt~~qck 105 (280)
|..+....|..|..+|+.| |-+..+|.
T Consensus 10 l~~ia~~iG~~Wk~Lar~L-Gls~~dI~ 36 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHL-EMKDKEIR 36 (86)
T ss_pred HHHHHHHHhhhHHHHHHHc-CCCHHHHH
Confidence 3346688899999999999 87877764
No 104
>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=30.41 E-value=88 Score=26.69 Aligned_cols=46 Identities=15% Similarity=0.154 Sum_probs=37.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCCccccccccCC----CCCHHHHHHHHHHh
Q 040841 66 KRGNITPDEDDLIIRLHSLLGNRWSLIAGRLP----GRTDNEIKNYWNTH 111 (280)
Q Consensus 66 kkg~WT~EED~~L~~lv~~~G~~W~~IA~~lp----gRt~~qck~Rw~~~ 111 (280)
....-|..|..-|..|+.+||.++...+.-.. =.|..||+.+...+
T Consensus 113 ~~~~ls~~e~~~i~~Li~KhGdDy~aMarD~KLN~~Q~T~~qlrrki~~~ 162 (164)
T PF09420_consen 113 KPRRLSEREIEYIEYLIEKHGDDYKAMARDRKLNYMQHTPGQLRRKIRKY 162 (164)
T ss_pred CCCCCCHHHHHHHHHHHHHHCccHHHHhccCCCCcccCCHHHHHHHHHHh
Confidence 34567999999999999999999988887442 36899998887654
No 105
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=29.95 E-value=51 Score=25.93 Aligned_cols=46 Identities=9% Similarity=0.039 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHHHHHh----CC----ccccccc----cC-CCCCHHHHHHHHHHhhh
Q 040841 68 GNITPDEDDLIIRLHSLL----GN----RWSLIAG----RL-PGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 68 g~WT~EED~~L~~lv~~~----G~----~W~~IA~----~l-pgRt~~qck~Rw~~~l~ 113 (280)
..||+|++..|++.+..| |. .|..+-. .| ..=+..|+.++-+.+-+
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 469999999999998776 62 3444333 33 12377888887776433
No 106
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptor
Probab=29.62 E-value=32 Score=26.00 Aligned_cols=33 Identities=27% Similarity=0.542 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHhCCccccccccCCCCCHHHHHH
Q 040841 72 PDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKN 106 (280)
Q Consensus 72 ~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~ 106 (280)
.||.++|+.. -..|.+|...|..| |=+...|++
T Consensus 2 ~~~v~~ll~~-~nlG~dW~~LA~~L-G~~~~~I~~ 34 (77)
T cd08311 2 QEEVEKLLES-GRPGRDWRSLAGEL-GYEDEAIDT 34 (77)
T ss_pred hHHHHHHHhC-CCCccCHHHHHHHc-CCCHHHHHH
Confidence 5788888732 24678999999999 888887765
No 107
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=29.39 E-value=90 Score=26.31 Aligned_cols=36 Identities=22% Similarity=0.181 Sum_probs=28.8
Q ss_pred HHHhCCccccccccCCCCCHHHHHHHHHHhhhhHHhh
Q 040841 82 HSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRLRV 118 (280)
Q Consensus 82 v~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~~~ 118 (280)
+...|-...+||..| |-+...|+.|....+..-+..
T Consensus 139 ~~~~g~s~~EIA~~l-gis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 139 ATLDGMKQKDIAQAL-DIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHHHh
Confidence 344477899999999 999999999998777665543
No 108
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=29.30 E-value=83 Score=26.19 Aligned_cols=36 Identities=25% Similarity=0.312 Sum_probs=27.7
Q ss_pred HHHHHhCCccccccccCCCCCHHHHHHHHHHhhhhHH
Q 040841 80 RLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKRL 116 (280)
Q Consensus 80 ~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~~~ 116 (280)
.|....|-...+||+.| |-+...|+.+-...+++-.
T Consensus 129 ~L~~~~g~s~~EIA~~l-gis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 129 LYNRLDGMGHAEIAERL-GVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred HHHHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHHHHH
Confidence 33444577899999999 9999999999877665543
No 109
>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=29.28 E-value=34 Score=25.29 Aligned_cols=18 Identities=28% Similarity=0.582 Sum_probs=14.8
Q ss_pred HHHHHHHHhCCccccccc
Q 040841 77 LIIRLHSLLGNRWSLIAG 94 (280)
Q Consensus 77 ~L~~lv~~~G~~W~~IA~ 94 (280)
.|.+|.+.||++|..|-.
T Consensus 31 vl~~LL~lY~~nW~lIEe 48 (65)
T PF10440_consen 31 VLKNLLKLYDGNWELIEE 48 (65)
T ss_pred HHHHHHHHHcCCchhhhc
Confidence 477888999999999864
No 110
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=28.94 E-value=59 Score=27.16 Aligned_cols=28 Identities=11% Similarity=-0.083 Sum_probs=23.0
Q ss_pred hCCccccccccCCCCCHHHHHHHHHHhhh
Q 040841 85 LGNRWSLIAGRLPGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 85 ~G~~W~~IA~~lpgRt~~qck~Rw~~~l~ 113 (280)
.|..+.+||..| |-|...++++.....+
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 9999999998876543
No 111
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.81 E-value=23 Score=23.56 Aligned_cols=37 Identities=32% Similarity=0.421 Sum_probs=18.8
Q ss_pred CCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHH
Q 040841 69 NITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNY 107 (280)
Q Consensus 69 ~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~R 107 (280)
.+|.+|-..|..++ .-|..=..||+.| ||+...|.+.
T Consensus 4 ~Lt~~eR~~I~~l~-~~G~s~~~IA~~l-g~s~sTV~re 40 (44)
T PF13936_consen 4 HLTPEERNQIEALL-EQGMSIREIAKRL-GRSRSTVSRE 40 (44)
T ss_dssp --------HHHHHH-CS---HHHHHHHT-T--HHHHHHH
T ss_pred chhhhHHHHHHHHH-HcCCCHHHHHHHH-CcCcHHHHHH
Confidence 57778877777665 4577789999999 9999888653
No 112
>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=28.35 E-value=63 Score=26.75 Aligned_cols=30 Identities=20% Similarity=0.274 Sum_probs=23.8
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhhhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHLSK 114 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~ 114 (280)
..|-...+||..| |-|...|++++...+++
T Consensus 133 ~~g~s~~eiA~~l-gis~~tv~~~l~Ra~~~ 162 (169)
T TIGR02954 133 YHDLTIKEIAEVM-NKPEGTVKTYLHRALKK 162 (169)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHHHH
Confidence 3466789999999 88999999998765443
No 113
>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=28.33 E-value=37 Score=26.09 Aligned_cols=30 Identities=33% Similarity=0.552 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCCccccccccCCCCCHHHHHH
Q 040841 76 DLIIRLHSLLGNRWSLIAGRLPGRTDNEIKN 106 (280)
Q Consensus 76 ~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~ 106 (280)
+.|-.+....|.+|..+|+.| |=+..+|..
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 345556688899999999999 888887765
No 114
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=27.72 E-value=51 Score=27.65 Aligned_cols=27 Identities=11% Similarity=-0.011 Sum_probs=22.3
Q ss_pred hCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 85 LGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 85 ~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
.|-...+||..| |-|...|+++....+
T Consensus 153 ~~~s~~EIA~~l-gis~~tv~~~l~rar 179 (190)
T TIGR02939 153 EGLSYEDIARIM-DCPVGTVRSRIFRAR 179 (190)
T ss_pred cCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 356789999999 889999999987654
No 115
>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=26.66 E-value=43 Score=24.81 Aligned_cols=30 Identities=27% Similarity=0.563 Sum_probs=22.1
Q ss_pred HHHHHHHHHH-hCCccccccccCCCCCHHHHH
Q 040841 75 DDLIIRLHSL-LGNRWSLIAGRLPGRTDNEIK 105 (280)
Q Consensus 75 D~~L~~lv~~-~G~~W~~IA~~lpgRt~~qck 105 (280)
.+.|..++.. .|..|..+|+.| |-+..+|.
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~L-g~~~~~i~ 35 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKL-GLSEADID 35 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHc-CCCHHHHH
Confidence 4556667777 899999999999 55555543
No 116
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=26.66 E-value=80 Score=25.65 Aligned_cols=29 Identities=10% Similarity=0.066 Sum_probs=23.6
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~ 113 (280)
..|-.-.+||..| |-+...|+.+....++
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~~ 148 (161)
T PRK09047 120 WEDMDVAETAAAM-GCSEGSVKTHCSRATH 148 (161)
T ss_pred HhcCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 3467789999999 9999999999876543
No 117
>PLN00032 DNA-directed RNA polymerase; Provisional
Probab=26.53 E-value=65 Score=24.25 Aligned_cols=27 Identities=22% Similarity=0.428 Sum_probs=18.2
Q ss_pred ChhhHHHHHHHHHHHHccCCchhh-hhh
Q 040841 247 GENSLEKLYEEYLQILKNDDEQLQ-LDC 273 (280)
Q Consensus 247 ~~~~~~~~~~~~~q~~~~~~~~~~-~~~ 273 (280)
+-..+-.+||||.++++-+.+..+ ||.
T Consensus 10 CGkvig~~we~y~~~~~~g~~~~~~LD~ 37 (71)
T PLN00032 10 CGKVIGNKWDTYLDLLQADYSEGDALDA 37 (71)
T ss_pred CCCCcHHHHHHHHHHHhcCCCHHHHHHH
Confidence 334567899999999976543333 554
No 118
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.11 E-value=78 Score=26.74 Aligned_cols=30 Identities=17% Similarity=0.205 Sum_probs=24.1
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhhhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHLSK 114 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~ 114 (280)
..|-...+||..| |-+...|+.+....+++
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 3467899999999 99999999988765443
No 119
>PF02216 B: B domain; InterPro: IPR003132 This entry represents the immunoglobulin-binding domain found in the Staphylococcus aureus virulence factor protein A (SpA). Protein A contains five highly homologous Ig-binding domains in tandem (designated domains E, D, A, B and C), which share a common structure consisting of three helices in a closed left-handed twist. Protein A can exist in both secreted and membrane-bound forms, and has two distinct Ig-binding activities: each domain can bind Fc-gamma (the constant region of IgG involved in effector functions) and Fab (the Ig fragment responsible for antigen recognition) [].; GO: 0019865 immunoglobulin binding, 0009405 pathogenesis; PDB: 1EDL_A 1EDI_A 1EDJ_A 1EDK_A 2B88_A 2B87_A 2B89_A 1FC2_C 1DEE_H 1ZXG_A ....
Probab=26.08 E-value=57 Score=23.19 Aligned_cols=21 Identities=19% Similarity=0.406 Sum_probs=13.1
Q ss_pred HHHHHccCC-chhhhhhHHHhh
Q 040841 258 YLQILKNDD-EQLQLDCFAESL 278 (280)
Q Consensus 258 ~~q~~~~~~-~~~~~~~~~~~~ 278 (280)
|++||+|++ .--|-+-|+++|
T Consensus 13 FY~vl~~~nLteeQrn~yI~~l 34 (54)
T PF02216_consen 13 FYEVLHMPNLTEEQRNGYIQSL 34 (54)
T ss_dssp HHHHHCSTTS-HHHHHHHHHHH
T ss_pred HHHHHcCCCcCHHHHHhHHHHH
Confidence 677888777 223566666655
No 120
>PF11427 HTH_Tnp_Tc3_1: Tc3 transposase; PDB: 1U78_A 1TC3_C.
Probab=26.02 E-value=61 Score=22.63 Aligned_cols=36 Identities=28% Similarity=0.414 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHH
Q 040841 71 TPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYW 108 (280)
Q Consensus 71 T~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw 108 (280)
|.. |+-.+.++.+.|-.-.+||+.+ ||+.+.|++.-
T Consensus 6 t~~-Eqaqid~m~qlG~s~~~isr~i-~RSr~~Ir~yl 41 (50)
T PF11427_consen 6 TDA-EQAQIDVMHQLGMSLREISRRI-GRSRTCIRRYL 41 (50)
T ss_dssp -HH-HHHHHHHHHHTT--HHHHHHHH-T--HHHHHHHH
T ss_pred CHH-HHHHHHHHHHhchhHHHHHHHh-CccHHHHHHHh
Confidence 444 4455667788899999999999 99999888654
No 121
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.61 E-value=1.2e+02 Score=24.35 Aligned_cols=57 Identities=16% Similarity=0.216 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCCCCCCCCHHHHHHH
Q 040841 19 PREDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDIKRGNITPDEDDLI 78 (280)
Q Consensus 19 ~EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~ikkg~WT~EED~~L 78 (280)
.-+.+.|.++|..++...=.+||+.++- ..+...|+.+.|.-..++..|..+++..-
T Consensus 56 Kid~~~L~~~v~~~pd~tl~Ela~~l~V---s~~ti~~~Lkrlg~t~KK~~~~~~~~~~~ 112 (119)
T PF01710_consen 56 KIDRDELKALVEENPDATLRELAERLGV---SPSTIWRALKRLGITRKKKTLHSEKDREK 112 (119)
T ss_pred cccHHHHHHHHHHCCCcCHHHHHHHcCC---CHHHHHHHHHHcCchhccCcccchhHHHH
Confidence 3356679999999998777789988863 66667777777877888888877666543
No 122
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=25.38 E-value=77 Score=26.93 Aligned_cols=28 Identities=25% Similarity=0.113 Sum_probs=23.2
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
..|-...+||..| |-+...|+.+....+
T Consensus 120 ~~g~~~~EIA~~l-gis~~tV~~~l~Rar 147 (181)
T PRK09637 120 LEGLSQKEIAEKL-GLSLSGAKSRVQRGR 147 (181)
T ss_pred hcCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 4477899999999 999999999887553
No 123
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=24.46 E-value=70 Score=28.24 Aligned_cols=45 Identities=24% Similarity=0.229 Sum_probs=35.5
Q ss_pred CCCCHHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHhhhhH
Q 040841 68 GNITPDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLSKR 115 (280)
Q Consensus 68 g~WT~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~~ 115 (280)
...|+.|-+.|.-+.+ |-.=+.||..| +.+...||+|..++++|-
T Consensus 147 ~~LT~RE~eVL~lla~--G~snkeIA~~L-~iS~~TVk~h~~~i~~KL 191 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLSNKEIAEEL-NLSEKTVKTHVSNILRKL 191 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCCHHHHHHHH-CCCHhHHHHHHHHHHHHc
Confidence 3688888886665543 55558999999 999999999999887653
No 124
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=24.30 E-value=89 Score=25.89 Aligned_cols=28 Identities=25% Similarity=0.260 Sum_probs=23.1
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
..|-.-.+||..| |.+...|+.+....+
T Consensus 132 ~~g~s~~EIA~~l-gis~~tV~~~l~ra~ 159 (173)
T PRK09645 132 YRGWSTAQIAADL-GIPEGTVKSRLHYAL 159 (173)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3466789999999 999999999987654
No 125
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=24.22 E-value=40 Score=27.56 Aligned_cols=44 Identities=11% Similarity=0.062 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCC
Q 040841 20 REDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDI 65 (280)
Q Consensus 20 EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~i 65 (280)
+-|.+++++.+..+...+..||+.++ -+...|+.|-.+..+-++
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lg--lS~~~v~~Ri~~L~~~Gi 51 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVG--LSPSTVLRRIKRLEEEGV 51 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--CCHHHHHHHHHHHHHCCc
Confidence 56889999999999989999999998 788899998777655444
No 126
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=24.20 E-value=78 Score=26.80 Aligned_cols=27 Identities=11% Similarity=-0.017 Sum_probs=22.1
Q ss_pred hCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 85 LGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 85 ~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
.|-....||..| |-+...|++++...+
T Consensus 153 ~g~s~~eIA~~l-gis~~tv~~~l~Rar 179 (193)
T PRK11923 153 DGLSYEDIASVM-QCPVGTVRSRIFRAR 179 (193)
T ss_pred cCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 356789999999 889999999987653
No 127
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=24.17 E-value=1.1e+02 Score=25.62 Aligned_cols=30 Identities=13% Similarity=0.201 Sum_probs=24.1
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhhhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHLSK 114 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~~ 114 (280)
..|-....||..| |-+...|+.+....+++
T Consensus 145 ~~g~s~~eIA~~l-~is~~tV~~~l~ra~~~ 174 (184)
T PRK12512 145 VEGASIKETAAKL-SMSEGAVRVALHRGLAA 174 (184)
T ss_pred HcCCCHHHHHHHh-CCCHHHHHHHHHHHHHH
Confidence 3467789999999 99999999998765433
No 128
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=24.12 E-value=90 Score=26.41 Aligned_cols=28 Identities=7% Similarity=-0.013 Sum_probs=23.3
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
..|-....||..| |-+...|++++...+
T Consensus 145 ~~~~s~~eIA~~l-gis~~tV~~~l~Rar 172 (189)
T PRK12515 145 YHEKSVEEVGEIV-GIPESTVKTRMFYAR 172 (189)
T ss_pred HcCCCHHHHHHHH-CcCHHHHHHHHHHHH
Confidence 3467799999999 889999999987654
No 129
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=23.85 E-value=53 Score=25.28 Aligned_cols=44 Identities=18% Similarity=0.123 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHHhCCCCccccccccCccccchhhhhhhhhccCCCC
Q 040841 20 REDTLLTEYIQVHGEGHWRSLPKKAGLLRCGKSCRLRWMNYLRPDI 65 (280)
Q Consensus 20 EED~~L~~lV~~~G~~~W~~IA~~~~~~Rt~~qCr~Rw~~~L~p~i 65 (280)
+.|.+++.++...+.-.+..||+.++ -+...|+.|.......++
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~--~s~~tv~~~l~~L~~~g~ 46 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVG--LSPSTVHNRVKRLEEEGV 46 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHC--cCHHHHHHHHHHHHHCCC
Confidence 57889999999998889999999997 688889888877655443
No 130
>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=23.52 E-value=54 Score=25.04 Aligned_cols=27 Identities=26% Similarity=0.437 Sum_probs=21.6
Q ss_pred HHHHHHHHHhCCccccccccCCCCCHHH
Q 040841 76 DLIIRLHSLLGNRWSLIAGRLPGRTDNE 103 (280)
Q Consensus 76 ~~L~~lv~~~G~~W~~IA~~lpgRt~~q 103 (280)
..|..+....|..|..+|..| |=+..+
T Consensus 3 ~~l~~ia~~LG~~Wk~lar~L-Glse~~ 29 (86)
T cd08779 3 SNLLSIAGRLGLDWQAIGLHL-GLSYRE 29 (86)
T ss_pred hHHHHHHHHHhHHHHHHHHHc-CCCHHH
Confidence 457888999999999999999 544443
No 131
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=23.21 E-value=93 Score=26.53 Aligned_cols=28 Identities=7% Similarity=-0.062 Sum_probs=23.3
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
..|-...+||..| |-+...|+.|....+
T Consensus 148 ~~g~s~~EIA~~l-gis~~tVk~~l~RAr 175 (189)
T PRK12530 148 YLELSSEQICQEC-DISTSNLHVLLYRAR 175 (189)
T ss_pred HcCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3467799999999 999999999977543
No 132
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=23.07 E-value=1.1e+02 Score=25.95 Aligned_cols=28 Identities=14% Similarity=0.129 Sum_probs=22.7
Q ss_pred HHhCCccccccccCCCCCHHHHHHHHHHh
Q 040841 83 SLLGNRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 83 ~~~G~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
...|-.-.+||..| |-+...|+.+....
T Consensus 149 ~~~g~s~~EIA~~l-gis~~tVk~~l~Ra 176 (195)
T PRK12532 149 EILGFSSDEIQQMC-GISTSNYHTIMHRA 176 (195)
T ss_pred HHhCCCHHHHHHHH-CCCHHHHHHHHHHH
Confidence 33467789999999 99999999987753
No 133
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=23.06 E-value=81 Score=26.31 Aligned_cols=26 Identities=12% Similarity=-0.056 Sum_probs=21.5
Q ss_pred CCccccccccCCCCCHHHHHHHHHHhh
Q 040841 86 GNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 86 G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
|-....||..| |-+...|+++.....
T Consensus 152 g~s~~eIA~~l-gis~~~v~~~l~Rar 177 (187)
T TIGR02948 152 DLSLKEISEIL-DLPVGTVKTRIHRGR 177 (187)
T ss_pred CCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 56788999999 889999999887653
No 134
>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=22.91 E-value=99 Score=26.37 Aligned_cols=31 Identities=13% Similarity=0.085 Sum_probs=24.5
Q ss_pred HHHHhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 81 LHSLLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 81 lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
++...|-....||..| |-+...|+.|....+
T Consensus 142 l~~~~g~s~~EIA~~l-gis~~tvk~rl~Rar 172 (188)
T TIGR02943 142 MREVLGFESDEICQEL-EISTSNCHVLLYRAR 172 (188)
T ss_pred HHHHhCCCHHHHHHHh-CCCHHHHHHHHHHHH
Confidence 3344567899999999 999999999877653
No 135
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=22.78 E-value=99 Score=26.39 Aligned_cols=29 Identities=10% Similarity=-0.017 Sum_probs=23.4
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~ 113 (280)
..|-...+||..| |-+...|+.|.+..++
T Consensus 155 ~eg~s~~EIA~~l-gis~~tVk~rl~ra~~ 183 (194)
T PRK12531 155 LEELPHQQVAEMF-DIPLGTVKSRLRLAVE 183 (194)
T ss_pred HcCCCHHHHHHHh-CcCHHHHHHHHHHHHH
Confidence 3467789999999 9999999998876543
No 136
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.65 E-value=1e+02 Score=25.13 Aligned_cols=28 Identities=11% Similarity=-0.091 Sum_probs=22.9
Q ss_pred HhCCccccccccCCCCCHHHHHHHHHHhh
Q 040841 84 LLGNRWSLIAGRLPGRTDNEIKNYWNTHL 112 (280)
Q Consensus 84 ~~G~~W~~IA~~lpgRt~~qck~Rw~~~l 112 (280)
..|-.-.+||..| |-+...|+++....+
T Consensus 120 ~~g~s~~EIA~~l-gis~~tV~~~l~Rar 147 (160)
T PRK09642 120 LEEKSYQEIALQE-KIEVKTVEMKLYRAR 147 (160)
T ss_pred HhCCCHHHHHHHH-CCCHHHHHHHHHHHH
Confidence 3467789999999 999999999877543
No 137
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=21.99 E-value=1e+02 Score=26.36 Aligned_cols=30 Identities=10% Similarity=-0.055 Sum_probs=23.8
Q ss_pred HHhCCccccccccCCCCCHHHHHHHHHHhhh
Q 040841 83 SLLGNRWSLIAGRLPGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 83 ~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~ 113 (280)
...|-.+.+||+.| |-+...|+++....++
T Consensus 149 ~~~g~s~~eIA~~l-gis~~tV~~~l~Ra~~ 178 (196)
T PRK12524 149 HIEGLSNPEIAEVM-EIGVEAVESLTARGKR 178 (196)
T ss_pred HHcCCCHHHHHHHH-CcCHHHHHHHHHHHHH
Confidence 34467899999999 9999999988776543
No 138
>PRK00118 putative DNA-binding protein; Validated
Probab=21.37 E-value=1.2e+02 Score=24.35 Aligned_cols=39 Identities=10% Similarity=0.068 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHhCCccccccccCCCCCHHHHHHHHHHh
Q 040841 72 PDEDDLIIRLHSLLGNRWSLIAGRLPGRTDNEIKNYWNTH 111 (280)
Q Consensus 72 ~EED~~L~~lv~~~G~~W~~IA~~lpgRt~~qck~Rw~~~ 111 (280)
++.+..++.+....|-...+||+.+ |-|...++.+-...
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~l-GIS~~TV~r~L~RA 57 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEF-NVSRQAVYDNIKRT 57 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHH-CcCHHHHHHHHHHH
Confidence 4556667778888889999999999 99999998886654
No 139
>cd08805 Death_ank1 Death domain of Ankyrin-1. Death Domain (DD) of the human protein ankyrin-1 (ANK-1) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-1, also called ankyrin-R (for restricted), is found in brain, muscle, and erythrocytes and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. It plays a critical nonredundant role in erythroid development and is associated with hereditary spherocytosis (HS), a common disorder of the red cell membrane. The small alternatively-spliced variant, sANK-1, found in striated muscle and concentrated in the sarcoplasmic reticulum (SR) binds obscurin and titin, which facilitates the anchoring of the network SR to the contractile apparatus. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common featur
Probab=21.21 E-value=67 Score=24.69 Aligned_cols=28 Identities=18% Similarity=0.305 Sum_probs=22.1
Q ss_pred HHHHHHHHHHhCCccccccccCCCCCHHH
Q 040841 75 DDLIIRLHSLLGNRWSLIAGRLPGRTDNE 103 (280)
Q Consensus 75 D~~L~~lv~~~G~~W~~IA~~lpgRt~~q 103 (280)
|.+|..+....|..|..+|..| |=+...
T Consensus 4 ~~~l~~Ia~~LG~dW~~Lar~L-~vs~~d 31 (84)
T cd08805 4 EMKMAVIREHLGLSWAELAREL-QFSVED 31 (84)
T ss_pred hhHHHHHHHHhcchHHHHHHHc-CCCHHH
Confidence 4567788899999999999998 554443
No 140
>PF01133 ER: Enhancer of rudimentary; InterPro: IPR000781 The Drosophila protein 'enhancer of rudimentary' (gene (e(r)) is a small protein of 104 residues whose function is not yet clear. From an evolutionary point of view, it is highly conserved [] and has been found to exist in probably all multicellular eukaryotic organisms. It has been proposed that this protein plays a role in the cell cycle.; GO: 0007049 cell cycle; PDB: 1W9G_A 2NML_A 1WWQ_A 1WZ7_B.
Probab=20.50 E-value=99 Score=24.87 Aligned_cols=31 Identities=29% Similarity=0.359 Sum_probs=20.8
Q ss_pred hhHHHHHHHHHHHHccCC-----chhhhhhHHHhhc
Q 040841 249 NSLEKLYEEYLQILKNDD-----EQLQLDCFAESLL 279 (280)
Q Consensus 249 ~~~~~~~~~~~q~~~~~~-----~~~~~~~~~~~~~ 279 (280)
+.+=++|||.+.-+|..- |-.||=.|+++|-
T Consensus 30 egIC~~YE~~LK~~nP~~~~ItYdIs~Lf~fID~l~ 65 (102)
T PF01133_consen 30 EGICKIYEEHLKRKNPNSPSITYDISDLFDFIDSLA 65 (102)
T ss_dssp HHHHHHHHHHHHHHSTT-SS----HHHHHHHHHHSS
T ss_pred HHHHHHHHHHHHHcCCCCCcccccHHHHHHHHhhhh
Confidence 345578888877776433 5678888988873
No 141
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=20.07 E-value=1.3e+02 Score=24.65 Aligned_cols=31 Identities=26% Similarity=0.289 Sum_probs=24.6
Q ss_pred HHHhCCccccccccCCCCCHHHHHHHHHHhhh
Q 040841 82 HSLLGNRWSLIAGRLPGRTDNEIKNYWNTHLS 113 (280)
Q Consensus 82 v~~~G~~W~~IA~~lpgRt~~qck~Rw~~~l~ 113 (280)
....|-...+||..| |-+...|+.|....++
T Consensus 125 ~~~~g~s~~EIA~~l-~is~~tV~~~l~ra~~ 155 (161)
T PRK12528 125 AQVDGLGYGEIATEL-GISLATVKRYLNKAAM 155 (161)
T ss_pred HHHcCCCHHHHHHHH-CCCHHHHHHHHHHHHH
Confidence 334567899999999 9999999999876543
Done!