Query 035712
Match_columns 563
No_of_seqs 249 out of 1899
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 05:39:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035712.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035712hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0051 RNA polymerase I termi 100.0 7.7E-31 1.7E-35 285.7 15.4 194 370-563 305-511 (607)
2 PLN03212 Transcription repress 99.9 2.3E-23 5.1E-28 207.4 9.0 113 425-561 10-125 (249)
3 PLN03212 Transcription repress 99.9 3E-22 6.4E-27 199.5 9.2 105 366-492 18-125 (249)
4 KOG0049 Transcription factor, 99.9 1.6E-21 3.5E-26 212.0 11.6 150 371-556 303-458 (939)
5 PLN03091 hypothetical protein; 99.8 1.5E-21 3.3E-26 206.8 9.6 101 443-561 11-114 (459)
6 PLN03091 hypothetical protein; 99.8 3.7E-21 8.1E-26 203.8 10.0 102 368-491 9-113 (459)
7 KOG0049 Transcription factor, 99.8 6.3E-21 1.4E-25 207.4 11.3 157 367-562 247-409 (939)
8 KOG0048 Transcription factor, 99.8 5.5E-21 1.2E-25 190.1 9.8 97 373-491 9-108 (238)
9 KOG0048 Transcription factor, 99.8 3.3E-21 7.2E-26 191.6 8.1 99 445-561 8-109 (238)
10 PF13921 Myb_DNA-bind_6: Myb-l 99.6 1.6E-15 3.6E-20 119.9 7.5 59 449-507 1-60 (60)
11 KOG0051 RNA polymerase I termi 99.6 5.7E-15 1.2E-19 162.3 12.4 223 277-560 311-568 (607)
12 COG5147 REB1 Myb superfamily p 99.5 8.7E-15 1.9E-19 159.3 5.0 174 374-558 219-395 (512)
13 PF13921 Myb_DNA-bind_6: Myb-l 99.3 3.8E-12 8.1E-17 100.8 7.1 59 376-457 1-60 (60)
14 KOG0050 mRNA splicing protein 99.3 3.3E-12 7.2E-17 137.7 6.6 100 370-491 4-104 (617)
15 COG5147 REB1 Myb superfamily p 99.2 1.9E-11 4.1E-16 133.6 6.5 123 367-512 14-138 (512)
16 PF00249 Myb_DNA-binding: Myb- 99.2 6.1E-11 1.3E-15 90.7 5.7 45 446-490 1-48 (48)
17 KOG0050 mRNA splicing protein 99.1 1.6E-10 3.5E-15 124.9 7.1 97 445-560 6-104 (617)
18 PF00249 Myb_DNA-binding: Myb- 99.0 6.7E-10 1.4E-14 84.9 5.7 47 496-559 1-48 (48)
19 smart00717 SANT SANT SWI3, AD 98.9 2.9E-09 6.3E-14 78.3 5.9 46 446-491 1-48 (49)
20 cd00167 SANT 'SWI3, ADA2, N-Co 98.8 1.4E-08 3E-13 73.8 5.5 43 448-490 1-45 (45)
21 smart00717 SANT SANT SWI3, AD 98.7 5.8E-08 1.3E-12 71.4 6.3 48 496-560 1-48 (49)
22 cd00167 SANT 'SWI3, ADA2, N-Co 98.5 2.7E-07 5.8E-12 67.0 5.8 45 498-559 1-45 (45)
23 TIGR01557 myb_SHAQKYF myb-like 97.0 0.0017 3.6E-08 52.5 5.7 45 446-490 3-54 (57)
24 TIGR02894 DNA_bind_RsfA transc 96.9 0.0009 2E-08 64.3 4.2 47 445-491 3-56 (161)
25 PF13837 Myb_DNA-bind_4: Myb/S 96.8 0.0017 3.7E-08 54.6 4.3 59 497-559 2-64 (90)
26 KOG0457 Histone acetyltransfer 96.7 0.002 4.4E-08 69.8 5.2 49 494-559 70-118 (438)
27 PF13837 Myb_DNA-bind_4: Myb/S 96.5 0.0027 5.8E-08 53.5 3.9 45 447-491 2-65 (90)
28 KOG0457 Histone acetyltransfer 96.5 0.004 8.6E-08 67.7 5.8 48 444-491 70-119 (438)
29 PF13325 MCRS_N: N-terminal re 96.4 0.019 4.1E-07 57.2 9.7 92 375-490 1-126 (199)
30 COG5259 RSC8 RSC chromatin rem 96.2 0.0052 1.1E-07 67.3 4.6 45 445-489 278-323 (531)
31 KOG1279 Chromatin remodeling f 96.0 0.0082 1.8E-07 66.9 5.0 45 445-489 252-297 (506)
32 PRK13923 putative spore coat p 95.6 0.011 2.3E-07 57.6 3.7 47 445-491 4-57 (170)
33 TIGR01557 myb_SHAQKYF myb-like 95.3 0.049 1.1E-06 44.1 5.8 47 496-559 3-54 (57)
34 PF08914 Myb_DNA-bind_2: Rap1 95.3 0.028 6.2E-07 46.6 4.5 55 375-443 4-59 (65)
35 PF13325 MCRS_N: N-terminal re 94.9 0.13 2.8E-06 51.4 8.6 95 448-558 1-125 (199)
36 COG5259 RSC8 RSC chromatin rem 94.8 0.051 1.1E-06 59.9 6.2 64 354-440 256-323 (531)
37 KOG1279 Chromatin remodeling f 94.6 0.047 1E-06 61.1 5.3 47 494-558 251-297 (506)
38 PF13873 Myb_DNA-bind_5: Myb/S 94.4 0.077 1.7E-06 44.0 5.1 46 446-491 2-70 (78)
39 PF08914 Myb_DNA-bind_2: Rap1 94.2 0.087 1.9E-06 43.8 4.9 46 447-492 3-59 (65)
40 PF13873 Myb_DNA-bind_5: Myb/S 93.2 0.21 4.4E-06 41.5 5.4 58 373-441 2-69 (78)
41 TIGR02894 DNA_bind_RsfA transc 93.1 0.11 2.4E-06 50.2 4.3 54 372-442 3-56 (161)
42 PRK13923 putative spore coat p 91.5 0.21 4.5E-06 48.8 3.9 54 372-442 4-57 (170)
43 KOG4282 Transcription factor G 90.3 0.46 1E-05 50.1 5.6 46 446-491 54-114 (345)
44 COG5114 Histone acetyltransfer 90.0 0.32 7E-06 51.7 4.0 50 494-560 61-110 (432)
45 COG5114 Histone acetyltransfer 90.0 0.35 7.6E-06 51.4 4.3 47 445-491 62-110 (432)
46 KOG1194 Predicted DNA-binding 88.5 1.8 3.9E-05 48.1 8.4 91 376-490 133-232 (534)
47 KOG4282 Transcription factor G 87.8 0.93 2E-05 47.8 5.7 56 496-559 54-113 (345)
48 PF08281 Sigma70_r4_2: Sigma-7 83.7 2.2 4.8E-05 32.8 4.5 40 451-490 12-51 (54)
49 PF09111 SLIDE: SLIDE; InterP 83.6 2.7 5.8E-05 38.8 5.8 47 444-490 47-110 (118)
50 PF12776 Myb_DNA-bind_3: Myb/S 82.7 2.8 6.1E-05 35.6 5.3 55 375-440 1-61 (96)
51 PF12776 Myb_DNA-bind_3: Myb/S 82.2 2.4 5.1E-05 36.1 4.6 56 498-558 1-61 (96)
52 PF13404 HTH_AsnC-type: AsnC-t 81.2 3.6 7.8E-05 31.2 4.7 37 453-489 4-41 (42)
53 COG5118 BDP1 Transcription ini 80.1 2.4 5.3E-05 46.2 4.8 43 497-557 366-408 (507)
54 COG5118 BDP1 Transcription ini 79.0 2.8 6.1E-05 45.8 4.8 69 445-513 364-441 (507)
55 PLN03142 Probable chromatin-re 77.4 12 0.00026 45.8 10.0 164 372-559 804-984 (1033)
56 smart00595 MADF subfamily of S 73.8 4.5 9.8E-05 34.0 3.9 24 467-490 29-52 (89)
57 KOG1194 Predicted DNA-binding 69.5 7.3 0.00016 43.5 5.1 42 374-438 188-229 (534)
58 PF04504 DUF573: Protein of un 69.5 24 0.00051 31.5 7.5 79 374-463 5-94 (98)
59 PRK11179 DNA-binding transcrip 68.6 9.4 0.0002 35.8 5.1 41 452-492 9-50 (153)
60 KOG2656 DNA methyltransferase 68.4 3.9 8.5E-05 44.8 2.8 44 447-490 131-181 (445)
61 PF09197 Rap1-DNA-bind: Rap1, 66.3 17 0.00037 33.2 6.0 67 375-441 1-75 (105)
62 PF04545 Sigma70_r4: Sigma-70, 61.1 20 0.00044 27.2 4.8 39 452-490 7-45 (50)
63 PF11626 Rap1_C: TRF2-interact 60.9 7.8 0.00017 33.5 2.8 22 444-465 45-74 (87)
64 PRK11169 leucine-responsive tr 60.8 14 0.0003 35.1 4.7 42 451-492 13-55 (164)
65 PF07750 GcrA: GcrA cell cycle 56.6 14 0.00029 35.9 3.9 41 448-489 2-43 (162)
66 PF10545 MADF_DNA_bdg: Alcohol 55.0 10 0.00023 30.8 2.5 24 467-490 28-53 (85)
67 smart00595 MADF subfamily of S 54.5 11 0.00025 31.6 2.7 23 535-558 29-51 (89)
68 TIGR02985 Sig70_bacteroi1 RNA 51.6 25 0.00054 31.5 4.6 36 455-490 119-154 (161)
69 PF13404 HTH_AsnC-type: AsnC-t 44.8 50 0.0011 25.0 4.5 37 503-557 4-40 (42)
70 PRK11179 DNA-binding transcrip 43.3 45 0.00097 31.3 5.0 42 502-561 9-50 (153)
71 PF09111 SLIDE: SLIDE; InterP 43.3 35 0.00076 31.6 4.2 51 372-441 48-110 (118)
72 PF07638 Sigma70_ECF: ECF sigm 39.9 45 0.00097 32.1 4.6 29 462-490 148-176 (185)
73 PF09420 Nop16: Ribosome bioge 39.3 50 0.0011 31.7 4.8 45 445-489 113-162 (164)
74 PRK11169 leucine-responsive tr 38.8 53 0.0011 31.2 4.8 43 501-561 13-55 (164)
75 cd08319 Death_RAIDD Death doma 38.7 40 0.00086 29.3 3.6 30 454-483 2-31 (83)
76 PF01388 ARID: ARID/BRIGHT DNA 38.7 46 0.001 28.3 4.0 36 456-491 40-89 (92)
77 smart00344 HTH_ASNC helix_turn 38.6 67 0.0015 27.8 5.1 41 452-492 3-44 (108)
78 TIGR00673 cynS cyanate hydrata 38.4 1.3E+02 0.0028 29.2 7.3 51 455-512 11-61 (150)
79 PF13936 HTH_38: Helix-turn-he 37.9 45 0.00098 25.2 3.4 37 447-484 3-39 (44)
80 KOG4167 Predicted DNA-binding 37.7 45 0.00098 39.6 4.8 45 445-489 618-663 (907)
81 PF11626 Rap1_C: TRF2-interact 36.6 36 0.00078 29.4 3.0 25 372-396 46-74 (87)
82 PF02954 HTH_8: Bacterial regu 35.1 98 0.0021 23.1 4.8 36 453-488 6-41 (42)
83 cd08803 Death_ank3 Death domai 34.9 51 0.0011 28.7 3.7 30 454-483 4-33 (84)
84 TIGR02957 SigX4 RNA polymerase 34.6 2.2E+02 0.0047 29.3 8.8 53 463-515 122-177 (281)
85 KOG2656 DNA methyltransferase 34.5 31 0.00067 38.2 2.8 90 416-559 74-181 (445)
86 PLN03142 Probable chromatin-re 33.6 76 0.0016 39.2 6.1 47 445-491 925-985 (1033)
87 KOG4167 Predicted DNA-binding 32.5 69 0.0015 38.2 5.2 42 374-438 620-661 (907)
88 TIGR02937 sigma70-ECF RNA poly 31.9 72 0.0016 27.6 4.2 42 448-490 110-151 (158)
89 cd06171 Sigma70_r4 Sigma70, re 31.7 1E+02 0.0022 22.0 4.4 41 448-489 10-50 (55)
90 PF04504 DUF573: Protein of un 31.1 1.1E+02 0.0024 27.2 5.3 67 446-512 4-93 (98)
91 smart00501 BRIGHT BRIGHT, ARID 30.9 68 0.0015 27.6 3.8 27 466-492 54-86 (93)
92 PRK09652 RNA polymerase sigma 30.4 80 0.0017 28.9 4.5 31 460-490 139-169 (182)
93 PF10545 MADF_DNA_bdg: Alcohol 30.2 44 0.00095 27.1 2.4 26 534-559 27-53 (85)
94 COG1522 Lrp Transcriptional re 29.7 87 0.0019 28.6 4.6 41 452-492 8-49 (154)
95 KOG4468 Polycomb-group transcr 28.1 75 0.0016 37.1 4.5 51 441-491 83-144 (782)
96 PF11198 DUF2857: Protein of u 28.0 2.6E+02 0.0057 27.4 7.8 60 452-512 74-136 (180)
97 PRK11924 RNA polymerase sigma 28.0 89 0.0019 28.5 4.3 28 463-490 139-166 (179)
98 cd08317 Death_ank Death domain 27.9 57 0.0012 27.8 2.8 29 454-482 4-32 (84)
99 PRK09641 RNA polymerase sigma 27.1 91 0.002 29.0 4.3 31 460-490 147-177 (187)
100 KOG2009 Transcription initiati 27.1 56 0.0012 37.9 3.3 45 445-489 408-453 (584)
101 TIGR02954 Sig70_famx3 RNA poly 26.5 98 0.0021 28.6 4.4 28 463-490 133-160 (169)
102 PRK09643 RNA polymerase sigma 26.3 1E+02 0.0022 29.6 4.5 28 463-490 148-175 (192)
103 PF11035 SnAPC_2_like: Small n 26.0 4.9E+02 0.011 28.5 9.8 101 446-560 21-127 (344)
104 PRK09636 RNA polymerase sigma 25.3 3.6E+02 0.0078 27.7 8.6 51 463-513 129-182 (293)
105 PRK09047 RNA polymerase factor 25.2 1.2E+02 0.0026 27.5 4.6 37 454-490 111-147 (161)
106 cd08804 Death_ank2 Death domai 24.9 88 0.0019 27.0 3.5 30 454-483 4-33 (84)
107 TIGR02939 RpoE_Sigma70 RNA pol 24.4 91 0.002 29.1 3.8 28 463-490 152-179 (190)
108 PRK09645 RNA polymerase sigma 24.4 1.2E+02 0.0026 28.1 4.6 30 461-490 130-159 (173)
109 cd07178 terB_like_YebE telluri 24.4 3.3E+02 0.0071 24.0 7.0 82 373-465 13-94 (95)
110 COG2963 Transposase and inacti 24.2 1.8E+02 0.0039 25.7 5.4 44 446-490 5-49 (116)
111 PRK12529 RNA polymerase sigma 24.1 1.2E+02 0.0027 28.5 4.6 31 460-490 138-168 (178)
112 PRK09642 RNA polymerase sigma 24.0 1.3E+02 0.0027 27.5 4.6 33 458-490 115-147 (160)
113 PRK09637 RNA polymerase sigma 23.8 1.2E+02 0.0025 29.0 4.4 31 460-490 117-147 (181)
114 PRK01905 DNA-binding protein F 23.7 3.1E+02 0.0068 23.1 6.5 40 450-489 35-74 (77)
115 PRK04217 hypothetical protein; 23.4 1.6E+02 0.0034 27.1 5.0 44 446-490 40-83 (110)
116 PRK09635 sigI RNA polymerase s 23.2 4.1E+02 0.0089 27.7 8.6 50 463-512 132-184 (290)
117 PF11035 SnAPC_2_like: Small n 23.1 3.8E+02 0.0081 29.3 8.3 87 374-491 22-127 (344)
118 PRK12530 RNA polymerase sigma 23.0 1.3E+02 0.0027 28.8 4.5 28 463-490 148-175 (189)
119 PRK11923 algU RNA polymerase s 22.9 1.2E+02 0.0026 28.7 4.3 28 463-490 152-179 (193)
120 PRK09413 IS2 repressor TnpA; R 22.9 5.7E+02 0.012 23.1 9.7 47 443-490 7-53 (121)
121 PF07750 GcrA: GcrA cell cycle 22.7 74 0.0016 30.9 2.8 43 375-441 2-44 (162)
122 PRK12515 RNA polymerase sigma 22.7 1.3E+02 0.0029 28.4 4.6 28 463-490 145-172 (189)
123 cd08318 Death_NMPP84 Death dom 22.6 1.1E+02 0.0024 26.4 3.6 26 457-482 10-35 (86)
124 PRK12523 RNA polymerase sigma 22.4 1.4E+02 0.0031 27.8 4.6 33 458-490 128-160 (172)
125 smart00005 DEATH DEATH domain, 22.3 1.1E+02 0.0023 25.5 3.4 29 454-482 5-34 (88)
126 TIGR02948 SigW_bacill RNA poly 22.0 1.2E+02 0.0026 28.2 4.1 27 464-490 151-177 (187)
127 PRK09648 RNA polymerase sigma 22.0 1.4E+02 0.0031 28.2 4.6 28 463-490 153-180 (189)
128 PF01527 HTH_Tnp_1: Transposas 21.9 1.5E+02 0.0032 23.9 4.1 45 445-490 3-47 (76)
129 PRK12531 RNA polymerase sigma 21.9 1.4E+02 0.0031 28.5 4.6 28 463-490 155-182 (194)
130 PF01726 LexA_DNA_bind: LexA D 21.8 2.4E+02 0.0051 23.3 5.2 49 376-442 4-52 (65)
131 cd00569 HTH_Hin_like Helix-tur 21.7 2.2E+02 0.0047 17.8 5.2 37 447-484 4-40 (42)
132 PRK12512 RNA polymerase sigma 21.6 1.4E+02 0.0031 27.9 4.5 28 463-490 145-172 (184)
133 TIGR02531 yecD_yerC TrpR-relat 20.6 2.2E+02 0.0048 25.1 5.1 69 417-489 4-73 (88)
134 PRK00118 putative DNA-binding 20.6 1.7E+02 0.0037 26.6 4.5 40 451-490 19-58 (104)
135 cd08311 Death_p75NR Death doma 20.5 99 0.0021 26.5 2.8 33 450-483 1-33 (77)
136 KOG3554 Histone deacetylase co 20.0 96 0.0021 35.3 3.3 64 375-461 287-355 (693)
No 1
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.97 E-value=7.7e-31 Score=285.72 Aligned_cols=194 Identities=31% Similarity=0.579 Sum_probs=175.2
Q ss_pred CcCCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCC-CcccccHHHHHhHCCCCCHHHHHHHHHHhcCCC--CC
Q 035712 370 FVRGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSH-PEVKHCWKEIGSALPWRPYDSIYYRAHIIFQRD--EN 446 (563)
Q Consensus 370 ~vKkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~-~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p~--kK 446 (563)
.++.+.||++|+.+|.++|..|+..+||+..++.+.++++.+ +....+|+.|...||.|+..++|++.++.+++. ++
T Consensus 305 e~~~~~F~~eed~ale~~V~~y~~~eg~s~~q~~~~i~s~~~~~~~~~l~n~~~~~Lp~R~~~siy~~~rR~y~~FE~~r 384 (607)
T KOG0051|consen 305 EINLKKFSKEEDAALENFVNEYLANEGWSSEQFCQRIWSKDWKTIIRNLYNNLYKLLPYRDRKSIYHHLRRAYTPFENKR 384 (607)
T ss_pred hhhhhhccHHHHHHHHHHHHHHHHhhCcchhhhhhheeccCcchHHHHHHHhhhhhcCcccchhHHHHHHhcCCcccccc
Confidence 456689999999999999999999999999999999999988 778999999999999999999999888777753 89
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhhccc--CCCCCCCHHHHHHHHHHHHhHHHHHHHHH--
Q 035712 447 RKWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVRLPN--QKKGQWSQEEYQKLFDLVNMDLRMRALEE-- 522 (563)
Q Consensus 447 GkWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL~p~--ikkG~WTqEED~kLielV~e~Lr~k~~~e-- 522 (563)
|.||+||++.|..+|.+||++|..|+..|||.|.+|++||+++..+. .++|.||.+|+..|+++|+++++...++-
T Consensus 385 g~wt~ee~eeL~~l~~~~g~~W~~Ig~~lgr~P~~crd~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~ 464 (607)
T KOG0051|consen 385 GKWTPEEEEELKKLVVEHGNDWKEIGKALGRMPMDCRDRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQPQAS 464 (607)
T ss_pred CCCCcchHHHHHHHHHHhcccHHHHHHHHccCcHHHHHHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhccccc
Confidence 99999999999999999999999999999999999999999998775 58999999999999999999887544331
Q ss_pred ------HhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccCCCC
Q 035712 523 ------KKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLTSPM 563 (563)
Q Consensus 523 ------~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~p~M 563 (563)
.-+..+++.++|+|+.|++.++||++.|||.+|+.+++++|
T Consensus 465 n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl~~~~s 511 (607)
T KOG0051|consen 465 NTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKLTTSPS 511 (607)
T ss_pred ccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHHHhhHH
Confidence 11234467799999999999999999999999999998875
No 2
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.89 E-value=2.3e-23 Score=207.35 Aligned_cols=113 Identities=19% Similarity=0.332 Sum_probs=100.5
Q ss_pred CCCCCHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHhCC-hhHHHHhhh--CCChhhHHHHHHHhhcccCCCCCCCH
Q 035712 425 LPWRPYDSIYYRAHIIFQRDENRKWTPEELELVRKFHEKHGS-NWKMLANAL--GKHRFHVKDAWRRVRLPNQKKGQWSQ 501 (563)
Q Consensus 425 LPgRs~kqcy~Rwrr~L~p~kKGkWT~EEDekLielV~kyGn-~W~~IAk~L--GRT~~QCRdRWr~iL~p~ikkG~WTq 501 (563)
+|.|++--|+. ...++++||+|||++|+.+|.+||. +|..||..| |||+.||+.||.++|.|.+++++||.
T Consensus 10 ~~~~~~pcc~K------~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L~P~I~kgpWT~ 83 (249)
T PLN03212 10 VSKKTTPCCTK------MGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYLRPSVKRGGITS 83 (249)
T ss_pred CCCCCCCCccc------CCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhhchhcccCCCCh
Confidence 45566655532 1237899999999999999999996 899999988 69999999999999999999999999
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccCC
Q 035712 502 EEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLTS 561 (563)
Q Consensus 502 EED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~p 561 (563)
+||.+|++++. .+| ..|+.||..|++||+.||++||+.+|.+
T Consensus 84 EED~lLlel~~-------------~~G-----nKWs~IAk~LpGRTDnqIKNRWns~LrK 125 (249)
T PLN03212 84 DEEDLILRLHR-------------LLG-----NRWSLIAGRIPGRTDNEIKNYWNTHLRK 125 (249)
T ss_pred HHHHHHHHHHH-------------hcc-----ccHHHHHhhcCCCCHHHHHHHHHHHHhH
Confidence 99999999998 678 5999999999999999999999988764
No 3
>PLN03212 Transcription repressor MYB5; Provisional
Probab=99.87 E-value=3e-22 Score=199.53 Aligned_cols=105 Identities=18% Similarity=0.278 Sum_probs=95.2
Q ss_pred CCCCCcCCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHC-CCCCHHHHHHHHHHhcCCC
Q 035712 366 KDDGFVRGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSAL-PWRPYDSIYYRAHIIFQRD 444 (563)
Q Consensus 366 k~~~~vKkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~L-PgRs~kqcy~Rwrr~L~p~ 444 (563)
.....+++|+||+|||++|+++|..|+. ..|..||..+ |+|+.+||+.||.++|+|.
T Consensus 18 c~K~glKRg~WT~EEDe~L~~lV~kyG~----------------------~nW~~IAk~~g~gRT~KQCReRW~N~L~P~ 75 (249)
T PLN03212 18 CTKMGMKRGPWTVEEDEILVSFIKKEGE----------------------GRWRSLPKRAGLLRCGKSCRLRWMNYLRPS 75 (249)
T ss_pred cccCCCcCCCCCHHHHHHHHHHHHHhCc----------------------ccHHHHHHhhhcCCCcchHHHHHHHhhchh
Confidence 3444567889999999999999999942 3899999988 6999999999999999986
Q ss_pred -CCCCCCHHHHHHHHHHHHHhCChhHHHHhhh-CCChhhHHHHHHHhhcc
Q 035712 445 -ENRKWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRVRLP 492 (563)
Q Consensus 445 -kKGkWT~EEDekLielV~kyGn~W~~IAk~L-GRT~~QCRdRWr~iL~p 492 (563)
.+++||+|||++|+++|..||++|..||..| |||..+|++||+.++..
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK 125 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRK 125 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhH
Confidence 8999999999999999999999999999999 99999999999988753
No 4
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.85 E-value=1.6e-21 Score=211.98 Aligned_cols=150 Identities=17% Similarity=0.282 Sum_probs=136.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcCCC-CCCCC
Q 035712 371 VRGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQRD-ENRKW 449 (563)
Q Consensus 371 vKkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p~-kKGkW 449 (563)
+....||.|||.+|..+|+.... .....|..|...||+|+..|+..||.+.|+|. ++|+|
T Consensus 303 L~ekeWsEEed~kL~alV~~~~~-------------------nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~w 363 (939)
T KOG0049|consen 303 LSEKEWSEEEDTKLIALVKITSI-------------------NSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRW 363 (939)
T ss_pred HHhhhcchhhhHHHHHHHHHhhc-------------------cCccchHHHHHhcCCcchhhhhhhheeccCccccCCCC
Confidence 34468999999999999988843 22349999999999999999999999999986 99999
Q ss_pred CHHHHHHHHHHHHHhCC-hhHHHHhhh-CCChhhHHHHHHHhhcccCCCCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhc
Q 035712 450 TPEELELVRKFHEKHGS-NWKMLANAL-GKHRFHVKDAWRRVRLPNQKKGQWSQEEYQKLFDLVNMDLRMRALEEKKTKH 527 (563)
Q Consensus 450 T~EEDekLielV~kyGn-~W~~IAk~L-GRT~~QCRdRWr~iL~p~ikkG~WTqEED~kLielV~e~Lr~k~~~e~k~~~ 527 (563)
|++||.+|+.+|.+||. +|..|-..+ |||..|||+||.+.|....+.|.||-.||.+|+.+|. .|
T Consensus 364 t~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~RY~nvL~~s~K~~rW~l~edeqL~~~V~-------------~Y 430 (939)
T KOG0049|consen 364 TDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRERYTNVLNRSAKVERWTLVEDEQLLYAVK-------------VY 430 (939)
T ss_pred CCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHHHHHHHHHhhccCceeecchHHHHHHHH-------------HH
Confidence 99999999999999987 999999999 9999999999999999999999999999999999998 78
Q ss_pred CCCCCCCChHHHHhHcCCCCH---HHHHHHHH
Q 035712 528 GMLRDNISWEAISDKLATRSN---AICCMKWY 556 (563)
Q Consensus 528 G~~~d~IsWs~IS~~LgtRS~---~QCR~RW~ 556 (563)
|. ..|..||..||.||. ..||.|+.
T Consensus 431 G~----g~WakcA~~Lp~~t~~q~~rrR~R~~ 458 (939)
T KOG0049|consen 431 GK----GNWAKCAMLLPKKTSRQLRRRRLRLI 458 (939)
T ss_pred cc----chHHHHHHHccccchhHHHHHHHHHH
Confidence 86 699999999999999 55766653
No 5
>PLN03091 hypothetical protein; Provisional
Probab=99.85 E-value=1.5e-21 Score=206.76 Aligned_cols=101 Identities=23% Similarity=0.397 Sum_probs=95.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCC-hhHHHHhhh--CCChhhHHHHHHHhhcccCCCCCCCHHHHHHHHHHHHhHHHHHH
Q 035712 443 RDENRKWTPEELELVRKFHEKHGS-NWKMLANAL--GKHRFHVKDAWRRVRLPNQKKGQWSQEEYQKLFDLVNMDLRMRA 519 (563)
Q Consensus 443 p~kKGkWT~EEDekLielV~kyGn-~W~~IAk~L--GRT~~QCRdRWr~iL~p~ikkG~WTqEED~kLielV~e~Lr~k~ 519 (563)
..++|+||+|||++|+.+|.+||. +|..||..+ ||++.|||+||.++|+|.+++|+||.|||.+|++++.
T Consensus 11 klrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyLdP~IkKgpWT~EED~lLLeL~k------- 83 (459)
T PLN03091 11 KLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYLRPDLKRGTFSQQEENLIIELHA------- 83 (459)
T ss_pred CCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhccCCcccCCCCCHHHHHHHHHHHH-------
Confidence 357899999999999999999997 899999988 6999999999999999999999999999999999998
Q ss_pred HHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccCC
Q 035712 520 LEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLTS 561 (563)
Q Consensus 520 ~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~p 561 (563)
.+| ..|+.||..|++||+.||++||+.+|.+
T Consensus 84 ------~~G-----nKWskIAk~LPGRTDnqIKNRWnslLKK 114 (459)
T PLN03091 84 ------VLG-----NRWSQIAAQLPGRTDNEIKNLWNSCLKK 114 (459)
T ss_pred ------HhC-----cchHHHHHhcCCCCHHHHHHHHHHHHHH
Confidence 688 5999999999999999999999988754
No 6
>PLN03091 hypothetical protein; Provisional
Probab=99.84 E-value=3.7e-21 Score=203.77 Aligned_cols=102 Identities=24% Similarity=0.398 Sum_probs=93.7
Q ss_pred CCCcCCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHC-CCCCHHHHHHHHHHhcCCC-C
Q 035712 368 DGFVRGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSAL-PWRPYDSIYYRAHIIFQRD-E 445 (563)
Q Consensus 368 ~~~vKkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~L-PgRs~kqcy~Rwrr~L~p~-k 445 (563)
...+++|+||+|||++|+++|.+|+. ..|..||..+ ++|+++||+.||.++|+|. .
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~----------------------~nWs~IAk~~g~gRT~KQCRERW~NyLdP~Ik 66 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGH----------------------GCWSSVPKQAGLQRCGKSCRLRWINYLRPDLK 66 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCc----------------------CCHHHHhhhhccCcCcchHhHHHHhccCCccc
Confidence 34568899999999999999999942 3899999887 4899999999999999985 8
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHHhhh-CCChhhHHHHHHHhhc
Q 035712 446 NRKWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRVRL 491 (563)
Q Consensus 446 KGkWT~EEDekLielV~kyGn~W~~IAk~L-GRT~~QCRdRWr~iL~ 491 (563)
+|+||+|||.+|+++|..||++|..||..| |||+.+|++||+.++.
T Consensus 67 KgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLK 113 (459)
T PLN03091 67 RGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLK 113 (459)
T ss_pred CCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHH
Confidence 999999999999999999999999999999 9999999999998764
No 7
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.84 E-value=6.3e-21 Score=207.43 Aligned_cols=157 Identities=19% Similarity=0.321 Sum_probs=139.2
Q ss_pred CCCCcCCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCC-CCHHHHHHHHHHhcCCCC
Q 035712 367 DDGFVRGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPW-RPYDSIYYRAHIIFQRDE 445 (563)
Q Consensus 367 ~~~~vKkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPg-Rs~kqcy~Rwrr~L~p~k 445 (563)
.+..+++..||+||++.|... +..|+.- .|..||..|.. |+..||+.+|+..+....
T Consensus 247 l~P~~nk~~WS~EE~E~L~Ai----A~A~~~~------------------~W~~IA~~Lgt~RS~yQC~~kF~t~~~~L~ 304 (939)
T KOG0049|consen 247 LNPKWNKEHWSNEEVEKLKAL----AEAPKFV------------------SWPMIALNLGTNRSSYQCMEKFKTEVSQLS 304 (939)
T ss_pred cCCccchhccChHHHHHHHHH----Hhccccc------------------cHHHHHHHhCCCcchHHHHHHHHHHHHHHH
Confidence 345567778999999999766 4444542 89999999987 999999999998877666
Q ss_pred CCCCCHHHHHHHHHHHHHhC--C--hhHHHHhhh-CCChhhHHHHHHHhhcccCCCCCCCHHHHHHHHHHHHhHHHHHHH
Q 035712 446 NRKWTPEELELVRKFHEKHG--S--NWKMLANAL-GKHRFHVKDAWRRVRLPNQKKGQWSQEEYQKLFDLVNMDLRMRAL 520 (563)
Q Consensus 446 KGkWT~EEDekLielV~kyG--n--~W~~IAk~L-GRT~~QCRdRWr~iL~p~ikkG~WTqEED~kLielV~e~Lr~k~~ 520 (563)
...||+|||.+|+.+|.... . +|.+|-.+| ||+..|+..||...|+|.+++|+||.+||.+|+.+|.
T Consensus 305 ekeWsEEed~kL~alV~~~~~nShI~w~kVV~Ympgr~~~qLI~R~~~~LdPsikhg~wt~~ED~~L~~AV~-------- 376 (939)
T KOG0049|consen 305 EKEWSEEEDTKLIALVKITSINSHIQWDKVVQYMPGRTRQQLITRFSHTLDPSVKHGRWTDQEDVLLVCAVS-------- 376 (939)
T ss_pred hhhcchhhhHHHHHHHHHhhccCccchHHHHHhcCCcchhhhhhhheeccCccccCCCCCCHHHHHHHHHHH--------
Confidence 68999999999999999873 3 999999999 9999999999999999999999999999999999998
Q ss_pred HHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccCCC
Q 035712 521 EEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLTSP 562 (563)
Q Consensus 521 ~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~p~ 562 (563)
.||. ..|..|-..+|+||..|||.||.+.|..+
T Consensus 377 -----~Yg~----kdw~k~R~~vPnRSdsQcR~RY~nvL~~s 409 (939)
T KOG0049|consen 377 -----RYGA----KDWAKVRQAVPNRSDSQCRERYTNVLNRS 409 (939)
T ss_pred -----HhCc----cchhhHHHhcCCccHHHHHHHHHHHHHHh
Confidence 5664 79999999999999999999999988653
No 8
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.84 E-value=5.5e-21 Score=190.06 Aligned_cols=97 Identities=23% Similarity=0.334 Sum_probs=91.9
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCC-CCCHHHHHHHHHHhcCCC-CCCCCC
Q 035712 373 GKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALP-WRPYDSIYYRAHIIFQRD-ENRKWT 450 (563)
Q Consensus 373 kGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LP-gRs~kqcy~Rwrr~L~p~-kKGkWT 450 (563)
+|+||+|||++|...|..|+. .+|..|+..++ +|+.+||+.||.++|+|. ++|.||
T Consensus 9 kGpWt~EED~~L~~~V~~~G~----------------------~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT 66 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGK----------------------HNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFS 66 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCC----------------------CCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCC
Confidence 599999999999999999953 38999999999 999999999999999986 999999
Q ss_pred HHHHHHHHHHHHHhCChhHHHHhhh-CCChhhHHHHHHHhhc
Q 035712 451 PEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRVRL 491 (563)
Q Consensus 451 ~EEDekLielV~kyGn~W~~IAk~L-GRT~~QCRdRWr~iL~ 491 (563)
+|||.+|++||..||+.|+.||++| |||++.|+++|..++.
T Consensus 67 ~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~lk 108 (238)
T KOG0048|consen 67 DEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTHLK 108 (238)
T ss_pred HHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHHHH
Confidence 9999999999999999999999999 9999999999988874
No 9
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=99.84 E-value=3.3e-21 Score=191.62 Aligned_cols=99 Identities=22% Similarity=0.338 Sum_probs=94.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-hhHHHHhhh--CCChhhHHHHHHHhhcccCCCCCCCHHHHHHHHHHHHhHHHHHHHH
Q 035712 445 ENRKWTPEELELVRKFHEKHGS-NWKMLANAL--GKHRFHVKDAWRRVRLPNQKKGQWSQEEYQKLFDLVNMDLRMRALE 521 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn-~W~~IAk~L--GRT~~QCRdRWr~iL~p~ikkG~WTqEED~kLielV~e~Lr~k~~~ 521 (563)
.+|+||+|||++|+.+|.+||. +|..||+.+ ||+..+||.||.++|.|.+++|.||+|||..|+++..
T Consensus 8 ~kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyLrP~ikrg~fT~eEe~~Ii~lH~--------- 78 (238)
T KOG0048|consen 8 VKGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYLRPDLKRGNFSDEEEDLIIKLHA--------- 78 (238)
T ss_pred cCCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhcccCCCccCCCCCHHHHHHHHHHHH---------
Confidence 3699999999999999999999 799999999 6999999999999999999999999999999999998
Q ss_pred HHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccCC
Q 035712 522 EKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLTS 561 (563)
Q Consensus 522 e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~p 561 (563)
.+| ..|+.||..||+||++.++++|+..|.+
T Consensus 79 ----~~G-----NrWs~IA~~LPGRTDNeIKN~Wnt~lkk 109 (238)
T KOG0048|consen 79 ----LLG-----NRWSLIAGRLPGRTDNEVKNHWNTHLKK 109 (238)
T ss_pred ----HHC-----cHHHHHHhhCCCcCHHHHHHHHHHHHHH
Confidence 788 6899999999999999999999988754
No 10
>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=99.61 E-value=1.6e-15 Score=119.94 Aligned_cols=59 Identities=37% Similarity=0.761 Sum_probs=54.4
Q ss_pred CCHHHHHHHHHHHHHhCChhHHHHhhhC-CChhhHHHHHHHhhcccCCCCCCCHHHHHHH
Q 035712 449 WTPEELELVRKFHEKHGSNWKMLANALG-KHRFHVKDAWRRVRLPNQKKGQWSQEEYQKL 507 (563)
Q Consensus 449 WT~EEDekLielV~kyGn~W~~IAk~LG-RT~~QCRdRWr~iL~p~ikkG~WTqEED~kL 507 (563)
||+|||.+|+.+|..||++|..||..|| ||+.||++||+.+|.+.+.+++||++||++|
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHHhcC
Confidence 9999999999999999999999999998 9999999999998888999999999999987
No 11
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=99.59 E-value=5.7e-15 Score=162.33 Aligned_cols=223 Identities=18% Similarity=0.184 Sum_probs=166.4
Q ss_pred CchhhhhccccchhhhhcccccccchhhHHhhhhhccccccCCCcc-ccccccCCCCCCCCCCccccccccccccCCCcc
Q 035712 277 GTQAEKLCNANSRVEEIEGHAVLEEDGIKEKKKATSVKKHSGGDKK-ASQTKKGVEPNDLSEGSAQKERSKKVSFSNDVQ 355 (563)
Q Consensus 277 ~~~~e~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~k~~-~~~~~~~~e~~s~S~~s~~k~~~KRvSf~d~le 355 (563)
.+.+|+....+.|.+|+..++++.++--+.+ -|+.. +.....+..+....+-...+...+-+ . .
T Consensus 311 F~~eed~ale~~V~~y~~~eg~s~~q~~~~i----------~s~~~~~~~~~l~n~~~~~Lp~R~~~siy~~~-r-R--- 375 (607)
T KOG0051|consen 311 FSKEEDAALENFVNEYLANEGWSSEQFCQRI----------WSKDWKTIIRNLYNNLYKLLPYRDRKSIYHHL-R-R--- 375 (607)
T ss_pred ccHHHHHHHHHHHHHHHHhhCcchhhhhhhe----------eccCcchHHHHHHHhhhhhcCcccchhHHHHH-H-h---
Confidence 4889999999999999999999998887777 44443 55555555554444431101101100 0 1
Q ss_pred cccCCCCCCCCCCCCc-CCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHH
Q 035712 356 VFPSSDAKNGKDDGFV-RGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIY 434 (563)
Q Consensus 356 ~~~s~d~~s~k~~~~v-KkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy 434 (563)
....+- .+|.||++|++.|..++.+.+. .|..|+..| +|.+.+|+
T Consensus 376 ----------~y~~FE~~rg~wt~ee~eeL~~l~~~~g~-----------------------~W~~Ig~~l-gr~P~~cr 421 (607)
T KOG0051|consen 376 ----------AYTPFENKRGKWTPEEEEELKKLVVEHGN-----------------------DWKEIGKAL-GRMPMDCR 421 (607)
T ss_pred ----------cCCccccccCCCCcchHHHHHHHHHHhcc-----------------------cHHHHHHHH-ccCcHHHH
Confidence 222222 6799999999999888766643 999999999 79999999
Q ss_pred HHHHHhcCCC---CCCCCCHHHHHHHHHHHH-------Hh-------------------CChhHHHHhhhC-CChhhHHH
Q 035712 435 YRAHIIFQRD---ENRKWTPEELELVRKFHE-------KH-------------------GSNWKMLANALG-KHRFHVKD 484 (563)
Q Consensus 435 ~Rwrr~L~p~---kKGkWT~EEDekLielV~-------ky-------------------Gn~W~~IAk~LG-RT~~QCRd 484 (563)
.||+.+...+ .+|+||.||.+.|+.+|+ +| +-+|..|++.+| |++.||+.
T Consensus 422 d~wr~~~~~g~~~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~ 501 (607)
T KOG0051|consen 422 DRWRQYVKCGSKRNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRY 501 (607)
T ss_pred HHHHHhhccccccccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHH
Confidence 9999988754 899999999999999995 23 117999999885 99999999
Q ss_pred HHHHhh-cccCCCCCCCH-HHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCC-HHHHHHHHHhccC
Q 035712 485 AWRRVR-LPNQKKGQWSQ-EEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRS-NAICCMKWYDQLT 560 (563)
Q Consensus 485 RWr~iL-~p~ikkG~WTq-EED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS-~~QCR~RW~~iL~ 560 (563)
+|..++ .+..+.+.|.. .+...|++-+.+ ..-.....|+|..|+...|+.+ +.+|+.+|.++.+
T Consensus 502 Kw~kl~~~~s~n~~~~~~~~~~v~l~ErL~d------------l~~~e~~~IDW~~l~~~~~g~~~~~e~r~q~~~lk~ 568 (607)
T KOG0051|consen 502 KWYKLTTSPSFNKRQESKGSDMVWLLERLSD------------LDLTEESPIDWKSLAEYAPGESTGEELRLQFERLKK 568 (607)
T ss_pred HHHHHHhhHHhhcccccccchhHHHHHHHHh------------cccccCCccCHHHHHHhCCCCCcHHHHHHHHHhHhh
Confidence 999998 56677788886 344555555542 1112455699999999999988 9999999998754
No 12
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.51 E-value=8.7e-15 Score=159.35 Aligned_cols=174 Identities=25% Similarity=0.401 Sum_probs=155.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcCCC-CCCCCCHH
Q 035712 374 KRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQRD-ENRKWTPE 452 (563)
Q Consensus 374 GkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p~-kKGkWT~E 452 (563)
+.|.+.+..++.+.++.|....|++..+|+.-+++.. .....||.-|...+|+|+..++|.+-++.+++. ..|.||.|
T Consensus 219 k~f~~~~~~~~e~~i~~~~~~~~~sr~q~~~~Iws~~-~~~~~f~~n~~~~l~~R~~ksiy~~~rrky~~f~~~~~wt~e 297 (512)
T COG5147 219 KAFKKGETLALEQEINEYKEKKGLSRKQFCERIWSTD-RDEDKFWPNIYKKLPYRDKKSIYKHLRRKYNIFEQRGKWTKE 297 (512)
T ss_pred cccchhHHHHHHHHHHHHHHHhcccHHHHHhhccccc-cccccccchhhcccccccccchHHHHHHhhhHHhhhccCccc
Confidence 5788999999999999999999999999998888777 667789999999999999999999999999975 89999999
Q ss_pred HHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhhcc--cCCCCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCC
Q 035712 453 ELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVRLP--NQKKGQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGML 530 (563)
Q Consensus 453 EDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL~p--~ikkG~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~ 530 (563)
|+..|..++..+|..|+.|+..+||-+..|++||+++..+ .+.+++||.+|+.+|...|.++....+.
T Consensus 298 ~~~eL~~~~~~~~~~w~~ig~~~~rmp~~crd~wr~~~~~g~t~~~~~ws~eee~~l~~vv~e~~~~~~~---------- 367 (512)
T COG5147 298 EEQELAKLVVEHGGSWTEIGKLLGRMPNDCRDRWRDYVKCGDTLKRNRWSIEEEELLDKVVNEMRLEAQQ---------- 367 (512)
T ss_pred cccccccccccccchhhHhhhhhccCcHHHHHHHhhhccccCccCCCCCchhhhhhHHHHHHHHHHHHhh----------
Confidence 9999999999999999999999999999999999999876 6788999999999999999865433221
Q ss_pred CCCCChHHHHhHcCCCCHHHHHHHHHhc
Q 035712 531 RDNISWEAISDKLATRSNAICCMKWYDQ 558 (563)
Q Consensus 531 ~d~IsWs~IS~~LgtRS~~QCR~RW~~i 558 (563)
...|.|..|+..+++|...+|+.++...
T Consensus 368 ~~~~~~~li~~~~~~~~~~~~~~~~~~~ 395 (512)
T COG5147 368 SSRILWLLIAQNIRNRLQHHCRDKYGVL 395 (512)
T ss_pred hhhhhHHHHHHhhhccccCCCCCccccc
Confidence 2338999999999999999999876553
No 13
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=99.32 E-value=3.8e-12 Score=100.76 Aligned_cols=59 Identities=29% Similarity=0.367 Sum_probs=51.3
Q ss_pred CCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcCC-CCCCCCCHHHH
Q 035712 376 FSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQR-DENRKWTPEEL 454 (563)
Q Consensus 376 WT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p-~kKGkWT~EED 454 (563)
||++||++|..+|..|+. .|..||..||+|++.+|+.||..+|.+ ..+++||++||
T Consensus 1 WT~eEd~~L~~~~~~~g~-----------------------~W~~Ia~~l~~Rt~~~~~~r~~~~l~~~~~~~~wt~eEd 57 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN-----------------------DWKKIAEHLGNRTPKQCRNRWRNHLRPKISRGPWTKEED 57 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS------------------------HHHHHHHSTTS-HHHHHHHHHHTTSTTSTSSSSSHHHH
T ss_pred CCHHHHHHHHHHHHHHCc-----------------------CHHHHHHHHCcCCHHHHHHHHHHHCcccccCCCcCHHHH
Confidence 999999999999999942 899999999889999999999997765 48999999999
Q ss_pred HHH
Q 035712 455 ELV 457 (563)
Q Consensus 455 ekL 457 (563)
+.|
T Consensus 58 ~~L 60 (60)
T PF13921_consen 58 QRL 60 (60)
T ss_dssp HHH
T ss_pred hcC
Confidence 987
No 14
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.29 E-value=3.3e-12 Score=137.66 Aligned_cols=100 Identities=21% Similarity=0.386 Sum_probs=94.4
Q ss_pred CcCCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcCCC-CCCC
Q 035712 370 FVRGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQRD-ENRK 448 (563)
Q Consensus 370 ~vKkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p~-kKGk 448 (563)
.+++|-|+.-||++|..+|..|+. ..|..|+..|+-.++.|||.||..+++|. ++.-
T Consensus 4 ~~kggvwrntEdeilkaav~kyg~----------------------nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~te 61 (617)
T KOG0050|consen 4 EIKGGVWRNTEDEVLKAAVMKYGK----------------------NQWSRIASLLNRKTARQCKARWEEWLDPAIKKTE 61 (617)
T ss_pred EEecceecccHHHHHHHHHHHcch----------------------HHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhh
Confidence 468899999999999999999964 48999999999999999999999999985 8899
Q ss_pred CCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhhc
Q 035712 449 WTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVRL 491 (563)
Q Consensus 449 WT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL~ 491 (563)
|+.|||++|+-+.....+.|..||.+|||+++||..||.+++.
T Consensus 62 ws~eederlLhlakl~p~qwrtIa~i~gr~~~qc~eRy~~ll~ 104 (617)
T KOG0050|consen 62 WSREEDERLLHLAKLEPTQWRTIADIMGRTSQQCLERYNNLLD 104 (617)
T ss_pred hhhhHHHHHHHHHHhcCCccchHHHHhhhhHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999999999874
No 15
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=99.19 E-value=1.9e-11 Score=133.59 Aligned_cols=123 Identities=16% Similarity=0.229 Sum_probs=107.4
Q ss_pred CCCCcCCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcCCC-C
Q 035712 367 DDGFVRGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQRD-E 445 (563)
Q Consensus 367 ~~~~vKkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p~-k 445 (563)
++...++|.|+..||+.|..+|..|.. ..|..||..|+.+++.+|..||..+++|. +
T Consensus 14 ~~~~~k~gsw~~~EDe~l~~~vk~l~~----------------------nnws~vas~~~~~~~kq~~~rw~~~lnp~lk 71 (512)
T COG5147 14 MQTKRKGGSWKRTEDEDLKALVKKLGP----------------------NNWSKVASLLISSTGKQSSNRWNNHLNPQLK 71 (512)
T ss_pred ccceecCCCCCCcchhHHHHHHhhccc----------------------ccHHHHHHHhcccccccccchhhhhhchhcc
Confidence 556778899999999999999988832 37999999999999999999999999985 8
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHHhhh-CCChhhHHHHHHHhhcccCCCCCCCHHHHHHHHHHHH
Q 035712 446 NRKWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRVRLPNQKKGQWSQEEYQKLFDLVN 512 (563)
Q Consensus 446 KGkWT~EEDekLielV~kyGn~W~~IAk~L-GRT~~QCRdRWr~iL~p~ikkG~WTqEED~kLielV~ 512 (563)
+..||.|||..|+.+...+|+.|+.||..+ |||..+|.+||.+.+.+... ..||.......+.-+.
T Consensus 72 ~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~~~~~~s-~~~s~~~~~~~f~k~d 138 (512)
T COG5147 72 KKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNTLEDLSS-THDSKLQRRNEFDKID 138 (512)
T ss_pred cccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHHHhhhhhc-cccccccchhhccccC
Confidence 999999999999999999999999999999 59999999999999865333 6777777666655554
No 16
>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=99.15 E-value=6.1e-11 Score=90.68 Aligned_cols=45 Identities=22% Similarity=0.428 Sum_probs=40.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCCh-hHHHHhhhC--CChhhHHHHHHHhh
Q 035712 446 NRKWTPEELELVRKFHEKHGSN-WKMLANALG--KHRFHVKDAWRRVR 490 (563)
Q Consensus 446 KGkWT~EEDekLielV~kyGn~-W~~IAk~LG--RT~~QCRdRWr~iL 490 (563)
+++||+|||.+|++++.+||.+ |..||..|+ ||+.||++||++++
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 5899999999999999999997 999999995 99999999999875
No 17
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=99.08 E-value=1.6e-10 Score=124.93 Aligned_cols=97 Identities=27% Similarity=0.515 Sum_probs=89.3
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-hhHHHHhhhC-CChhhHHHHHHHhhcccCCCCCCCHHHHHHHHHHHHhHHHHHHHHH
Q 035712 445 ENRKWTPEELELVRKFHEKHGS-NWKMLANALG-KHRFHVKDAWRRVRLPNQKKGQWSQEEYQKLFDLVNMDLRMRALEE 522 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn-~W~~IAk~LG-RT~~QCRdRWr~iL~p~ikkG~WTqEED~kLielV~e~Lr~k~~~e 522 (563)
+.|.|+.-||+.|...|.+||. .|+.|+..|. .|+.||+.||...++|.+++.-||.+||.+|+.+..
T Consensus 6 kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp~i~~tews~eederlLhlak---------- 75 (617)
T KOG0050|consen 6 KGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDPAIKKTEWSREEDERLLHLAK---------- 75 (617)
T ss_pred ecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCHHHhhhhhhhhHHHHHHHHHH----------
Confidence 5689999999999999999998 8999999996 589999999999999999999999999999999997
Q ss_pred HhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccC
Q 035712 523 KKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLT 560 (563)
Q Consensus 523 ~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~ 560 (563)
... -.|..|+..|+ |+..||-.||+++|.
T Consensus 76 ---l~p-----~qwrtIa~i~g-r~~~qc~eRy~~ll~ 104 (617)
T KOG0050|consen 76 ---LEP-----TQWRTIADIMG-RTSQQCLERYNNLLD 104 (617)
T ss_pred ---hcC-----CccchHHHHhh-hhHHHHHHHHHHHHH
Confidence 233 59999999997 999999999998764
No 18
>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=99.00 E-value=6.7e-10 Score=84.94 Aligned_cols=47 Identities=30% Similarity=0.690 Sum_probs=40.8
Q ss_pred CCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcC-CCCHHHHHHHHHhcc
Q 035712 496 KGQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLA-TRSNAICCMKWYDQL 559 (563)
Q Consensus 496 kG~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~Lg-tRS~~QCR~RW~~iL 559 (563)
+++||++|+.+|+++|. .+|. .+|..||..|| +||..||++||+++|
T Consensus 1 r~~Wt~eE~~~l~~~v~-------------~~g~----~~W~~Ia~~~~~~Rt~~qc~~~~~~~~ 48 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVK-------------KYGK----DNWKKIAKRMPGGRTAKQCRSRYQNLL 48 (48)
T ss_dssp S-SS-HHHHHHHHHHHH-------------HSTT----THHHHHHHHHSSSSTHHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHH-------------HhCC----cHHHHHHHHcCCCCCHHHHHHHHHhhC
Confidence 57999999999999999 7884 25999999999 999999999999875
No 19
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.90 E-value=2.9e-09 Score=78.30 Aligned_cols=46 Identities=30% Similarity=0.645 Sum_probs=42.8
Q ss_pred CCCCCHHHHHHHHHHHHHhC-ChhHHHHhhh-CCChhhHHHHHHHhhc
Q 035712 446 NRKWTPEELELVRKFHEKHG-SNWKMLANAL-GKHRFHVKDAWRRVRL 491 (563)
Q Consensus 446 KGkWT~EEDekLielV~kyG-n~W~~IAk~L-GRT~~QCRdRWr~iL~ 491 (563)
+++||++||..|+.++..|| .+|..||..| +||+.+|+.||+.++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 36899999999999999999 8999999999 6999999999998753
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=98.76 E-value=1.4e-08 Score=73.76 Aligned_cols=43 Identities=35% Similarity=0.698 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHHHhC-ChhHHHHhhh-CCChhhHHHHHHHhh
Q 035712 448 KWTPEELELVRKFHEKHG-SNWKMLANAL-GKHRFHVKDAWRRVR 490 (563)
Q Consensus 448 kWT~EEDekLielV~kyG-n~W~~IAk~L-GRT~~QCRdRWr~iL 490 (563)
+||++|+..|+.++..|| .+|..||..| +||+.+|+.+|.+++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999999999 7999999999 699999999998763
No 21
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.66 E-value=5.8e-08 Score=71.36 Aligned_cols=48 Identities=38% Similarity=0.778 Sum_probs=43.3
Q ss_pred CCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccC
Q 035712 496 KGQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLT 560 (563)
Q Consensus 496 kG~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~ 560 (563)
+++||++|+..|+.++. .+|. .+|..||..|++||+.+|+.+|+.++.
T Consensus 1 ~~~Wt~~E~~~l~~~~~-------------~~g~----~~w~~Ia~~~~~rt~~~~~~~~~~~~~ 48 (49)
T smart00717 1 KGEWTEEEDELLIELVK-------------KYGK----NNWEKIAKELPGRTAEQCRERWNNLLK 48 (49)
T ss_pred CCCCCHHHHHHHHHHHH-------------HHCc----CCHHHHHHHcCCCCHHHHHHHHHHHcC
Confidence 46899999999999998 5663 599999999999999999999998775
No 22
>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=98.50 E-value=2.7e-07 Score=66.95 Aligned_cols=45 Identities=33% Similarity=0.701 Sum_probs=40.7
Q ss_pred CCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhcc
Q 035712 498 QWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQL 559 (563)
Q Consensus 498 ~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL 559 (563)
+||.+|+..|+.++. .+|. .+|..||..|++||..+|+.+|+.++
T Consensus 1 ~Wt~eE~~~l~~~~~-------------~~g~----~~w~~Ia~~~~~rs~~~~~~~~~~~~ 45 (45)
T cd00167 1 PWTEEEDELLLEAVK-------------KYGK----NNWEKIAKELPGRTPKQCRERWRNLL 45 (45)
T ss_pred CCCHHHHHHHHHHHH-------------HHCc----CCHHHHHhHcCCCCHHHHHHHHHHhC
Confidence 599999999999998 5663 69999999999999999999998764
No 23
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=96.99 E-value=0.0017 Score=52.50 Aligned_cols=45 Identities=20% Similarity=0.334 Sum_probs=40.6
Q ss_pred CCCCCHHHHHHHHHHHHHhCC-hh---HHHHhhhC--C-ChhhHHHHHHHhh
Q 035712 446 NRKWTPEELELVRKFHEKHGS-NW---KMLANALG--K-HRFHVKDAWRRVR 490 (563)
Q Consensus 446 KGkWT~EEDekLielV~kyGn-~W---~~IAk~LG--R-T~~QCRdRWr~iL 490 (563)
+-.||+||...+++++..||. +| ..|+..|+ | |+.||+.+++.+.
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 458999999999999999998 99 99999984 6 9999999998764
No 24
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=96.92 E-value=0.0009 Score=64.28 Aligned_cols=47 Identities=23% Similarity=0.330 Sum_probs=42.9
Q ss_pred CCCCCCHHHHHHHHHHHHHh---CC----hhHHHHhhhCCChhhHHHHHHHhhc
Q 035712 445 ENRKWTPEELELVRKFHEKH---GS----NWKMLANALGKHRFHVKDAWRRVRL 491 (563)
Q Consensus 445 kKGkWT~EEDekLielV~ky---Gn----~W~~IAk~LGRT~~QCRdRWr~iL~ 491 (563)
.+..||.|||.+|.+.|-.| |. .+..+|..|+||+.+|.-||+.++.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRALNRTAAACGFRWNAYVR 56 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHcccHHHhcchHHHHHH
Confidence 45789999999999999999 44 7999999999999999999999875
No 25
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.76 E-value=0.0017 Score=54.62 Aligned_cols=59 Identities=27% Similarity=0.544 Sum_probs=35.6
Q ss_pred CCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcC----CCCHHHHHHHHHhcc
Q 035712 497 GQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLA----TRSNAICCMKWYDQL 559 (563)
Q Consensus 497 G~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~Lg----tRS~~QCR~RW~~iL 559 (563)
-.||.+|...||.++.+.+....... .+......-|..||..|. .||+.||+.||.++.
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~----~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~ 64 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDN----GGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLK 64 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH------SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhh----hccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 47999999999999986321111111 011112236999999993 799999999999864
No 26
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.69 E-value=0.002 Score=69.82 Aligned_cols=49 Identities=18% Similarity=0.480 Sum_probs=44.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhcc
Q 035712 494 QKKGQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQL 559 (563)
Q Consensus 494 ikkG~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL 559 (563)
+-...||.+|+..|++++. .+|. .||..||.++|+++...|+.+|++++
T Consensus 70 i~~~~WtadEEilLLea~~-------------t~G~----GNW~dIA~hIGtKtkeeck~hy~k~f 118 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAE-------------TYGF----GNWQDIADHIGTKTKEECKEHYLKHF 118 (438)
T ss_pred CCCCCCChHHHHHHHHHHH-------------HhCC----CcHHHHHHHHcccchHHHHHHHHHHH
Confidence 5567899999999999998 6775 69999999999999999999999865
No 27
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=96.54 E-value=0.0027 Score=53.46 Aligned_cols=45 Identities=27% Similarity=0.665 Sum_probs=35.0
Q ss_pred CCCCHHHHHHHHHHHHH------hC---C-----hhHHHHhhh---C--CChhhHHHHHHHhhc
Q 035712 447 RKWTPEELELVRKFHEK------HG---S-----NWKMLANAL---G--KHRFHVKDAWRRVRL 491 (563)
Q Consensus 447 GkWT~EEDekLielV~k------yG---n-----~W~~IAk~L---G--RT~~QCRdRWr~iL~ 491 (563)
-.||.+|...|+.++.. ++ . -|..||..| | ||+.||+++|.++..
T Consensus 2 ~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~L~~ 65 (90)
T PF13837_consen 2 RNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKNLKK 65 (90)
T ss_dssp -SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 47999999999999877 21 1 599999998 4 999999999999863
No 28
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=96.49 E-value=0.004 Score=67.65 Aligned_cols=48 Identities=25% Similarity=0.421 Sum_probs=44.4
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC-hhHHHHhhhC-CChhhHHHHHHHhhc
Q 035712 444 DENRKWTPEELELVRKFHEKHGS-NWKMLANALG-KHRFHVKDAWRRVRL 491 (563)
Q Consensus 444 ~kKGkWT~EEDekLielV~kyGn-~W~~IAk~LG-RT~~QCRdRWr~iL~ 491 (563)
.-...||.+|+-.|++++..||- +|..||.++| +|..+|+++|.++..
T Consensus 70 i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv 119 (438)
T KOG0457|consen 70 ILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFV 119 (438)
T ss_pred CCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHh
Confidence 35679999999999999999999 9999999997 899999999999963
No 29
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=96.43 E-value=0.019 Score=57.20 Aligned_cols=92 Identities=15% Similarity=0.266 Sum_probs=62.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCC---CCHHHHHHHHHHhc----------
Q 035712 375 RFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPW---RPYDSIYYRAHIIF---------- 441 (563)
Q Consensus 375 kWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPg---Rs~kqcy~Rwrr~L---------- 441 (563)
+|++.+|-.|+.+|..-. +...|+.+++- -|..-+..||..++
T Consensus 1 rW~~~DDl~Li~av~~~~------------------------~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~ 56 (199)
T PF13325_consen 1 RWKPEDDLLLINAVEQTN------------------------DLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAV 56 (199)
T ss_pred CCCchhhHHHHHHHHHhc------------------------CHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHH
Confidence 699999999999998764 23333332221 34444555555433
Q ss_pred ------CC------CCCCCCCHHHHHHHHHHHHHhCC---hhHHHHh----hh--CCChhhHHHHHHHhh
Q 035712 442 ------QR------DENRKWTPEELELVRKFHEKHGS---NWKMLAN----AL--GKHRFHVKDAWRRVR 490 (563)
Q Consensus 442 ------~p------~kKGkWT~EEDekLielV~kyGn---~W~~IAk----~L--GRT~~QCRdRWr~iL 490 (563)
+| ..+-+||.+|++.|........+ .|..|-. .| +||+.++.++|+.+.
T Consensus 57 ~~m~~l~p~~~~~iq~kalfS~~EE~lL~~v~s~~~p~le~Fq~LL~~n~~vFh~sRTak~L~~HW~lmk 126 (199)
T PF13325_consen 57 AAMRNLHPELIAAIQSKALFSKEEEQLLGTVASSSQPSLETFQELLDKNRSVFHPSRTAKSLQDHWRLMK 126 (199)
T ss_pred HHHHhCCcchhhcccccCCCCHHHHHHHHhhhhccCCcHHHHHHHHHhChhhhccccCHHHHHHHHHHHH
Confidence 21 14679999999999998877655 5666533 24 699999999999874
No 30
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=96.19 E-value=0.0052 Score=67.33 Aligned_cols=45 Identities=22% Similarity=0.447 Sum_probs=41.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCChhHHHHhhhC-CChhhHHHHHHHh
Q 035712 445 ENRKWTPEELELVRKFHEKHGSNWKMLANALG-KHRFHVKDAWRRV 489 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn~W~~IAk~LG-RT~~QCRdRWr~i 489 (563)
....||.+|..+|++.++.||.+|..||.++| +|..||..||.++
T Consensus 278 ~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~FL~L 323 (531)
T COG5259 278 RDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILHFLQL 323 (531)
T ss_pred ccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHHHHcC
Confidence 34589999999999999999999999999995 9999999999877
No 31
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=95.97 E-value=0.0082 Score=66.89 Aligned_cols=45 Identities=22% Similarity=0.374 Sum_probs=42.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCChhHHHHhhh-CCChhhHHHHHHHh
Q 035712 445 ENRKWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRV 489 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn~W~~IAk~L-GRT~~QCRdRWr~i 489 (563)
..+.||.+|..+|++.++.||.+|..||.++ .||..||-.++.++
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 5689999999999999999999999999999 59999999999877
No 32
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=95.63 E-value=0.011 Score=57.56 Aligned_cols=47 Identities=19% Similarity=0.286 Sum_probs=41.0
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-------hhHHHHhhhCCChhhHHHHHHHhhc
Q 035712 445 ENRKWTPEELELVRKFHEKHGS-------NWKMLANALGKHRFHVKDAWRRVRL 491 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn-------~W~~IAk~LGRT~~QCRdRWr~iL~ 491 (563)
.+..||.|+|.+|.+.|..|+. -...++..|+||+.+|..||..++.
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tql~afe~~g~~L~rt~aac~fRwNs~vr 57 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQLKAFEEVGDALKRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchHHHHHHHHHHHHhhhHHHHHhHHHHHHH
Confidence 4679999999999999999955 6888889999999999999976653
No 33
>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=95.29 E-value=0.049 Score=44.09 Aligned_cols=47 Identities=13% Similarity=0.281 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCCh---HHHHhHcC-CC-CHHHHHHHHHhcc
Q 035712 496 KGQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISW---EAISDKLA-TR-SNAICCMKWYDQL 559 (563)
Q Consensus 496 kG~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsW---s~IS~~Lg-tR-S~~QCR~RW~~iL 559 (563)
+-.||+||...++++|. .+|. .+| ..|++.|. ++ |..||+.+.....
T Consensus 3 r~~WT~eeh~~Fl~ai~-------------~~G~----g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 3 RVVWTEDLHDRFLQAVQ-------------KLGG----PDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCHHHHHHHHHHHH-------------HhCC----CcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 45799999999999998 5662 389 99999997 67 9999999876643
No 34
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=95.28 E-value=0.028 Score=46.60 Aligned_cols=55 Identities=20% Similarity=0.258 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCC-CCCHHHHHHHHHHhcCC
Q 035712 375 RFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALP-WRPYDSIYYRAHIIFQR 443 (563)
Q Consensus 375 kWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LP-gRs~kqcy~Rwrr~L~p 443 (563)
+||.+||++|...|..+.. ++. .......|+.++..-| .+|..|.+.||.+.|.+
T Consensus 4 ~fT~edD~~l~~~v~~~~~-~~~-------------~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~ 59 (65)
T PF08914_consen 4 PFTEEDDAALLDYVKENER-QGG-------------SVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRG 59 (65)
T ss_dssp ---HHHHHHHHHHHHHT---STT-------------TTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT--
T ss_pred CCCHHHHHHHHHHHHHhcc-CCC-------------CCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Confidence 7999999999999887743 111 1123458999999988 89999999999988764
No 35
>PF13325 MCRS_N: N-terminal region of micro-spherule protein
Probab=94.86 E-value=0.13 Score=51.36 Aligned_cols=95 Identities=18% Similarity=0.259 Sum_probs=66.8
Q ss_pred CCCHHHHHHHHHHHHHhCChhHHHHhhh--C--CChhhHHHHHHHhhc-cc--------------------CCCCCCCHH
Q 035712 448 KWTPEELELVRKFHEKHGSNWKMLANAL--G--KHRFHVKDAWRRVRL-PN--------------------QKKGQWSQE 502 (563)
Q Consensus 448 kWT~EEDekLielV~kyGn~W~~IAk~L--G--RT~~QCRdRWr~iL~-p~--------------------ikkG~WTqE 502 (563)
+|++++|-.|+..|. +|++-..|+..+ . -|-..+..||+.+|. |. ..+-+||.+
T Consensus 1 rW~~~DDl~Li~av~-~~~~L~~v~~gvkFS~~fT~~Ei~~RW~~llyd~~is~~a~~~m~~l~p~~~~~iq~kalfS~~ 79 (199)
T PF13325_consen 1 RWKPEDDLLLINAVE-QTNDLESVHLGVKFSCKFTLQEIEERWYALLYDPVISRIAVAAMRNLHPELIAAIQSKALFSKE 79 (199)
T ss_pred CCCchhhHHHHHHHH-HhcCHHHHHccCCcCCcCcHHHHHHHHHHHHcChhhHHHHHHHHHhCCcchhhcccccCCCCHH
Confidence 699999999999986 456666776655 2 488999999999984 21 246789999
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHh----Hc-CCCCHHHHHHHHHhc
Q 035712 503 EYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISD----KL-ATRSNAICCMKWYDQ 558 (563)
Q Consensus 503 ED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~----~L-gtRS~~QCR~RW~~i 558 (563)
|++.|.......... .-.|..|=. .| ++||+.+...+|..+
T Consensus 80 EE~lL~~v~s~~~p~---------------le~Fq~LL~~n~~vFh~sRTak~L~~HW~lm 125 (199)
T PF13325_consen 80 EEQLLGTVASSSQPS---------------LETFQELLDKNRSVFHPSRTAKSLQDHWRLM 125 (199)
T ss_pred HHHHHHhhhhccCCc---------------HHHHHHHHHhChhhhccccCHHHHHHHHHHH
Confidence 999999976421000 012222211 13 479999999999864
No 36
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=94.82 E-value=0.051 Score=59.85 Aligned_cols=64 Identities=14% Similarity=0.225 Sum_probs=50.9
Q ss_pred cccccCCCCCCC----CCCCCcCCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCC
Q 035712 354 VQVFPSSDAKNG----KDDGFVRGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRP 429 (563)
Q Consensus 354 le~~~s~d~~s~----k~~~~vKkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs 429 (563)
..+|++....++ .....+....||.+|-.+|.+.|+.|+. .|..||.++.+++
T Consensus 256 qg~f~s~~~ssDf~~v~~~~~~~dk~WS~qE~~LLLEGIe~ygD-----------------------dW~kVA~HVgtKt 312 (531)
T COG5259 256 QGRFPSEFTSSDFKPVTISLLIRDKNWSRQELLLLLEGIEMYGD-----------------------DWDKVARHVGTKT 312 (531)
T ss_pred cCcCCCccccccchhhhhhcccccccccHHHHHHHHHHHHHhhh-----------------------hHHHHHHHhCCCC
Confidence 345555544444 4444545668999999999999999975 9999999999999
Q ss_pred HHHHHHHHHHh
Q 035712 430 YDSIYYRAHII 440 (563)
Q Consensus 430 ~kqcy~Rwrr~ 440 (563)
..||..||.++
T Consensus 313 ~EqCIl~FL~L 323 (531)
T COG5259 313 KEQCILHFLQL 323 (531)
T ss_pred HHHHHHHHHcC
Confidence 99999999754
No 37
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=94.57 E-value=0.047 Score=61.06 Aligned_cols=47 Identities=21% Similarity=0.579 Sum_probs=42.3
Q ss_pred CCCCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhc
Q 035712 494 QKKGQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQ 558 (563)
Q Consensus 494 ikkG~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~i 558 (563)
...+.||.+|..+|+++|. .||. +|..||.++++||..||-.|+.++
T Consensus 251 ~~~~~WT~qE~lLLLE~ie-------------~y~d-----dW~kVa~hVg~ks~eqCI~kFL~L 297 (506)
T KOG1279|consen 251 SARPNWTEQETLLLLEAIE-------------MYGD-----DWNKVADHVGTKSQEQCILKFLRL 297 (506)
T ss_pred cCCCCccHHHHHHHHHHHH-------------Hhcc-----cHHHHHhccCCCCHHHHHHHHHhc
Confidence 4567899999999999998 6774 999999999999999999998764
No 38
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=94.43 E-value=0.077 Score=44.02 Aligned_cols=46 Identities=26% Similarity=0.572 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHHh-----C--C----------hhHHHHhhh------CCChhhHHHHHHHhhc
Q 035712 446 NRKWTPEELELVRKFHEKH-----G--S----------NWKMLANAL------GKHRFHVKDAWRRVRL 491 (563)
Q Consensus 446 KGkWT~EEDekLielV~ky-----G--n----------~W~~IAk~L------GRT~~QCRdRWr~iL~ 491 (563)
...||++|...|++++.+| | . .|..|+..| .||..||+.+|.++..
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 4589999999999999987 3 1 699999998 2999999999999863
No 39
>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=94.22 E-value=0.087 Score=43.76 Aligned_cols=46 Identities=15% Similarity=0.227 Sum_probs=32.2
Q ss_pred CCCCHHHHHHHHHHHHHh--------CC-hhHHHHhhh--CCChhhHHHHHHHhhcc
Q 035712 447 RKWTPEELELVRKFHEKH--------GS-NWKMLANAL--GKHRFHVKDAWRRVRLP 492 (563)
Q Consensus 447 GkWT~EEDekLielV~ky--------Gn-~W~~IAk~L--GRT~~QCRdRWr~iL~p 492 (563)
-+||.|||++|+.+|..+ |+ =|..++..- .+|.+..++||...|.+
T Consensus 3 ~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L~~ 59 (65)
T PF08914_consen 3 TPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHLRG 59 (65)
T ss_dssp ----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT--
T ss_pred CCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHHhc
Confidence 589999999999999655 33 699999875 67899999999998854
No 40
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=93.16 E-value=0.21 Score=41.49 Aligned_cols=58 Identities=22% Similarity=0.364 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccC-----CCcccccHHHHHhHC-----CCCCHHHHHHHHHHhc
Q 035712 373 GKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRS-----HPEVKHCWKEIGSAL-----PWRPYDSIYYRAHIIF 441 (563)
Q Consensus 373 kGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r-----~~e~k~~Wk~IA~~L-----PgRs~kqcy~Rwrr~L 441 (563)
...||++|..+|.++|..|.. ++.... .......|..|+..| +.|+..++...|.++.
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~-----------il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk 69 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKD-----------ILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLK 69 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHH-----------HHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHH
Confidence 357999999999999999854 222211 112456999998765 2499999999998765
No 41
>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=93.15 E-value=0.11 Score=50.23 Aligned_cols=54 Identities=22% Similarity=0.340 Sum_probs=43.0
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcC
Q 035712 372 RGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQ 442 (563)
Q Consensus 372 KkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~ 442 (563)
+.-.||.+||.+|.+.|.+|+..-+ + + -..+.++|..| +||+-+|--||..++.
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~-T--Q-------------L~AFeEvg~~L-~RTsAACGFRWNs~VR 56 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGS-T--Q-------------LSAFEEVGRAL-NRTAAACGFRWNAYVR 56 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcch-H--H-------------HHHHHHHHHHH-cccHHHhcchHHHHHH
Confidence 4557999999999999999975211 1 1 13788999999 7999999999987663
No 42
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=91.46 E-value=0.21 Score=48.84 Aligned_cols=54 Identities=22% Similarity=0.399 Sum_probs=42.3
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcC
Q 035712 372 RGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQ 442 (563)
Q Consensus 372 KkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~ 442 (563)
+...||.|+|.+|.+.|.+|+..-+.- -.....++..| +|++-+|+.||...+.
T Consensus 4 rqdawt~e~d~llae~vl~~i~eg~tq----------------l~afe~~g~~L-~rt~aac~fRwNs~vr 57 (170)
T PRK13923 4 RQDAWTQERDGLLAEVVLRHIREGGTQ----------------LKAFEEVGDAL-KRTAAACGFRWNSVVR 57 (170)
T ss_pred hhhhhhhHHHHHHHHHHHHHHhccchH----------------HHHHHHHHHHH-hhhHHHHHhHHHHHHH
Confidence 557899999999999999997643321 12567788888 7999999999965553
No 43
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=90.32 E-value=0.46 Score=50.08 Aligned_cols=46 Identities=17% Similarity=0.401 Sum_probs=39.1
Q ss_pred CCCCCHHHHHHHHHHHHHh----------CChhHHHHhhh---C--CChhhHHHHHHHhhc
Q 035712 446 NRKWTPEELELVRKFHEKH----------GSNWKMLANAL---G--KHRFHVKDAWRRVRL 491 (563)
Q Consensus 446 KGkWT~EEDekLielV~ky----------Gn~W~~IAk~L---G--RT~~QCRdRWr~iL~ 491 (563)
...||.+|-..|+.+.... +..|..||..| | ||+.||+.+|.++..
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k 114 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKK 114 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 3789999999999988743 45899999966 4 999999999999963
No 44
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=90.03 E-value=0.32 Score=51.71 Aligned_cols=50 Identities=18% Similarity=0.386 Sum_probs=43.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccC
Q 035712 494 QKKGQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLT 560 (563)
Q Consensus 494 ikkG~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~ 560 (563)
+--..|+.+|+..|+++.. ..|. .+|..||..+|.|....|+.+|..+..
T Consensus 61 I~~e~WgadEEllli~~~~-------------TlGl----GNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 61 IGEEGWGADEELLLIECLD-------------TLGL----GNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred ccCCCcCchHHHHHHHHHH-------------hcCC----CcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 3445799999999999998 5554 599999999999999999999988754
No 45
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=90.00 E-value=0.35 Score=51.43 Aligned_cols=47 Identities=19% Similarity=0.420 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-hhHHHHhhhC-CChhhHHHHHHHhhc
Q 035712 445 ENRKWTPEELELVRKFHEKHGS-NWKMLANALG-KHRFHVKDAWRRVRL 491 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn-~W~~IAk~LG-RT~~QCRdRWr~iL~ 491 (563)
---.|+..|+-.|++.....|- +|.-||.++| |+...|+++|..++.
T Consensus 62 ~~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 62 GEEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred cCCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 4458999999999999999998 9999999996 999999999998865
No 46
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=88.48 E-value=1.8 Score=48.07 Aligned_cols=91 Identities=18% Similarity=0.310 Sum_probs=66.9
Q ss_pred CCHH---HHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHH-----HhHCCCCCHHHHHHHHHHhcCCCCCC
Q 035712 376 FSKE---EDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEI-----GSALPWRPYDSIYYRAHIIFQRDENR 447 (563)
Q Consensus 376 WT~E---EDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~I-----A~~LPgRs~kqcy~Rwrr~L~p~kKG 447 (563)
|++- .|..|.+.|..-...||+..+++..|| +|..- -..|+.|+. ...
T Consensus 133 Wsp~~~i~D~kL~EYI~~A~~rY~i~ieqAL~iL----------~~h~~d~d~A~~~l~rr~~--------------~~d 188 (534)
T KOG1194|consen 133 WSPPLEIQDDKLEEYISEAKERYGIPIEQALFIL----------FWHKHDFDLAHADLARRTE--------------FPD 188 (534)
T ss_pred ecCcccCcHHHHHHHHHHHHHhcCCcHHHHHHHH----------HhhcccchHHHHHHhhcCC--------------Ccc
Confidence 6543 355888888888888999877766555 34322 111222221 347
Q ss_pred CCCHHHHHHHHHHHHHhCChhHHHHhhh-CCChhhHHHHHHHhh
Q 035712 448 KWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRVR 490 (563)
Q Consensus 448 kWT~EEDekLielV~kyGn~W~~IAk~L-GRT~~QCRdRWr~iL 490 (563)
.||.||--++-.++..||.++..|-++| -|+-..+...|+...
T Consensus 189 ~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqyYy~~K 232 (534)
T KOG1194|consen 189 EWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQYYYSWK 232 (534)
T ss_pred cchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHHHHHHH
Confidence 9999999999999999999999999999 799888888777664
No 47
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=87.85 E-value=0.93 Score=47.84 Aligned_cols=56 Identities=27% Similarity=0.373 Sum_probs=41.1
Q ss_pred CCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcC----CCCHHHHHHHHHhcc
Q 035712 496 KGQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLA----TRSNAICCMKWYDQL 559 (563)
Q Consensus 496 kG~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~Lg----tRS~~QCR~RW~~iL 559 (563)
...|+.+|...||.+-.+...... .+.. ..--|..||..|. .||+.||+.||.++.
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~-------~~~~-k~~~We~va~k~~~~g~~rs~~qck~K~~nl~ 113 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALR-------RGKL-KGPLWEEVARKMAELGYPRSPKQCKAKIENLK 113 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHH-------hhhh-cccHHHHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 368999999999999985332211 1111 1257999999774 699999999999865
No 48
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=83.65 E-value=2.2 Score=32.75 Aligned_cols=40 Identities=28% Similarity=0.344 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 451 PEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 451 ~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
|+.+..++.++-..|-.|..||..+|.|...|+.+.++.+
T Consensus 12 ~~~~r~i~~l~~~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 12 PERQREIFLLRYFQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp -HHHHHHHHHHHTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4778888999999999999999999999999999887654
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=83.64 E-value=2.7 Score=38.84 Aligned_cols=47 Identities=13% Similarity=0.283 Sum_probs=37.7
Q ss_pred CCCCCCCHHHHHHHHHHHHHhCC----hhHHHHhhh-------------CCChhhHHHHHHHhh
Q 035712 444 DENRKWTPEELELVRKFHEKHGS----NWKMLANAL-------------GKHRFHVKDAWRRVR 490 (563)
Q Consensus 444 ~kKGkWT~EEDekLielV~kyGn----~W~~IAk~L-------------GRT~~QCRdRWr~iL 490 (563)
+.+..||++||.-|+-++.+||- .|..|-..+ .||+..+..|...++
T Consensus 47 ~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~tLi 110 (118)
T PF09111_consen 47 NKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNTLI 110 (118)
T ss_dssp SS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHHHH
Confidence 46789999999999999999998 999998763 388888888877665
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=82.68 E-value=2.8 Score=35.59 Aligned_cols=55 Identities=11% Similarity=0.232 Sum_probs=39.3
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCC-CccchhhhhcccCCCcccccHHHHHhHCCC-----CCHHHHHHHHHHh
Q 035712 375 RFSKEEDEMIKRAVMNYIETHGL-GEEGLNMVLHCRSHPEVKHCWKEIGSALPW-----RPYDSIYYRAHII 440 (563)
Q Consensus 375 kWT~EEDeiL~kaV~ky~~~hGl-see~L~~ll~s~r~~e~k~~Wk~IA~~LPg-----Rs~kqcy~Rwrr~ 440 (563)
.||++.++.|..++.+.....+. +...|. ...|..|+..|.. .+..||..||..+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk-----------~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFK-----------KEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcC-----------HHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999999888766555 333332 3479999877632 5667888887654
No 51
>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=82.18 E-value=2.4 Score=36.08 Aligned_cols=56 Identities=16% Similarity=0.259 Sum_probs=39.0
Q ss_pred CCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcC-----CCCHHHHHHHHHhc
Q 035712 498 QWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLA-----TRSNAICCMKWYDQ 558 (563)
Q Consensus 498 ~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~Lg-----tRS~~QCR~RW~~i 558 (563)
.||++.+..|++++.+....-.. ..+......-|..|+..|- ..+..||++||..+
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~-----~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~l 61 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNR-----PTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKTL 61 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCC-----CCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHHH
Confidence 59999999999999753321111 0122334567999999983 57889999998764
No 52
>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=81.21 E-value=3.6 Score=31.23 Aligned_cols=37 Identities=22% Similarity=0.317 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHhCC-hhHHHHhhhCCChhhHHHHHHHh
Q 035712 453 ELELVRKFHEKHGS-NWKMLANALGKHRFHVKDAWRRV 489 (563)
Q Consensus 453 EDekLielV~kyGn-~W~~IAk~LGRT~~QCRdRWr~i 489 (563)
=|..|+.+...-|. .|..||+.+|=|+..|..|++.+
T Consensus 4 ~D~~Il~~Lq~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 4 LDRKILRLLQEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HHHHHHHHHHH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 46778888887787 99999999999999999999865
No 53
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=80.07 E-value=2.4 Score=46.19 Aligned_cols=43 Identities=21% Similarity=0.401 Sum_probs=39.4
Q ss_pred CCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHh
Q 035712 497 GQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYD 557 (563)
Q Consensus 497 G~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~ 557 (563)
.+||..|-.++..|+. ..| +.++.||..||+|++.|++.+|.+
T Consensus 366 ~~Ws~~e~ekFYKALs-------------~wG-----tdF~LIs~lfP~R~RkqIKaKfi~ 408 (507)
T COG5118 366 LRWSKKEIEKFYKALS-------------IWG-----TDFSLISSLFPNRERKQIKAKFIK 408 (507)
T ss_pred CcccHHHHHHHHHHHH-------------Hhc-----chHHHHHHhcCchhHHHHHHHHHH
Confidence 4799999999999998 667 799999999999999999999865
No 54
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=78.97 E-value=2.8 Score=45.75 Aligned_cols=69 Identities=20% Similarity=0.399 Sum_probs=56.6
Q ss_pred CCCCCCHHHHHHHHHHHHHhCChhHHHHhhh-CCChhhHHHHHHHhh--ccc------CCCCCCCHHHHHHHHHHHHh
Q 035712 445 ENRKWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRVR--LPN------QKKGQWSQEEYQKLFDLVNM 513 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn~W~~IAk~L-GRT~~QCRdRWr~iL--~p~------ikkG~WTqEED~kLielV~e 513 (563)
+.-+||.+|-++...+...+|.++..||.++ .|...||+.+|.+-- +|. ..+-++.++|+-.|...+.+
T Consensus 364 ~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaKfi~Eek~nP~rIn~aL~~kkp~d~~eY~k~~~~~~e 441 (507)
T COG5118 364 GALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEEKVNPERINEALNEKKPFDQVEYNKLRSYLLE 441 (507)
T ss_pred CCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHHHHHHhhhCHHHHHHHHhccCCCCHHHHhhHHHHHHH
Confidence 5579999999999999999999999999999 899999999997653 221 24568889998876665553
No 55
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=77.40 E-value=12 Score=45.79 Aligned_cols=164 Identities=15% Similarity=0.220 Sum_probs=96.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcCCCCCCCCCH
Q 035712 372 RGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQRDENRKWTP 451 (563)
Q Consensus 372 KkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p~kKGkWT~ 451 (563)
...+.|.+|.+.-.+++.+- -..|+..+|..++.... .-.+.+...||..|.+.+...|..+..-.+.+... -
T Consensus 804 ~~~~lt~~e~~~k~~l~~~g--f~~w~~~~f~~f~~~~~-~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~~~----~ 876 (1033)
T PLN03142 804 PGDPLTAEEQEEKEQLLEEG--FSTWSRRDFNAFIRACE-KYGRNDIKSIASEMEGKTEEEVERYAKVFWERYKE----L 876 (1033)
T ss_pred cCCCCCHHHHHHHHHHHhcC--cCcccHHHHHHHHHHHH-HhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhhhh----h
Confidence 34578888877776665432 23455556665554321 11245899999999999999987665555433211 1
Q ss_pred HHHHHHHHHHHHhCC---hhHHHHhhhCCChhhHHHHHHHhh--cccCCCCCCCHHHHHHHHHHHHhHHHHHHHHHHhhh
Q 035712 452 EELELVRKFHEKHGS---NWKMLANALGKHRFHVKDAWRRVR--LPNQKKGQWSQEEYQKLFDLVNMDLRMRALEEKKTK 526 (563)
Q Consensus 452 EEDekLielV~kyGn---~W~~IAk~LGRT~~QCRdRWr~iL--~p~ikkG~WTqEED~kLielV~e~Lr~k~~~e~k~~ 526 (563)
.+-++++.-++.--. .=..+...|.+--.+|.+-|..+. .+..+.-.+|.+||+-|+-.+. .
T Consensus 877 ~~~~~~~~~ie~~e~~~~~~~~~~~~~~~k~~~~~~p~~~l~~~~~~~~~~~~~~~~d~~~~~~~~-------------~ 943 (1033)
T PLN03142 877 NDYDRIIKNIERGEARISRKDEIMKAIGKKLDRYKNPWLELKIQYGQNKGKLYNEECDRFMLCMVH-------------K 943 (1033)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCcHHHceeecCCCCCCcCCHHHHHHHHHHHH-------------H
Confidence 222333333332211 222233333444556666777664 2233444699999999999998 5
Q ss_pred cCCCCCCCChHHHHhHc------------CCCCHHHHHHHHHhcc
Q 035712 527 HGMLRDNISWEAISDKL------------ATRSNAICCMKWYDQL 559 (563)
Q Consensus 527 ~G~~~d~IsWs~IS~~L------------gtRS~~QCR~RW~~iL 559 (563)
+|. -+|..|-..+ .+||+..+..|=..+|
T Consensus 944 ~g~----~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~ 984 (1033)
T PLN03142 944 LGY----GNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLI 984 (1033)
T ss_pred hcc----chHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHH
Confidence 663 2598885443 2688888887766554
No 56
>smart00595 MADF subfamily of SANT domain.
Probab=73.80 E-value=4.5 Score=34.00 Aligned_cols=24 Identities=29% Similarity=0.678 Sum_probs=22.3
Q ss_pred hhHHHHhhhCCChhhHHHHHHHhh
Q 035712 467 NWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 467 ~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
.|..||..||-|..+|+.+|.++-
T Consensus 29 aW~~Ia~~l~~~~~~~~~kw~~LR 52 (89)
T smart00595 29 AWEEIAEELGLSVEECKKRWKNLR 52 (89)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHHH
Confidence 699999999999999999999884
No 57
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=69.48 E-value=7.3 Score=43.54 Aligned_cols=42 Identities=19% Similarity=0.258 Sum_probs=37.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHH
Q 035712 374 KRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAH 438 (563)
Q Consensus 374 GkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwr 438 (563)
-.||.||.-++.++...|++ .+.+|.+.||+|+..++..+|.
T Consensus 188 d~WT~Ed~vlFe~aF~~~GK-----------------------~F~kIrq~LP~rsLaSlvqyYy 229 (534)
T KOG1194|consen 188 DEWTAEDIVLFEQAFQFFGK-----------------------DFHKIRQALPHRSLASLVQYYY 229 (534)
T ss_pred ccchHHHHHHHHHHHHHhcc-----------------------cHHHHHHHccCccHHHHHHHHH
Confidence 36999999999999998865 8999999999999999877664
No 58
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=69.45 E-value=24 Score=31.46 Aligned_cols=79 Identities=11% Similarity=0.326 Sum_probs=50.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCC-CCHHHHHHHHHH-------hcCCCC
Q 035712 374 KRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPW-RPYDSIYYRAHI-------IFQRDE 445 (563)
Q Consensus 374 GkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPg-Rs~kqcy~Rwrr-------~L~p~k 445 (563)
.-||+++.-.|.+++..|...+|.+.. +....+...|...|.. =+..|++...++ ...+..
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~-----------~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k~~ 73 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQ-----------PDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKKSK 73 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCC-----------ccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhhcc
Confidence 359999999999999999999997521 1111244555555433 245566654443 333322
Q ss_pred CC---CCCHHHHHHHHHHHHH
Q 035712 446 NR---KWTPEELELVRKFHEK 463 (563)
Q Consensus 446 KG---kWT~EEDekLielV~k 463 (563)
.| .++..-|..+.+|..+
T Consensus 74 ~g~~~~~~~~hd~~~f~Lsk~ 94 (98)
T PF04504_consen 74 NGKDPSFSKPHDRRLFELSKK 94 (98)
T ss_pred cCcCCCCCCHhHHHHHHHHHH
Confidence 23 7888888888888653
No 59
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=68.64 E-value=9.4 Score=35.79 Aligned_cols=41 Identities=7% Similarity=0.007 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhCC-hhHHHHhhhCCChhhHHHHHHHhhcc
Q 035712 452 EELELVRKFHEKHGS-NWKMLANALGKHRFHVKDAWRRVRLP 492 (563)
Q Consensus 452 EEDekLielV~kyGn-~W~~IAk~LGRT~~QCRdRWr~iL~p 492 (563)
+-|..|+.+....|. .|+.||+.+|-|+..|+.|++.+...
T Consensus 9 ~~D~~Il~~Lq~d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 9 NLDRGILEALMENARTPYAELAKQFGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 468888888888888 99999999999999999999999753
No 60
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=68.37 E-value=3.9 Score=44.76 Aligned_cols=44 Identities=14% Similarity=0.323 Sum_probs=40.5
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHHhh-----h--CCChhhHHHHHHHhh
Q 035712 447 RKWTPEELELVRKFHEKHGSNWKMLANA-----L--GKHRFHVKDAWRRVR 490 (563)
Q Consensus 447 GkWT~EEDekLielV~kyGn~W~~IAk~-----L--GRT~~QCRdRWr~iL 490 (563)
..||.+|.+.|..|+..|--.|-.||.. + .||-..+++||+.+.
T Consensus 131 n~WskeETD~LF~lck~fDLRf~VIaDRyd~qq~~~sRTvEdLKeRyY~v~ 181 (445)
T KOG2656|consen 131 NSWSKEETDYLFDLCKRFDLRFFVIADRYDNQQYKKSRTVEDLKERYYSVC 181 (445)
T ss_pred ccccHHHHHHHHHHHHhcCeeEEEEeeccchhhccccccHHHHHHHHHHHH
Confidence 5899999999999999999999999987 4 399999999999885
No 61
>PF09197 Rap1-DNA-bind: Rap1, DNA-binding; InterPro: IPR015280 Members of this entry, which are predominantly found in the yeast protein Rap1, assume a secondary structure consisting of a three-helix bundle and an N-terminal arm. They contain an Arg-Asp-Arg-Lys sequence that interacts with an ACAregion in the 3, region of the DNA-binding site []. ; PDB: 1IGN_A 3UKG_A.
Probab=66.32 E-value=17 Score=33.21 Aligned_cols=67 Identities=10% Similarity=0.170 Sum_probs=39.1
Q ss_pred CCCHHHHHHHHHHHHHHHHH--cCCCccchhhhhc-cc-C----CCcccccHHHHHhHCCCCCHHHHHHHHHHhc
Q 035712 375 RFSKEEDEMIKRAVMNYIET--HGLGEEGLNMVLH-CR-S----HPEVKHCWKEIGSALPWRPYDSIYYRAHIIF 441 (563)
Q Consensus 375 kWT~EEDeiL~kaV~ky~~~--hGlsee~L~~ll~-s~-r----~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L 441 (563)
+||++||-.|..+|..|... ...+...-..++. .. . ......++..++...|..|..+=+.||+..+
T Consensus 1 kfTA~dDY~Lc~~i~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~fF~~~~~~~p~HT~~sWRDR~RKfv 75 (105)
T PF09197_consen 1 KFTADDDYALCKAIKKQFYRDIYQKDPDTGSSLISDGDSKEFIPKRDMRSFFKDLARKNPRHTENSWRDRYRKFV 75 (105)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHSB-TTSS-B----------------TTHHHHHHHHTTTS-HHHHHHHHHHTH
T ss_pred CCChHHHHHHHHHHHHHHHHHHHhhCcccccccccCCCccccccchhhHHHHHHHHHcCCccchhHHHHHHHHHH
Confidence 59999999999999877653 1111100000000 00 0 0012569999999999999999999999875
No 62
>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=61.13 E-value=20 Score=27.21 Aligned_cols=39 Identities=21% Similarity=0.206 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 452 EELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 452 EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
+++..++.++-..|..+..||..||-|...|+.+....+
T Consensus 7 ~~er~vi~~~y~~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 7 PREREVIRLRYFEGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp HHHHHHHHHHHTST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 344555555556677999999999999999998877765
No 63
>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=60.90 E-value=7.8 Score=33.50 Aligned_cols=22 Identities=36% Similarity=0.771 Sum_probs=12.8
Q ss_pred CCCCCCCHHHHHHH--------HHHHHHhC
Q 035712 444 DENRKWTPEELELV--------RKFHEKHG 465 (563)
Q Consensus 444 ~kKGkWT~EEDekL--------ielV~kyG 465 (563)
+..|-||+|+|..| ..|+.+||
T Consensus 45 n~~GiWT~eDD~~L~~~~~~~~~~L~~khG 74 (87)
T PF11626_consen 45 NMPGIWTPEDDEMLRSGDKDDIERLIKKHG 74 (87)
T ss_dssp T-TT---HHHHHHHTS--HHHHHHHHHHH-
T ss_pred CCCCCcCHHHHHHHHcCCHHHHHHHHHHhC
Confidence 57899999999999 34555665
No 64
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=60.78 E-value=14 Score=35.15 Aligned_cols=42 Identities=14% Similarity=0.045 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHhCC-hhHHHHhhhCCChhhHHHHHHHhhcc
Q 035712 451 PEELELVRKFHEKHGS-NWKMLANALGKHRFHVKDAWRRVRLP 492 (563)
Q Consensus 451 ~EEDekLielV~kyGn-~W~~IAk~LGRT~~QCRdRWr~iL~p 492 (563)
.+-|.+|+.+....|. .|+.||+.+|-|+..|+.|++++...
T Consensus 13 D~~D~~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 13 DRIDRNILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQ 55 (164)
T ss_pred HHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 4567888888888887 99999999999999999999999754
No 65
>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=56.65 E-value=14 Score=35.87 Aligned_cols=41 Identities=32% Similarity=0.443 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHHHHhCChhHHHHhhhC-CChhhHHHHHHHh
Q 035712 448 KWTPEELELVRKFHEKHGSNWKMLANALG-KHRFHVKDAWRRV 489 (563)
Q Consensus 448 kWT~EEDekLielV~kyGn~W~~IAk~LG-RT~~QCRdRWr~i 489 (563)
.||.|..+.|.+|. .-|..=..||..|| .|.+.|.-+.+++
T Consensus 2 ~Wtde~~~~L~~lw-~~G~SasqIA~~lg~vsRnAViGk~hRl 43 (162)
T PF07750_consen 2 SWTDERVERLRKLW-AEGLSASQIARQLGGVSRNAVIGKAHRL 43 (162)
T ss_pred CCCHHHHHHHHHHH-HcCCCHHHHHHHhCCcchhhhhhhhhcc
Confidence 59999999999998 56888999999997 9999999888876
No 66
>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=55.01 E-value=10 Score=30.82 Aligned_cols=24 Identities=29% Similarity=0.649 Sum_probs=21.2
Q ss_pred hhHHHHhhhC--CChhhHHHHHHHhh
Q 035712 467 NWKMLANALG--KHRFHVKDAWRRVR 490 (563)
Q Consensus 467 ~W~~IAk~LG--RT~~QCRdRWr~iL 490 (563)
.|..||..|| -+..+|+.+|.++.
T Consensus 28 aw~~Ia~~l~~~~~~~~~~~~w~~Lr 53 (85)
T PF10545_consen 28 AWQEIARELGKEFSVDDCKKRWKNLR 53 (85)
T ss_pred HHHHHHHHHccchhHHHHHHHHHHHH
Confidence 6999999997 68889999999874
No 67
>smart00595 MADF subfamily of SANT domain.
Probab=54.53 E-value=11 Score=31.55 Aligned_cols=23 Identities=30% Similarity=0.741 Sum_probs=21.4
Q ss_pred ChHHHHhHcCCCCHHHHHHHHHhc
Q 035712 535 SWEAISDKLATRSNAICCMKWYDQ 558 (563)
Q Consensus 535 sWs~IS~~LgtRS~~QCR~RW~~i 558 (563)
-|..||..|+. +...|+.+|.++
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~L 51 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKNL 51 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHHH
Confidence 79999999987 999999999886
No 68
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=51.58 E-value=25 Score=31.48 Aligned_cols=36 Identities=17% Similarity=0.157 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 455 ELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 455 ekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..++.+.-..|-.+..||..||.|...|+.++.+.+
T Consensus 119 r~il~l~~~~~~~~~eIA~~lgis~~tv~~~~~ra~ 154 (161)
T TIGR02985 119 RKIFILSRFEGKSYKEIAEELGISVKTVEYHISKAL 154 (161)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 334444344588999999999999999999988764
No 69
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=44.80 E-value=50 Score=25.04 Aligned_cols=37 Identities=16% Similarity=0.264 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHh
Q 035712 503 EYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYD 557 (563)
Q Consensus 503 ED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~ 557 (563)
=|..|+.+++ ..|. .+|.+||..+| =|...|..|+..
T Consensus 4 ~D~~Il~~Lq-------------~d~r----~s~~~la~~lg-lS~~~v~~Ri~r 40 (42)
T PF13404_consen 4 LDRKILRLLQ-------------EDGR----RSYAELAEELG-LSESTVRRRIRR 40 (42)
T ss_dssp HHHHHHHHHH-------------H-TT----S-HHHHHHHHT-S-HHHHHHHHHH
T ss_pred HHHHHHHHHH-------------HcCC----ccHHHHHHHHC-cCHHHHHHHHHH
Confidence 3778888887 3343 79999999998 678888888765
No 70
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=43.29 E-value=45 Score=31.27 Aligned_cols=42 Identities=2% Similarity=0.077 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccCC
Q 035712 502 EEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLTS 561 (563)
Q Consensus 502 EED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~p 561 (563)
+-|.+|+.+++ ..|- ++|++||+.++ -|...|+.||..+...
T Consensus 9 ~~D~~Il~~Lq-------------~d~R----~s~~eiA~~lg-lS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 9 NLDRGILEALM-------------ENAR----TPYAELAKQFG-VSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHHHHHHHHHH-------------HcCC----CCHHHHHHHHC-cCHHHHHHHHHHHHHC
Confidence 46888999998 4443 79999999997 7889999999887654
No 71
>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=43.28 E-value=35 Score=31.59 Aligned_cols=51 Identities=24% Similarity=0.457 Sum_probs=33.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhH------------CCCCCHHHHHHHHHH
Q 035712 372 RGKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSA------------LPWRPYDSIYYRAHI 439 (563)
Q Consensus 372 KkGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~------------LPgRs~kqcy~Rwrr 439 (563)
++..||.+||..|.-.+..| |++.+ +.|..|... |-.||+..+..|+..
T Consensus 48 ~~k~yseeEDRfLl~~~~~~----G~~~~---------------~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~t 108 (118)
T PF09111_consen 48 KKKVYSEEEDRFLLCMLYKY----GYDAE---------------GNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNT 108 (118)
T ss_dssp S-SSS-HHHHHHHHHHHHHH----TTTST---------------THHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHH
T ss_pred CCCCcCcHHHHHHHHHHHHh----CCCCC---------------chHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHH
Confidence 55689999999998888777 55321 256666432 124999999999887
Q ss_pred hc
Q 035712 440 IF 441 (563)
Q Consensus 440 ~L 441 (563)
++
T Consensus 109 Li 110 (118)
T PF09111_consen 109 LI 110 (118)
T ss_dssp HH
T ss_pred HH
Confidence 65
No 72
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=39.88 E-value=45 Score=32.10 Aligned_cols=29 Identities=28% Similarity=0.284 Sum_probs=25.3
Q ss_pred HHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 462 EKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 462 ~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
.-.|-.|.+||..||-|+..|+.+|+.+-
T Consensus 148 ~~~Gls~~EIA~~lgiS~~tV~r~l~~aR 176 (185)
T PF07638_consen 148 FFEGLSVEEIAERLGISERTVRRRLRRAR 176 (185)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34588999999999999999999998763
No 73
>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=39.34 E-value=50 Score=31.73 Aligned_cols=45 Identities=22% Similarity=0.412 Sum_probs=36.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhCChhHHHHhhh--C---CChhhHHHHHHHh
Q 035712 445 ENRKWTPEELELVRKFHEKHGSNWKMLANAL--G---KHRFHVKDAWRRV 489 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn~W~~IAk~L--G---RT~~QCRdRWr~i 489 (563)
...+-|+.|..-|..|+.+||.++..+|.-. + .|+.||+.+...+
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 4467899999999999999999999998754 2 6888888776654
No 74
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=38.85 E-value=53 Score=31.21 Aligned_cols=43 Identities=16% Similarity=0.182 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhHcCCCCHHHHHHHHHhccCC
Q 035712 501 QEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDKLATRSNAICCMKWYDQLTS 561 (563)
Q Consensus 501 qEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~LgtRS~~QCR~RW~~iL~p 561 (563)
.+-|.+|+.+++ ..|- ++|++||+.++ =|...|+.||..+...
T Consensus 13 D~~D~~IL~~Lq-------------~d~R----~s~~eiA~~lg-lS~~tv~~Ri~rL~~~ 55 (164)
T PRK11169 13 DRIDRNILNELQ-------------KDGR----ISNVELSKRVG-LSPTPCLERVRRLERQ 55 (164)
T ss_pred HHHHHHHHHHhc-------------cCCC----CCHHHHHHHHC-cCHHHHHHHHHHHHHC
Confidence 345888999888 4553 79999999997 7888899999887643
No 75
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=38.73 E-value=40 Score=29.35 Aligned_cols=30 Identities=13% Similarity=0.329 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhCChhHHHHhhhCCChhhHH
Q 035712 454 LELVRKFHEKHGSNWKMLANALGKHRFHVK 483 (563)
Q Consensus 454 DekLielV~kyGn~W~~IAk~LGRT~~QCR 483 (563)
|+.|..+....|.+|..+|..||=|..+|.
T Consensus 2 ~~~L~~la~~LG~~W~~Lar~Lgls~~~I~ 31 (83)
T cd08319 2 DRELNQLAQRLGPEWEQVLLDLGLSQTDIY 31 (83)
T ss_pred HHHHHHHHHHHhhhHHHHHHHcCCCHHHHH
Confidence 567889999999999999999996655543
No 76
>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=38.71 E-value=46 Score=28.29 Aligned_cols=36 Identities=22% Similarity=0.394 Sum_probs=25.0
Q ss_pred HHHHHHHHhCC--------hhHHHHhhhCC------ChhhHHHHHHHhhc
Q 035712 456 LVRKFHEKHGS--------NWKMLANALGK------HRFHVKDAWRRVRL 491 (563)
Q Consensus 456 kLielV~kyGn--------~W~~IAk~LGR------T~~QCRdRWr~iL~ 491 (563)
.|-.+|..+|. .|..||..||= ++.+++..|..+|.
T Consensus 40 ~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~ 89 (92)
T PF01388_consen 40 KLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLL 89 (92)
T ss_dssp HHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTH
T ss_pred HHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhH
Confidence 44555555553 69999999962 13678888888874
No 77
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=38.65 E-value=67 Score=27.75 Aligned_cols=41 Identities=17% Similarity=0.109 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHhCC-hhHHHHhhhCCChhhHHHHHHHhhcc
Q 035712 452 EELELVRKFHEKHGS-NWKMLANALGKHRFHVKDAWRRVRLP 492 (563)
Q Consensus 452 EEDekLielV~kyGn-~W~~IAk~LGRT~~QCRdRWr~iL~p 492 (563)
+-|..|+.+....|. .|..||+.+|-++..|+.++..+...
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKVGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 457778888888776 99999999999999999999998653
No 78
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=38.41 E-value=1.3e+02 Score=29.23 Aligned_cols=51 Identities=16% Similarity=0.184 Sum_probs=38.1
Q ss_pred HHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhhcccCCCCCCCHHHHHHHHHHHH
Q 035712 455 ELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVRLPNQKKGQWSQEEYQKLFDLVN 512 (563)
Q Consensus 455 ekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL~p~ikkG~WTqEED~kLielV~ 512 (563)
+.|+.+=..-|-.|..||+.+|++..-+..-.+ ....-+.++-.+|.+++.
T Consensus 11 ~~Ll~AK~~KGLTwe~IAe~iG~sevwvaaa~l-------GQ~~ls~e~A~kla~lLg 61 (150)
T TIGR00673 11 DALLESKKKKGLTFADIADGLGLAEVFVAAALY-------GQAAAPADEARLVGAKLD 61 (150)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHh-------CCCCCCHHHHHHHHHHhC
Confidence 467777778899999999999999875554332 233467888888888775
No 79
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=37.88 E-value=45 Score=25.24 Aligned_cols=37 Identities=27% Similarity=0.460 Sum_probs=19.1
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHH
Q 035712 447 RKWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKD 484 (563)
Q Consensus 447 GkWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRd 484 (563)
..||++|-..|..++ .-|..-..||..|||++..|..
T Consensus 3 ~~Lt~~eR~~I~~l~-~~G~s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 3 KHLTPEERNQIEALL-EQGMSIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp ---------HHHHHH-CS---HHHHHHHTT--HHHHHH
T ss_pred cchhhhHHHHHHHHH-HcCCCHHHHHHHHCcCcHHHHH
Confidence 368888888888775 4678999999999999988864
No 80
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=37.65 E-value=45 Score=39.59 Aligned_cols=45 Identities=18% Similarity=0.250 Sum_probs=40.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCChhHHHHhhh-CCChhhHHHHHHHh
Q 035712 445 ENRKWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRV 489 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn~W~~IAk~L-GRT~~QCRdRWr~i 489 (563)
....||+-|-.++..+.-.|-.++-.|+.++ +.|-.||-..|+.-
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVeyYYtW 663 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEYYYTW 663 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHHHHHH
Confidence 4569999999999999999999999999999 99999998776654
No 81
>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=36.57 E-value=36 Score=29.39 Aligned_cols=25 Identities=32% Similarity=0.551 Sum_probs=13.3
Q ss_pred CCCCCCHHHHHHH----HHHHHHHHHHcC
Q 035712 372 RGKRFSKEEDEMI----KRAVMNYIETHG 396 (563)
Q Consensus 372 KkGkWT~EEDeiL----~kaV~ky~~~hG 396 (563)
-.|-||+++|+.| ...+.+....||
T Consensus 46 ~~GiWT~eDD~~L~~~~~~~~~~L~~khG 74 (87)
T PF11626_consen 46 MPGIWTPEDDEMLRSGDKDDIERLIKKHG 74 (87)
T ss_dssp -TT---HHHHHHHTS--HHHHHHHHHHH-
T ss_pred CCCCcCHHHHHHHHcCCHHHHHHHHHHhC
Confidence 4579999999999 444444444444
No 82
>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=35.08 E-value=98 Score=23.07 Aligned_cols=36 Identities=28% Similarity=0.350 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHH
Q 035712 453 ELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRR 488 (563)
Q Consensus 453 EDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~ 488 (563)
|-..|..+...+|.+....|+.||=++..++.+...
T Consensus 6 E~~~i~~aL~~~~gn~~~aA~~Lgisr~tL~~klkk 41 (42)
T PF02954_consen 6 EKQLIRQALERCGGNVSKAARLLGISRRTLYRKLKK 41 (42)
T ss_dssp HHHHHHHHHHHTTT-HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHCCCHHHHHHHHHh
Confidence 667888999999999999999999888888776543
No 83
>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=34.88 E-value=51 Score=28.68 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhCChhHHHHhhhCCChhhHH
Q 035712 454 LELVRKFHEKHGSNWKMLANALGKHRFHVK 483 (563)
Q Consensus 454 DekLielV~kyGn~W~~IAk~LGRT~~QCR 483 (563)
|..|..+....|.+|..+|..||=+...+.
T Consensus 4 d~~l~~ia~~LG~dW~~LA~eLg~s~~dI~ 33 (84)
T cd08803 4 DIRMAIVADHLGLSWTELARELNFSVDEIN 33 (84)
T ss_pred HHHHHHHHHHhhccHHHHHHHcCCCHHHHH
Confidence 567888889999999999999997766554
No 84
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=34.62 E-value=2.2e+02 Score=29.27 Aligned_cols=53 Identities=17% Similarity=0.207 Sum_probs=37.2
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhhc---ccCCCCCCCHHHHHHHHHHHHhHH
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVRL---PNQKKGQWSQEEYQKLFDLVNMDL 515 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL~---p~ikkG~WTqEED~kLielV~e~L 515 (563)
-+|-.-..||..||.|...|+.+.++... ..........++...|+......+
T Consensus 122 ~~g~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~f~~a~ 177 (281)
T TIGR02957 122 VFDYPYEEIASIVGKSEANCRQLVSRARRHLDARRPRFEVSREESRQLLERFVEAA 177 (281)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHHHHHHH
Confidence 45779999999999999999988776642 222333466677776766665433
No 85
>KOG2656 consensus DNA methyltransferase 1-associated protein-1 [Chromatin structure and dynamics; Transcription]
Probab=34.54 E-value=31 Score=38.15 Aligned_cols=90 Identities=21% Similarity=0.275 Sum_probs=63.9
Q ss_pred ccHHHHHhHCCCCCHHHHHHHHHHhcCCCCC------------CCCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHH
Q 035712 416 HCWKEIGSALPWRPYDSIYYRAHIIFQRDEN------------RKWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVK 483 (563)
Q Consensus 416 ~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p~kK------------GkWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCR 483 (563)
..|.-+.-.-|.|.....++||.+.-++... -.+|.||.
T Consensus 74 ~~W~w~pFtn~aRkD~~~l~HWvr~~d~~~dypfakfNk~vdipsYt~eEY----------------------------- 124 (445)
T KOG2656|consen 74 RPWKWVPFTNSARKDDATLHHWVRVGDTPKDYPFAKFNKHVDIPSYTDEEY----------------------------- 124 (445)
T ss_pred CCceeeccCCccccCCceEEeeeeccCCCCCCchhhhccccCccccchHHH-----------------------------
Confidence 4677776666667777777888776443221 24455443
Q ss_pred HHHHHhhcccCCCCCCCHHHHHHHHHHHHhHHHHHHHHHHhhhcCCCCCCCChHHHHhH-----cCC-CCHHHHHHHHHh
Q 035712 484 DAWRRVRLPNQKKGQWSQEEYQKLFDLVNMDLRMRALEEKKTKHGMLRDNISWEAISDK-----LAT-RSNAICCMKWYD 557 (563)
Q Consensus 484 dRWr~iL~p~ikkG~WTqEED~kLielV~e~Lr~k~~~e~k~~~G~~~d~IsWs~IS~~-----Lgt-RS~~QCR~RW~~ 557 (563)
..+|. -..||.+|...|+++.+ .+. ..|-.|+.. +++ ||-...+.|||.
T Consensus 125 ---e~~l~----dn~WskeETD~LF~lck-------------~fD-----LRf~VIaDRyd~qq~~~sRTvEdLKeRyY~ 179 (445)
T KOG2656|consen 125 ---EAHLN----DNSWSKEETDYLFDLCK-------------RFD-----LRFFVIADRYDNQQYKKSRTVEDLKERYYS 179 (445)
T ss_pred ---HHhhc----cccccHHHHHHHHHHHH-------------hcC-----eeEEEEeeccchhhccccccHHHHHHHHHH
Confidence 33332 26799999999999998 454 689999988 565 999999999997
Q ss_pred cc
Q 035712 558 QL 559 (563)
Q Consensus 558 iL 559 (563)
+.
T Consensus 180 v~ 181 (445)
T KOG2656|consen 180 VC 181 (445)
T ss_pred HH
Confidence 54
No 86
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=33.60 E-value=76 Score=39.22 Aligned_cols=47 Identities=15% Similarity=0.200 Sum_probs=37.8
Q ss_pred CCCCCCHHHHHHHHHHHHHhCC-hhHHHHhhh-------------CCChhhHHHHHHHhhc
Q 035712 445 ENRKWTPEELELVRKFHEKHGS-NWKMLANAL-------------GKHRFHVKDAWRRVRL 491 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn-~W~~IAk~L-------------GRT~~QCRdRWr~iL~ 491 (563)
++..||.|||..|+-++.+||- +|..|-..+ .||+..+..|...++.
T Consensus 925 ~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~ 985 (1033)
T PLN03142 925 KGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIR 985 (1033)
T ss_pred CCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHH
Confidence 4556999999999999999996 899996653 3788888877776653
No 87
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=32.52 E-value=69 Score=38.15 Aligned_cols=42 Identities=7% Similarity=0.103 Sum_probs=36.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHH
Q 035712 374 KRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAH 438 (563)
Q Consensus 374 GkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwr 438 (563)
-.||+.|..+..+|+-.|-+ ++-.|+..+++.+..+|-.+|.
T Consensus 620 d~WTp~E~~lF~kA~y~~~K-----------------------DF~~v~km~~~KtVaqCVeyYY 661 (907)
T KOG4167|consen 620 DKWTPLERKLFNKALYTYSK-----------------------DFIFVQKMVKSKTVAQCVEYYY 661 (907)
T ss_pred ccccHHHHHHHHHHHHHhcc-----------------------cHHHHHHHhccccHHHHHHHHH
Confidence 47999999999999988843 8889999999999999966553
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=31.93 E-value=72 Score=27.56 Aligned_cols=42 Identities=29% Similarity=0.332 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 448 KWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 448 kWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..++.+-..| .++-..|-.+..||+.||=|+..|+.+....+
T Consensus 110 ~L~~~~~~ii-~~~~~~g~s~~eIA~~l~~s~~~v~~~~~~~~ 151 (158)
T TIGR02937 110 KLPEREREVL-VLRYLEGLSYKEIAEILGISVGTVKRRLKRAR 151 (158)
T ss_pred hCCHHHHHHH-hhHHhcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444444333 34334688999999999999999998888765
No 89
>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=31.66 E-value=1e+02 Score=21.99 Aligned_cols=41 Identities=24% Similarity=0.270 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHh
Q 035712 448 KWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRV 489 (563)
Q Consensus 448 kWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~i 489 (563)
.+++++- .++.++-..|..+..||..||=+...|+.+....
T Consensus 10 ~l~~~~~-~~~~~~~~~~~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 10 KLPERER-EVILLRFGEGLSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred hCCHHHH-HHHHHHHhcCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3555544 4444444577899999999998888887766554
No 90
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=31.09 E-value=1.1e+02 Score=27.21 Aligned_cols=67 Identities=21% Similarity=0.401 Sum_probs=46.2
Q ss_pred CCCCCHHHHHHHHHHHHHh----CC----hhHHHHhhh-C-----CChhhHHHHHHHhhcc------cCCCC---CCCHH
Q 035712 446 NRKWTPEELELVRKFHEKH----GS----NWKMLANAL-G-----KHRFHVKDAWRRVRLP------NQKKG---QWSQE 502 (563)
Q Consensus 446 KGkWT~EEDekLielV~ky----Gn----~W~~IAk~L-G-----RT~~QCRdRWr~iL~p------~ikkG---~WTqE 502 (563)
+..||++++-.|++.+..| |. +|..+-..+ + =|..|+.++.+++... ....| .++..
T Consensus 4 qR~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~KirrLK~Ky~~~~~k~~~g~~~~~~~~ 83 (98)
T PF04504_consen 4 QRLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKIRRLKKKYRNAVKKSKNGKDPSFSKP 83 (98)
T ss_pred cCCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHhhhcccCcCCCCCCH
Confidence 4579999999998877666 73 777766665 3 2677877776666321 12233 67888
Q ss_pred HHHHHHHHHH
Q 035712 503 EYQKLFDLVN 512 (563)
Q Consensus 503 ED~kLielV~ 512 (563)
-|+.++++-.
T Consensus 84 hd~~~f~Lsk 93 (98)
T PF04504_consen 84 HDRRLFELSK 93 (98)
T ss_pred hHHHHHHHHH
Confidence 8888888865
No 91
>smart00501 BRIGHT BRIGHT, ARID (A/T-rich interaction domain) domain. DNA-binding domain containing a helix-turn-helix structure
Probab=30.94 E-value=68 Score=27.63 Aligned_cols=27 Identities=30% Similarity=0.585 Sum_probs=20.3
Q ss_pred ChhHHHHhhhCCC------hhhHHHHHHHhhcc
Q 035712 466 SNWKMLANALGKH------RFHVKDAWRRVRLP 492 (563)
Q Consensus 466 n~W~~IAk~LGRT------~~QCRdRWr~iL~p 492 (563)
..|..||..||-. ..+++..|.++|.+
T Consensus 54 ~~W~~Va~~lg~~~~~~~~~~~lk~~Y~k~L~~ 86 (93)
T smart00501 54 KKWKEIARELGIPDTSTSAASSLRKHYERYLLP 86 (93)
T ss_pred CCHHHHHHHhCCCcccchHHHHHHHHHHHHhHH
Confidence 3799999999743 46778888887743
No 92
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=30.38 E-value=80 Score=28.93 Aligned_cols=31 Identities=23% Similarity=0.288 Sum_probs=24.9
Q ss_pred HHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 460 FHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 460 lV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
+.-..|..+..||..||-|...|+.+..+.+
T Consensus 139 l~~~~~~s~~eIA~~lgis~~tV~~~l~ra~ 169 (182)
T PRK09652 139 LREIEGLSYEEIAEIMGCPIGTVRSRIFRAR 169 (182)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3334578999999999999999988877664
No 93
>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=30.25 E-value=44 Score=27.11 Aligned_cols=26 Identities=23% Similarity=0.487 Sum_probs=21.8
Q ss_pred CChHHHHhHcC-CCCHHHHHHHHHhcc
Q 035712 534 ISWEAISDKLA-TRSNAICCMKWYDQL 559 (563)
Q Consensus 534 IsWs~IS~~Lg-tRS~~QCR~RW~~iL 559 (563)
--|..|+..|+ .-+...|+.+|.++.
T Consensus 27 ~aw~~Ia~~l~~~~~~~~~~~~w~~Lr 53 (85)
T PF10545_consen 27 EAWQEIARELGKEFSVDDCKKRWKNLR 53 (85)
T ss_pred HHHHHHHHHHccchhHHHHHHHHHHHH
Confidence 46999999998 467889999999864
No 94
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=29.74 E-value=87 Score=28.57 Aligned_cols=41 Identities=12% Similarity=0.084 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHhCC-hhHHHHhhhCCChhhHHHHHHHhhcc
Q 035712 452 EELELVRKFHEKHGS-NWKMLANALGKHRFHVKDAWRRVRLP 492 (563)
Q Consensus 452 EEDekLielV~kyGn-~W~~IAk~LGRT~~QCRdRWr~iL~p 492 (563)
+-|.+|+.+....|. .+..||+.+|-|+..|..|-+++...
T Consensus 8 ~~D~~IL~~L~~d~r~~~~eia~~lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 8 DIDRRILRLLQEDARISNAELAERVGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 446777777777777 99999999999999999999998653
No 95
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=28.15 E-value=75 Score=37.07 Aligned_cols=51 Identities=20% Similarity=0.253 Sum_probs=41.4
Q ss_pred cCCCCCCCCCHHHHHHHHHHHHHhCChhHHHHhhh-C----------CChhhHHHHHHHhhc
Q 035712 441 FQRDENRKWTPEELELVRKFHEKHGSNWKMLANAL-G----------KHRFHVKDAWRRVRL 491 (563)
Q Consensus 441 L~p~kKGkWT~EEDekLielV~kyGn~W~~IAk~L-G----------RT~~QCRdRWr~iL~ 491 (563)
|.-..+..||-.|......+..+||.++..|-..+ - .|-.|++.+|++.+.
T Consensus 83 Lkt~~ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~ 144 (782)
T KOG4468|consen 83 LKTWAKTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVR 144 (782)
T ss_pred cccccccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHH
Confidence 44345789999999999999999999999995444 2 467899999988864
No 96
>PF11198 DUF2857: Protein of unknown function (DUF2857); InterPro: IPR021364 This is a bacterial family of uncharacterised proteins.
Probab=28.02 E-value=2.6e+02 Score=27.44 Aligned_cols=60 Identities=18% Similarity=0.201 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhhcccCCCC---CCCHHHHHHHHHHHH
Q 035712 452 EELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVRLPNQKKG---QWSQEEYQKLFDLVN 512 (563)
Q Consensus 452 EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL~p~ikkG---~WTqEED~kLielV~ 512 (563)
++...++.-.-.+|-....+..+||-|+..|..| |.++.-..+.| .-|++++..|...-+
T Consensus 74 ~~~~~~idr~L~lGAS~~mm~~~FGls~~ev~~r-R~llgi~~~~GR~~~~~ee~~~~iW~~W~ 136 (180)
T PF11198_consen 74 QQEQQLIDRALRLGASIEMMQRLFGLSSAEVAAR-RRLLGIPVRKGRPPALSEEEEAAIWRRWQ 136 (180)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHH-HHHhCCCCCCCCCCCcCHHHHHHHHHHHH
Confidence 5567778888899999999999999999999875 55654334444 456777877777776
No 97
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=27.98 E-value=89 Score=28.54 Aligned_cols=28 Identities=32% Similarity=0.412 Sum_probs=23.9
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..|..+..||..||-|+..|+.++....
T Consensus 139 ~~~~~~~eIA~~lgis~~tv~~~~~ra~ 166 (179)
T PRK11924 139 VEGLSYREIAEILGVPVGTVKSRLRRAR 166 (179)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4577999999999999999998887764
No 98
>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=27.95 E-value=57 Score=27.80 Aligned_cols=29 Identities=24% Similarity=0.360 Sum_probs=23.1
Q ss_pred HHHHHHHHHHhCChhHHHHhhhCCChhhH
Q 035712 454 LELVRKFHEKHGSNWKMLANALGKHRFHV 482 (563)
Q Consensus 454 DekLielV~kyGn~W~~IAk~LGRT~~QC 482 (563)
|..|..+....|.+|..+|..||=+..++
T Consensus 4 ~~~l~~ia~~lG~dW~~LAr~Lg~~~~dI 32 (84)
T cd08317 4 DIRLADISNLLGSDWPQLARELGVSETDI 32 (84)
T ss_pred cchHHHHHHHHhhHHHHHHHHcCCCHHHH
Confidence 45677888888999999999998665443
No 99
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=27.13 E-value=91 Score=29.05 Aligned_cols=31 Identities=19% Similarity=0.066 Sum_probs=25.0
Q ss_pred HHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 460 FHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 460 lV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
+.-..|..+..||..||-|...|+.++++..
T Consensus 147 l~~~~~~s~~eIA~~lgis~~~v~~~l~Rar 177 (187)
T PRK09641 147 LKYIEDLSLKEISEILDLPVGTVKTRIHRGR 177 (187)
T ss_pred hHHhhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3334577999999999999999998877664
No 100
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=27.07 E-value=56 Score=37.86 Aligned_cols=45 Identities=27% Similarity=0.526 Sum_probs=41.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhCChhHHHHhhh-CCChhhHHHHHHHh
Q 035712 445 ENRKWTPEELELVRKFHEKHGSNWKMLANAL-GKHRFHVKDAWRRV 489 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn~W~~IAk~L-GRT~~QCRdRWr~i 489 (563)
..++||.+|-++.-.....+|.+.+.|+..+ +|+..|++.+|..-
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K~~~e 453 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAKFKKE 453 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHHHhhh
Confidence 4679999999999999999999999999999 89999999998754
No 101
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=26.52 E-value=98 Score=28.61 Aligned_cols=28 Identities=25% Similarity=0.182 Sum_probs=24.2
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..|.+...||..||-|...|+.++.+.+
T Consensus 133 ~~g~s~~eiA~~lgis~~tv~~~l~Ra~ 160 (169)
T TIGR02954 133 YHDLTIKEIAEVMNKPEGTVKTYLHRAL 160 (169)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4577999999999999999999888765
No 102
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=26.25 E-value=1e+02 Score=29.56 Aligned_cols=28 Identities=29% Similarity=0.171 Sum_probs=24.1
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
.+|..+..||..||-|...|+.|+.+.+
T Consensus 148 ~~g~s~~EIA~~lg~s~~tV~~rl~rar 175 (192)
T PRK09643 148 MQGYSVADAARMLGVAEGTVKSRCARGR 175 (192)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4577999999999999999999987664
No 103
>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=26.04 E-value=4.9e+02 Score=28.46 Aligned_cols=101 Identities=14% Similarity=0.256 Sum_probs=60.8
Q ss_pred CCCCCHHHHHHHHHHHHHh-CC---hhHHHHhhh-CCChhhHHHHHHHhhcccCCCCCCCHHHHHHHHHHHHhHHHHHHH
Q 035712 446 NRKWTPEELELVRKFHEKH-GS---NWKMLANAL-GKHRFHVKDAWRRVRLPNQKKGQWSQEEYQKLFDLVNMDLRMRAL 520 (563)
Q Consensus 446 KGkWT~EEDekLielV~ky-Gn---~W~~IAk~L-GRT~~QCRdRWr~iL~p~ikkG~WTqEED~kLielV~e~Lr~k~~ 520 (563)
...||.-|-..|+.+..-. |. +-..|++.| ||+..+|++--+.+. ...+.++++..-. -+.
T Consensus 21 p~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK-------------~rvareaiqkv~~-~g~ 86 (344)
T PF11035_consen 21 PAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLK-------------GRVAREAIQKVHP-GGL 86 (344)
T ss_pred cccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHH-------------HHHHHHHHHHhcc-ccc
Confidence 4689999999888877644 65 777899999 999999998665553 3445555542100 000
Q ss_pred HHHhhhcCCCCCCC-ChHHHHhHcCCCCHHHHHHHHHhccC
Q 035712 521 EEKKTKHGMLRDNI-SWEAISDKLATRSNAICCMKWYDQLT 560 (563)
Q Consensus 521 ~e~k~~~G~~~d~I-sWs~IS~~LgtRS~~QCR~RW~~iL~ 560 (563)
...+-........| -|..++..+.+.-....-.-|-++|+
T Consensus 87 ~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 87 KGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred ccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 00000000011111 49999999987777666666666553
No 104
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=25.34 E-value=3.6e+02 Score=27.71 Aligned_cols=51 Identities=20% Similarity=0.208 Sum_probs=34.0
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhhc---ccCCCCCCCHHHHHHHHHHHHh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVRL---PNQKKGQWSQEEYQKLFDLVNM 513 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL~---p~ikkG~WTqEED~kLielV~e 513 (563)
.+|-.-..||+.||.|...|+.+.++... .......-..++...|+.....
T Consensus 129 ~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~v~~f~~ 182 (293)
T PRK09636 129 VFGVPFDEIASTLGRSPAACRQLASRARKHVRAARPRFPVSDEEGAELVEAFFA 182 (293)
T ss_pred HhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHhhCCCCCCCchHHHHHHHHHHH
Confidence 34779999999999999999988776642 2222233455555555554443
No 105
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=25.21 E-value=1.2e+02 Score=27.52 Aligned_cols=37 Identities=16% Similarity=-0.022 Sum_probs=28.9
Q ss_pred HHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 454 LELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 454 DekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
...++.++...|-....||..||-|...|+.+..+.+
T Consensus 111 ~r~v~~l~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 147 (161)
T PRK09047 111 QREAFLLRYWEDMDVAETAAAMGCSEGSVKTHCSRAT 147 (161)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3444455555688999999999999999999887764
No 106
>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=24.94 E-value=88 Score=27.00 Aligned_cols=30 Identities=20% Similarity=0.283 Sum_probs=24.4
Q ss_pred HHHHHHHHHHhCChhHHHHhhhCCChhhHH
Q 035712 454 LELVRKFHEKHGSNWKMLANALGKHRFHVK 483 (563)
Q Consensus 454 DekLielV~kyGn~W~~IAk~LGRT~~QCR 483 (563)
+..|-.+....|.+|..+|..||=|...|.
T Consensus 4 ~~~l~~ia~~LG~dWk~LAr~Lg~se~dI~ 33 (84)
T cd08804 4 EERLAVIADHLGFSWTELARELDFTEEQIH 33 (84)
T ss_pred hhHHHHHHHHHhhhHHHHHHHcCCCHHHHH
Confidence 456778888999999999999997666554
No 107
>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=24.45 E-value=91 Score=29.13 Aligned_cols=28 Identities=18% Similarity=0.153 Sum_probs=23.9
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..|.++..||..||=|...|+.+.++.+
T Consensus 152 ~~~~s~~EIA~~lgis~~tv~~~l~rar 179 (190)
T TIGR02939 152 LEGLSYEDIARIMDCPVGTVRSRIFRAR 179 (190)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 3477999999999999999999887764
No 108
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=24.44 E-value=1.2e+02 Score=28.06 Aligned_cols=30 Identities=20% Similarity=0.050 Sum_probs=24.8
Q ss_pred HHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 461 HEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 461 V~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
.--+|-.-..||..||.+...|+.++++.+
T Consensus 130 ~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 159 (173)
T PRK09645 130 SYYRGWSTAQIAADLGIPEGTVKSRLHYAL 159 (173)
T ss_pred HHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 334577999999999999999998887764
No 109
>cd07178 terB_like_YebE tellurium resistance terB-like protein, subgroup 3. This family includes several uncharacterized bacterial proteins including an Escherichia coli protein called YebE. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=24.37 E-value=3.3e+02 Score=23.96 Aligned_cols=82 Identities=16% Similarity=0.101 Sum_probs=48.8
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcCCCCCCCCCHH
Q 035712 373 GKRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQRDENRKWTPE 452 (563)
Q Consensus 373 kGkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p~kKGkWT~E 452 (563)
.|.++.+|.+.|...+... +++.+.-..+...-..|. .=..|+..+++.......+++..+.. +..|+.
T Consensus 13 DG~id~~E~~~I~~~~~~~----~~~~~~~~~~~~~l~~p~---~~~~la~~~~~~~~a~~~y~~s~~~~----d~~s~a 81 (95)
T cd07178 13 DGHIDEAERARILGELGEA----GLDAEERAFLEAELAAPL---DPDALAAAVPDPELAAEVYAASLLAI----DPDTFA 81 (95)
T ss_pred cCCCCHHHHHHHHHHHHHh----CCCHHHHHHHHHHHHCCC---CHHHHHHHcCCHHHHHHHHHHHHHHH----cCCCHH
Confidence 4899999999998876655 444322111111111221 33388888876433333334443333 477999
Q ss_pred HHHHHHHHHHHhC
Q 035712 453 ELELVRKFHEKHG 465 (563)
Q Consensus 453 EDekLielV~kyG 465 (563)
|...|-++..-.|
T Consensus 82 E~~~L~~la~aLg 94 (95)
T cd07178 82 ERAYLDELAAALG 94 (95)
T ss_pred HHHHHHHHHHHhC
Confidence 9999999887665
No 110
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=24.18 E-value=1.8e+02 Score=25.73 Aligned_cols=44 Identities=18% Similarity=0.243 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHHhhhCC-ChhhHHHHHHHhh
Q 035712 446 NRKWTPEELELVRKFHEKHGSNWKMLANALGK-HRFHVKDAWRRVR 490 (563)
Q Consensus 446 KGkWT~EEDekLielV~kyGn~W~~IAk~LGR-T~~QCRdRWr~iL 490 (563)
..+||+|.-..+..++..-|..=..||..+|- ++.+++ +|...+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l~-~W~~~~ 49 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQLY-KWRIQL 49 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHHH-HHHHHH
Confidence 46899999999999999999999999999997 565555 555544
No 111
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.12 E-value=1.2e+02 Score=28.52 Aligned_cols=31 Identities=23% Similarity=0.101 Sum_probs=25.4
Q ss_pred HHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 460 FHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 460 lV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
|+...|-....||..||-|...|+.|..+.+
T Consensus 138 L~~~~g~s~~EIA~~lgis~~tVk~~l~rAl 168 (178)
T PRK12529 138 MATLDGMKQKDIAQALDIALPTVKKYIHQAY 168 (178)
T ss_pred HHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3334588999999999999999999887665
No 112
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=24.00 E-value=1.3e+02 Score=27.54 Aligned_cols=33 Identities=15% Similarity=-0.018 Sum_probs=26.0
Q ss_pred HHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 458 RKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 458 ielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
+.+.-..|-....||..||-|...|+.+..+.+
T Consensus 115 ~~l~~~~g~s~~EIA~~lgis~~tV~~~l~Rar 147 (160)
T PRK09642 115 VLAHYLEEKSYQEIALQEKIEVKTVEMKLYRAR 147 (160)
T ss_pred HHHHHHhCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 333344578999999999999999998877664
No 113
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=23.81 E-value=1.2e+02 Score=28.98 Aligned_cols=31 Identities=29% Similarity=0.252 Sum_probs=25.3
Q ss_pred HHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 460 FHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 460 lV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
+.-..|-.+..||..||-|...|+.+..+.+
T Consensus 117 l~~~~g~~~~EIA~~lgis~~tV~~~l~Rar 147 (181)
T PRK09637 117 LTELEGLSQKEIAEKLGLSLSGAKSRVQRGR 147 (181)
T ss_pred HHHhcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 3334578999999999999999998887764
No 114
>PRK01905 DNA-binding protein Fis; Provisional
Probab=23.67 E-value=3.1e+02 Score=23.05 Aligned_cols=40 Identities=23% Similarity=0.267 Sum_probs=32.2
Q ss_pred CHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHh
Q 035712 450 TPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRV 489 (563)
Q Consensus 450 T~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~i 489 (563)
..-|...|..++..+|.++...|+.||=++..++.+.+.+
T Consensus 35 ~~~E~~~i~~aL~~~~gn~s~aAr~LGIsrstL~rklkk~ 74 (77)
T PRK01905 35 SCVEKPLLEVVMEQAGGNQSLAAEYLGINRNTLRKKLQQH 74 (77)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHh
Confidence 3446778889999999999999999998877777666543
No 115
>PRK04217 hypothetical protein; Provisional
Probab=23.43 E-value=1.6e+02 Score=27.06 Aligned_cols=44 Identities=20% Similarity=0.058 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 446 NRKWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 446 KGkWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
-..-|+++ ..++.+....|-....||+.||-|...|+.+|+...
T Consensus 40 ~~~Lt~ee-reai~l~~~eGlS~~EIAk~LGIS~sTV~r~L~RAr 83 (110)
T PRK04217 40 PIFMTYEE-FEALRLVDYEGLTQEEAGKRMGVSRGTVWRALTSAR 83 (110)
T ss_pred cccCCHHH-HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45667777 577777777888999999999999999999988763
No 116
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=23.18 E-value=4.1e+02 Score=27.72 Aligned_cols=50 Identities=10% Similarity=0.118 Sum_probs=34.9
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh---cccCCCCCCCHHHHHHHHHHHH
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR---LPNQKKGQWSQEEYQKLFDLVN 512 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL---~p~ikkG~WTqEED~kLielV~ 512 (563)
-+|-.-..||..||.|...|+.+.++.. .........+.++...|+...-
T Consensus 132 ~~g~s~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~f~ 184 (290)
T PRK09635 132 IFGLPYQQIATTIGSQASTCRQLAHRARRKINESRIAASVEPAQHRVVTRAFI 184 (290)
T ss_pred HhCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHhhCCCCCCChHHHHHHHHHHH
Confidence 4577999999999999999998776654 2222223466777666666554
No 117
>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=23.13 E-value=3.8e+02 Score=29.32 Aligned_cols=87 Identities=23% Similarity=0.264 Sum_probs=61.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcCCCCCCCCCHHH
Q 035712 374 KRFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQRDENRKWTPEE 453 (563)
Q Consensus 374 GkWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~p~kKGkWT~EE 453 (563)
-.||.-|...|..+++.- .|-. ..+..+|+..|++|+...|......+-.+
T Consensus 22 ~~Ws~rEkr~Llr~Lqar---~g~~----------------epd~ael~~~l~~Rs~aEI~~fl~~LK~r---------- 72 (344)
T PF11035_consen 22 AAWSAREKRQLLRLLQAR---RGQP----------------EPDAAELAKELPGRSEAEIRDFLQQLKGR---------- 72 (344)
T ss_pred ccCcHHHHHHHHHHHHHh---cCCC----------------CcCHHHHHhhccCcCHHHHHHHHHHHHHH----------
Confidence 479999999998887642 2221 12778899999999999988766554322
Q ss_pred HHHHHHHHHH-h-----CC------------hhHHHHhhh-CCChhhHHHHHHHhhc
Q 035712 454 LELVRKFHEK-H-----GS------------NWKMLANAL-GKHRFHVKDAWRRVRL 491 (563)
Q Consensus 454 DekLielV~k-y-----Gn------------~W~~IAk~L-GRT~~QCRdRWr~iL~ 491 (563)
.+.+++.+ | |. -|..+|..+ |.....+-.-|.++|.
T Consensus 73 --vareaiqkv~~~g~~~~R~~e~q~paPIEvW~dla~k~tg~~ee~~t~afsq~l~ 127 (344)
T PF11035_consen 73 --VAREAIQKVHPGGLKGPRRREAQPPAPIEVWMDLAEKVTGPLEEALTAAFSQVLT 127 (344)
T ss_pred --HHHHHHHHhcccccccccccccCCCccHHHHHHHHHHhcCchHHHHHHHHHHHHH
Confidence 23333332 1 11 599999999 8888888888888874
No 118
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=23.00 E-value=1.3e+02 Score=28.80 Aligned_cols=28 Identities=7% Similarity=-0.060 Sum_probs=24.2
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
-.|-....||..||-|...|+.|.++.+
T Consensus 148 ~~g~s~~EIA~~lgis~~tVk~~l~RAr 175 (189)
T PRK12530 148 YLELSSEQICQECDISTSNLHVLLYRAR 175 (189)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3477999999999999999999877664
No 119
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=22.89 E-value=1.2e+02 Score=28.67 Aligned_cols=28 Identities=18% Similarity=0.144 Sum_probs=24.3
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..|-....||..||-|...|+.++++.+
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~~~l~Rar 179 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVRSRIFRAR 179 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3477999999999999999999988774
No 120
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=22.88 E-value=5.7e+02 Score=23.09 Aligned_cols=47 Identities=17% Similarity=0.235 Sum_probs=38.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 443 RDENRKWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 443 p~kKGkWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
+..+..||+|+-..++..+...|..=..||..+|=++.+++ +|.+..
T Consensus 7 ~~~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~tl~-~W~r~y 53 (121)
T PRK09413 7 PEKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAASQLF-LWRKQY 53 (121)
T ss_pred CCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHHHHH-HHHHHH
Confidence 44567899999999999888889999999999988666654 577664
No 121
>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=22.70 E-value=74 Score=30.86 Aligned_cols=43 Identities=19% Similarity=0.227 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhc
Q 035712 375 RFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIF 441 (563)
Q Consensus 375 kWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L 441 (563)
.||.|..+.|.++..+ |+ .-.+||..|.+.+..+|.-+.+++-
T Consensus 2 ~Wtde~~~~L~~lw~~-----G~-------------------SasqIA~~lg~vsRnAViGk~hRlg 44 (162)
T PF07750_consen 2 SWTDERVERLRKLWAE-----GL-------------------SASQIARQLGGVSRNAVIGKAHRLG 44 (162)
T ss_pred CCCHHHHHHHHHHHHc-----CC-------------------CHHHHHHHhCCcchhhhhhhhhccc
Confidence 4999999999888533 33 5689999997799999999888753
No 122
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=22.67 E-value=1.3e+02 Score=28.36 Aligned_cols=28 Identities=18% Similarity=0.126 Sum_probs=24.5
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..|-....||..||-|...|+.++.+.+
T Consensus 145 ~~~~s~~eIA~~lgis~~tV~~~l~Rar 172 (189)
T PRK12515 145 YHEKSVEEVGEIVGIPESTVKTRMFYAR 172 (189)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4577999999999999999999988775
No 123
>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=22.55 E-value=1.1e+02 Score=26.42 Aligned_cols=26 Identities=31% Similarity=0.544 Sum_probs=20.9
Q ss_pred HHHHHHHhCChhHHHHhhhCCChhhH
Q 035712 457 VRKFHEKHGSNWKMLANALGKHRFHV 482 (563)
Q Consensus 457 LielV~kyGn~W~~IAk~LGRT~~QC 482 (563)
|..+....|.+|..+|..||=+..+|
T Consensus 10 l~~ia~~iG~~Wk~Lar~LGls~~dI 35 (86)
T cd08318 10 ITVFANKLGEDWKTLAPHLEMKDKEI 35 (86)
T ss_pred HHHHHHHHhhhHHHHHHHcCCCHHHH
Confidence 33466778999999999999877766
No 124
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=22.37 E-value=1.4e+02 Score=27.77 Aligned_cols=33 Identities=15% Similarity=0.119 Sum_probs=25.8
Q ss_pred HHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 458 RKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 458 ielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
+.|....|-....||..||-+...|+.+..+-+
T Consensus 128 ~~L~~~~g~s~~EIA~~lgis~~tV~~~l~ra~ 160 (172)
T PRK12523 128 FLYNRLDGMGHAEIAERLGVSVSRVRQYLAQGL 160 (172)
T ss_pred HHHHHHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 333444588999999999999999998876654
No 125
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=22.27 E-value=1.1e+02 Score=25.52 Aligned_cols=29 Identities=28% Similarity=0.495 Sum_probs=21.9
Q ss_pred HHHHHHHHHH-hCChhHHHHhhhCCChhhH
Q 035712 454 LELVRKFHEK-HGSNWKMLANALGKHRFHV 482 (563)
Q Consensus 454 DekLielV~k-yGn~W~~IAk~LGRT~~QC 482 (563)
...|..++.. .|.+|..+|..||=+..++
T Consensus 5 ~~~~~~l~~~~~g~~W~~la~~Lg~~~~~i 34 (88)
T smart00005 5 REKLAKLLDHPLGLDWRELARKLGLSEADI 34 (88)
T ss_pred HHHHHHHHcCccchHHHHHHHHcCCCHHHH
Confidence 4566667766 7999999999998655444
No 126
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.03 E-value=1.2e+02 Score=28.21 Aligned_cols=27 Identities=22% Similarity=0.102 Sum_probs=23.1
Q ss_pred hCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 464 HGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 464 yGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
.|.....||..||-|...|+.+..+.+
T Consensus 151 ~g~s~~eIA~~lgis~~~v~~~l~Rar 177 (187)
T TIGR02948 151 EDLSLKEISEILDLPVGTVKTRIHRGR 177 (187)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 477999999999999999998887764
No 127
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=22.00 E-value=1.4e+02 Score=28.16 Aligned_cols=28 Identities=25% Similarity=0.111 Sum_probs=23.7
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..|..+..||..||-+...|+.+.++.+
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 180 (189)
T PRK09648 153 VVGLSAEETAEAVGSTPGAVRVAQHRAL 180 (189)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3477999999999999999998887664
No 128
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=21.94 E-value=1.5e+02 Score=23.94 Aligned_cols=45 Identities=18% Similarity=0.253 Sum_probs=33.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 445 ENRKWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 445 kKGkWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
....||+|+-..++..+...|.....||..+|=++.+++ +|....
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~~l~-~W~~~~ 47 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREYGISPSTLY-NWRKQY 47 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HHHHH-HHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeeccccccccccc-HHHHHH
Confidence 346899999999999998889999999999988666554 577665
No 129
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=21.87 E-value=1.4e+02 Score=28.49 Aligned_cols=28 Identities=14% Similarity=-0.043 Sum_probs=23.2
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..|-....||..||-|...|+.|.++.+
T Consensus 155 ~eg~s~~EIA~~lgis~~tVk~rl~ra~ 182 (194)
T PRK12531 155 LEELPHQQVAEMFDIPLGTVKSRLRLAV 182 (194)
T ss_pred HcCCCHHHHHHHhCcCHHHHHHHHHHHH
Confidence 3477899999999999999988877664
No 130
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=21.77 E-value=2.4e+02 Score=23.33 Aligned_cols=49 Identities=18% Similarity=0.316 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHHHhHCCCCCHHHHHHHHHHhcC
Q 035712 376 FSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEIGSALPWRPYDSIYYRAHIIFQ 442 (563)
Q Consensus 376 WT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~IA~~LPgRs~kqcy~Rwrr~L~ 442 (563)
.|+-..++ ..+|..|...+|... --.+||..|.-++..++..+...+-.
T Consensus 4 LT~rQ~~v-L~~I~~~~~~~G~~P-----------------t~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 4 LTERQKEV-LEFIREYIEENGYPP-----------------TVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp --HHHHHH-HHHHHHHHHHHSS--------------------HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred CCHHHHHH-HHHHHHHHHHcCCCC-----------------CHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 34444444 478899999899863 78899999987999999988876653
No 131
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=21.75 E-value=2.2e+02 Score=17.82 Aligned_cols=37 Identities=30% Similarity=0.400 Sum_probs=24.9
Q ss_pred CCCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHH
Q 035712 447 RKWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKD 484 (563)
Q Consensus 447 GkWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRd 484 (563)
..+++++-..++.++ .-|..+..|+..+|.+...+..
T Consensus 4 ~~~~~~~~~~i~~~~-~~~~s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 4 PKLTPEQIEEARRLL-AAGESVAEIARRLGVSRSTLYR 40 (42)
T ss_pred CcCCHHHHHHHHHHH-HcCCCHHHHHHHHCCCHHHHHH
Confidence 346665555555554 3566899999999988766653
No 132
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=21.57 E-value=1.4e+02 Score=27.90 Aligned_cols=28 Identities=25% Similarity=0.109 Sum_probs=24.0
Q ss_pred HhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 463 KHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 463 kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
..|.....||..||-|...|+.++.+.+
T Consensus 145 ~~g~s~~eIA~~l~is~~tV~~~l~ra~ 172 (184)
T PRK12512 145 VEGASIKETAAKLSMSEGAVRVALHRGL 172 (184)
T ss_pred HcCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 4477999999999999999999887764
No 133
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=20.59 E-value=2.2e+02 Score=25.08 Aligned_cols=69 Identities=16% Similarity=0.160 Sum_probs=45.9
Q ss_pred cHHHHHhHC-CCCCHHHHHHHHHHhcCCCCCCCCCHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHh
Q 035712 417 CWKEIGSAL-PWRPYDSIYYRAHIIFQRDENRKWTPEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRV 489 (563)
Q Consensus 417 ~Wk~IA~~L-PgRs~kqcy~Rwrr~L~p~kKGkWT~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~i 489 (563)
.|..++..| ..-++..|+..+.-++-|.-....|+- ..+..+ ..-|.....||..+|.|...|.. |.+.
T Consensus 4 ~~~~~~~~~~~~~~~~~~~~~~~~l~t~~e~~~Ls~R--~~I~~l-l~~G~S~~eIA~~LgISrsTIyR-i~R~ 73 (88)
T TIGR02531 4 LLDELFDAILTLKNREECYRFFDDIATINEIQSLAQR--LQVAKM-LKQGKTYSDIEAETGASTATISR-VKRC 73 (88)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhCCHHHHHhhhHH--HHHHHH-HHCCCCHHHHHHHHCcCHHHHHH-HHHh
Confidence 577776553 347888998888887765422234443 233333 23478999999999999999876 5543
No 134
>PRK00118 putative DNA-binding protein; Validated
Probab=20.58 E-value=1.7e+02 Score=26.58 Aligned_cols=40 Identities=15% Similarity=0.081 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHhCChhHHHHhhhCCChhhHHHHHHHhh
Q 035712 451 PEELELVRKFHEKHGSNWKMLANALGKHRFHVKDAWRRVR 490 (563)
Q Consensus 451 ~EEDekLielV~kyGn~W~~IAk~LGRT~~QCRdRWr~iL 490 (563)
++.+..++.++-..|.....||+.||-|+..|+.+..+..
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RAr 58 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTE 58 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4566777788888899999999999999999988876654
No 135
>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=20.51 E-value=99 Score=26.52 Aligned_cols=33 Identities=27% Similarity=0.476 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHHHhCChhHHHHhhhCCChhhHH
Q 035712 450 TPEELELVRKFHEKHGSNWKMLANALGKHRFHVK 483 (563)
Q Consensus 450 T~EEDekLielV~kyGn~W~~IAk~LGRT~~QCR 483 (563)
+.||.++|+..- ..|.+|..+|..||=+...|.
T Consensus 1 ~~~~v~~ll~~~-nlG~dW~~LA~~LG~~~~~I~ 33 (77)
T cd08311 1 KQEEVEKLLESG-RPGRDWRSLAGELGYEDEAID 33 (77)
T ss_pred ChHHHHHHHhCC-CCccCHHHHHHHcCCCHHHHH
Confidence 357888887322 457799999999997766554
No 136
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=20.04 E-value=96 Score=35.30 Aligned_cols=64 Identities=20% Similarity=0.302 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHcCCCccchhhhhcccCCCcccccHHHH-HhHCCCCCHHHHHHHHHHhc--CCC--CCCCC
Q 035712 375 RFSKEEDEMIKRAVMNYIETHGLGEEGLNMVLHCRSHPEVKHCWKEI-GSALPWRPYDSIYYRAHIIF--QRD--ENRKW 449 (563)
Q Consensus 375 kWT~EEDeiL~kaV~ky~~~hGlsee~L~~ll~s~r~~e~k~~Wk~I-A~~LPgRs~kqcy~Rwrr~L--~p~--kKGkW 449 (563)
-||..|--+..+++++|++ +++.| +..||+.+..+|..+|.-.- ++. .+.-=
T Consensus 287 EWSasEanLFEeALeKyGK-----------------------DFndIrqdfLPWKSl~sIveyYYmwKttdRYvqqKrlK 343 (693)
T KOG3554|consen 287 EWSASEANLFEEALEKYGK-----------------------DFNDIRQDFLPWKSLTSIVEYYYMWKTTDRYVQQKRLK 343 (693)
T ss_pred hccchhhHHHHHHHHHhcc-----------------------cHHHHHHhhcchHHHHHHHHHHHHHhhhhHHHHHHhhh
Confidence 4999999999999999976 67777 46788877777766553221 111 11122
Q ss_pred CHHHHHHHHHHH
Q 035712 450 TPEELELVRKFH 461 (563)
Q Consensus 450 T~EEDekLielV 461 (563)
..|-|.+|...+
T Consensus 344 aaeadsKlkqvY 355 (693)
T KOG3554|consen 344 AAEADSKLKQVY 355 (693)
T ss_pred hhhhhhhhheee
Confidence 566677777665
Done!