Query 004715
Match_columns 734
No_of_seqs 187 out of 531
Neff 2.9
Searched_HMMs 46136
Date Thu Mar 28 11:41:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/004715.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/004715hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01557 myb_SHAQKYF myb-like 99.6 1.5E-15 3.3E-20 124.3 5.6 50 22-71 1-56 (57)
2 PF00249 Myb_DNA-binding: Myb- 99.3 3.2E-12 6.9E-17 99.0 6.3 45 24-68 1-47 (48)
3 KOG0724 Zuotin and related mol 98.9 5.4E-11 1.2E-15 122.6 -2.8 100 6-111 34-134 (335)
4 smart00717 SANT SANT SWI3, AD 98.9 3.2E-09 7E-14 78.1 5.2 46 24-69 1-47 (49)
5 cd00167 SANT 'SWI3, ADA2, N-Co 98.9 3.7E-09 8E-14 77.0 5.4 43 26-68 1-44 (45)
6 PF13921 Myb_DNA-bind_6: Myb-l 98.6 3.4E-08 7.4E-13 78.8 4.9 42 27-68 1-42 (60)
7 COG5259 RSC8 RSC chromatin rem 98.1 2.5E-06 5.5E-11 93.9 5.1 51 14-64 267-319 (531)
8 PLN03212 Transcription repress 98.1 6.1E-06 1.3E-10 85.2 6.5 62 8-69 7-72 (249)
9 KOG0457 Histone acetyltransfer 98.0 7.2E-06 1.6E-10 89.7 6.9 67 5-71 46-120 (438)
10 KOG1279 Chromatin remodeling f 98.0 8.1E-06 1.7E-10 91.1 6.3 53 20-76 249-301 (506)
11 PLN03212 Transcription repress 98.0 2.1E-05 4.6E-10 81.3 8.6 51 22-72 76-126 (249)
12 PLN03091 hypothetical protein; 97.9 1E-05 2.3E-10 88.9 5.1 51 19-69 9-61 (459)
13 PLN03091 hypothetical protein; 97.7 6.1E-05 1.3E-09 83.0 7.2 53 22-74 65-117 (459)
14 COG5114 Histone acetyltransfer 97.5 0.00023 5.1E-09 76.3 6.9 47 24-70 63-110 (432)
15 PLN03162 golden-2 like transcr 97.1 0.0013 2.7E-08 71.9 7.5 86 21-106 234-327 (526)
16 KOG0048 Transcription factor, 96.9 0.00094 2E-08 67.5 4.3 46 24-69 9-56 (238)
17 KOG0048 Transcription factor, 96.7 0.0039 8.4E-08 63.2 7.2 46 23-68 61-106 (238)
18 KOG4329 DNA-binding protein [G 96.4 0.014 3.1E-07 63.9 9.4 58 14-74 264-325 (445)
19 KOG0049 Transcription factor, 95.9 0.011 2.4E-07 68.3 5.9 53 22-77 358-411 (939)
20 KOG4468 Polycomb-group transcr 95.1 0.028 6.1E-07 64.6 5.4 51 24-74 88-148 (782)
21 KOG0049 Transcription factor, 93.0 0.14 3.1E-06 59.7 5.6 46 23-68 411-457 (939)
22 PF13837 Myb_DNA-bind_4: Myb/S 92.8 0.22 4.8E-06 42.2 5.2 44 24-67 1-62 (90)
23 KOG0724 Zuotin and related mol 92.8 0.068 1.5E-06 56.0 2.5 55 22-76 162-223 (335)
24 COG5118 BDP1 Transcription ini 92.6 0.22 4.7E-06 55.3 6.0 44 21-64 362-405 (507)
25 PLN03142 Probable chromatin-re 92.2 0.25 5.3E-06 60.3 6.5 48 25-72 825-873 (1033)
26 KOG4167 Predicted DNA-binding 91.9 0.28 6E-06 58.0 6.1 49 23-74 618-666 (907)
27 KOG0051 RNA polymerase I termi 90.9 0.27 5.8E-06 57.0 4.6 47 22-68 434-506 (607)
28 smart00426 TEA TEA domain. 90.4 0.26 5.6E-06 43.1 3.0 43 24-66 3-66 (68)
29 KOG3841 TEF-1 and related tran 90.1 0.55 1.2E-05 52.2 5.9 54 23-76 75-149 (455)
30 KOG0050 mRNA splicing protein 89.9 0.37 8E-06 55.2 4.5 50 22-71 5-55 (617)
31 KOG3554 Histone deacetylase co 89.5 0.8 1.7E-05 52.2 6.7 48 21-71 282-330 (693)
32 KOG0051 RNA polymerase I termi 89.1 0.45 9.8E-06 55.2 4.6 51 17-68 376-427 (607)
33 PF13873 Myb_DNA-bind_5: Myb/S 86.5 3.3 7.3E-05 34.8 7.2 51 24-74 2-74 (78)
34 KOG1194 Predicted DNA-binding 85.0 1.8 3.9E-05 49.2 6.2 41 24-64 187-227 (534)
35 PF01285 TEA: TEA/ATTS domain 83.7 1.1 2.3E-05 50.3 3.9 48 21-68 46-112 (431)
36 COG5147 REB1 Myb superfamily p 75.6 1.7 3.8E-05 49.8 2.2 60 16-75 12-72 (512)
37 PF11035 SnAPC_2_like: Small n 71.5 23 0.00049 39.3 9.2 58 22-79 19-80 (344)
38 PF09111 SLIDE: SLIDE; InterP 69.9 13 0.00027 35.4 6.1 50 18-67 43-108 (118)
39 PF12776 Myb_DNA-bind_3: Myb/S 65.4 28 0.00061 29.9 7.0 42 26-67 1-60 (96)
40 COG5147 REB1 Myb superfamily p 55.1 15 0.00033 42.5 4.5 50 23-72 71-120 (512)
41 COG4425 Predicted membrane pro 53.6 13 0.00028 43.0 3.6 50 360-420 87-136 (588)
42 KOG1194 Predicted DNA-binding 51.9 23 0.00049 40.9 5.1 55 22-76 367-421 (534)
43 KOG0050 mRNA splicing protein 50.1 17 0.00037 42.4 3.9 44 23-67 58-101 (617)
44 KOG2009 Transcription initiati 49.3 11 0.00023 44.3 2.2 42 23-64 408-449 (584)
45 KOG0385 Chromatin remodeling c 45.6 35 0.00075 41.8 5.6 60 16-76 787-847 (971)
46 COG0315 MoaC Molybdenum cofact 41.8 22 0.00047 35.8 2.7 27 405-431 55-81 (157)
47 PRK13923 putative spore coat p 40.6 51 0.0011 33.5 5.1 48 23-70 4-57 (170)
48 PF04504 DUF573: Protein of un 40.1 68 0.0015 29.4 5.5 41 25-65 5-58 (98)
49 KOG4282 Transcription factor G 39.8 83 0.0018 33.7 6.9 55 24-78 54-122 (345)
50 cd08780 Death_TRADD Death Doma 35.8 59 0.0013 30.3 4.3 38 28-68 1-42 (90)
51 TIGR02894 DNA_bind_RsfA transc 34.0 82 0.0018 32.0 5.4 53 23-76 3-62 (161)
52 PLN03142 Probable chromatin-re 33.7 1.9E+02 0.0041 36.5 9.4 54 22-75 924-990 (1033)
53 cd01420 MoaC_PE MoaC family, p 33.0 44 0.00095 33.1 3.2 27 405-431 41-67 (140)
54 PRK12343 putative molybdenum c 32.9 41 0.00088 33.7 3.0 25 407-431 51-75 (151)
55 KOG1019 Retinoblastoma pathway 32.9 22 0.00047 43.4 1.4 60 5-64 25-85 (837)
56 PF12451 VPS11_C: Vacuolar pro 32.2 37 0.00081 27.7 2.2 28 28-55 17-44 (49)
57 cd00528 MoaC MoaC family. Memb 30.6 48 0.001 32.7 3.1 27 405-431 41-67 (136)
58 TIGR00581 moaC molybdenum cofa 30.4 46 0.00099 33.2 2.9 25 407-431 54-78 (147)
59 PF08914 Myb_DNA-bind_2: Rap1 29.5 1.1E+02 0.0023 26.5 4.7 46 24-69 2-57 (65)
60 KOG1079 Transcriptional repres 28.0 43 0.00094 40.3 2.7 53 15-67 399-452 (739)
61 cd01419 MoaC_A MoaC family, ar 26.8 61 0.0013 32.2 3.1 26 406-431 42-67 (141)
62 PF08281 Sigma70_r4_2: Sigma-7 26.1 2.2E+02 0.0047 22.3 5.5 35 32-67 15-49 (54)
63 smart00595 MADF subfamily of S 25.9 1.5E+02 0.0033 25.2 5.0 22 45-67 29-50 (89)
64 PRK09364 moaC molybdenum cofac 25.2 66 0.0014 32.4 3.0 24 408-431 58-81 (159)
65 PF06461 DUF1086: Domain of Un 22.6 2.1E+02 0.0045 28.8 5.8 49 26-74 40-91 (145)
66 TIGR02937 sigma70-ECF RNA poly 22.0 2.7E+02 0.0059 24.1 5.9 46 26-73 110-155 (158)
67 PF01388 ARID: ARID/BRIGHT DNA 21.2 2.6E+02 0.0057 24.2 5.6 40 32-71 39-90 (92)
68 PLN02375 molybderin biosynthes 20.5 86 0.0019 34.0 3.0 27 405-431 167-193 (270)
No 1
>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=99.59 E-value=1.5e-15 Score=124.26 Aligned_cols=50 Identities=42% Similarity=0.651 Sum_probs=46.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCh-hh---HHHHHHhC-CC-CHHHHHHHHHHHHHH
Q 004715 22 KQRERWTEEEHNRFLEALKLYGR-AW---QRIEEHIG-TK-KAVQIRSHAQKFFSK 71 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe~YGr-dW---KkIAe~Vg-TR-T~~QVRSHAQKYF~K 71 (734)
+.+..||+|||.+||+||+.||+ +| ++|+++++ ++ |+.||+||+||||++
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 45789999999999999999999 99 99999764 78 999999999999986
No 2
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=99.32 E-value=3.2e-12 Score=99.00 Aligned_cols=45 Identities=42% Similarity=0.786 Sum_probs=41.3
Q ss_pred CCCCCHHHHHHHHHHHHHhChh-hHHHHHHhC-CCCHHHHHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKLYGRA-WQRIEEHIG-TKKAVQIRSHAQKF 68 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~YGrd-WKkIAe~Vg-TRT~~QVRSHAQKY 68 (734)
++.||+||+++|++||++||.+ |+.||.+|+ +||..||++|+++|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~~Ia~~~~~~Rt~~qc~~~~~~~ 47 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWKKIAKRMPGGRTAKQCRSRYQNL 47 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHHHHHHHHSSSSTHHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHHHHHHHcCCCCCHHHHHHHHHhh
Confidence 5789999999999999999996 999999999 99999999999987
No 3
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=98.94 E-value=5.4e-11 Score=122.56 Aligned_cols=100 Identities=32% Similarity=0.313 Sum_probs=89.5
Q ss_pred cccccccccCCCeecccCCCC-CCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHhhhcCCCCC
Q 004715 6 SGEDLVLKTRKPYTITKQRER-WTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEALSKGVPIG 84 (734)
Q Consensus 6 ~ge~~v~K~RKPytitk~r~~-WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k~~~~kG~~~g 84 (734)
.+++..++++|+|.+...+.+ ||.+||..|.++|..|++.|++|-+|++.++.+|+|+|+|+||-++.+.. .+
T Consensus 34 ~~~~~~k~i~ka~~i~~~~~~~~t~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~p~~~~~~------~~ 107 (335)
T KOG0724|consen 34 WTEEEFKKIEKALAILDDDEPRRTPDSWDKFAEALPLEKRLEDKIEEYIGLVFDVNIRESGQKPFPKYGKSD------TS 107 (335)
T ss_pred hHHHHHHHHHHHHHHHhccccccchhhhhHHHhcCccccccchhHHhhhhhHHHHhhhhccCCCccccCccc------cc
Confidence 466778899999999997654 99999999999999998899999999999999999999999999997754 24
Q ss_pred ccccccCCCCCCCCCCCCCCCCccCCC
Q 004715 85 QAIDIDIPPPRPKRKPRNPYPRKTCTN 111 (734)
Q Consensus 85 ~~~~I~IPPpRPKRkps~PYPrK~~~g 111 (734)
..+.+.+|++++++++.+|||++...+
T Consensus 108 ~~~~~~~~~~~~~~k~~~~y~~~~~~~ 134 (335)
T KOG0724|consen 108 LAEVEEFYNFWPKFKSWRQYPQKDEPD 134 (335)
T ss_pred cccccccCCccccccccccCCCCCCcc
Confidence 566788999999999999999998664
No 4
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=98.87 E-value=3.2e-09 Score=78.07 Aligned_cols=46 Identities=30% Similarity=0.653 Sum_probs=42.7
Q ss_pred CCCCCHHHHHHHHHHHHHhC-hhhHHHHHHhCCCCHHHHHHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKLYG-RAWQRIEEHIGTKKAVQIRSHAQKFF 69 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~YG-rdWKkIAe~VgTRT~~QVRSHAQKYF 69 (734)
+..||.+|..+|+.++..|| .+|..|+.++++||+.||+.++..++
T Consensus 1 ~~~Wt~~E~~~l~~~~~~~g~~~w~~Ia~~~~~rt~~~~~~~~~~~~ 47 (49)
T smart00717 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWNNLL 47 (49)
T ss_pred CCCCCHHHHHHHHHHHHHHCcCCHHHHHHHcCCCCHHHHHHHHHHHc
Confidence 46899999999999999999 89999999999999999999987654
No 5
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=98.87 E-value=3.7e-09 Score=76.97 Aligned_cols=43 Identities=35% Similarity=0.686 Sum_probs=40.9
Q ss_pred CCCHHHHHHHHHHHHHhC-hhhHHHHHHhCCCCHHHHHHHHHHH
Q 004715 26 RWTEEEHNRFLEALKLYG-RAWQRIEEHIGTKKAVQIRSHAQKF 68 (734)
Q Consensus 26 ~WTeEEHelFLeGLe~YG-rdWKkIAe~VgTRT~~QVRSHAQKY 68 (734)
.||.||+.+|+.+++.|| .+|..|+.++++||..||+.|++++
T Consensus 1 ~Wt~eE~~~l~~~~~~~g~~~w~~Ia~~~~~rs~~~~~~~~~~~ 44 (45)
T cd00167 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRERWRNL 44 (45)
T ss_pred CCCHHHHHHHHHHHHHHCcCCHHHHHhHcCCCCHHHHHHHHHHh
Confidence 599999999999999999 7999999999999999999998765
No 6
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=98.65 E-value=3.4e-08 Score=78.81 Aligned_cols=42 Identities=38% Similarity=0.790 Sum_probs=37.2
Q ss_pred CCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHH
Q 004715 27 WTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKF 68 (734)
Q Consensus 27 WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKY 68 (734)
||+||.++++++++.||.+|+.||+++|+||+.||+.|+.++
T Consensus 1 WT~eEd~~L~~~~~~~g~~W~~Ia~~l~~Rt~~~~~~r~~~~ 42 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGNDWKKIAEHLGNRTPKQCRNRWRNH 42 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-HHHHHHHSTTS-HHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHHHHCcCHHHHHHHHCcCCHHHHHHHHHHH
Confidence 999999999999999999999999999999999999997763
No 7
>COG5259 RSC8 RSC chromatin remodeling complex subunit RSC8 [Chromatin structure and dynamics / Transcription]
Probab=98.12 E-value=2.5e-06 Score=93.93 Aligned_cols=51 Identities=33% Similarity=0.658 Sum_probs=43.7
Q ss_pred cCCCeecccC--CCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHH
Q 004715 14 TRKPYTITKQ--RERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSH 64 (734)
Q Consensus 14 ~RKPytitk~--r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSH 64 (734)
.-+|.++.-. ...||.+|..++|+||+.||.+|.+||.||||||+.||.-|
T Consensus 267 Df~~v~~~~~~~dk~WS~qE~~LLLEGIe~ygDdW~kVA~HVgtKt~EqCIl~ 319 (531)
T COG5259 267 DFKPVTISLLIRDKNWSRQELLLLLEGIEMYGDDWDKVARHVGTKTKEQCILH 319 (531)
T ss_pred cchhhhhhcccccccccHHHHHHHHHHHHHhhhhHHHHHHHhCCCCHHHHHHH
Confidence 3344444333 34899999999999999999999999999999999999999
No 8
>PLN03212 Transcription repressor MYB5; Provisional
Probab=98.07 E-value=6.1e-06 Score=85.17 Aligned_cols=62 Identities=21% Similarity=0.380 Sum_probs=51.6
Q ss_pred cccccccCCCeec--ccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhC-CCCHHHHHHHHHHHH
Q 004715 8 EDLVLKTRKPYTI--TKQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIG-TKKAVQIRSHAQKFF 69 (734)
Q Consensus 8 e~~v~K~RKPyti--tk~r~~WTeEEHelFLeGLe~YGr-dWKkIAe~Vg-TRT~~QVRSHAQKYF 69 (734)
.+.+.+.+.|+-. ...+++||.||.+++++++++||. +|+.||.+++ .||..|||-++.+|+
T Consensus 7 ~~~~~~~~~pcc~K~glKRg~WT~EEDe~L~~lV~kyG~~nW~~IAk~~g~gRT~KQCReRW~N~L 72 (249)
T PLN03212 7 KKPVSKKTTPCCTKMGMKRGPWTVEEDEILVSFIKKEGEGRWRSLPKRAGLLRCGKSCRLRWMNYL 72 (249)
T ss_pred CCCCCCCCCCCcccCCCcCCCCCHHHHHHHHHHHHHhCcccHHHHHHhhhcCCCcchHHHHHHHhh
Confidence 3455566666543 346889999999999999999996 8999999886 899999999988875
No 9
>KOG0457 consensus Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=98.05 E-value=7.2e-06 Score=89.72 Aligned_cols=67 Identities=36% Similarity=0.613 Sum_probs=54.8
Q ss_pred Cccccccc-ccCCCeecccC------CCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHH
Q 004715 5 SSGEDLVL-KTRKPYTITKQ------RERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSK 71 (734)
Q Consensus 5 s~ge~~v~-K~RKPytitk~------r~~WTeEEHelFLeGLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~K 71 (734)
+.|-+..+ +.--||.+-.. ...||.+|.-+||+|++.||= +|..||+||||||..+|+.|.-|+|..
T Consensus 46 s~GaE~~~H~~~H~Yrim~~~s~~i~~~~WtadEEilLLea~~t~G~GNW~dIA~hIGtKtkeeck~hy~k~fv~ 120 (438)
T KOG0457|consen 46 SVGAETGKHQNDHPYRIMDTNSFPILDPSWTADEEILLLEAAETYGFGNWQDIADHIGTKTKEECKEHYLKHFVN 120 (438)
T ss_pred hcccccCCCCCCCCceeecCCCCCCCCCCCChHHHHHHHHHHHHhCCCcHHHHHHHHcccchHHHHHHHHHHHhc
Confidence 34444322 45567776444 569999999999999999998 999999999999999999998888865
No 10
>KOG1279 consensus Chromatin remodeling factor subunit and related transcription factors [Chromatin structure and dynamics]
Probab=98.00 E-value=8.1e-06 Score=91.12 Aligned_cols=53 Identities=36% Similarity=0.663 Sum_probs=47.2
Q ss_pred cccCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHh
Q 004715 20 ITKQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEA 76 (734)
Q Consensus 20 itk~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k~~ 76 (734)
....+..||++|-.++|+||+.||.+|.+|+.||||||..||-.| |.+|....
T Consensus 249 ~~~~~~~WT~qE~lLLLE~ie~y~ddW~kVa~hVg~ks~eqCI~k----FL~LPieD 301 (506)
T KOG1279|consen 249 GESARPNWTEQETLLLLEAIEMYGDDWNKVADHVGTKSQEQCILK----FLRLPIED 301 (506)
T ss_pred cccCCCCccHHHHHHHHHHHHHhcccHHHHHhccCCCCHHHHHHH----HHhcCccc
Confidence 345688999999999999999999999999999999999999999 66665544
No 11
>PLN03212 Transcription repressor MYB5; Provisional
Probab=97.99 E-value=2.1e-05 Score=81.28 Aligned_cols=51 Identities=22% Similarity=0.330 Sum_probs=46.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 004715 22 KQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKL 72 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~Kl 72 (734)
.+++.||.||.+++|+....||..|..||.+|+.||..||+.|+..++.+.
T Consensus 76 I~kgpWT~EED~lLlel~~~~GnKWs~IAk~LpGRTDnqIKNRWns~LrK~ 126 (249)
T PLN03212 76 VKRGGITSDEEDLILRLHRLLGNRWSLIAGRIPGRTDNEIKNYWNTHLRKK 126 (249)
T ss_pred cccCCCChHHHHHHHHHHHhccccHHHHHhhcCCCCHHHHHHHHHHHHhHH
Confidence 467899999999999999999999999999999999999999977655544
No 12
>PLN03091 hypothetical protein; Provisional
Probab=97.91 E-value=1e-05 Score=88.89 Aligned_cols=51 Identities=18% Similarity=0.485 Sum_probs=45.4
Q ss_pred ecccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhC-CCCHHHHHHHHHHHH
Q 004715 19 TITKQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIG-TKKAVQIRSHAQKFF 69 (734)
Q Consensus 19 titk~r~~WTeEEHelFLeGLe~YGr-dWKkIAe~Vg-TRT~~QVRSHAQKYF 69 (734)
+....+++||.||.+++++++++||. +|+.||.+++ .||..|||-++.+|+
T Consensus 9 KqklrKg~WTpEEDe~L~~~V~kyG~~nWs~IAk~~g~gRT~KQCRERW~NyL 61 (459)
T PLN03091 9 KQKLRKGLWSPEEDEKLLRHITKYGHGCWSSVPKQAGLQRCGKSCRLRWINYL 61 (459)
T ss_pred CCCCcCCCCCHHHHHHHHHHHHHhCcCCHHHHhhhhccCcCcchHhHHHHhcc
Confidence 34456789999999999999999997 8999999886 899999999988775
No 13
>PLN03091 hypothetical protein; Provisional
Probab=97.72 E-value=6.1e-05 Score=83.03 Aligned_cols=53 Identities=17% Similarity=0.364 Sum_probs=47.2
Q ss_pred cCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Q 004715 22 KQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEK 74 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k 74 (734)
-.++.||.||.+++|+..++||..|.+||.+|+.||..||+.|+...++|..+
T Consensus 65 IkKgpWT~EED~lLLeL~k~~GnKWskIAk~LPGRTDnqIKNRWnslLKKklr 117 (459)
T PLN03091 65 LKRGTFSQQEENLIIELHAVLGNRWSQIAAQLPGRTDNEIKNLWNSCLKKKLR 117 (459)
T ss_pred ccCCCCCHHHHHHHHHHHHHhCcchHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999999999999999999999999998766555444
No 14
>COG5114 Histone acetyltransferase complex SAGA/ADA, subunit ADA2 [Chromatin structure and dynamics]
Probab=97.46 E-value=0.00023 Score=76.26 Aligned_cols=47 Identities=30% Similarity=0.633 Sum_probs=44.7
Q ss_pred CCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFS 70 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~ 70 (734)
..-|+.+|..+|++|++-.|- +|..||.|||+|+...|++|.-|||.
T Consensus 63 ~e~WgadEEllli~~~~TlGlGNW~dIadyiGsr~kee~k~HylK~y~ 110 (432)
T COG5114 63 EEGWGADEELLLIECLDTLGLGNWEDIADYIGSRAKEEIKSHYLKMYD 110 (432)
T ss_pred CCCcCchHHHHHHHHHHhcCCCcHHHHHHHHhhhhhHHHHHHHHHHHh
Confidence 468999999999999999998 99999999999999999999988887
No 15
>PLN03162 golden-2 like transcription factor; Provisional
Probab=97.09 E-value=0.0013 Score=71.91 Aligned_cols=86 Identities=29% Similarity=0.331 Sum_probs=60.3
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCh---hhHHHHHH--hCCCCHHHHHHHHHHHHHHHHHHhhhc---CCCCCccccccCC
Q 004715 21 TKQRERWTEEEHNRFLEALKLYGR---AWQRIEEH--IGTKKAVQIRSHAQKFFSKLEKEALSK---GVPIGQAIDIDIP 92 (734)
Q Consensus 21 tk~r~~WTeEEHelFLeGLe~YGr---dWKkIAe~--VgTRT~~QVRSHAQKYF~Kl~k~~~~k---G~~~g~~~~I~IP 92 (734)
.|.|-+||.|=|++|++|++..|- -=|+|-++ |..=|..+|+||-|||...+.+..... +...........|
T Consensus 234 KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaEa~swt~kr~~~~~P 313 (526)
T PLN03162 234 KKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAEAASWTHRRAYTQAP 313 (526)
T ss_pred CCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhhhccchhhhhhccCC
Confidence 356789999999999999999994 46788886 567899999999999999887543211 1111111223345
Q ss_pred CCCCCCCCCCCCCC
Q 004715 93 PPRPKRKPRNPYPR 106 (734)
Q Consensus 93 PpRPKRkps~PYPr 106 (734)
.+|-+|+..+||--
T Consensus 314 ~~rs~~~~g~p~~~ 327 (526)
T PLN03162 314 WPRSSRRDGLPYLV 327 (526)
T ss_pred cccCCCCCCCcccc
Confidence 56667777666653
No 16
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.90 E-value=0.00094 Score=67.52 Aligned_cols=46 Identities=17% Similarity=0.374 Sum_probs=43.8
Q ss_pred CCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhC-CCCHHHHHHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKLYGR-AWQRIEEHIG-TKKAVQIRSHAQKFF 69 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~YGr-dWKkIAe~Vg-TRT~~QVRSHAQKYF 69 (734)
++.||.||.+++++-|++||. .|..|+...| -|+-.|||-++-.|+
T Consensus 9 kGpWt~EED~~L~~~V~~~G~~~W~~i~k~~gl~R~GKSCRlRW~NyL 56 (238)
T KOG0048|consen 9 KGPWTQEEDLTQIRSIKSFGKHNGTALPKLAGLRRCGKSCRLRWTNYL 56 (238)
T ss_pred CCCCChHHHHHHHHHHHHhCCCCcchhhhhcCCCccchHHHHHhhccc
Confidence 799999999999999999998 7999999999 899999999998874
No 17
>KOG0048 consensus Transcription factor, Myb superfamily [Transcription]
Probab=96.72 E-value=0.0039 Score=63.17 Aligned_cols=46 Identities=17% Similarity=0.442 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHH
Q 004715 23 QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKF 68 (734)
Q Consensus 23 ~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKY 68 (734)
.++.||+||.++.+++-.+||-+|..||.+++.||.-.|+.|+--.
T Consensus 61 krg~fT~eEe~~Ii~lH~~~GNrWs~IA~~LPGRTDNeIKN~Wnt~ 106 (238)
T KOG0048|consen 61 KRGNFSDEEEDLIIKLHALLGNRWSLIAGRLPGRTDNEVKNHWNTH 106 (238)
T ss_pred cCCCCCHHHHHHHHHHHHHHCcHHHHHHhhCCCcCHHHHHHHHHHH
Confidence 5899999999999999999999999999999999999999997544
No 18
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=96.42 E-value=0.014 Score=63.88 Aligned_cols=58 Identities=22% Similarity=0.487 Sum_probs=46.1
Q ss_pred cCCCeec---ccCCCCCCHHHHHHHHHHHHHhChhhHHHHH-HhCCCCHHHHHHHHHHHHHHHHH
Q 004715 14 TRKPYTI---TKQRERWTEEEHNRFLEALKLYGRAWQRIEE-HIGTKKAVQIRSHAQKFFSKLEK 74 (734)
Q Consensus 14 ~RKPyti---tk~r~~WTeEEHelFLeGLe~YGrdWKkIAe-~VgTRT~~QVRSHAQKYF~Kl~k 74 (734)
.|+++.+ +..-..|+++|-+.|.+||++||+++-.|.. -|.||++-.|--+ ||++...
T Consensus 264 rr~rfnvk~~rd~l~~wsEeEcr~FEegl~~yGKDF~lIr~nkvrtRsvgElVey---YYlWKkS 325 (445)
T KOG4329|consen 264 RRLRFNVKTVRDDLSGWSEEECRNFEEGLELYGKDFHLIRANKVRTRSVGELVEY---YYLWKKS 325 (445)
T ss_pred HhcCCcceecccccccCCHHHHHHHHHHHHHhcccHHHHHhcccccchHHHHHHH---HHHhhcC
Confidence 4444443 3344599999999999999999999999987 6999999998777 6666543
No 19
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=95.95 E-value=0.011 Score=68.33 Aligned_cols=53 Identities=23% Similarity=0.525 Sum_probs=46.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHhh
Q 004715 22 KQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEAL 77 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k~~~ 77 (734)
...++||++|.-+++.|+.+||- +|-+|-+.|+.|+..|||.+ |...|....+
T Consensus 358 ikhg~wt~~ED~~L~~AV~~Yg~kdw~k~R~~vPnRSdsQcR~R---Y~nvL~~s~K 411 (939)
T KOG0049|consen 358 VKHGRWTDQEDVLLVCAVSRYGAKDWAKVRQAVPNRSDSQCRER---YTNVLNRSAK 411 (939)
T ss_pred ccCCCCCCHHHHHHHHHHHHhCccchhhHHHhcCCccHHHHHHH---HHHHHHHhhc
Confidence 46789999999999999999986 99999999999999999998 6666655543
No 20
>KOG4468 consensus Polycomb-group transcriptional regulator [Transcription]
Probab=95.14 E-value=0.028 Score=64.63 Aligned_cols=51 Identities=22% Similarity=0.565 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHhChhhHHH----------HHHhCCCCHHHHHHHHHHHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKLYGRAWQRI----------EEHIGTKKAVQIRSHAQKFFSKLEK 74 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~YGrdWKkI----------Ae~VgTRT~~QVRSHAQKYF~Kl~k 74 (734)
+..||..|.+-|..||++||+++.+| -.-+..||.-|||.|+-+-..++.+
T Consensus 88 ktaWt~~E~~~Ffdal~~~GKdFe~VinaklKRrna~s~~~~Ktkdqvr~~yY~~~~~m~k 148 (782)
T KOG4468|consen 88 KTAWTHQEEESFFDALRQVGKDFEKVINAKLKRRNATSRVQSKTKDQVRHYYYRLVRRMNK 148 (782)
T ss_pred ccccchhhHHHHHHHHHHhcccHHHHHHHHHHhcccccchhhhhhHHHHHHHHHHHHHHHh
Confidence 77999999999999999999999999 3346678999999986555445444
No 21
>KOG0049 consensus Transcription factor, Myb superfamily [Transcription]
Probab=93.03 E-value=0.14 Score=59.67 Aligned_cols=46 Identities=30% Similarity=0.609 Sum_probs=41.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHH
Q 004715 23 QRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKF 68 (734)
Q Consensus 23 ~r~~WTeEEHelFLeGLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKY 68 (734)
..++||-.|.++++.++++||. .|-+||.++|.||-.|.++.-..+
T Consensus 411 K~~rW~l~edeqL~~~V~~YG~g~WakcA~~Lp~~t~~q~~rrR~R~ 457 (939)
T KOG0049|consen 411 KVERWTLVEDEQLLYAVKVYGKGNWAKCAMLLPKKTSRQLRRRRLRL 457 (939)
T ss_pred ccCceeecchHHHHHHHHHHccchHHHHHHHccccchhHHHHHHHHH
Confidence 3679999999999999999999 899999999999999988875543
No 22
>PF13837 Myb_DNA-bind_4: Myb/SANT-like DNA-binding domain; PDB: 2EBI_A 2JMW_A.
Probab=92.83 E-value=0.22 Score=42.17 Aligned_cols=44 Identities=30% Similarity=0.659 Sum_probs=31.2
Q ss_pred CCCCCHHHHHHHHHHHHH------hC---h-----hhHHHHHHh---C-CCCHHHHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKL------YG---R-----AWQRIEEHI---G-TKKAVQIRSHAQK 67 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~------YG---r-----dWKkIAe~V---g-TRT~~QVRSHAQK 67 (734)
|..||++|..+||+.+.. |+ . -|+.||+.+ | .||+.||+.....
T Consensus 1 R~~Wt~~et~~Li~~~~~~~~~~~~~~~~~~~~~~~w~~Ia~~l~~~G~~rt~~qc~~Kw~~ 62 (90)
T PF13837_consen 1 RRNWTDEETKLLIELWKENLMELRFDNGGKKRNKKVWKEIAEELAEHGYNRTPEQCRNKWKN 62 (90)
T ss_dssp --SS-HHHHHHHHHHHHH--HHHHHHH--SS--HHHHHHHHHHHHHHC----HHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhccccchHHHHHHHHHHHHcCCCCCHHHHHHHHHH
Confidence 458999999999998877 32 1 699999865 3 6999999999765
No 23
>KOG0724 consensus Zuotin and related molecular chaperones (DnaJ superfamily), contains DNA-binding domains [Posttranslational modification, protein turnover, chaperones]
Probab=92.83 E-value=0.068 Score=56.03 Aligned_cols=55 Identities=29% Similarity=0.411 Sum_probs=49.3
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCh-hhHHHHH-HhCCCCHHHHHHHHH-----HHHHHHHHHh
Q 004715 22 KQRERWTEEEHNRFLEALKLYGR-AWQRIEE-HIGTKKAVQIRSHAQ-----KFFSKLEKEA 76 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe~YGr-dWKkIAe-~VgTRT~~QVRSHAQ-----KYF~Kl~k~~ 76 (734)
+.+..|+..+|.+|+.++..||+ .|.+|.+ ++.+|++.|+.+|+| +||.+.....
T Consensus 162 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~s~a~~~~~~~~~~~~~~~~ 223 (335)
T KOG0724|consen 162 RKGTPVTERERKLVLLALKKDGKIDWRKISQNVEKERTPEQVASHAQEKAFEKALARQKSGE 223 (335)
T ss_pred hccchhHHHHHHHHHhhhcccccccceechhhhhhhhcchhhhhhhhhhhhHHHHHHHhhhc
Confidence 45679999999999999999999 9999998 789999999999999 8888885544
No 24
>COG5118 BDP1 Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=92.58 E-value=0.22 Score=55.31 Aligned_cols=44 Identities=25% Similarity=0.539 Sum_probs=40.6
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHH
Q 004715 21 TKQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSH 64 (734)
Q Consensus 21 tk~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSH 64 (734)
.+...+||.+|-++|..||..+|-+|..|+.++++|...||...
T Consensus 362 ~~~~~~Ws~~e~ekFYKALs~wGtdF~LIs~lfP~R~RkqIKaK 405 (507)
T COG5118 362 KKGALRWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAK 405 (507)
T ss_pred CCCCCcccHHHHHHHHHHHHHhcchHHHHHHhcCchhHHHHHHH
Confidence 34567999999999999999999999999999999999999865
No 25
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=92.23 E-value=0.25 Score=60.33 Aligned_cols=48 Identities=23% Similarity=0.528 Sum_probs=44.7
Q ss_pred CCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 004715 25 ERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSKL 72 (734)
Q Consensus 25 ~~WTeEEHelFLeGLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~Kl 72 (734)
..||..+-..|+.|.++||| +..+||..|+.||+.+|+-|++-|+.+.
T Consensus 825 ~~w~~~~f~~f~~~~~~~gr~~~~~i~~~~~~k~~~ev~~y~~~f~~~~ 873 (1033)
T PLN03142 825 STWSRRDFNAFIRACEKYGRNDIKSIASEMEGKTEEEVERYAKVFWERY 873 (1033)
T ss_pred CcccHHHHHHHHHHHHHhCHhHHHHHHHHhcCCCHHHHHHHHHHHHHhh
Confidence 36999999999999999999 8999999999999999999999888664
No 26
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=91.91 E-value=0.28 Score=57.97 Aligned_cols=49 Identities=18% Similarity=0.356 Sum_probs=43.5
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Q 004715 23 QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEK 74 (734)
Q Consensus 23 ~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k 74 (734)
....||..|..+|-.||-.|-+||..|+..|.+||+.||--+ ||.+...
T Consensus 618 gSd~WTp~E~~lF~kA~y~~~KDF~~v~km~~~KtVaqCVey---YYtWKK~ 666 (907)
T KOG4167|consen 618 GSDKWTPLERKLFNKALYTYSKDFIFVQKMVKSKTVAQCVEY---YYTWKKI 666 (907)
T ss_pred CcccccHHHHHHHHHHHHHhcccHHHHHHHhccccHHHHHHH---HHHHHHh
Confidence 467999999999999999999999999999999999999655 7766533
No 27
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=90.88 E-value=0.27 Score=57.01 Aligned_cols=47 Identities=28% Similarity=0.569 Sum_probs=40.5
Q ss_pred cCCCCCCHHHHHHHHHHHH-------Hh-------C------------hhhHHHHHHhCCCCHHHHHHHHHHH
Q 004715 22 KQRERWTEEEHNRFLEALK-------LY-------G------------RAWQRIEEHIGTKKAVQIRSHAQKF 68 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe-------~Y-------G------------rdWKkIAe~VgTRT~~QVRSHAQKY 68 (734)
.++++||-||.+++|..++ .| | -.|..|++.+|||+..|||.|++|-
T Consensus 434 ~~r~~Ws~eEe~~Llk~V~~~~~~~~q~q~~n~~~~~q~sp~s~~~d~I~Wt~vse~~~TR~~~qCr~Kw~kl 506 (607)
T KOG0051|consen 434 RNRGAWSIEEEEKLLKTVNEMIREALQPQASNTDTGLQESPESTLKDDINWTLVSEMLGTRSRIQCRYKWYKL 506 (607)
T ss_pred cccCcchHHHHHHHHHHHHHHHHHhhcccccccchhhhcCccccccCCcchhhhhHhhcCCCcchHHHHHHHH
Confidence 3789999999999999996 44 1 1799999999999999999997763
No 28
>smart00426 TEA TEA domain.
Probab=90.36 E-value=0.26 Score=43.12 Aligned_cols=43 Identities=30% Similarity=0.447 Sum_probs=34.3
Q ss_pred CCCCCHHHHHHHHHHHHHhCh--hh--------------HHHHHHhC-----CCCHHHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKLYGR--AW--------------QRIEEHIG-----TKKAVQIRSHAQ 66 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~YGr--dW--------------KkIAe~Vg-----TRT~~QVRSHAQ 66 (734)
...|.++=...|++||+.|-. .| .-|++||- .||..||.||-|
T Consensus 3 ~~vWp~~lE~Af~~aL~~~~~~g~~kik~~~r~k~~gRNelIs~YI~~~tGk~Rt~KQVsShIQ 66 (68)
T smart00426 3 EGVWSPDIEQAFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQ 66 (68)
T ss_pred CCcCcHHHHHHHHHHHHHcCccCcccchhhhcCcccchhHHHHHHHHHHhCCccchhhhcchhe
Confidence 468999999999999999864 12 13677653 599999999987
No 29
>KOG3841 consensus TEF-1 and related transcription factor, TEAD family [Transcription]
Probab=90.10 E-value=0.55 Score=52.19 Aligned_cols=54 Identities=28% Similarity=0.386 Sum_probs=43.7
Q ss_pred CCCCCCHHHHHHHHHHHHHhC---h-------------hhHHHHHHhC-----CCCHHHHHHHHHHHHHHHHHHh
Q 004715 23 QRERWTEEEHNRFLEALKLYG---R-------------AWQRIEEHIG-----TKKAVQIRSHAQKFFSKLEKEA 76 (734)
Q Consensus 23 ~r~~WTeEEHelFLeGLe~YG---r-------------dWKkIAe~Vg-----TRT~~QVRSHAQKYF~Kl~k~~ 76 (734)
..+.|+.+=.+.|+|||..|. | +=..||.||. |||..||-||-|=+-+|..+.-
T Consensus 75 aegvWSpdIEqsFqEALaiyppcGrrKIilsdegkmyGRNELIarYIKlrtgktRTrKQVSSHIQVlarrk~rei 149 (455)
T KOG3841|consen 75 AEGVWSPDIEQSFQEALAIYPPCGRRKIILSDEGKMYGRNELIARYIKLRTGKTRTRKQVSSHIQVLARRKLREI 149 (455)
T ss_pred cccccChhHHHHHHHHHhhcCCCCceeEEEccCccccchHHHHHHHHHHhcCCchhHHHHHHHHHHHHHHHHHHH
Confidence 457999999999999999974 2 2357899874 8999999999997766666654
No 30
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=89.86 E-value=0.37 Score=55.20 Aligned_cols=50 Identities=22% Similarity=0.466 Sum_probs=45.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHH
Q 004715 22 KQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSK 71 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~K 71 (734)
..++.|+.-|.+.+--|+.+||. .|.+|+..+..+|+.||+..+-+|..-
T Consensus 5 ~kggvwrntEdeilkaav~kyg~nqws~i~sll~~kt~rqC~~rw~e~ldp 55 (617)
T KOG0050|consen 5 IKGGVWRNTEDEVLKAAVMKYGKNQWSRIASLLNRKTARQCKARWEEWLDP 55 (617)
T ss_pred EecceecccHHHHHHHHHHHcchHHHHHHHHHHhhcchhHHHHHHHHHhCH
Confidence 45789999999999999999999 799999999999999999998877543
No 31
>KOG3554 consensus Histone deacetylase complex, MTA1 component [Chromatin structure and dynamics]
Probab=89.46 E-value=0.8 Score=52.16 Aligned_cols=48 Identities=27% Similarity=0.498 Sum_probs=37.9
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhChhhHHHHH-HhCCCCHHHHHHHHHHHHHH
Q 004715 21 TKQRERWTEEEHNRFLEALKLYGRAWQRIEE-HIGTKKAVQIRSHAQKFFSK 71 (734)
Q Consensus 21 tk~r~~WTeEEHelFLeGLe~YGrdWKkIAe-~VgTRT~~QVRSHAQKYF~K 71 (734)
.-+-+-|+..|-.+|.+||++||+|+..|-. |++=|+..-|- +-||+.
T Consensus 282 RDemEEWSasEanLFEeALeKyGKDFndIrqdfLPWKSl~sIv---eyYYmw 330 (693)
T KOG3554|consen 282 RDEMEEWSASEANLFEEALEKYGKDFNDIRQDFLPWKSLTSIV---EYYYMW 330 (693)
T ss_pred hhhhhhccchhhHHHHHHHHHhcccHHHHHHhhcchHHHHHHH---HHHHHH
Confidence 3345689999999999999999999999965 88888865554 335543
No 32
>KOG0051 consensus RNA polymerase I termination factor, Myb superfamily [Transcription]
Probab=89.13 E-value=0.45 Score=55.22 Aligned_cols=51 Identities=24% Similarity=0.551 Sum_probs=44.4
Q ss_pred Ceeccc-CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHH
Q 004715 17 PYTITK-QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKF 68 (734)
Q Consensus 17 Pytitk-~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKY 68 (734)
-|++-. .++.||.||.+.+-.-...+|.+|+.|+..|| |.+.-||.|+..|
T Consensus 376 ~y~~FE~~rg~wt~ee~eeL~~l~~~~g~~W~~Ig~~lg-r~P~~crd~wr~~ 427 (607)
T KOG0051|consen 376 AYTPFENKRGKWTPEEEEELKKLVVEHGNDWKEIGKALG-RMPMDCRDRWRQY 427 (607)
T ss_pred cCCccccccCCCCcchHHHHHHHHHHhcccHHHHHHHHc-cCcHHHHHHHHHh
Confidence 344444 89999999999999999999999999999998 5678899998865
No 33
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=86.51 E-value=3.3 Score=34.81 Aligned_cols=51 Identities=25% Similarity=0.485 Sum_probs=41.1
Q ss_pred CCCCCHHHHHHHHHHHHHh-----C------------hhhHHHHHHh-----CCCCHHHHHHHHHHHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKLY-----G------------RAWQRIEEHI-----GTKKAVQIRSHAQKFFSKLEK 74 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~Y-----G------------rdWKkIAe~V-----gTRT~~QVRSHAQKYF~Kl~k 74 (734)
...||.+|-+.+|+-|+.| | +.|..|+..| +.||..|++-.++.+-..+.+
T Consensus 2 ~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk 74 (78)
T PF13873_consen 2 KPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKK 74 (78)
T ss_pred CCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHH
Confidence 3579999999999999997 3 2799999843 379999999998886555544
No 34
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=84.97 E-value=1.8 Score=49.24 Aligned_cols=41 Identities=17% Similarity=0.496 Sum_probs=37.3
Q ss_pred CCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSH 64 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSH 64 (734)
...||.||.-||-.++..||+++.+|-..++-|+..-++-+
T Consensus 187 ~d~WT~Ed~vlFe~aF~~~GK~F~kIrq~LP~rsLaSlvqy 227 (534)
T KOG1194|consen 187 PDEWTAEDIVLFEQAFQFFGKDFHKIRQALPHRSLASLVQY 227 (534)
T ss_pred cccchHHHHHHHHHHHHHhcccHHHHHHHccCccHHHHHHH
Confidence 47899999999999999999999999999999997776654
No 35
>PF01285 TEA: TEA/ATTS domain family; InterPro: IPR000818 Transcriptional enhancer activators are nuclear proteins that contain a TEA/ATTSdomain, a DNA-binding region of 66-68 amino acids. The TEA/ATTS domain is found in the N-termini of certain gene regulatory proteins, such as the Simian virus 40 (SV40) enhancer factor TEF-1, yeast trans-acting factor TEC-1 (which is required for TY1 enhancer activity), and the Aspergillus abaA regulatory gene product. SV40 and retroviral enhancers, and those to which TEF-1, TEC-1 and abaA proteins bind, contain GT-IIC sites: the TEA/ATTS domain may therefore recognise and bind such sites. Secondary structure predictions suggest the presence of 3 helices, but have not confirmed the presence of the helix-turn-helix motif characteristic of many DNA-binding proteins: DNA-binding may therefore be effected by a different mechanism [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3L15_B 2HZD_A 3KYS_A 3JUA_C 4EAZ_B.
Probab=83.68 E-value=1.1 Score=50.29 Aligned_cols=48 Identities=27% Similarity=0.407 Sum_probs=32.6
Q ss_pred ccCCCCCCHHHHHHHHHHHHHhCh----hh----------HHHHHHhC-----CCCHHHHHHHHHHH
Q 004715 21 TKQRERWTEEEHNRFLEALKLYGR----AW----------QRIEEHIG-----TKKAVQIRSHAQKF 68 (734)
Q Consensus 21 tk~r~~WTeEEHelFLeGLe~YGr----dW----------KkIAe~Vg-----TRT~~QVRSHAQKY 68 (734)
....+.|+++=...|++||+.|.. .| +-|++||. +||..||.||.|-.
T Consensus 46 ~~~~~vw~~~~e~af~~al~~~~~~g~~k~~~~~~~~grn~li~~yi~~~tg~~rt~kqvsshiqvl 112 (431)
T PF01285_consen 46 GDGEGVWPPDIEQAFQEALAIYPPCGRRKLSDEGKMYGRNELISDYIKLKTGKTRTRKQVSSHIQVL 112 (431)
T ss_dssp GGGS--S-HHHHHHHHHHHHHS-SSS---HHHH-----THHHHHHHHHHHHS----SHHHHHHHHHH
T ss_pred CCCCCCCCHHHHHHHHHHHHhCCCCCCcccccccccccchhHHHHHHHHHhCcccchhHHHHHHHHH
Confidence 456789999999999999999852 22 25788763 69999999999964
No 36
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=75.55 E-value=1.7 Score=49.82 Aligned_cols=60 Identities=13% Similarity=0.269 Sum_probs=50.0
Q ss_pred CCeecccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHHHHHH
Q 004715 16 KPYTITKQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSKLEKE 75 (734)
Q Consensus 16 KPytitk~r~~WTeEEHelFLeGLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k~ 75 (734)
|++......+.|+..|.+..+-+.+.||. .|-+||..++.||..||+.|+-.|...+.+.
T Consensus 12 ~~~~~~~k~gsw~~~EDe~l~~~vk~l~~nnws~vas~~~~~~~kq~~~rw~~~lnp~lk~ 72 (512)
T COG5147 12 KLMQTKRKGGSWKRTEDEDLKALVKKLGPNNWSKVASLLISSTGKQSSNRWNNHLNPQLKK 72 (512)
T ss_pred ccccceecCCCCCCcchhHHHHHHhhcccccHHHHHHHhcccccccccchhhhhhchhccc
Confidence 44555567789999999999999999998 8999999888899999999996665554443
No 37
>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=71.45 E-value=23 Score=39.25 Aligned_cols=58 Identities=19% Similarity=0.412 Sum_probs=48.5
Q ss_pred cCCCCCCHHHHHHHHHHHHHh-Ch---hhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHhhhc
Q 004715 22 KQRERWTEEEHNRFLEALKLY-GR---AWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEALSK 79 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe~Y-Gr---dWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k~~~~k 79 (734)
.....||..|...+|.+|+.- |. +-..|+..|..|+..+|+..-|+.-.|+.++...+
T Consensus 19 ~gp~~Ws~rEkr~Llr~Lqar~g~~epd~ael~~~l~~Rs~aEI~~fl~~LK~rvareaiqk 80 (344)
T PF11035_consen 19 TGPAAWSAREKRQLLRLLQARRGQPEPDAAELAKELPGRSEAEIRDFLQQLKGRVAREAIQK 80 (344)
T ss_pred CCcccCcHHHHHHHHHHHHHhcCCCCcCHHHHHhhccCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 446799999999999999875 55 55567778999999999999999888888887654
No 38
>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=69.94 E-value=13 Score=35.37 Aligned_cols=50 Identities=20% Similarity=0.497 Sum_probs=39.4
Q ss_pred eecccCCCCCCHHHHHHHHHHHHHhCh----hhHHHHH------------HhCCCCHHHHHHHHHH
Q 004715 18 YTITKQRERWTEEEHNRFLEALKLYGR----AWQRIEE------------HIGTKKAVQIRSHAQK 67 (734)
Q Consensus 18 ytitk~r~~WTeEEHelFLeGLe~YGr----dWKkIAe------------~VgTRT~~QVRSHAQK 67 (734)
|..+..+..||++|..-+|-.|-+||- .|.+|-. |+.+||+..|.=++.-
T Consensus 43 y~~~~~~k~yseeEDRfLl~~~~~~G~~~~~~~e~Ik~~Ir~~p~FrFDwf~kSRt~~el~rR~~t 108 (118)
T PF09111_consen 43 YPPNNKKKVYSEEEDRFLLCMLYKYGYDAEGNWEKIKQEIRESPLFRFDWFFKSRTPQELQRRCNT 108 (118)
T ss_dssp STSTSS-SSS-HHHHHHHHHHHHHHTTTSTTHHHHHHHHHHH-CGGCT-HHHHTS-HHHHHHHHHH
T ss_pred cCCCCCCCCcCcHHHHHHHHHHHHhCCCCCchHHHHHHHHHhCCCcccchhcccCCHHHHHHHHHH
Confidence 555667889999999999999999997 7999854 4569999999988874
No 39
>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=65.38 E-value=28 Score=29.90 Aligned_cols=42 Identities=26% Similarity=0.491 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHHh---C----------hhhHHHHHHh----C-CCCHHHHHHHHHH
Q 004715 26 RWTEEEHNRFLEALKLY---G----------RAWQRIEEHI----G-TKKAVQIRSHAQK 67 (734)
Q Consensus 26 ~WTeEEHelFLeGLe~Y---G----------rdWKkIAe~V----g-TRT~~QVRSHAQK 67 (734)
+||+++.+.||+.|... | ..|+.|++.+ | ..|..||++|.+.
T Consensus 1 ~Wt~~~~~~ll~~~~e~~~~g~~~~~~~fk~~~w~~i~~~~~~~~~~~~t~~qlknk~~~ 60 (96)
T PF12776_consen 1 SWTPEMTRFLLDLLIEQINKGNRPTNGGFKKEGWNNIAEEFNEKTGLNYTKKQLKNKWKT 60 (96)
T ss_pred CCChHHHHHHHHHHHHHHHhCCCCCCCCcCHHHHHHHHHHHHHHhCCcccHHHHHHHHHH
Confidence 59999999999999654 1 1699998733 3 4689999999764
No 40
>COG5147 REB1 Myb superfamily proteins, including transcription factors and mRNA splicing factors [Transcription / RNA processing and modification / Cell division and chromosome partitioning]
Probab=55.11 E-value=15 Score=42.55 Aligned_cols=50 Identities=22% Similarity=0.442 Sum_probs=43.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHH
Q 004715 23 QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKL 72 (734)
Q Consensus 23 ~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~Kl 72 (734)
.+..|+.||.+..+..=..+|-.|..|+.+|+.||..||--....-+..+
T Consensus 71 k~~~~~~eed~~li~l~~~~~~~wstia~~~d~rt~~~~~ery~~~~~~~ 120 (512)
T COG5147 71 KKKNWSEEEDEQLIDLDKELGTQWSTIADYKDRRTAQQCVERYVNTLEDL 120 (512)
T ss_pred ccccccHHHHHHHHHHHHhcCchhhhhccccCccchHHHHHHHHHHhhhh
Confidence 57799999999999999999999999999999999999976655443333
No 41
>COG4425 Predicted membrane protein [Function unknown]
Probab=53.62 E-value=13 Score=42.98 Aligned_cols=50 Identities=30% Similarity=0.312 Sum_probs=38.6
Q ss_pred HHHHHHhhhhccCCCCCCCCCCCCCCCCCCCCCCCCCCCchhHHHHHHHHHHHHHHHHHHc
Q 004715 360 AAHAAASFAATFWPYTNMETSADSPTCPQGGFLSRQMSSPPSMAAIAAATVAAATAWWAAH 420 (734)
Q Consensus 360 AaHAAAsfAAsfWP~an~e~s~ds~~~~~~g~~~r~~~s~PSmAAIaAATVAAAtAWWAah 420 (734)
+-|+|+.|+-..|+|-+...|..-+ .|-+ =..+|||+|.+|..++|||+|
T Consensus 87 ~Gy~~gv~~~wl~~y~elp~~s~~~--------~R~~---~~~~ai~~~~~a~~fl~qa~~ 136 (588)
T COG4425 87 AGYGAGVFLHWLWRYLELPESSPRP--------PRWA---KPAAAIVGAAGAVGFLVQAAV 136 (588)
T ss_pred hhhHHHHHHHHHHHHhhCCCCCCCC--------cchh---hhHHHHHHHHHHHHHHHHHHH
Confidence 5699999999999999886544332 2222 236889999999999999997
No 42
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=51.93 E-value=23 Score=40.88 Aligned_cols=55 Identities=7% Similarity=0.007 Sum_probs=47.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHh
Q 004715 22 KQRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEA 76 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k~~ 76 (734)
+...+||.+|..+.+.+|++||++...|.-.||.++..|+.-..-.|-.+..-.+
T Consensus 367 ~~n~~~~T~~~la~v~~I~~~~~~~~pl~wrik~t~cmee~e~l~~~~Rr~mfea 421 (534)
T KOG1194|consen 367 RMNRCFDTPAALALIDNIKRKHHMCVPLVWRVKQTKCMEENEILNEEARRQMFEA 421 (534)
T ss_pred hhccccCcHHHHHHHHHHHHhccCcchhhhHhcCcchhhHHHHHHHHHHHHHHHH
Confidence 4457999999999999999999999999999999999999887777766655444
No 43
>KOG0050 consensus mRNA splicing protein CDC5 (Myb superfamily) [RNA processing and modification; Cell cycle control, cell division, chromosome partitioning]
Probab=50.12 E-value=17 Score=42.37 Aligned_cols=44 Identities=25% Similarity=0.541 Sum_probs=39.9
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHH
Q 004715 23 QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQK 67 (734)
Q Consensus 23 ~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQK 67 (734)
++.-|+.||.+++|.+.+++.--|..|+..|| ||..||--+..+
T Consensus 58 ~~tews~eederlLhlakl~p~qwrtIa~i~g-r~~~qc~eRy~~ 101 (617)
T KOG0050|consen 58 KKTEWSREEDERLLHLAKLEPTQWRTIADIMG-RTSQQCLERYNN 101 (617)
T ss_pred hhhhhhhhHHHHHHHHHHhcCCccchHHHHhh-hhHHHHHHHHHH
Confidence 46789999999999999999999999999998 899999887654
No 44
>KOG2009 consensus Transcription initiation factor TFIIIB, Bdp1 subunit [Transcription]
Probab=49.27 E-value=11 Score=44.26 Aligned_cols=42 Identities=21% Similarity=0.433 Sum_probs=39.2
Q ss_pred CCCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHH
Q 004715 23 QRERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSH 64 (734)
Q Consensus 23 ~r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSH 64 (734)
..++||.+|-++|-.+|..+|-++.-|+.....|+..||+--
T Consensus 408 ~~~~w~~se~e~fyka~~~~gs~~slis~l~p~R~rk~iK~K 449 (584)
T KOG2009|consen 408 ETDKWDASETELFYKALSERGSDFSLISNLFPLRDRKQIKAK 449 (584)
T ss_pred ccCcccchhhHHhhhHHhhhcccccccccccccccHHHHHHH
Confidence 467999999999999999999999999999999999999843
No 45
>KOG0385 consensus Chromatin remodeling complex WSTF-ISWI, small subunit [Transcription]
Probab=45.56 E-value=35 Score=41.84 Aligned_cols=60 Identities=23% Similarity=0.467 Sum_probs=50.5
Q ss_pred CCeecccCCCCCCHHHHHHHHHHHHHhCh-hhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHh
Q 004715 16 KPYTITKQRERWTEEEHNRFLEALKLYGR-AWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEA 76 (734)
Q Consensus 16 KPytitk~r~~WTeEEHelFLeGLe~YGr-dWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k~~ 76 (734)
|+--.+..-+.||+.+-..|+.|-++||| +-..|+.-|-. |+.-|..+|.-||.++.+..
T Consensus 787 k~~ll~~gft~w~k~df~~fi~a~eKygr~di~~ia~~~e~-~~eev~~y~rvfwer~~el~ 847 (971)
T KOG0385|consen 787 KEELLSQGFTNWTKRDFNQFIKANEKYGRDDIENIAAEVEG-TPEEVGEYARVFWERLEELS 847 (971)
T ss_pred hhhhhhccccchhhhhHHHHHHHhhccCcchhhhhHHhhcC-CHHHHHHHHHHHHHHHHHhh
Confidence 33334455568999999999999999999 89999997755 99999999999999988754
No 46
>COG0315 MoaC Molybdenum cofactor biosynthesis enzyme [Coenzyme metabolism]
Probab=41.77 E-value=22 Score=35.81 Aligned_cols=27 Identities=33% Similarity=0.535 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 004715 405 IAAATVAAATAWWAAHGLLPLCAPFHA 431 (734)
Q Consensus 405 IaAATVAAAtAWWAahGLLPlcaP~~~ 431 (734)
|++|=+|+..|==-+.-|+|||-||+.
T Consensus 55 l~tAriAgimaaKkT~elIPlCHpi~l 81 (157)
T COG0315 55 LATARIAGIMAAKRTSELIPLCHPLPL 81 (157)
T ss_pred HHHHHHHHHHHhhhhhhhCccCCCCcc
Confidence 556666666666677799999999654
No 47
>PRK13923 putative spore coat protein regulator protein YlbO; Provisional
Probab=40.63 E-value=51 Score=33.54 Aligned_cols=48 Identities=15% Similarity=0.250 Sum_probs=36.4
Q ss_pred CCCCCCHHHHHHHHHHHHHhCh-hhHHHHHH--hC---CCCHHHHHHHHHHHHH
Q 004715 23 QRERWTEEEHNRFLEALKLYGR-AWQRIEEH--IG---TKKAVQIRSHAQKFFS 70 (734)
Q Consensus 23 ~r~~WTeEEHelFLeGLe~YGr-dWKkIAe~--Vg---TRT~~QVRSHAQKYF~ 70 (734)
....||.||..++-+-+-.|++ .=.+++.| || .||+.+|..++--|..
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 4578999999999999999987 44555543 33 6999999999954443
No 48
>PF04504 DUF573: Protein of unknown function, DUF573; InterPro: IPR007592 This is a family of uncharacterised proteins.
Probab=40.13 E-value=68 Score=29.36 Aligned_cols=41 Identities=17% Similarity=0.336 Sum_probs=31.1
Q ss_pred CCCCHHHHHHHHHHHHHh----Ch----hhHHHHHHhCCC-----CHHHHHHHH
Q 004715 25 ERWTEEEHNRFLEALKLY----GR----AWQRIEEHIGTK-----KAVQIRSHA 65 (734)
Q Consensus 25 ~~WTeEEHelFLeGLe~Y----Gr----dWKkIAe~VgTR-----T~~QVRSHA 65 (734)
..||+|+.-.+|+||-.| |+ +|..+-++|... |..|+..-.
T Consensus 5 R~WS~eDEi~iL~gl~~~~~~~G~~p~~d~~~f~~~vk~~l~~~~s~~Ql~~Ki 58 (98)
T PF04504_consen 5 RLWSEEDEIVILQGLIDFRAKTGKSPQPDMNAFYDFVKGSLSFDVSKNQLYDKI 58 (98)
T ss_pred CCCCchHHHHHHHHHHHHHHhcCCCCCccHHHHHHHHHHHccCCCCHHHHHHHH
Confidence 469999999999999999 74 788877776543 556654443
No 49
>KOG4282 consensus Transcription factor GT-2 and related proteins, contains trihelix DNA-binding/SANT domain [Transcription]
Probab=39.77 E-value=83 Score=33.69 Aligned_cols=55 Identities=22% Similarity=0.451 Sum_probs=41.8
Q ss_pred CCCCCHHHHHHHHHHHHHhC----------hhhHHHHH---HhC-CCCHHHHHHHHHHHHHHHHHHhhh
Q 004715 24 RERWTEEEHNRFLEALKLYG----------RAWQRIEE---HIG-TKKAVQIRSHAQKFFSKLEKEALS 78 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~YG----------rdWKkIAe---~Vg-TRT~~QVRSHAQKYF~Kl~k~~~~ 78 (734)
...|+.+|-..||+.....- ..|..||. ..| -||+.||+.-..+-..+..+....
T Consensus 54 ~~~Ws~~et~~Li~~~~~~~~~~~~~~~k~~~We~va~k~~~~g~~rs~~qck~K~~nl~k~Yk~~k~~ 122 (345)
T KOG4282|consen 54 EPRWSEEETLTLIEIRGEMDVALRRGKLKGPLWEEVARKMAELGYPRSPKQCKAKIENLKKKYKKEKAK 122 (345)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHhhhhcccHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 47999999999998876532 26999998 244 699999999987766666665543
No 50
>cd08780 Death_TRADD Death Domain of Tumor Necrosis Factor Receptor 1-Associated Death Domain protein. Death domain (DD) of TRADD (TNF Receptor 1-Associated Death Domain or TNFRSF1A-associated via death domain) protein. TRADD is a central signaling adaptor for TNF-receptor 1 (TNFR1), mediating activation of Nuclear Factor -kappaB (NF-kB) and c-Jun N-terminal kinase (JNK), as well as caspase-dependent apoptosis. It also carries important immunological roles including germinal center formation, DR3-mediated T-cell stimulation, and TNFalpha-mediated inflammatory responses. 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 s
Probab=35.77 E-value=59 Score=30.31 Aligned_cols=38 Identities=16% Similarity=0.442 Sum_probs=26.1
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHHHhCC----CCHHHHHHHHHHH
Q 004715 28 TEEEHNRFLEALKLYGRAWQRIEEHIGT----KKAVQIRSHAQKF 68 (734)
Q Consensus 28 TeEEHelFLeGLe~YGrdWKkIAe~VgT----RT~~QVRSHAQKY 68 (734)
|.++++.|-+. .|++||+++..+|- =|..+|..-+.+|
T Consensus 1 ~~~~~q~~~~n---vGr~WK~laR~Lg~~cral~d~~ID~I~~~y 42 (90)
T cd08780 1 TPADQQHFAKS---VGKKWKPVGRSLQKNCRALRDPAIDNLAYEY 42 (90)
T ss_pred CHHHHHHHHHH---HhHHHHHHHHHHcccccccchhHHHHHHhhc
Confidence 45666666654 58999999999982 3555666655554
No 51
>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=33.98 E-value=82 Score=31.95 Aligned_cols=53 Identities=21% Similarity=0.297 Sum_probs=40.1
Q ss_pred CCCCCCHHHHHHHHHHHHHhCh-------hhHHHHHHhCCCCHHHHHHHHHHHHHHHHHHh
Q 004715 23 QRERWTEEEHNRFLEALKLYGR-------AWQRIEEHIGTKKAVQIRSHAQKFFSKLEKEA 76 (734)
Q Consensus 23 ~r~~WTeEEHelFLeGLe~YGr-------dWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k~~ 76 (734)
....||.||..++-+.+-.|=| .+..++.-+ +||+.=|..+|--|..|.-..+
T Consensus 3 RQDAWT~eeDlLLAEtVLrhIReG~TQL~AFeEvg~~L-~RTsAACGFRWNs~VRkqY~~~ 62 (161)
T TIGR02894 3 RQDAWTHEEDLLLAETVLRHIREGSTQLSAFEEVGRAL-NRTAAACGFRWNAYVRKQYEEA 62 (161)
T ss_pred cccccccHHHHHHHHHHHHHHhcchHHHHHHHHHHHHH-cccHHHhcchHHHHHHHHHHHH
Confidence 3568999999999999988844 344444333 6999999999998877655544
No 52
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=33.67 E-value=1.9e+02 Score=36.50 Aligned_cols=54 Identities=15% Similarity=0.356 Sum_probs=43.4
Q ss_pred cCCCCCCHHHHHHHHHHHHHhCh-hhHHHHH------------HhCCCCHHHHHHHHHHHHHHHHHH
Q 004715 22 KQRERWTEEEHNRFLEALKLYGR-AWQRIEE------------HIGTKKAVQIRSHAQKFFSKLEKE 75 (734)
Q Consensus 22 k~r~~WTeEEHelFLeGLe~YGr-dWKkIAe------------~VgTRT~~QVRSHAQKYF~Kl~k~ 75 (734)
.++..||+||.+.+|-.|-+||- .|.+|-. |+.+||+..|.-++.-...-+.|+
T Consensus 924 ~~~~~~~~~~d~~~~~~~~~~g~~~~~~~~~~i~~~~~f~fd~~~~srt~~~~~~r~~~l~~~~~~e 990 (1033)
T PLN03142 924 NKGKLYNEECDRFMLCMVHKLGYGNWDELKAAFRTSPLFRFDWFVKSRTPQELARRCDTLIRLIEKE 990 (1033)
T ss_pred CCCCcCCHHHHHHHHHHHHHhccchHHHHHHHHHhCCceeeehhhccCCHHHHHHHHHHHHHHHHHH
Confidence 34557999999999999999996 8999833 466999999999988655555554
No 53
>cd01420 MoaC_PE MoaC family, prokaryotic and eukaryotic. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=32.97 E-value=44 Score=33.06 Aligned_cols=27 Identities=33% Similarity=0.529 Sum_probs=18.2
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 004715 405 IAAATVAAATAWWAAHGLLPLCAPFHA 431 (734)
Q Consensus 405 IaAATVAAAtAWWAahGLLPlcaP~~~ 431 (734)
++.|-+|+..|==-+.-|+|||-|++.
T Consensus 41 l~vAriAgI~aaK~T~~LIPlCHpi~l 67 (140)
T cd01420 41 LAVARIAGIMAAKRTSELIPLCHPLPL 67 (140)
T ss_pred HHHHHHHHHHHHHhhhcccccCCCCcc
Confidence 344555555555567789999999644
No 54
>PRK12343 putative molybdenum cofactor biosynthesis protein MoaC; Reviewed
Probab=32.92 E-value=41 Score=33.72 Aligned_cols=25 Identities=32% Similarity=0.484 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHHHcCCCCCCCCCCC
Q 004715 407 AATVAAATAWWAAHGLLPLCAPFHA 431 (734)
Q Consensus 407 AATVAAAtAWWAahGLLPlcaP~~~ 431 (734)
+|-+|+-.|==-+.-|||||-|++.
T Consensus 51 ~AriAgi~aAK~T~~LIPlCHPl~l 75 (151)
T PRK12343 51 TARVAGILAVKKTPELIPMCHPIPI 75 (151)
T ss_pred HHHHHHHHHHHhhhhhccCCCCccc
Confidence 3334444444456689999999654
No 55
>KOG1019 consensus Retinoblastoma pathway protein LIN-9/chromatin-associated protein Aly [Chromatin structure and dynamics; Cell cycle control, cell division, chromosome partitioning; Signal transduction mechanisms]
Probab=32.88 E-value=22 Score=43.36 Aligned_cols=60 Identities=23% Similarity=0.405 Sum_probs=46.8
Q ss_pred CcccccccccCCCeecccCCCCCCHHHHHHHHHHHHHhChhhHHHHHHh-CCCCHHHHHHH
Q 004715 5 SSGEDLVLKTRKPYTITKQRERWTEEEHNRFLEALKLYGRAWQRIEEHI-GTKKAVQIRSH 64 (734)
Q Consensus 5 s~ge~~v~K~RKPytitk~r~~WTeEEHelFLeGLe~YGrdWKkIAe~V-gTRT~~QVRSH 64 (734)
+++.-...+-|++....+-.--|+..|-.+|+++..+||+.|++.+..+ ++|...+|..-
T Consensus 25 ~~~~~sKt~qR~~~~~d~l~pq~s~~~~e~~~k~~~k~~~~~r~~~~~~~~~R~s~~vell 85 (837)
T KOG1019|consen 25 DSGSTSKTPQRKRKLADKLSPQWSKLELERFYKAYRKRGREWRKSPAAVRSTRSSNMVELL 85 (837)
T ss_pred cccccccCCCCCcccccccCcchhHhhhhhhhhcccccccccccccccccchhhhhHHHHH
Confidence 3444444566777776677779999999999999999999999999876 56887777543
No 56
>PF12451 VPS11_C: Vacuolar protein sorting protein 11 C terminal; InterPro: IPR024763 Vps 11 is one of the evolutionarily conserved class C vacuolar protein sorting genes (c-vps: vps11, vps16, vps18, and vps33), whose products physically associate to form the c-vps protein complex required for vesicle docking and fusion. This entry represents the C-terminal domain of vps11.
Probab=32.18 E-value=37 Score=27.74 Aligned_cols=28 Identities=21% Similarity=0.421 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHHHHhChhhHHHHHHhCC
Q 004715 28 TEEEHNRFLEALKLYGRAWQRIEEHIGT 55 (734)
Q Consensus 28 TeEEHelFLeGLe~YGrdWKkIAe~VgT 55 (734)
..+.|++|...|+.-...++-||+|+|-
T Consensus 17 ~~~~~d~F~~~L~~s~D~F~vIaeyfGr 44 (49)
T PF12451_consen 17 SADQHDLFFKQLEESEDRFSVIAEYFGR 44 (49)
T ss_pred HhhcHHHHHHHHHhCCCCchhHHHHHcc
Confidence 3567999999998888899999999984
No 57
>cd00528 MoaC MoaC family. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=30.60 E-value=48 Score=32.67 Aligned_cols=27 Identities=33% Similarity=0.529 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 004715 405 IAAATVAAATAWWAAHGLLPLCAPFHA 431 (734)
Q Consensus 405 IaAATVAAAtAWWAahGLLPlcaP~~~ 431 (734)
++.|-+|+-.|==-+.-|+|||-|++.
T Consensus 41 l~~AriAgI~aaK~T~~LIPlCHpl~l 67 (136)
T cd00528 41 LAVARIAGIMAAKRTSELIPLCHPLPL 67 (136)
T ss_pred HHHHHHHHHHHHHhcccccccCCCCcc
Confidence 344555555555667899999999644
No 58
>TIGR00581 moaC molybdenum cofactor biosynthesis protein MoaC. MoaC catalyzes an early step in molybdenum cofactor biosynthesis in E. coli. The Arabidopsis homolog Cnx3 complements MoaC deficiency in E. coli (MUID:95197640). Eukarotic members of this family branch within the bacterial branch, with the archaeal members as an apparent outgroup. This protein is absent in a number of the pathogens with smaller genomes, including Mycoplasmas, Chlamydias, and spirochetes, but is found in most other complete genomes to date. The homolog form Synechocystis sp. is fused to a MobA-homologous region and is an outlier to all other bacterial forms by both neighbor-joining and UPGMA analyses. Members of this family are well-conserved. The seed for this model excludes both archaeal sequences and the most divergent bacterial sequences, but still finds all candidate MoaC sequences easily between trusted and noise cutoffs. We suggest that sequences branching outside the set that contains all seed members
Probab=30.41 E-value=46 Score=33.18 Aligned_cols=25 Identities=32% Similarity=0.505 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHcCCCCCCCCCCC
Q 004715 407 AATVAAATAWWAAHGLLPLCAPFHA 431 (734)
Q Consensus 407 AATVAAAtAWWAahGLLPlcaP~~~ 431 (734)
.|-||+-.|==-+.-|+|||-|++.
T Consensus 54 ~AriAgi~aaK~T~~lIPlCHpi~l 78 (147)
T TIGR00581 54 TARIAGIMAAKRTGDLIPLCHPLPL 78 (147)
T ss_pred HHHHHHHHHHHhhhhhcCCCCCccc
Confidence 3344444444455689999999654
No 59
>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=29.49 E-value=1.1e+02 Score=26.53 Aligned_cols=46 Identities=24% Similarity=0.375 Sum_probs=29.5
Q ss_pred CCCCCHHHHHHHHHHHHHhC---------hhhHHHHHH-hCCCCHHHHHHHHHHHH
Q 004715 24 RERWTEEEHNRFLEALKLYG---------RAWQRIEEH-IGTKKAVQIRSHAQKFF 69 (734)
Q Consensus 24 r~~WTeEEHelFLeGLe~YG---------rdWKkIAe~-VgTRT~~QVRSHAQKYF 69 (734)
|...|.||...++.-|+.+. +-|+.+++. +-..|-.=.|.|.-|.+
T Consensus 2 R~~fT~edD~~l~~~v~~~~~~~~~~~Gn~iwk~le~~~~t~HtwQSwR~Ry~K~L 57 (65)
T PF08914_consen 2 RTPFTEEDDAALLDYVKENERQGGSVSGNKIWKELEEKHPTRHTWQSWRDRYLKHL 57 (65)
T ss_dssp -----HHHHHHHHHHHHHT--STTTTTSSHHHHHHHHS-SSS--SHHHHHHHHHHT
T ss_pred CCCCCHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 56789999999999996653 169999995 44778777888855543
No 60
>KOG1079 consensus Transcriptional repressor EZH1 [Transcription]
Probab=28.02 E-value=43 Score=40.26 Aligned_cols=53 Identities=26% Similarity=0.329 Sum_probs=44.6
Q ss_pred CCCeecccC-CCCCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHH
Q 004715 15 RKPYTITKQ-RERWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQK 67 (734)
Q Consensus 15 RKPytitk~-r~~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQK 67 (734)
++|+...+. ...|+--|.-+|..+...||.+.-.|+..+++||=.||--+.|+
T Consensus 399 ~~~~~~~~~~~~ew~~~ek~~fr~~~~~~~~n~c~Iar~l~~ktC~~v~~~~~~ 452 (739)
T KOG1079|consen 399 QNPVHGKKDTNVEWNGAEKVLFRVGSTLYGTNRCSIARNLLTKTCRQVYEYEQK 452 (739)
T ss_pred cCcccccCCcccccchhhhHHHHhccccccchhhHHHHHhcchHHHHHHHHhhc
Confidence 445544333 34899999999999999999999999999999999999888775
No 61
>cd01419 MoaC_A MoaC family, archaeal. Members of this family are involved in molybdenum cofactor (Moco) biosynthesis, an essential cofactor of a diverse group of redox enzymes. MoaC, a small hexameric protein, converts, together with MoaA, a guanosine derivative to the precursor Z by inserting the carbon-8 of the purine between the 2' and 3' ribose carbon atoms, which is the first of three phases of Moco biosynthesis.
Probab=26.85 E-value=61 Score=32.19 Aligned_cols=26 Identities=31% Similarity=0.492 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHcCCCCCCCCCCC
Q 004715 406 AAATVAAATAWWAAHGLLPLCAPFHA 431 (734)
Q Consensus 406 aAATVAAAtAWWAahGLLPlcaP~~~ 431 (734)
+.|-+|+-.|==-+.-|+|||-|++.
T Consensus 42 ~vAriAgI~aaK~T~~LIPlCHpl~l 67 (141)
T cd01419 42 ATARIAGILAVKKTPELIPMCHPIPI 67 (141)
T ss_pred HHHHHHHHHHHHhhhhhccCCCCccc
Confidence 34445555554566789999999644
No 62
>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=26.05 E-value=2.2e+02 Score=22.26 Aligned_cols=35 Identities=11% Similarity=0.270 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHH
Q 004715 32 HNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQK 67 (734)
Q Consensus 32 HelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQK 67 (734)
....+.-....|..|+.||+.+| .|...|+.|-++
T Consensus 15 ~r~i~~l~~~~g~s~~eIa~~l~-~s~~~v~~~l~r 49 (54)
T PF08281_consen 15 QREIFLLRYFQGMSYAEIAEILG-ISESTVKRRLRR 49 (54)
T ss_dssp HHHHHHHHHTS---HHHHHHHCT-S-HHHHHHHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHHC-cCHHHHHHHHHH
Confidence 33344444556789999999987 677777777554
No 63
>smart00595 MADF subfamily of SANT domain.
Probab=25.87 E-value=1.5e+02 Score=25.23 Aligned_cols=22 Identities=23% Similarity=0.543 Sum_probs=19.5
Q ss_pred hhHHHHHHhCCCCHHHHHHHHHH
Q 004715 45 AWQRIEEHIGTKKAVQIRSHAQK 67 (734)
Q Consensus 45 dWKkIAe~VgTRT~~QVRSHAQK 67 (734)
.|..|+.-+|. |+.+|+.++..
T Consensus 29 aW~~Ia~~l~~-~~~~~~~kw~~ 50 (89)
T smart00595 29 AWEEIAEELGL-SVEECKKRWKN 50 (89)
T ss_pred HHHHHHHHHCc-CHHHHHHHHHH
Confidence 79999999988 99999988764
No 64
>PRK09364 moaC molybdenum cofactor biosynthesis protein MoaC; Provisional
Probab=25.15 E-value=66 Score=32.44 Aligned_cols=24 Identities=33% Similarity=0.531 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHcCCCCCCCCCCC
Q 004715 408 ATVAAATAWWAAHGLLPLCAPFHA 431 (734)
Q Consensus 408 ATVAAAtAWWAahGLLPlcaP~~~ 431 (734)
|-+|+..|==-+.-|||||-|++.
T Consensus 58 AriAgi~aaK~T~~LIPlCHpi~i 81 (159)
T PRK09364 58 ARIAGIMAAKRTSDLIPLCHPLML 81 (159)
T ss_pred HHHHHHHHHHhhhhhcccCCCCcc
Confidence 333333443456689999999644
No 65
>PF06461 DUF1086: Domain of Unknown Function (DUF1086); InterPro: IPR009462 This entry represents several eukaryotic domains of unknown function, which are present in chromodomain helicase DNA binding proteins. This domain is often found in conjunction with IPR000330 from INTERPRO, IPR001650 from INTERPRO, IPR009463 from INTERPRO, IPR000953 from INTERPRO and IPR001965 from INTERPRO.
Probab=22.55 E-value=2.1e+02 Score=28.79 Aligned_cols=49 Identities=22% Similarity=0.444 Sum_probs=43.2
Q ss_pred CCCHHHHHHHHHHHHHhCh---hhHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Q 004715 26 RWTEEEHNRFLEALKLYGR---AWQRIEEHIGTKKAVQIRSHAQKFFSKLEK 74 (734)
Q Consensus 26 ~WTeEEHelFLeGLe~YGr---dWKkIAe~VgTRT~~QVRSHAQKYF~Kl~k 74 (734)
-.+..+...||.+|-.||- +|+-+-..+.-||...|+.|+-=|+..|.-
T Consensus 40 GFn~rQR~~Fln~vMR~G~~~f~~~w~~~~Lr~Ks~~ei~aY~~LFm~HL~E 91 (145)
T PF06461_consen 40 GFNPRQRKAFLNAVMRYGMGAFDWKWFVPRLRGKSEKEIRAYGSLFMRHLCE 91 (145)
T ss_pred ccCHHHHHHHHHHHHHHCcCcccchHHhhhhccccHHHHHHHHHHHHHHhcC
Confidence 5689999999999999996 899888888999999999999877776643
No 66
>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=21.99 E-value=2.7e+02 Score=24.07 Aligned_cols=46 Identities=20% Similarity=0.312 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHHhChhhHHHHHHhCCCCHHHHHHHHHHHHHHHH
Q 004715 26 RWTEEEHNRFLEALKLYGRAWQRIEEHIGTKKAVQIRSHAQKFFSKLE 73 (734)
Q Consensus 26 ~WTeEEHelFLeGLe~YGrdWKkIAe~VgTRT~~QVRSHAQKYF~Kl~ 73 (734)
.+++.|...|..- -..|..+..||+.+|. +...|+.+-++-..+|.
T Consensus 110 ~L~~~~~~ii~~~-~~~g~s~~eIA~~l~~-s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLR-YLEGLSYKEIAEILGI-SVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhH-HhcCCCHHHHHHHHCC-CHHHHHHHHHHHHHHHH
Confidence 4555565555322 2347799999998886 66666666655555554
No 67
>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=21.17 E-value=2.6e+02 Score=24.21 Aligned_cols=40 Identities=23% Similarity=0.502 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhC-------hhhHHHHHHhCC---CC--HHHHHHHHHHHHHH
Q 004715 32 HNRFLEALKLYG-------RAWQRIEEHIGT---KK--AVQIRSHAQKFFSK 71 (734)
Q Consensus 32 HelFLeGLe~YG-------rdWKkIAe~VgT---RT--~~QVRSHAQKYF~K 71 (734)
+.+|..-.+.-| +.|..|++.+|= .+ ..+++.|-.+|+..
T Consensus 39 ~~Ly~~V~~~GG~~~V~~~~~W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 39 YKLYKAVMKRGGFDKVTKNKKWREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHHHHTSHHHHHHHTTHHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHHhCcCcccCcccchHHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 345555444444 279999997753 22 47888888887654
No 68
>PLN02375 molybderin biosynthesis protein CNX3
Probab=20.50 E-value=86 Score=33.97 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCCCC
Q 004715 405 IAAATVAAATAWWAAHGLLPLCAPFHA 431 (734)
Q Consensus 405 IaAATVAAAtAWWAahGLLPlcaP~~~ 431 (734)
++.|-||+-.|==-+.-|+|||-||+.
T Consensus 167 LavArIAGImAAKkTseLIPLCHPLpL 193 (270)
T PLN02375 167 LGVAKIAGINGAKQTSSLIPLCHNIAL 193 (270)
T ss_pred HHHHHHHHHHHhhccccccccCCCccc
Confidence 445555555555667899999999644
Done!