Query 028386
Match_columns 210
No_of_seqs 125 out of 210
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 10:42:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028386.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028386hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3219 Transcription initiati 100.0 5.4E-45 1.2E-49 311.1 12.2 114 96-210 81-195 (195)
2 PF04719 TAFII28: hTAFII28-lik 100.0 4.6E-43 1E-47 268.3 9.5 90 105-194 1-90 (90)
3 cd08048 TAF11 TATA Binding Pro 100.0 2.4E-38 5.2E-43 239.5 10.6 83 112-195 1-85 (85)
4 COG5251 TAF40 Transcription in 100.0 8.6E-32 1.9E-36 227.7 11.2 94 103-197 91-184 (199)
5 KOG3902 Histone acetyltransfer 99.3 2.4E-11 5.3E-16 110.9 10.3 99 98-197 191-330 (352)
6 PF00808 CBFD_NFYB_HMF: Histon 97.9 4.8E-05 1E-09 53.7 6.1 65 126-191 1-65 (65)
7 smart00803 TAF TATA box bindin 96.3 0.024 5.2E-07 41.1 7.0 65 126-192 1-65 (65)
8 cd07981 TAF12 TATA Binding Pro 95.7 0.093 2E-06 38.3 8.0 67 128-195 2-68 (72)
9 cd00074 H2A Histone 2A; H2A is 95.4 0.066 1.4E-06 43.0 7.0 66 127-193 20-85 (115)
10 PF00125 Histone: Core histone 94.9 0.1 2.2E-06 37.1 5.9 66 127-193 5-74 (75)
11 COG5262 HTA1 Histone H2A [Chro 94.1 0.13 2.8E-06 42.4 5.6 66 126-192 25-90 (132)
12 KOG0871 Class 2 transcription 93.5 0.39 8.4E-06 40.8 7.6 69 126-195 11-80 (156)
13 PF02969 TAF: TATA box binding 93.3 0.47 1E-05 34.8 6.8 65 126-192 2-66 (66)
14 smart00414 H2A Histone 2A. 93.3 0.31 6.7E-06 38.6 6.3 66 127-193 9-74 (106)
15 COG2036 HHT1 Histones H3 and H 92.8 0.58 1.3E-05 36.4 7.1 80 115-196 7-86 (91)
16 cd00076 H4 Histone H4, one of 92.0 1.1 2.4E-05 34.4 7.6 67 126-194 12-78 (85)
17 PTZ00017 histone H2A; Provisio 91.9 0.43 9.3E-06 39.6 5.6 66 127-193 27-92 (134)
18 PTZ00015 histone H4; Provision 90.4 1.7 3.7E-05 34.5 7.5 68 126-195 29-96 (102)
19 PLN00154 histone H2A; Provisio 89.9 1.2 2.7E-05 37.1 6.6 66 127-193 38-104 (136)
20 PLN00153 histone H2A; Provisio 89.7 1 2.2E-05 37.2 5.9 65 128-193 25-89 (129)
21 PLN00035 histone H4; Provision 89.6 2.2 4.7E-05 34.0 7.5 66 128-195 30-95 (103)
22 PLN00156 histone H2AX; Provisi 89.5 1.1 2.4E-05 37.4 6.0 65 128-193 30-94 (139)
23 PLN00157 histone H2A; Provisio 89.5 0.95 2.1E-05 37.5 5.5 65 128-193 27-91 (132)
24 smart00576 BTP Bromodomain tra 89.4 2.7 5.8E-05 30.8 7.4 64 130-195 9-72 (77)
25 KOG1659 Class 2 transcription 88.5 1.4 3E-05 39.4 6.3 68 125-193 11-78 (224)
26 PTZ00252 histone H2A; Provisio 88.3 1.7 3.8E-05 36.1 6.3 66 128-193 26-92 (134)
27 PF09415 CENP-X: CENP-S associ 87.0 1.5 3.2E-05 32.6 4.7 64 129-192 1-66 (72)
28 smart00417 H4 Histone H4. 86.8 2.3 4.9E-05 32.0 5.7 48 127-175 13-60 (74)
29 PF03847 TFIID_20kDa: Transcri 86.0 3.2 6.9E-05 30.5 6.0 64 129-193 1-64 (68)
30 cd08050 TAF6 TATA Binding Prot 83.3 6.3 0.00014 36.4 8.0 67 130-198 2-68 (343)
31 KOG1756 Histone 2A [Chromatin 81.8 5.2 0.00011 33.3 6.2 65 127-192 27-91 (131)
32 COG5208 HAP5 CCAAT-binding fac 81.5 3.6 7.9E-05 37.4 5.6 74 119-193 101-174 (286)
33 PF07524 Bromo_TP: Bromodomain 79.2 19 0.00042 25.9 7.9 64 130-195 9-72 (77)
34 COG5247 BUR6 Class 2 transcrip 73.2 12 0.00027 30.3 5.9 68 123-191 19-86 (113)
35 PRK07194 fliG flagellar motor 69.8 30 0.00066 31.9 8.5 90 104-200 215-323 (334)
36 PF07526 POX: Associated with 69.0 43 0.00093 27.7 8.4 41 116-162 89-132 (140)
37 smart00427 H2B Histone H2B. 68.2 34 0.00074 26.7 7.2 66 133-200 7-72 (89)
38 COG5150 Class 2 transcription 67.3 31 0.00067 29.1 7.2 67 126-195 10-79 (148)
39 PF01706 FliG_C: FliG C-termin 62.1 17 0.00037 28.0 4.6 69 127-200 27-107 (110)
40 PRK13916 plasmid segregation p 59.8 6.7 0.00014 30.9 1.9 18 182-199 31-48 (97)
41 PLN00158 histone H2B; Provisio 58.6 61 0.0013 26.6 7.3 62 133-195 33-94 (116)
42 smart00574 POX domain associat 54.5 76 0.0017 26.8 7.4 43 115-163 88-133 (140)
43 PTZ00463 histone H2B; Provisio 52.5 73 0.0016 26.2 6.9 66 133-200 34-99 (117)
44 PRK05686 fliG flagellar motor 51.2 38 0.00082 31.1 5.7 69 127-200 249-329 (339)
45 TIGR00207 fliG flagellar motor 50.6 40 0.00088 31.2 5.8 69 127-200 246-326 (338)
46 KOG0870 DNA polymerase epsilon 48.6 1E+02 0.0022 26.9 7.5 50 126-175 9-60 (172)
47 KOG1657 CCAAT-binding factor, 46.9 32 0.00068 30.9 4.3 71 122-193 69-139 (236)
48 KOG1142 Transcription initiati 46.5 34 0.00073 31.5 4.5 49 128-176 155-203 (258)
49 PF13443 HTH_26: Cro/C1-type H 46.1 7.1 0.00015 26.3 0.1 52 113-166 7-58 (63)
50 cd07978 TAF13 The TATA Binding 45.0 1.4E+02 0.0031 22.9 7.2 63 128-193 4-66 (92)
51 COG2074 2-phosphoglycerate kin 44.4 34 0.00073 32.0 4.2 78 101-201 58-138 (299)
52 PF12174 RST: RCD1-SRO-TAF4 (R 41.9 79 0.0017 23.3 5.1 38 106-143 16-57 (70)
53 KOG2140 Uncharacterized conser 39.7 1.3E+02 0.0028 31.1 7.6 78 98-175 137-244 (739)
54 PF03540 TFIID_30kDa: Transcri 39.5 1.4E+02 0.0029 21.2 6.4 47 128-175 3-49 (51)
55 KOG1757 Histone 2A [Chromatin 39.1 33 0.00071 28.4 2.9 65 127-192 30-95 (131)
56 PF04147 Nop14: Nop14-like fam 39.0 2.8E+02 0.0061 29.0 10.3 71 102-172 428-517 (840)
57 PF13335 Mg_chelatase_2: Magne 37.4 1.2E+02 0.0026 23.1 5.7 27 165-192 68-94 (96)
58 COG3492 Uncharacterized protei 35.2 1.6E+02 0.0034 23.7 6.1 53 109-170 3-56 (104)
59 PF02269 TFIID-18kDa: Transcri 34.7 51 0.0011 25.2 3.3 60 133-193 7-66 (93)
60 PRK14703 glutaminyl-tRNA synth 32.7 32 0.00069 35.8 2.4 94 106-204 586-683 (771)
61 PRK15398 aldehyde dehydrogenas 31.5 66 0.0014 30.9 4.2 46 131-177 8-53 (465)
62 PF05236 TAF4: Transcription i 30.6 96 0.0021 27.4 4.8 52 127-178 43-97 (264)
63 PF07462 MSP1_C: Merozoite sur 29.5 77 0.0017 32.2 4.3 14 145-158 463-476 (574)
64 PF11011 DUF2849: Protein of u 28.8 36 0.00077 26.4 1.5 18 177-194 64-81 (90)
65 COG5123 TOA2 Transcription ini 28.7 54 0.0012 26.6 2.6 32 120-152 5-36 (113)
66 PF02978 SRP_SPB: Signal pepti 28.6 80 0.0017 24.6 3.5 35 99-138 47-81 (104)
67 cd04411 Ribosomal_P1_P2_L12p R 27.1 35 0.00076 27.0 1.3 11 78-88 92-102 (105)
68 PF03115 Astro_capsid: Astrovi 26.8 21 0.00046 37.2 0.0 14 106-119 715-729 (787)
69 PF15510 CENP-W: Centromere ki 26.4 2.8E+02 0.0061 22.2 6.2 67 127-196 16-98 (102)
70 PF11521 TFIIE-A_C-term: C-ter 25.8 56 0.0012 25.2 2.2 21 105-125 58-78 (86)
71 KOG1819 FYVE finger-containing 25.5 74 0.0016 32.7 3.4 22 75-96 426-447 (990)
72 KOG3449 60S acidic ribosomal p 23.8 44 0.00095 27.3 1.3 9 80-88 100-108 (112)
73 KOG3467 Histone H4 [Chromatin 23.6 2.3E+02 0.0051 22.5 5.2 47 126-173 28-74 (103)
74 cd04404 RhoGAP-p50rhoGAP RhoGA 23.6 2.4E+02 0.0052 23.4 5.7 45 121-166 43-90 (195)
75 PF02268 TFIIA_gamma_N: Transc 23.6 23 0.00051 24.8 -0.3 34 119-153 2-35 (49)
76 PTZ00373 60S Acidic ribosomal 23.4 47 0.001 26.8 1.4 10 80-89 100-109 (112)
77 COG3937 Uncharacterized conser 23.1 1.1E+02 0.0024 24.8 3.4 36 157-195 43-78 (108)
78 KOG3463 Transcription initiati 22.5 81 0.0018 25.6 2.5 33 119-152 3-35 (109)
79 cd04378 RhoGAP_GMIP_PARG1 RhoG 22.0 1.7E+02 0.0037 24.7 4.6 45 122-167 37-84 (203)
80 PF08971 GlgS: Glycogen synthe 21.7 65 0.0014 24.1 1.7 23 104-126 29-55 (66)
81 COG3763 Uncharacterized protei 21.7 3.7E+02 0.0079 20.4 5.8 43 150-194 8-51 (71)
82 cd08768 Cdc6_C Winged-helix do 21.3 3E+02 0.0066 19.4 6.3 40 161-201 24-63 (87)
83 KOG1744 Histone H2B [Chromatin 20.4 4.2E+02 0.0092 22.0 6.4 77 122-201 33-109 (127)
84 PF09628 YvfG: YvfG protein; 20.3 3.6E+02 0.0077 20.2 5.3 39 149-196 24-67 (68)
85 cd07979 TAF9 TATA Binding Prot 20.2 4.5E+02 0.0097 20.9 7.9 63 132-196 6-68 (117)
No 1
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=100.00 E-value=5.4e-45 Score=311.08 Aligned_cols=114 Identities=51% Similarity=0.848 Sum_probs=108.5
Q ss_pred CCcHHHHHHHHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028386 96 SSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 175 (210)
Q Consensus 96 ~~d~e~~~km~~Ll~~fteEQl~RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E 175 (210)
+.+.++..+|+.||++||+||++|||.||||+|+|+.|||||++|||. +|++|++|+|+||||||||||||+|++||++
T Consensus 81 ~~~~ee~~r~q~L~s~fseEQl~RYEvfRrs~f~Ka~iKkL~~~itg~-~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~ 159 (195)
T KOG3219|consen 81 TVDAEEAQRMQTLLSNFSEEQLSRYEVFRRSAFPKAQIKKLMSSITGQ-SVSENVAIAMAGIAKVFVGEVVEEALDVREE 159 (195)
T ss_pred CcCHHHHHHHHHHHHhcCHHHHHHHHHHHHhcCCHHHHHHHHHHHhCC-ccCcceeeeecchhhHhHHHHHHHHHHHHHH
Confidence 335666679999999999999999999999999999999999999986 5999999999999999999999999999999
Q ss_pred hCcCCCCCchHHHHHHHHHHhcCCCC-CCCCCCCCC
Q 028386 176 RNESGPIRPCHIREAYRRLKLEGKVP-KRSVPRLFR 210 (210)
Q Consensus 176 ~~e~gPLqP~HIREA~RRL~~~Gkvp-~r~~~rlfr 210 (210)
|++++||||+|||||||||+.+|++| ++.++++||
T Consensus 160 ~~e~~PLqP~HIREA~rrL~~qgk~~~~~~~~~~fr 195 (195)
T KOG3219|consen 160 WGESGPLQPKHIREAYRRLKLQGKLPNSRYKKSMFR 195 (195)
T ss_pred hccCCCCCcHHHHHHHHHHHhcCCCCCCcccccccC
Confidence 99999999999999999999999999 888999998
No 2
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=100.00 E-value=4.6e-43 Score=268.28 Aligned_cols=90 Identities=51% Similarity=0.894 Sum_probs=68.4
Q ss_pred HHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCc
Q 028386 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRP 184 (210)
Q Consensus 105 m~~Ll~~fteEQl~RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP 184 (210)
|+.|+++||+||++|||+||||+|+|++|||||++++|+|+||+|++|+|+||||||||||||+|++||++|++++||+|
T Consensus 1 ~~~L~~~f~~eQ~~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P 80 (90)
T PF04719_consen 1 MQLLLSNFDEEQLDRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQP 80 (90)
T ss_dssp ---------HHHHHHHHHHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--H
T ss_pred ChHHHHcCCHHHHHHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence 78999999999999999999999999999999999999899999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHH
Q 028386 185 CHIREAYRRL 194 (210)
Q Consensus 185 ~HIREA~RRL 194 (210)
+|||||||||
T Consensus 81 ~hlreA~rrL 90 (90)
T PF04719_consen 81 DHLREAYRRL 90 (90)
T ss_dssp HHHHHHHHHH
T ss_pred HHHHHHHHhC
Confidence 9999999998
No 3
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=100.00 E-value=2.4e-38 Score=239.47 Aligned_cols=83 Identities=59% Similarity=0.965 Sum_probs=80.8
Q ss_pred CCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCc--CCCCCchHHHH
Q 028386 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNE--SGPIRPCHIRE 189 (210)
Q Consensus 112 fteEQl~RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e--~gPLqP~HIRE 189 (210)
||+|||+|||.||||+|+|++|||||+++++ |+||+||+|+|+||||+|||||||+|++||++|++ ++||+|+||||
T Consensus 1 f~~eQ~~Rye~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~Hire 79 (85)
T cd08048 1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLRE 79 (85)
T ss_pred CCHHHHHHHHHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHH
Confidence 8999999999999999999999999999987 79999999999999999999999999999999999 89999999999
Q ss_pred HHHHHH
Q 028386 190 AYRRLK 195 (210)
Q Consensus 190 A~RRL~ 195 (210)
|||||+
T Consensus 80 A~rrl~ 85 (85)
T cd08048 80 AYRRLK 85 (85)
T ss_pred HHHHhC
Confidence 999985
No 4
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=99.97 E-value=8.6e-32 Score=227.71 Aligned_cols=94 Identities=36% Similarity=0.653 Sum_probs=90.1
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCC
Q 028386 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPI 182 (210)
Q Consensus 103 ~km~~Ll~~fteEQl~RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPL 182 (210)
.++..|+.+||+||+.|||.|||++|||..||||+++|.+ |+|++|++|+|+|++|||||||||.|+.||++|.++|||
T Consensus 91 ~r~k~l~~~~deeq~~RyEvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl 169 (199)
T COG5251 91 ERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPL 169 (199)
T ss_pred HHHHHHHhhcCHHHHHHHHHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCC
Confidence 5788899999999999999999999999999999999875 899999999999999999999999999999999999999
Q ss_pred CchHHHHHHHHHHhc
Q 028386 183 RPCHIREAYRRLKLE 197 (210)
Q Consensus 183 qP~HIREA~RRL~~~ 197 (210)
.|.|+|||||++..+
T Consensus 170 ~p~h~reayr~~~k~ 184 (199)
T COG5251 170 IPFHKREAYRYKLKK 184 (199)
T ss_pred ChHHHHHHHHHHHHh
Confidence 999999999998865
No 5
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=99.27 E-value=2.4e-11 Score=110.94 Aligned_cols=99 Identities=21% Similarity=0.278 Sum_probs=80.1
Q ss_pred cHHHHHHHHH---HHhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcC----CCCCCccHHHHHHHHHHHHHHHHHHHHH
Q 028386 98 DPAKMAKMQA---ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITG----SQKISLPMTIVVCGIAKMFVGELVETAR 170 (210)
Q Consensus 98 d~e~~~km~~---Ll~~fteEQl~RYE~fRRS~f~K~~IKRLi~~vtg----sqsVs~nvvIavaGlaKvFVGELVEeAr 170 (210)
|+..+++|.. .-..||.+||..|..||+++|.+.+-||+ ..+.+ ..+++.++.-+++.||...|+-||+.|+
T Consensus 191 devt~~RLkrADrrTrimt~eqYvefsE~RqaSFt~RkgkrF-Rdwld~s~ld~rp~~~~mdILayLafEtVa~Lvd~AL 269 (352)
T KOG3902|consen 191 DEVTMRRLKRADRRTRIMTGEQYVEFSECRQASFTCRKGKRF-RDWLDLSALDLRPPTDTMDILAYLAFETVAALVDYAL 269 (352)
T ss_pred HHHHHHHHHHHHHHHhhccHHHHHHHHHHhhhhhhhhcchhH-HhhhCCchhccCCCccHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444443 55799999999999999999999999986 33333 2257888999999999999999999999
Q ss_pred HHHHHh----------------------------------CcCCCCCchHHHHHHHHHHhc
Q 028386 171 MVMTER----------------------------------NESGPIRPCHIREAYRRLKLE 197 (210)
Q Consensus 171 ~Vq~E~----------------------------------~e~gPLqP~HIREA~RRL~~~ 197 (210)
.|+... ....||+|+||+||||+|+-.
T Consensus 270 lvrq~~~~ka~~p~S~~~sa~~s~~~~H~~~e~t~~~G~e~v~~~lqp~hieea~R~~q~~ 330 (352)
T KOG3902|consen 270 LVRQRSDNKATEPYSSVTSAGGSSAMMHVCKEVTLFDGMEVVKPPLQPEHIEEARRRLQMS 330 (352)
T ss_pred HHHhhhhhcccCccccccCCCCchHHhccCcccccccCccccCCCcchHHHHHHHHHHhcc
Confidence 996641 136899999999999999964
No 6
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=97.86 E-value=4.8e-05 Score=53.69 Aligned_cols=65 Identities=15% Similarity=0.210 Sum_probs=53.5
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHH
Q 028386 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY 191 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~ 191 (210)
+.||.+.|||||...-+...||.+...+|+-.+-+||.+|..+|.++... +.+.=|+|.||..|+
T Consensus 1 ~~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~-~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 1 ASLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQR-DKRKTITYEDVAKAV 65 (65)
T ss_dssp -SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHH-TTSSEE-HHHHHHHH
T ss_pred CCCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCccCHHHHHHHC
Confidence 47999999999998755557999999999999999999999999998774 456689999999885
No 7
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=96.28 E-value=0.024 Score=41.06 Aligned_cols=65 Identities=20% Similarity=0.236 Sum_probs=55.4
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 028386 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (210)
+.||+..||+|..+. |-..+|+.+.-.++...+.|+-+|+..|.+++..-+ +.-|.+.+|.-|++
T Consensus 1 ~~~p~~~i~ria~~~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hak-Rktlt~~DI~~Alk 65 (65)
T smart00803 1 SWLPKETIKDVAESL-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSK-RTTLTTSDIDSALR 65 (65)
T ss_pred CCCCHHHHHHHHHHC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCeecHHHHHHHhC
Confidence 358999999998874 666799999999999999999999999999988653 34588999988764
No 8
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=95.70 E-value=0.093 Score=38.33 Aligned_cols=67 Identities=21% Similarity=0.279 Sum_probs=60.2
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 028386 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (210)
Q Consensus 128 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (210)
++|.++..|+..+.++..+++++..++.-++=-||-.+++.|..+...++.. -|.+..|.-+++|..
T Consensus 2 ~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~-tv~~~Di~l~l~r~~ 68 (72)
T cd07981 2 LTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSD-TLEVKDVQLHLERNW 68 (72)
T ss_pred CcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHhc
Confidence 5789999999999988889999999999999999999999999999887543 499999999988753
No 9
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=95.44 E-value=0.066 Score=43.04 Aligned_cols=66 Identities=15% Similarity=0.260 Sum_probs=57.0
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
.||-+.|.|+|..-.+...|+....+.++++--.++.||.|.|-...... ...-|.|.||..|++-
T Consensus 20 ~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~-k~krItp~hi~lAi~n 85 (115)
T cd00074 20 QFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDN-KKKRITPRHLQLAVRN 85 (115)
T ss_pred cCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCeEcHHHHHHHHhc
Confidence 57888899999875566789999999999999999999999999887654 3578999999999875
No 10
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=94.87 E-value=0.1 Score=37.15 Aligned_cols=66 Identities=23% Similarity=0.262 Sum_probs=52.6
Q ss_pred cCChhHHHHHHHHhcCC----CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 127 ALQKSNMRRLLVSITGS----QKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgs----qsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
..++.-++|++..+... ..++.....+|..+...|+.+|.+.|..+...-+ .-=|.|.||.-|.|.
T Consensus 5 ~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~k-R~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 5 LIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAK-RKTITPRDIQLAVRI 74 (75)
T ss_dssp SSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-BSEEGHHHHHHHHHH
T ss_pred ccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcC-CcEecHHHHHHHHhc
Confidence 34566677776666443 4789999999999999999999999999987654 345999999999874
No 11
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=94.14 E-value=0.13 Score=42.43 Aligned_cols=66 Identities=18% Similarity=0.255 Sum_probs=56.2
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 028386 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (210)
+-|+=..|||||..-...+.|+....+.++++--.++.||.|.|-.+.... ...-|-|.||..|.|
T Consensus 25 l~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~-kkkri~PrHlqlAIr 90 (132)
T COG5262 25 LIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDN-KKKRIIPRHLQLAIR 90 (132)
T ss_pred ccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhc-CcceechHHHHHHhc
Confidence 468888899999866667789999999999999999999999999886643 345689999999987
No 12
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=93.55 E-value=0.39 Score=40.84 Aligned_cols=69 Identities=13% Similarity=0.249 Sum_probs=52.8
Q ss_pred ccCChhHHHHHHHHhcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 028386 126 SALQKSNMRRLLVSITG-SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtg-sqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (210)
.+|||++|-|+|..+.. .-.|....--++---+=.||--|..+|-+|+.+. ...-|-|.|+-.|+..|-
T Consensus 11 ~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e-~KKTIa~EHV~KALe~Lg 80 (156)
T KOG0871|consen 11 LSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKE-AKKTIAPEHVIKALENLG 80 (156)
T ss_pred ccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHH-hcccCCHHHHHHHHHHcc
Confidence 47999999999999876 3345554433444445589999999999999876 456799999999988774
No 13
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=93.28 E-value=0.47 Score=34.80 Aligned_cols=65 Identities=15% Similarity=0.194 Sum_probs=47.6
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 028386 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (210)
+-|++..||-+..+ .|-.+++++++..++-=.-.-+.+||+.|.++|..- .+.-|.+.+|..|+|
T Consensus 2 s~~~~esvk~iAes-~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hs-kR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 2 SVFSQESVKDIAES-LGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHS-KRTKLTTDDINSALR 66 (66)
T ss_dssp ----HHHHHHHHHH-TT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHT-T-SSB-HHHHHHHH-
T ss_pred CcCCHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCCCCHHHHHHHhC
Confidence 45888999998766 465579999999999999999999999999998854 356799999998876
No 14
>smart00414 H2A Histone 2A.
Probab=93.27 E-value=0.31 Score=38.64 Aligned_cols=66 Identities=18% Similarity=0.293 Sum_probs=54.3
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
.||=..|.|+|..-+-...|+....+-++++--.++.||.|.|-.....- ...-|.|.||.-|.+-
T Consensus 9 ~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~-k~~rItp~hi~lAi~n 74 (106)
T smart00414 9 QFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDN-KKRRITPRHLQLAIRN 74 (106)
T ss_pred cCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccchHHHhhhccC
Confidence 46777899999876556789999999999999999999999998775543 3567999999977653
No 15
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=92.85 E-value=0.58 Score=36.41 Aligned_cols=80 Identities=19% Similarity=0.274 Sum_probs=68.5
Q ss_pred HHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHH
Q 028386 115 DQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL 194 (210)
Q Consensus 115 EQl~RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL 194 (210)
-+..||..+=...||++.|+|||.++.. ..||....-.+.-....|+=+|.+.|-.....- .+--+++..|.-|++++
T Consensus 7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~~~-~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha-~RKTV~~~DI~la~~~~ 84 (91)
T COG2036 7 KEIRRYQRSTDLLLPKAPVRRILRKAGA-ERVSSSAIEELQEALEEYLEEIAEDAVELAEHA-KRKTVKAEDIKLALKRL 84 (91)
T ss_pred HHHHhhhhhhhhhcCchHHHHHHHHHhH-HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCeecHHHHHHHHHHh
Confidence 4667899899999999999999999754 489999999999999999999999999887654 46679999999999887
Q ss_pred Hh
Q 028386 195 KL 196 (210)
Q Consensus 195 ~~ 196 (210)
..
T Consensus 85 ~~ 86 (91)
T COG2036 85 GR 86 (91)
T ss_pred cc
Confidence 64
No 16
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=92.03 E-value=1.1 Score=34.37 Aligned_cols=67 Identities=18% Similarity=0.244 Sum_probs=55.6
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHH
Q 028386 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL 194 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL 194 (210)
+.++|+.|+||+.. .|-..||..+...+..+.+.|+-+|+..|....+.- ...-+....|.-|++|.
T Consensus 12 ~gi~k~~I~RLarr-~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha-~RKTVt~~DV~~alkr~ 78 (85)
T cd00076 12 KGITKPAIRRLARR-GGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHA-KRKTVTAMDVVYALKRQ 78 (85)
T ss_pred ccCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcCcHHHHHHHHHHC
Confidence 36999999999877 465689999999999999999999999999886643 34458888888887764
No 17
>PTZ00017 histone H2A; Provisional
Probab=91.92 E-value=0.43 Score=39.62 Aligned_cols=66 Identities=17% Similarity=0.264 Sum_probs=53.1
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
.||=..|.|++..-.-...|+....+-++++--.++.||.|.|-...... ...-|.|.||.-|.+-
T Consensus 27 ~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~-kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 27 QFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDN-KKKRITPRHIQLAIRN 92 (134)
T ss_pred ccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhc-CCCeecHHHHHhhccC
Confidence 46667788888764445578888999999999999999999998876544 3568999999988874
No 18
>PTZ00015 histone H4; Provisional
Probab=90.42 E-value=1.7 Score=34.49 Aligned_cols=68 Identities=21% Similarity=0.266 Sum_probs=57.0
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 028386 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (210)
..++|+.|+||+.. .|-..||..+...+..+.+.|+-+|+..|..+.+.- ...-+....|.-|++|..
T Consensus 29 ~gI~k~~IrRLarr-~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA-~RKTVt~~DV~~AlKr~g 96 (102)
T PTZ00015 29 RGITKGAIRRLARR-GGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA-RRKTVTAMDVVYALKRQG 96 (102)
T ss_pred cCCCHHHHHHHHHH-cCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcccHHHHHHHHHhcC
Confidence 57999999999877 466689999999999999999999999999886643 455588889988877653
No 19
>PLN00154 histone H2A; Provisional
Probab=89.88 E-value=1.2 Score=37.08 Aligned_cols=66 Identities=17% Similarity=0.246 Sum_probs=51.8
Q ss_pred cCChhHHHHHHHHhc-CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 127 ALQKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 127 ~f~K~~IKRLi~~vt-gsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
.||=.-|.|++..-+ -.+.|+....+.++++--.++.||.|.|-......+ ..-|.|.||.-|.|-
T Consensus 38 ~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~k-k~RItPrHi~lAIrn 104 (136)
T PLN00154 38 QFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLK-VKRITPRHLQLAIRG 104 (136)
T ss_pred cCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhC-CceecHHHhhhhccC
Confidence 355666788877743 235789999999999999999999999987755443 456999999988764
No 20
>PLN00153 histone H2A; Provisional
Probab=89.73 E-value=1 Score=37.22 Aligned_cols=65 Identities=18% Similarity=0.271 Sum_probs=51.2
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 128 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
||=.-|.|++..-.-...|+....+-++++--.++.||.|.|-...... ....|.|.||.-|.|-
T Consensus 25 FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~n 89 (129)
T PLN00153 25 FPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDN-KKNRIVPRHIQLAIRN 89 (129)
T ss_pred cchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhc-CCCccChHHHHhhccC
Confidence 5556678887653334568888889999999999999999998876544 3579999999988764
No 21
>PLN00035 histone H4; Provisional
Probab=89.62 E-value=2.2 Score=34.04 Aligned_cols=66 Identities=20% Similarity=0.275 Sum_probs=56.5
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 028386 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (210)
Q Consensus 128 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (210)
||++.|+||+.. .|-..||..+...+..+.+.|+-+|+..|....+.- .+.-+....|.-|++|+.
T Consensus 30 ipk~~IrRLARr-~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA-~RKTV~~~DV~~Alkr~g 95 (103)
T PLN00035 30 ITKPAIRRLARR-GGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHA-RRKTVTAMDVVYALKRQG 95 (103)
T ss_pred CCHHHHHHHHHH-cCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcCcHHHHHHHHHHcC
Confidence 999999999877 466689999999999999999999999999887654 455688899998888764
No 22
>PLN00156 histone H2AX; Provisional
Probab=89.47 E-value=1.1 Score=37.45 Aligned_cols=65 Identities=17% Similarity=0.279 Sum_probs=51.6
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 128 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
||=.-|.|++..-.-...|+....+.++++--.++.||.|.|-...... ....|.|.||.-|+|-
T Consensus 30 FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~-kk~RItPrHi~lAIrn 94 (139)
T PLN00156 30 FPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDN-KKNRIVPRHIQLAVRN 94 (139)
T ss_pred cchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcCcHHHHHhhccC
Confidence 5556678887664334578888889999999999999999998876554 3579999999988764
No 23
>PLN00157 histone H2A; Provisional
Probab=89.46 E-value=0.95 Score=37.54 Aligned_cols=65 Identities=17% Similarity=0.262 Sum_probs=51.9
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 128 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
|+=..|.|++..-.-...|+....+-++++--.++.||.|.|-...... ...-|.|.||.-|.|-
T Consensus 27 FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~n 91 (132)
T PLN00157 27 FPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDN-KKSRIVPRHIQLAVRN 91 (132)
T ss_pred cchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhc-CCccccHHHHhhcccC
Confidence 5556688887664445578888899999999999999999998876544 3569999999988764
No 24
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=89.39 E-value=2.7 Score=30.75 Aligned_cols=64 Identities=17% Similarity=0.166 Sum_probs=52.1
Q ss_pred hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 028386 130 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (210)
Q Consensus 130 K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (210)
|..|.+++.. +|..++++...-.+.-+.--|+.+|...++..++--+.+.|. +..|..|+..+.
T Consensus 9 ~~~Vaqil~~-~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~-~~Dv~~Al~~~g 72 (77)
T smart00576 9 RIAVAQILES-AGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPN-LGDVVLALENLG 72 (77)
T ss_pred HHHHHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhC
Confidence 4556666655 577789999999999999999999999999999766666665 889999988764
No 25
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=88.49 E-value=1.4 Score=39.44 Aligned_cols=68 Identities=10% Similarity=0.345 Sum_probs=52.1
Q ss_pred hccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 125 RSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 125 RS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
-+.|+-+.|||||+.--.-.+|.+.|=++|+=---+|+-+||-.+.++-..++ ..-|.|.||+.|+..
T Consensus 11 ~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~-aKt~s~~hlkq~v~~ 78 (224)
T KOG1659|consen 11 KTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRG-AKTVSSSHLKQAVES 78 (224)
T ss_pred hccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcC-ccccCHHHHHHHHhc
Confidence 46899999999998642222566666566666667999999999999977764 557899999988754
No 26
>PTZ00252 histone H2A; Provisional
Probab=88.29 E-value=1.7 Score=36.15 Aligned_cols=66 Identities=14% Similarity=0.213 Sum_probs=52.4
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHh-CcCCCCCchHHHHHHHH
Q 028386 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTER-NESGPIRPCHIREAYRR 193 (210)
Q Consensus 128 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~-~e~gPLqP~HIREA~RR 193 (210)
|+=.-|.|++..-.-...|+....+-++++--.++.||.|.|-...... +...-|.|.||.-|+|-
T Consensus 26 FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 26 FPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred CchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 5555678887654444578888889999999999999999999987543 44679999999988764
No 27
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=86.99 E-value=1.5 Score=32.58 Aligned_cols=64 Identities=20% Similarity=0.190 Sum_probs=45.7
Q ss_pred ChhHHHHHHHHhcC--CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 028386 129 QKSNMRRLLVSITG--SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (210)
Q Consensus 129 ~K~~IKRLi~~vtg--sqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (210)
|+..|.||+..... +.+|+.+...+++-+-++||-|-|-.|.......+..+=|.+.||..-.=
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 46678888764322 23588889999999999999999999988766665555589999976543
No 28
>smart00417 H4 Histone H4.
Probab=86.85 E-value=2.3 Score=31.96 Aligned_cols=48 Identities=23% Similarity=0.259 Sum_probs=42.6
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028386 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 175 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E 175 (210)
.++|+.|+||+.. .|-..||..+...+..+.|.|+-+|+..|....+.
T Consensus 13 gI~k~~IrRLaRr-~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~h 60 (74)
T smart00417 13 GITKPAIRRLARR-GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEH 60 (74)
T ss_pred CCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 6999999999877 46668999999999999999999999999887653
No 29
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=85.98 E-value=3.2 Score=30.46 Aligned_cols=64 Identities=17% Similarity=0.273 Sum_probs=47.6
Q ss_pred ChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 129 QKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 129 ~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
.|.++..||.+|-++..+.+.+.-++.=||=-||-.+|+.|..+.+.|+. .-|.+..|.-.+.|
T Consensus 1 ~K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s-~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 1 SKRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKS-STLEVKDVQLHLER 64 (68)
T ss_dssp -HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SEE-HHHHHHHHHH
T ss_pred ChHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC-CCCCHHHHHHHHHh
Confidence 37889999999988888999999999999999999999999999988753 34666666665555
No 30
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=83.25 E-value=6.3 Score=36.40 Aligned_cols=67 Identities=13% Similarity=0.224 Sum_probs=57.0
Q ss_pred hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHhcC
Q 028386 130 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEG 198 (210)
Q Consensus 130 K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~G 198 (210)
+..||-+..++ |-..+++.++..++-....++.+|+++|.+.|..- .+.=|.+.||..|+|.+.-+-
T Consensus 2 ~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hs-kR~~l~~~Di~~Al~~~n~ep 68 (343)
T cd08050 2 QESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHS-KRRKLTTSDVNHALRLRNVEP 68 (343)
T ss_pred hhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCcCCHHHHHHHHHHhCCCc
Confidence 56788877664 54589999999999999999999999999998865 357899999999999887663
No 31
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=81.80 E-value=5.2 Score=33.30 Aligned_cols=65 Identities=18% Similarity=0.293 Sum_probs=49.2
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 028386 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (210)
-||=..|.|++..-...+.|+....+.|+++--....||.|.|-.+..+. ...-|.|.||+-|++
T Consensus 27 ~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardn-kk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 27 QFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDN-KKTRITPRHLQLAIR 91 (131)
T ss_pred ccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhc-CccccChHHHHHHHh
Confidence 35556677877652223467777777888999999999999998876653 345789999999998
No 32
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=81.55 E-value=3.6 Score=37.37 Aligned_cols=74 Identities=18% Similarity=0.308 Sum_probs=55.8
Q ss_pred HHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 119 RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
|-..+..-+|+-+.|||+|..--+---|+..+-++.+-++-+||.||+-.|--+ .|++.+.-||-..|.+|+.+
T Consensus 101 ~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~-ae~NkRRtLQksDia~Av~k 174 (286)
T COG5208 101 RQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWIN-AEENKRRTLQKSDIAAAVKK 174 (286)
T ss_pred HHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHH-HhHhhhhHHHHHHHHHHHHH
Confidence 336677778999999999865333223666666777889999999999988665 44456677888899998875
No 33
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=79.21 E-value=19 Score=25.93 Aligned_cols=64 Identities=16% Similarity=0.212 Sum_probs=51.0
Q ss_pred hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 028386 130 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (210)
Q Consensus 130 K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (210)
+..|..++.+ .|..++++...-++.-++.-|+-+|...++..++.-+.+.|. +.+|..|+..+-
T Consensus 9 ~~~va~il~~-~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~-~~Dv~~al~~~g 72 (77)
T PF07524_consen 9 RRSVAQILKH-AGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPN-LQDVEQALEEMG 72 (77)
T ss_pred HHHHHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhC
Confidence 3345555544 577788899999999999999999999999999777777777 888888887653
No 34
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=73.21 E-value=12 Score=30.26 Aligned_cols=68 Identities=10% Similarity=0.207 Sum_probs=43.6
Q ss_pred HHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHH
Q 028386 123 FRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY 191 (210)
Q Consensus 123 fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~ 191 (210)
|-.++||-+.|||||+---.-.+|++.+-++++----+|+.+||-+.++-.... .+.-+.-.||..|.
T Consensus 19 ~~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~-~skR~t~e~lk~a~ 86 (113)
T COG5247 19 KKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKK-SSKRMTSEFLKRAT 86 (113)
T ss_pred hhhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhc-cchhhHHHHHHHHH
Confidence 667899999999998743222256666555555555788888887776543322 23345556666554
No 35
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=69.82 E-value=30 Score=31.89 Aligned_cols=90 Identities=13% Similarity=0.286 Sum_probs=60.6
Q ss_pred HHHHHHhcCCHHHHHH-------HHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHH----HHHHH-H
Q 028386 104 KMQAILNQFTEDQMNR-------YESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGEL----VETAR-M 171 (210)
Q Consensus 104 km~~Ll~~fteEQl~R-------YE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGEL----VEeAr-~ 171 (210)
.+..-|..++++.... |+... ++....|..|+..+. ++..+.+++|+..-+.-+| -..|. .
T Consensus 215 ~il~~L~~~dp~~a~~Ir~~mF~FedL~--~~~~qtia~iL~~v~-----~~~la~aLkg~~~e~r~~il~nmS~Raa~~ 287 (334)
T PRK07194 215 QLMEMLKEHDEEVVNEIEDNMYDFFILS--RQSEETLQRLMDEVP-----MELWAVALKGTEPALRQAILRVMPKRQAQA 287 (334)
T ss_pred HHHHHHHhhCHHHHHHHHHhcCCHHHHh--cCCHHHHHHHHHhCC-----HHHHHHHHccCCHHHHHHHHHHccHHHHHH
Confidence 3444566667777666 55554 366777777776652 3578888988876555444 44444 4
Q ss_pred HHHHhCcCCCCCchHHHHH-------HHHHHhcCCC
Q 028386 172 VMTERNESGPIRPCHIREA-------YRRLKLEGKV 200 (210)
Q Consensus 172 Vq~E~~e~gPLqP~HIREA-------~RRL~~~Gkv 200 (210)
++++....||++...+.+| .|+|-.+|+|
T Consensus 288 l~eele~~gpV~~sdvE~Aq~~Iv~~~r~L~~~G~I 323 (334)
T PRK07194 288 LEAQIERLGPVPLSRVEQARKEIMALVRELAEAGEI 323 (334)
T ss_pred HHHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCE
Confidence 5667777999999988876 5677777764
No 36
>PF07526 POX: Associated with HOX; InterPro: IPR006563 This domain in found exclusively in plant proteins, associated with HOX domains which may suggest these proteins are homeodomain transcription factors.
Probab=69.00 E-value=43 Score=27.68 Aligned_cols=41 Identities=12% Similarity=0.294 Sum_probs=28.3
Q ss_pred HHHHHHHHHhccCChhHHHHHHH---HhcCCCCCCccHHHHHHHHHHHHH
Q 028386 116 QMNRYESFRRSALQKSNMRRLLV---SITGSQKISLPMTIVVCGIAKMFV 162 (210)
Q Consensus 116 Ql~RYE~fRRS~f~K~~IKRLi~---~vtgsqsVs~nvvIavaGlaKvFV 162 (210)
=-.||..|+. .|.-++. .++|...-..-...++..|+|.|=
T Consensus 89 Vd~RY~qY~~------Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR 132 (140)
T PF07526_consen 89 VDRRYRQYYD------QMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFR 132 (140)
T ss_pred HHHHHHHHHH------HHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHH
Confidence 3469999987 5666654 446643344557888999999884
No 37
>smart00427 H2B Histone H2B.
Probab=68.24 E-value=34 Score=26.68 Aligned_cols=66 Identities=14% Similarity=0.200 Sum_probs=47.4
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHhcCCC
Q 028386 133 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKV 200 (210)
Q Consensus 133 IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkv 200 (210)
|.|++.++-....++....-+|.+|..=+.-.|..+|-....- +...-|.+.+|+.|+|-+. .|++
T Consensus 7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~-nkr~TltsreIqtAvrl~L-pgeL 72 (89)
T smart00427 7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARY-NKKSTLSSREIQTAVRLIL-PGEL 72 (89)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCCcCCHHHHHHHHHHHc-cHHH
Confidence 7888888877777777777777766666666666677666543 3567899999999987664 3443
No 38
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=67.33 E-value=31 Score=29.08 Aligned_cols=67 Identities=19% Similarity=0.258 Sum_probs=46.6
Q ss_pred ccCChhHHHHHHHHhcCCC-CCCccH--HHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 028386 126 SALQKSNMRRLLVSITGSQ-KISLPM--TIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtgsq-sVs~nv--vIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (210)
-+|||++|.|.|.++..-- .++... +++=+|| .|+--|..+|-+++++. ...-|-|.|+-.|+.-|-
T Consensus 10 ~sLPKATVqKMvS~iLp~dl~ftKearei~in~ci--eFi~~lsseAne~ce~E-aKKTIa~EHviKALenLe 79 (148)
T COG5150 10 NSLPKATVQKMVSSILPKDLVFTKEAREIFINACI--EFINMLSSEANEACEEE-AKKTIAYEHVIKALENLE 79 (148)
T ss_pred ccCcHHHHHHHHHHhccccccccHHHHHHHHHHHH--HHHHHHHHHHHHHHHHH-HhccccHHHHHHHHHhcc
Confidence 3799999999988876522 122222 2333444 67888888999998865 345789999998887653
No 39
>PF01706 FliG_C: FliG C-terminal domain; InterPro: IPR023087 The flagellar motor switch in Escherichia coli and Salmonella typhimurium regulates the direction of flagellar rotation and hence controls swimming behaviour []. The switch is a complex apparatus that responds to signals transduced by the chemotaxis sensory signalling system during chemotactic behaviour []. CheY, the chemotaxis response regulator, is believed to act directly on the switch to induce tumbles in the swimming pattern, but no physical interactions of CheY and switch proteins have yet been demonstrated. The switch complex comprises at least three proteins - FliG, FliM and FliN. It has been shown that FliG interacts with FliM, FliM interacts with itself, and FliM interacts with FliN []. Several residues within the middle third of FliG appear to be strongly involved in the FliG-FliM interaction, with residues near the N- or C-termini being less important []. Such clustering suggests that FliG-FliM interaction plays a central role in switching. Analysis of the FliG, FliM and FliN sequences shows that none are especially hydrophobic or appear to be integral membrane proteins []. This result is consistent with other evidence suggesting that the proteins may be peripheral to the membrane, possibly mounted on the basal body M ring [, ]. FliG is present in about 25 copies per flagellum. This entry represents the C-terminal domain of FliG, the structure of which is known. This domain functions specifically in motor rotation [].; PDB: 3USY_B 3USW_A 3HJL_A 3AJC_A 1LKV_X 1QC7_B.
Probab=62.14 E-value=17 Score=27.96 Aligned_cols=69 Identities=26% Similarity=0.496 Sum_probs=40.4
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHH----HHHHHH-HHHHHHHHhCcCCCCCchHHHHH-------HHHH
Q 028386 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMF----VGELVE-TARMVMTERNESGPIRPCHIREA-------YRRL 194 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvF----VGELVE-eAr~Vq~E~~e~gPLqP~HIREA-------~RRL 194 (210)
.++...+.+|+.++. ++.+++++.|-..-| ++.|-. .|..|+.+....||+.+..+.+| .|+|
T Consensus 27 ~l~~~~l~~ll~~v~-----~~~la~ALkga~~e~~~~il~nms~r~a~~l~~e~~~~g~v~~~di~~Aq~~iv~~~r~l 101 (110)
T PF01706_consen 27 RLDDRDLQKLLREVD-----PDDLALALKGASEELREKILSNMSKRAAEMLREEMEALGPVRLSDIEEAQREIVEIVRRL 101 (110)
T ss_dssp GS-HHHHHHHHTTS------HHHHHHHHCTS-HHHHHHHHTTS-HHHHHHHHHHHHHH-S--HHHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHCC-----HhHHHHHHccCCHHHHHHHHHHcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHH
Confidence 355666666665542 356888887766554 444444 34566777778899999988876 4566
Q ss_pred HhcCCC
Q 028386 195 KLEGKV 200 (210)
Q Consensus 195 ~~~Gkv 200 (210)
..+|.|
T Consensus 102 ~~~G~I 107 (110)
T PF01706_consen 102 EEEGEI 107 (110)
T ss_dssp HHTTSS
T ss_pred HHCcCE
Confidence 666664
No 40
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=59.80 E-value=6.7 Score=30.92 Aligned_cols=18 Identities=44% Similarity=0.481 Sum_probs=15.7
Q ss_pred CCchHHHHHHHHHHhcCC
Q 028386 182 IRPCHIREAYRRLKLEGK 199 (210)
Q Consensus 182 LqP~HIREA~RRL~~~Gk 199 (210)
-.|.|||+|+|||..+|-
T Consensus 31 T~~~~iR~~L~rYI~~~G 48 (97)
T PRK13916 31 TKTAHIREALRRYIEEIG 48 (97)
T ss_pred CccHHHHHHHHHHHHhcC
Confidence 468999999999999864
No 41
>PLN00158 histone H2B; Provisional
Probab=58.60 E-value=61 Score=26.55 Aligned_cols=62 Identities=13% Similarity=0.149 Sum_probs=43.6
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 028386 133 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (210)
Q Consensus 133 IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (210)
|.|++.+|-....||....-+|.+|..=++-.|..+|-.+..- +...-|.+.+|+.|+|-+.
T Consensus 33 I~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~-nkr~TltsrEIqtAvrLvL 94 (116)
T PLN00158 33 IYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARY-NKKPTVTSREIQTAVRLIL 94 (116)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCCcCCHHHHHHHHHHhc
Confidence 8888888877777777766667765555555555566555432 4567899999999987664
No 42
>smart00574 POX domain associated with HOX domains.
Probab=54.46 E-value=76 Score=26.75 Aligned_cols=43 Identities=14% Similarity=0.249 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhccCChhHHHHHHH---HhcCCCCCCccHHHHHHHHHHHHHH
Q 028386 115 DQMNRYESFRRSALQKSNMRRLLV---SITGSQKISLPMTIVVCGIAKMFVG 163 (210)
Q Consensus 115 EQl~RYE~fRRS~f~K~~IKRLi~---~vtgsqsVs~nvvIavaGlaKvFVG 163 (210)
|=-.||..|+. .|.-++. .++|...-..-...++..|++.|=+
T Consensus 88 eVd~RY~qY~~------qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr~ 133 (140)
T smart00574 88 EVDRRYKHYYE------QMQTVVSSFDQAAGLGAAKPYTALALKTISRHFRC 133 (140)
T ss_pred HHHHHHHHHHH------HHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHH
Confidence 34579999986 5666654 3455433333467788888888843
No 43
>PTZ00463 histone H2B; Provisional
Probab=52.54 E-value=73 Score=26.16 Aligned_cols=66 Identities=12% Similarity=0.124 Sum_probs=43.3
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHhcCCC
Q 028386 133 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKV 200 (210)
Q Consensus 133 IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkv 200 (210)
|.|++.+|-....||....-+|.+|..=++-.|..+|-.+..- +...-|.+.+|+.|+|-+. .|+|
T Consensus 34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~-nkr~TltsrEIQtAvrLlL-pGEL 99 (117)
T PTZ00463 34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKY-TRRDTLSSREIQTAIRLVL-PGEL 99 (117)
T ss_pred HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCcCCHHHHHHHHhhcc-cHHH
Confidence 7888888877767777666666654444444444455554332 4577899999999987554 4554
No 44
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=51.16 E-value=38 Score=31.12 Aligned_cols=69 Identities=25% Similarity=0.476 Sum_probs=49.7
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHHHH----HHHHHHHHHHH-HHHHHhCcCCCCCchHHHHHH-------HHH
Q 028386 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAK----MFVGELVETAR-MVMTERNESGPIRPCHIREAY-------RRL 194 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaK----vFVGELVEeAr-~Vq~E~~e~gPLqP~HIREA~-------RRL 194 (210)
+++...+.+|+..|. ++.+++++.|-.. .|..-|-..+. .++++....||+++..+.+|- |+|
T Consensus 249 ~l~~~~l~~ll~~v~-----~~~L~~ALkga~~~~~~~il~nmS~R~a~~l~eel~~~g~v~~~dve~Aq~~I~~~~r~l 323 (339)
T PRK05686 249 DLDDRSIQRLLREVD-----NDVLALALKGASEELREKFLSNMSKRAAEMLREDLEALGPVRLSDVEEAQKKIVQIARRL 323 (339)
T ss_pred cCCHHHHHHHHHhCC-----HHHHHHHHCCCCHHHHHHHHHhcCHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHHH
Confidence 477777888887763 3678899987554 55666666554 556677779999999988774 577
Q ss_pred HhcCCC
Q 028386 195 KLEGKV 200 (210)
Q Consensus 195 ~~~Gkv 200 (210)
-.+|+|
T Consensus 324 ~~~G~I 329 (339)
T PRK05686 324 AEAGEI 329 (339)
T ss_pred HHCCCE
Confidence 777764
No 45
>TIGR00207 fliG flagellar motor switch protein FliG. The fliG protein along with fliM and fliN interact to form the switch complex of the bacterial flagellar motor located at the base of the basal body. This complex interacts with chemotaxis proteins (eg CHEY). In addition the complex interacts with other components of the motor that determine the direction of flagellar rotation. The model contains putative members of the fliG family at scores of less than 100 from Agrobacterium radiobacter and Sinorhizobium meliloti as well as fliG-like genes from treponema pallidum and Borrelia burgdorferi. That is why the suggested cutoff is set at 20 but was set at 100 to construct the family.
Probab=50.58 E-value=40 Score=31.17 Aligned_cols=69 Identities=22% Similarity=0.409 Sum_probs=50.1
Q ss_pred cCChhHHHHHHHHhcCCCCCCccHHHHHHHH----HHHHHHHHHHHHHH-HHHHhCcCCCCCchHHHHH-------HHHH
Q 028386 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGI----AKMFVGELVETARM-VMTERNESGPIRPCHIREA-------YRRL 194 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgsqsVs~nvvIavaGl----aKvFVGELVEeAr~-Vq~E~~e~gPLqP~HIREA-------~RRL 194 (210)
.+....|.+|+..|. ++.+++++.|- -.-|..-+-..|.+ ++++....||++...+.+| .|+|
T Consensus 246 ~ld~~~l~~llrev~-----~~~L~~ALkga~~e~~~~il~nmS~R~a~~l~ee~~~~GpV~~sdvE~Aq~~Iv~~~r~L 320 (338)
T TIGR00207 246 DLDDRSIQRVLREVD-----SEDLLLALKGAEQPLREKFLNNMSQRAAEILKEDMEFLGPVRLKDVEEAQKKIVSIVRKL 320 (338)
T ss_pred cCCHHHHHHHHHhCC-----HHHHHHHHCcCCHHHHHHHHHHhhHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHHHHH
Confidence 477777888887762 35788888774 45666677776654 4667777999999988876 5677
Q ss_pred HhcCCC
Q 028386 195 KLEGKV 200 (210)
Q Consensus 195 ~~~Gkv 200 (210)
-.+|.|
T Consensus 321 ~~~G~I 326 (338)
T TIGR00207 321 EETGEI 326 (338)
T ss_pred HHCCCE
Confidence 788874
No 46
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=48.62 E-value=1e+02 Score=26.86 Aligned_cols=50 Identities=18% Similarity=0.222 Sum_probs=41.3
Q ss_pred ccCChhHHHHHHHHhcCC--CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028386 126 SALQKSNMRRLLVSITGS--QKISLPMTIVVCGIAKMFVGELVETARMVMTE 175 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtgs--qsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E 175 (210)
-.||++.|.||+..+..- .+|+.....+|+=-|-|||--|...|.+++..
T Consensus 9 l~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~ 60 (172)
T KOG0870|consen 9 LNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKD 60 (172)
T ss_pred hhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 368999999998887542 24777788889999999999999999998774
No 47
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=46.89 E-value=32 Score=30.90 Aligned_cols=71 Identities=18% Similarity=0.319 Sum_probs=52.1
Q ss_pred HHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 122 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 122 ~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
.|....|+.+.|||+|.+=-.-++|+....+.++-.+-+||-||...+- +..+.+.+..|+=.||-.|..+
T Consensus 69 d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw-~~Tee~~rrtl~~sdia~av~~ 139 (236)
T KOG1657|consen 69 DFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSW-VHTEENKRRTLQKSDIAAAVTQ 139 (236)
T ss_pred chhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhh-hhhcccccccchHHHHHHHhcc
Confidence 4667799999999998764444478888899999999999999988742 3333345556666777666544
No 48
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=46.49 E-value=34 Score=31.46 Aligned_cols=49 Identities=22% Similarity=0.358 Sum_probs=42.2
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028386 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTER 176 (210)
Q Consensus 128 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~ 176 (210)
+.|.+|..|+..|.+...+-++|-.+|.=||==||-.||..|..+.+.|
T Consensus 155 l~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHR 203 (258)
T KOG1142|consen 155 LSKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHR 203 (258)
T ss_pred ccccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4467788888888888778889999999999999999999998887765
No 49
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=46.10 E-value=7.1 Score=26.34 Aligned_cols=52 Identities=17% Similarity=0.207 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHH
Q 028386 113 TEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELV 166 (210)
Q Consensus 113 teEQl~RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELV 166 (210)
.+-.+..++..+++.++++.|.++++.-. .+++-..+..|+-+-.+=++||+
T Consensus 7 ~~~~it~~~La~~~gis~~tl~~~~~~~~--~~~~~~~l~~ia~~l~~~~~el~ 58 (63)
T PF13443_consen 7 AERGITQKDLARKTGISRSTLSRILNGKP--SNPSLDTLEKIAKALNCSPEELF 58 (63)
T ss_dssp HHTT--HHHHHHHHT--HHHHHHHHTTT-------HHHHHHHHHHHT--HHHCT
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHhccc--ccccHHHHHHHHHHcCCCHHHHh
Confidence 34456788889999999999999986421 23444444444444333344443
No 50
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=45.02 E-value=1.4e+02 Score=22.93 Aligned_cols=63 Identities=17% Similarity=0.213 Sum_probs=46.4
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 128 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
|.+. |+.+|=..-..+.+.+..+.+|-.|.--||-+|+-+|..+.. | ..+.+.+..|.=++|+
T Consensus 4 f~~e-i~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~-r~~k~~~eD~~FliR~ 66 (92)
T cd07978 4 FTKE-IRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-R-RRGKVKVEDLIFLLRK 66 (92)
T ss_pred cHHH-HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-c-CCCCCCHHHHHHHHhc
Confidence 4433 777775543334556678888899999999999999999977 4 3455699999888775
No 51
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=44.39 E-value=34 Score=32.00 Aligned_cols=78 Identities=22% Similarity=0.303 Sum_probs=47.0
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHH---HhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 028386 101 KMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLV---SITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERN 177 (210)
Q Consensus 101 ~~~km~~Ll~~fteEQl~RYE~fRRS~f~K~~IKRLi~---~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~ 177 (210)
-++-.+.|+..-++|...||..||+ ||+.+. -..|+ ++|++|.-| |..|..+.+
T Consensus 58 ir~~~~~l~~k~~~e~a~rY~lwR~-------ir~~~~p~IILIGG----------asGVGkStI------A~ElA~rLg 114 (299)
T COG2074 58 IREVYQKLLEKGDPEVAKRYLLWRR-------IRKMKRPLIILIGG----------ASGVGKSTI------AGELARRLG 114 (299)
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHH-------HhccCCCeEEEecC----------CCCCChhHH------HHHHHHHcC
Confidence 3456778999999999999999999 444321 11222 245555433 444555555
Q ss_pred cCCCCCchHHHHHHHHHHhcCCCC
Q 028386 178 ESGPIRPCHIREAYRRLKLEGKVP 201 (210)
Q Consensus 178 e~gPLqP~HIREA~RRL~~~Gkvp 201 (210)
=+.-|--++|||-+|.+...-.+|
T Consensus 115 I~~visTD~IREvlR~ii~~~l~P 138 (299)
T COG2074 115 IRSVISTDSIREVLRKIISPELLP 138 (299)
T ss_pred CceeecchHHHHHHHHhCCHHhcc
Confidence 455566666776666665433333
No 52
>PF12174 RST: RCD1-SRO-TAF4 (RST) plant domain; InterPro: IPR022003 This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=41.87 E-value=79 Score=23.33 Aligned_cols=38 Identities=24% Similarity=0.545 Sum_probs=29.9
Q ss_pred HHHHhcCCHHHHH----HHHHHHhccCChhHHHHHHHHhcCC
Q 028386 106 QAILNQFTEDQMN----RYESFRRSALQKSNMRRLLVSITGS 143 (210)
Q Consensus 106 ~~Ll~~fteEQl~----RYE~fRRS~f~K~~IKRLi~~vtgs 143 (210)
..|...+++.+++ .|+.||+..++|...=|.+..|+|.
T Consensus 16 ~~l~~~l~~~~~~~l~~~Y~~~k~~kIsR~~fvr~lR~IVGD 57 (70)
T PF12174_consen 16 SALSKHLPPSKMDLLQKHYEEFKKKKISREEFVRKLRQIVGD 57 (70)
T ss_pred HHHHHHCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 3455677777664 7999999999999977777888885
No 53
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=39.69 E-value=1.3e+02 Score=31.12 Aligned_cols=78 Identities=24% Similarity=0.386 Sum_probs=53.8
Q ss_pred cHHHHHHHHHHHhcCCHHHHHH--HHHHHhc------cCChhHHHHHHH----------------HhcCCCCCCccHHHH
Q 028386 98 DPAKMAKMQAILNQFTEDQMNR--YESFRRS------ALQKSNMRRLLV----------------SITGSQKISLPMTIV 153 (210)
Q Consensus 98 d~e~~~km~~Ll~~fteEQl~R--YE~fRRS------~f~K~~IKRLi~----------------~vtgsqsVs~nvvIa 153 (210)
.|.+.+.|+.-+..=+..+|.| ||+.|.+ ++|..+|+-+|. +|.-.|.-+++.+-|
T Consensus 137 PPaKL~~mq~qi~Dk~s~~yQRmnWEalkksInglInkvn~sNi~~ii~eLfqeNiirgRgl~crsv~~aq~asp~ft~v 216 (739)
T KOG2140|consen 137 PPAKLRMMQAQITDKNSIEYQRMNWEALKKSINGLINKVNASNIQEIIRELFQENIIRGRGLLCRSVMQAQAASPGFTPV 216 (739)
T ss_pred CHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHhccchhHHHHHHHHhcCCCCcHH
Confidence 5666677777776666666666 8888886 677777766632 222234456677777
Q ss_pred HHHHHHHH------HHHHHHHHHHHHHH
Q 028386 154 VCGIAKMF------VGELVETARMVMTE 175 (210)
Q Consensus 154 vaGlaKvF------VGELVEeAr~Vq~E 175 (210)
.++|+-|+ ||||+-+-+-||..
T Consensus 217 yaALvAviNskfP~IgElLlkrLilqf~ 244 (739)
T KOG2140|consen 217 YAALVAVINSKFPQIGELLLKRLILQFK 244 (739)
T ss_pred HHHHHHHHccCCchHHHHHHHHHHHHHH
Confidence 77777765 89999888877764
No 54
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=39.48 E-value=1.4e+02 Score=21.15 Aligned_cols=47 Identities=15% Similarity=0.129 Sum_probs=37.2
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028386 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 175 (210)
Q Consensus 128 f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E 175 (210)
+|...+.-+++. .|.+.....++=.|+=.+-=||-+|+..|++.++-
T Consensus 3 IPD~v~~~yL~~-~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 3 IPDEVTDYYLER-SGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCHHHHHHHHHH-CCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 567777777766 57665556788889999999999999999887653
No 55
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=39.07 E-value=33 Score=28.39 Aligned_cols=65 Identities=18% Similarity=0.279 Sum_probs=44.7
Q ss_pred cCChhHHHHHHHH-hcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 028386 127 ALQKSNMRRLLVS-ITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (210)
Q Consensus 127 ~f~K~~IKRLi~~-vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (210)
-||=..|.|.+.+ ++...+|...-++-+++|-..+-.|+.|.|=..-+.. .-.-|.|.||+-|.|
T Consensus 30 qFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdL-KvKRitprHlqLAiR 95 (131)
T KOG1757|consen 30 QFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDL-KVKRITPRHLQLAIR 95 (131)
T ss_pred ccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccc-eeeeccchhheeeec
Confidence 3555567777654 3444567778888899999999999999874332211 123488999998876
No 56
>PF04147 Nop14: Nop14-like family ; InterPro: IPR007276 Emg1 and Nop14 are novel proteins whose interaction is required for the maturation of the 18S rRNA and for 40S ribosome production [].
Probab=38.97 E-value=2.8e+02 Score=29.02 Aligned_cols=71 Identities=17% Similarity=0.280 Sum_probs=45.8
Q ss_pred HHHHHHHHhcCCHHH----HHHHHHHHhccC---ChhHHHHHHH----Hh--cCCCCCCc------cHHHHHHHHHHHHH
Q 028386 102 MAKMQAILNQFTEDQ----MNRYESFRRSAL---QKSNMRRLLV----SI--TGSQKISL------PMTIVVCGIAKMFV 162 (210)
Q Consensus 102 ~~km~~Ll~~fteEQ----l~RYE~fRRS~f---~K~~IKRLi~----~v--tgsqsVs~------nvvIavaGlaKvFV 162 (210)
.+.+..||...+.++ ..|.-.|...+| ||.++.+|.. .+ ..++.-+. .++-.|-.||+.|.
T Consensus 428 ~eel~~lL~~~~~~~~~~iI~RIrk~~hpsLa~~NK~Kl~~f~~vLlq~i~~la~~~~~~~~~~ld~L~~~L~~Laq~~p 507 (840)
T PF04147_consen 428 HEELLELLDGYSPEDQPTIIQRIRKCYHPSLAEGNKEKLQVFFGVLLQHILYLASQDSPPPFEVLDSLIPHLYDLAQKYP 507 (840)
T ss_pred HHHHHHHHhcCCHHHHhHHHHHHHHhCCCCCCcchHHHHHHHHHHHHHHHHHHhcccCCcCHHHHHHHHHHHHHHHHHHH
Confidence 356888998888775 367778878887 6777776622 11 11221012 24555778888888
Q ss_pred HHHHHHHHHH
Q 028386 163 GELVETARMV 172 (210)
Q Consensus 163 GELVEeAr~V 172 (210)
-.+.+..+.+
T Consensus 508 ~~~a~~~r~~ 517 (840)
T PF04147_consen 508 EEAAECFREV 517 (840)
T ss_pred HHHHHHHHHH
Confidence 8777777766
No 57
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=37.35 E-value=1.2e+02 Score=23.13 Aligned_cols=27 Identities=30% Similarity=0.332 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhCcCCCCCchHHHHHHH
Q 028386 165 LVETARMVMTERNESGPIRPCHIREAYR 192 (210)
Q Consensus 165 LVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (210)
|+-.|++|.+- .+..-|.+.||.||+.
T Consensus 68 ilrvARTIADL-~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 68 ILRVARTIADL-EGSERITREHIAEALS 94 (96)
T ss_pred HHHHHHHHHhH-cCCCCCCHHHHHHHHh
Confidence 45668888664 4677899999999974
No 58
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.21 E-value=1.6e+02 Score=23.67 Aligned_cols=53 Identities=17% Similarity=0.333 Sum_probs=34.6
Q ss_pred HhcCCHHHHHHHHHHHhccCChhHHHHHHHHhcCCCCCCccH-HHHHHHHHHHHHHHHHHHHH
Q 028386 109 LNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPM-TIVVCGIAKMFVGELVETAR 170 (210)
Q Consensus 109 l~~fteEQl~RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nv-vIavaGlaKvFVGELVEeAr 170 (210)
+.+||++|.+|+++ +..|+|+.+.--. +=-+|| .+.++||+.--++.-+.+|-
T Consensus 3 ~~~ls~~q~~~leA--------AaFRrLv~HL~~r-sdvQNIDLMnLAgFCRNCLs~Wy~eaa 56 (104)
T COG3492 3 MQELSEEQRDRLEA--------AAFRRLVEHLQER-SDVQNIDLMNLAGFCRNCLSNWYREAA 56 (104)
T ss_pred hHhcCHHHHHHHHH--------HHHHHHHHHHHHh-cccchhHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999985 3455666654322 112344 45678998888887776653
No 59
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=34.74 E-value=51 Score=25.19 Aligned_cols=60 Identities=18% Similarity=0.196 Sum_probs=27.7
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHH
Q 028386 133 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (210)
Q Consensus 133 IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (210)
|+.+|=..-.+..+.+..+.+|--|...||-+|+-.|..+...+ .++-|.+.+|.=++|+
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~r-g~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRR-GSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccCcCcHHHHHHHHhc
Confidence 56666443223456667888899999999999999999986555 4778899999888886
No 60
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=32.69 E-value=32 Score=35.79 Aligned_cols=94 Identities=17% Similarity=0.202 Sum_probs=59.6
Q ss_pred HHHHhcCCHHHHHHHHHHHhc-cCChhHHHHHHHHhcCCCCCCccHHH---HHHHHHHHHHHHHHHHHHHHHHHhCcCCC
Q 028386 106 QAILNQFTEDQMNRYESFRRS-ALQKSNMRRLLVSITGSQKISLPMTI---VVCGIAKMFVGELVETARMVMTERNESGP 181 (210)
Q Consensus 106 ~~Ll~~fteEQl~RYE~fRRS-~f~K~~IKRLi~~vtgsqsVs~nvvI---avaGlaKvFVGELVEeAr~Vq~E~~e~gP 181 (210)
+.=+..||++|-.|.+-|-.. +|+..-.+-|+++..... .=..++- --..+|..+++||.....+- . -..-|
T Consensus 586 ~~~~~~~~~~~~~r~~Rlv~eyGLs~~dA~~L~~d~~la~-yFE~~v~~~~~pk~aANWl~~El~~~Lne~--~-i~~~~ 661 (771)
T PRK14703 586 RAEAAALNPEQRARFDRYLSELGLNEEDARTLARDPALAA-FFEAALAAGKSPVQLANWVVNDLAGLLRDR--E-LAALP 661 (771)
T ss_pred ccccccCCHhHHHHHHHHHHHcCCCHHHHHHHHcChHHHH-HHHHHHHcCCCHHHHHHHHHHHHHHHHhcC--C-CccCC
Confidence 335678999999999999875 888887766643221100 0001110 01246788888888776653 1 24568
Q ss_pred CCchHHHHHHHHHHhcCCCCCCC
Q 028386 182 IRPCHIREAYRRLKLEGKVPKRS 204 (210)
Q Consensus 182 LqP~HIREA~RRL~~~Gkvp~r~ 204 (210)
|.|.||-+-+ +|...|+|-...
T Consensus 662 l~pe~LaeLv-~lV~~g~IS~~~ 683 (771)
T PRK14703 662 FTPAALARLV-ALVDAGRISTRI 683 (771)
T ss_pred CCHHHHHHHH-HHHHcCCccHHH
Confidence 9999999987 555667775544
No 61
>PRK15398 aldehyde dehydrogenase EutE; Provisional
Probab=31.54 E-value=66 Score=30.91 Aligned_cols=46 Identities=20% Similarity=0.303 Sum_probs=36.0
Q ss_pred hHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Q 028386 131 SNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERN 177 (210)
Q Consensus 131 ~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~ 177 (210)
..||++|.+...||+||++.+.-+-|..+- |-+.|+.|+.-+.+|.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d-v~~av~~A~~A~~~w~ 53 (465)
T PRK15398 8 QVVKAVLAEMLSSQTVSPPAAVGEMGVFAS-VDDAVAAAKVAQQRYQ 53 (465)
T ss_pred HHHHHHHHHhhcccccccccccccccHHHH-HHHHHHHHHHHHHHHH
Confidence 358888888888899999887777777666 5678888888877773
No 62
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=30.62 E-value=96 Score=27.42 Aligned_cols=52 Identities=15% Similarity=0.227 Sum_probs=32.4
Q ss_pred cCChhHHHHHHHHhc---CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCc
Q 028386 127 ALQKSNMRRLLVSIT---GSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNE 178 (210)
Q Consensus 127 ~f~K~~IKRLi~~vt---gsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e 178 (210)
=|+...+.+.|..|. |...+..+++-.|+--++.++-+|||.+..+...|-+
T Consensus 43 fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~ 97 (264)
T PF05236_consen 43 FLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRD 97 (264)
T ss_dssp -S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH--------
T ss_pred ccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 356666666666654 4346888999999999999999999999999776643
No 63
>PF07462 MSP1_C: Merozoite surface protein 1 (MSP1) C-terminus; InterPro: IPR010901 This entry represents the C-terminal region of merozoite surface protein 1 (MSP1), which is found in a number of Plasmodium species. MSP-1 is a 200 kDa protein expressed on the surface of the Plasmodium vivax merozoite. MSP-1 of Plasmodium species is synthesised as a high-molecular-weight precursor and then processed into several fragments. At the time of red cell invasion by the merozoite, only the 19 kDa C-terminal fragment (MSP-119), which contains two epidermal growth factor-like domains, remains on the surface. Antibodies against MSP-119 inhibit merozoite entry into red cells, and immunisation with MSP-119 protects monkeys from challenging infections. Hence, MSP-119 is considered a promising vaccine candidate [].; GO: 0009405 pathogenesis, 0016020 membrane
Probab=29.46 E-value=77 Score=32.17 Aligned_cols=14 Identities=21% Similarity=0.259 Sum_probs=7.6
Q ss_pred CCCccHHHHHHHHH
Q 028386 145 KISLPMTIVVCGIA 158 (210)
Q Consensus 145 sVs~nvvIavaGla 158 (210)
+|..+|+++=-||+
T Consensus 463 SIdkDi~tAnDGl~ 476 (574)
T PF07462_consen 463 SIDKDIATANDGLA 476 (574)
T ss_pred HHhhhHHHhhhHHH
Confidence 45666666644443
No 64
>PF11011 DUF2849: Protein of unknown function (DUF2849); InterPro: IPR021270 This bacterial family of proteins has no known function.
Probab=28.81 E-value=36 Score=26.39 Aligned_cols=18 Identities=39% Similarity=0.630 Sum_probs=15.1
Q ss_pred CcCCCCCchHHHHHHHHH
Q 028386 177 NESGPIRPCHIREAYRRL 194 (210)
Q Consensus 177 ~e~gPLqP~HIREA~RRL 194 (210)
.+.|.++|.|+||.+|..
T Consensus 64 ~~dG~~~P~~~RE~iRa~ 81 (90)
T PF11011_consen 64 GADGRPRPVHLRERIRAR 81 (90)
T ss_pred cCCCCccchhHHHhhhcc
Confidence 357889999999998863
No 65
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=28.71 E-value=54 Score=26.63 Aligned_cols=32 Identities=31% Similarity=0.345 Sum_probs=19.4
Q ss_pred HHHHHhccCChhHHHHHHHHhcCCCCCCccHHH
Q 028386 120 YESFRRSALQKSNMRRLLVSITGSQKISLPMTI 152 (210)
Q Consensus 120 YE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvI 152 (210)
||.||||.+-|.-.+-|=.-|..+ .++++.+.
T Consensus 5 YElYRrs~ig~~L~dalD~lis~g-~isp~lam 36 (113)
T COG5123 5 YELYRRSMIGKVLEDALDELISAG-VISPNLAM 36 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcC-CcCHHHHH
Confidence 999999988766555442222222 56766543
No 66
>PF02978 SRP_SPB: Signal peptide binding domain; InterPro: IPR004125 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the M domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0048500 signal recognition particle; PDB: 2FFH_B 3NDB_B 2V3C_C 1QZW_G 1QZX_B 3KL4_A 2JQE_A 1HQ1_A 1RY1_W 1MFQ_C ....
Probab=28.59 E-value=80 Score=24.63 Aligned_cols=35 Identities=23% Similarity=0.404 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhccCChhHHHHHHH
Q 028386 99 PAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLV 138 (210)
Q Consensus 99 ~e~~~km~~Ll~~fteEQl~RYE~fRRS~f~K~~IKRLi~ 138 (210)
+.+..++..++++||+++++--..+.. +-++||..
T Consensus 47 ~~~lk~~~~Ii~SMT~~Er~~p~ll~~-----sR~~RIA~ 81 (104)
T PF02978_consen 47 EKKLKRMEAIIDSMTPEERDNPKLLNE-----SRRRRIAR 81 (104)
T ss_dssp HHHHHHHHHHHTTSBHHHHHCGGGHHH-----HHHHHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHhCccccch-----HHHHHHHH
Confidence 444588999999999999977776643 55777753
No 67
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=27.15 E-value=35 Score=26.96 Aligned_cols=11 Identities=36% Similarity=0.628 Sum_probs=5.2
Q ss_pred ccccccccccc
Q 028386 78 YDEEDDENVDV 88 (210)
Q Consensus 78 ~d~e~ed~~e~ 88 (210)
+++|+||+|-+
T Consensus 92 e~eE~dddmgf 102 (105)
T cd04411 92 EEEEEDEDFGF 102 (105)
T ss_pred cccccccccCc
Confidence 33444555544
No 68
>PF03115 Astro_capsid: Astrovirus capsid protein precursor; InterPro: IPR004337 The astrovirus genome is apparently organised with nonstructural proteins encoded at the 5' end and structural proteins at the 3' end []. Proteins in this family are encoded by astrovirus ORF2, one of the three astrovirus ORFs (1a, 1b, 2). The proteins contain a viral RNA-dependent RNA polymerase motif []. The 87kDa precursor polyprotein undergoes an intracellular cleavage to form a 79kDa protein. Subsequently, extracellular trypsin cleavage yields the three proteins forming the infectious virion [].; PDB: 3QSQ_A 3TS3_D.
Probab=26.84 E-value=21 Score=37.22 Aligned_cols=14 Identities=14% Similarity=0.434 Sum_probs=0.0
Q ss_pred HHHH-hcCCHHHHHH
Q 028386 106 QAIL-NQFTEDQMNR 119 (210)
Q Consensus 106 ~~Ll-~~fteEQl~R 119 (210)
..|| ..+++||-.|
T Consensus 715 nTLVNqGi~eerAar 729 (787)
T PF03115_consen 715 NTLVNQGIPEERAAR 729 (787)
T ss_dssp ---------------
T ss_pred HHHHHcCCCHHHHHh
Confidence 3355 6778887776
No 69
>PF15510 CENP-W: Centromere kinetochore component W
Probab=26.40 E-value=2.8e+02 Score=22.23 Aligned_cols=67 Identities=21% Similarity=0.270 Sum_probs=42.9
Q ss_pred cCChhHHHHHHHHhcCCCCC--CccHH--------------HHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHH
Q 028386 127 ALQKSNMRRLLVSITGSQKI--SLPMT--------------IVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREA 190 (210)
Q Consensus 127 ~f~K~~IKRLi~~vtgsqsV--s~nvv--------------IavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA 190 (210)
+-|+..+||++...-....+ +-++. +=+.+ =+||-.|-|+||.=.-| +..+-|.++|+-.|
T Consensus 16 kaPrgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLnc--LLFvhrLAEEaRtnA~E-nK~~~Ik~~Hv~Aa 92 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNC--LLFVHRLAEEARTNACE-NKCGTIKKEHVLAA 92 (102)
T ss_pred hCchHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhH--HHHHHHHHHHHHHHHHH-HhhccccHHHHHHH
Confidence 45788888887643222111 11222 22233 37999999999965433 35889999999998
Q ss_pred HHHHHh
Q 028386 191 YRRLKL 196 (210)
Q Consensus 191 ~RRL~~ 196 (210)
..-+..
T Consensus 93 aKviLK 98 (102)
T PF15510_consen 93 AKVILK 98 (102)
T ss_pred HHHHHH
Confidence 876654
No 70
>PF11521 TFIIE-A_C-term: C-terminal general transcription factor TFIIE alpha; InterPro: IPR021600 TFIIE is compiled of two subunits, alpha and beta. This family of proteins are the C-terminal domain of the alpha subunit of the protein which is the largest subunit and contains several functional domains which are important for basal transcription and cell growth. The C-terminal end of the protein binds directly to the amino-terminal PH domain of p62/Tfb1 (of IIH) which is involved in the recruitment of the general transcription factor IIH to the transcription preinitiation complex. P53 competes for the same binding site as TFIIE alpha which shows their structural similarity. Like p53, TFIIE alpha 336-439 can activate transcription in vivo []. ; PDB: 2RNR_A 2RNQ_A 2JTX_A.
Probab=25.83 E-value=56 Score=25.20 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=15.2
Q ss_pred HHHHHhcCCHHHHHHHHHHHh
Q 028386 105 MQAILNQFTEDQMNRYESFRR 125 (210)
Q Consensus 105 m~~Ll~~fteEQl~RYE~fRR 125 (210)
.-.||..||+++.+.|-.--+
T Consensus 58 ~p~LV~qMT~~EKEaYi~v~Q 78 (86)
T PF11521_consen 58 RPELVAQMTPEEKEAYIQVGQ 78 (86)
T ss_dssp -HHHHHHS-HHHHHHHHHHHH
T ss_pred chHHHHHcCHHHHHHHHHHHH
Confidence 356899999999999965443
No 71
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=25.46 E-value=74 Score=32.66 Aligned_cols=22 Identities=32% Similarity=0.558 Sum_probs=12.0
Q ss_pred CCcccccccccccccccCCCCC
Q 028386 75 KDEYDEEDDENVDVELGKFPSS 96 (210)
Q Consensus 75 ~~e~d~e~ed~~e~~l~~~~~~ 96 (210)
+.|++++++|+.+|+...+.++
T Consensus 426 dgdde~eddddidvdeediess 447 (990)
T KOG1819|consen 426 DGDDEAEDDDDIDVDEEDIESS 447 (990)
T ss_pred cCcccccCcccccccccccccc
Confidence 3344555556666665555553
No 72
>KOG3449 consensus 60S acidic ribosomal protein P2 [Translation, ribosomal structure and biogenesis]
Probab=23.80 E-value=44 Score=27.27 Aligned_cols=9 Identities=33% Similarity=0.708 Sum_probs=4.6
Q ss_pred ccccccccc
Q 028386 80 EEDDENVDV 88 (210)
Q Consensus 80 ~e~ed~~e~ 88 (210)
||.||||.+
T Consensus 100 eesddDmgf 108 (112)
T KOG3449|consen 100 EESDDDMGF 108 (112)
T ss_pred ccccccccc
Confidence 444555554
No 73
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=23.64 E-value=2.3e+02 Score=22.54 Aligned_cols=47 Identities=23% Similarity=0.334 Sum_probs=34.3
Q ss_pred ccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHH
Q 028386 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVM 173 (210)
Q Consensus 126 S~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq 173 (210)
+.++|..||||... .|--.|+--+---..++.|+|+-.++.-|..--
T Consensus 28 qgitKpaIRRlARr-~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt 74 (103)
T KOG3467|consen 28 QGITKPAIRRLARR-GGVKRISGLIYEETRGVLKVFLENVIRDAVTYT 74 (103)
T ss_pred cccchHHHHHHHHh-cCcchhchhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35779999998654 343345555566678999999999999887653
No 74
>cd04404 RhoGAP-p50rhoGAP RhoGAP-p50rhoGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of p50RhoGAP-like proteins; p50RhoGAP, also known as RhoGAP-1, contains a C-terminal RhoGAP domain and an N-terminal Sec14 domain which binds phosphatidylinositol 3,4,5-trisphosphate (PtdIns(3,4,5)P3). It is ubiquitously expressed and preferentially active on Cdc42. This subgroup also contains closely related ARHGAP8. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=23.62 E-value=2.4e+02 Score=23.43 Aligned_cols=45 Identities=22% Similarity=0.256 Sum_probs=29.1
Q ss_pred HHHHhccCChhHHHHHHHHhcCCCCCCcc---HHHHHHHHHHHHHHHHH
Q 028386 121 ESFRRSALQKSNMRRLLVSITGSQKISLP---MTIVVCGIAKMFVGELV 166 (210)
Q Consensus 121 E~fRRS~f~K~~IKRLi~~vtgsqsVs~n---vvIavaGlaKvFVGELV 166 (210)
..||.+. +...|+++...+.-+..++-+ -+.+++++-|.|+-+|-
T Consensus 43 GIFR~~g-~~~~i~~l~~~~~~~~~~~~~~~~d~~~va~~LK~~lr~Lp 90 (195)
T cd04404 43 GIFRRSA-NTQVVKEVQQKYNMGEPVDFDQYEDVHLPAVILKTFLRELP 90 (195)
T ss_pred CeeeCCC-cHHHHHHHHHHHhCCCCCCcccccCHHHHHHHHHHHHHhCC
Confidence 4577765 566678887666433222211 35678999999998874
No 75
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=23.60 E-value=23 Score=24.77 Aligned_cols=34 Identities=26% Similarity=0.342 Sum_probs=19.3
Q ss_pred HHHHHHhccCChhHHHHHHHHhcCCCCCCccHHHH
Q 028386 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIV 153 (210)
Q Consensus 119 RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIa 153 (210)
-|+.||+|++-.+=..-| .....++.+++.++.-
T Consensus 2 ~yelYR~stlG~aL~dtL-Deli~~~~I~p~La~k 35 (49)
T PF02268_consen 2 YYELYRRSTLGIALTDTL-DELIQEGKITPQLAMK 35 (49)
T ss_dssp --CGGGCSHHHHHHHHHH-HHHHHTTSS-HHHHHH
T ss_pred cHHHHHcchHHHHHHHHH-HHHHHcCCCCHHHHHH
Confidence 489999998766544443 3333345788776543
No 76
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=23.40 E-value=47 Score=26.81 Aligned_cols=10 Identities=20% Similarity=0.657 Sum_probs=4.8
Q ss_pred cccccccccc
Q 028386 80 EEDDENVDVE 89 (210)
Q Consensus 80 ~e~ed~~e~~ 89 (210)
+|+||+|-+.
T Consensus 100 ee~ddDmgf~ 109 (112)
T PTZ00373 100 EEEEDDLGFS 109 (112)
T ss_pred cccccccccc
Confidence 4444555543
No 77
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=23.12 E-value=1.1e+02 Score=24.83 Aligned_cols=36 Identities=33% Similarity=0.402 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHH
Q 028386 157 IAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (210)
Q Consensus 157 laKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (210)
=+|-||-+|+..++.-+.+|.+. .|..|++....|-
T Consensus 43 Eak~~vddl~~q~k~~~~e~e~K---~~r~i~~ml~~~~ 78 (108)
T COG3937 43 EAKRFVDDLLRQAKEAQGELEEK---IPRKIEEMLSDLE 78 (108)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHh---hhHHHHHHHhhcc
Confidence 46889999999999777777555 7778887776654
No 78
>KOG3463 consensus Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=22.47 E-value=81 Score=25.64 Aligned_cols=33 Identities=21% Similarity=0.352 Sum_probs=21.9
Q ss_pred HHHHHHhccCChhHHHHHHHHhcCCCCCCccHHH
Q 028386 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTI 152 (210)
Q Consensus 119 RYE~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvI 152 (210)
-|+.|||+.+-+.-.+-| -.....+.++++++.
T Consensus 3 ~YelYR~ttlG~~L~~tL-De~v~~g~itp~la~ 35 (109)
T KOG3463|consen 3 YYELYRRTTLGNALQKTL-DELVSDGVITPSLAK 35 (109)
T ss_pred HHHHHHHhhHHHHHHHHH-HHHHHcCCCCHHHHH
Confidence 599999999877655544 333344567777654
No 79
>cd04378 RhoGAP_GMIP_PARG1 RhoGAP_GMIP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of GMIP (Gem interacting protein) and PARG1 (PTPL1-associated RhoGAP1). GMIP plays important roles in neurite growth and axonal guidance, and interacts with Gem, a member of the RGK subfamily of the Ras small GTPase superfamily, through the N-terminal half of the protein. GMIP contains a C-terminal RhoGAP domain. GMIP inhibits RhoA function, but is inactive towards Rac1 and Cdc41. PARG1 interacts with Rap2, also a member of the Ras small GTPase superfamily whose exact function is unknown, and shows strong preference for Rho. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases ge
Probab=22.01 E-value=1.7e+02 Score=24.67 Aligned_cols=45 Identities=20% Similarity=0.330 Sum_probs=29.5
Q ss_pred HHHhccCChhHHHHHHHHhcCCCC---CCccHHHHHHHHHHHHHHHHHH
Q 028386 122 SFRRSALQKSNMRRLLVSITGSQK---ISLPMTIVVCGIAKMFVGELVE 167 (210)
Q Consensus 122 ~fRRS~f~K~~IKRLi~~vtgsqs---Vs~nvvIavaGlaKvFVGELVE 167 (210)
.||.+. ++..|++|...+..+.. .++.-+..++++-|.|+-||-+
T Consensus 37 IfR~sG-~~~~i~~l~~~~~~~~~~~~~~~~~~h~va~~LK~fLReLpe 84 (203)
T cd04378 37 IYRVSG-SKARVEKLCQAFENGKDLVELSELSPHDISSVLKLFLRQLPE 84 (203)
T ss_pred ceeCCC-cHHHHHHHHHHHhcCCCccccccCCHHHHHHHHHHHHHhCCC
Confidence 588887 57778888765532211 1223366789999999877644
No 80
>PF08971 GlgS: Glycogen synthesis protein; InterPro: IPR015065 Members of this protein are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them []. ; GO: 0005978 glycogen biosynthetic process; PDB: 1RRZ_A.
Probab=21.73 E-value=65 Score=24.07 Aligned_cols=23 Identities=30% Similarity=0.642 Sum_probs=16.3
Q ss_pred HHHHHHhcCCHHHH----HHHHHHHhc
Q 028386 104 KMQAILNQFTEDQM----NRYESFRRS 126 (210)
Q Consensus 104 km~~Ll~~fteEQl----~RYE~fRRS 126 (210)
....+-.|||++|. +||+.||+-
T Consensus 29 d~~~I~gnM~ee~r~~F~~R~~~Yr~q 55 (66)
T PF08971_consen 29 DVDAITGNMSEEQREWFCERYAHYRQQ 55 (66)
T ss_dssp -HHHHHHH--TTHHHHHHHHHHHHHHH
T ss_pred CHHHHhccCCHHHHHHHHHHHHHHHHH
Confidence 45668899999995 699999983
No 81
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.65 E-value=3.7e+02 Score=20.41 Aligned_cols=43 Identities=23% Similarity=0.343 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHhCcCCCCCchHHHHHHHHH
Q 028386 150 MTIVVCGIAKMFVGELVETARM-VMTERNESGPIRPCHIREAYRRL 194 (210)
Q Consensus 150 vvIavaGlaKvFVGELVEeAr~-Vq~E~~e~gPLqP~HIREA~RRL 194 (210)
+.|+++-++-+|.|-.| ||+ ++++..+..||-++-||.=+-..
T Consensus 8 l~ivl~ll~G~~~G~fi--ark~~~k~lk~NPpine~~iR~M~~qm 51 (71)
T COG3763 8 LLIVLALLAGLIGGFFI--ARKQMKKQLKDNPPINEEMIRMMMAQM 51 (71)
T ss_pred HHHHHHHHHHHHHHHHH--HHHHHHHHHhhCCCCCHHHHHHHHHHh
Confidence 46777888888888666 444 45667899999999888766544
No 82
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=21.31 E-value=3e+02 Score=19.36 Aligned_cols=40 Identities=20% Similarity=0.282 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHhcCCCC
Q 028386 161 FVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201 (210)
Q Consensus 161 FVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkvp 201 (210)
=.|+|.+.=..+++.. ...||....+.+-...|...|-|-
T Consensus 24 ~~~~vy~~Y~~~c~~~-~~~~l~~~~~~~~l~~L~~~gli~ 63 (87)
T cd08768 24 TTGEVYEVYEELCEEI-GVDPLTQRRISDLLSELEMLGLLE 63 (87)
T ss_pred cHHHHHHHHHHHHHHc-CCCCCcHHHHHHHHHHHHHcCCeE
Confidence 3588888888888765 788999999999999999988764
No 83
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=20.37 E-value=4.2e+02 Score=22.04 Aligned_cols=77 Identities=16% Similarity=0.170 Sum_probs=43.8
Q ss_pred HHHhccCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHhcCCCC
Q 028386 122 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201 (210)
Q Consensus 122 ~fRRS~f~K~~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkvp 201 (210)
.+|..+|..- |.|++.++..+..++..-..||.+|--.++-.|.-+|=....-.+. .-|--.||+-|+|-|. -|+++
T Consensus 33 ~~~~e~~s~y-v~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~kr-stisSreiqta~rLll-Pgel~ 109 (127)
T KOG1744|consen 33 TRRKESYSEY-VYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKR-STISSREIQTAVRLLL-PGELA 109 (127)
T ss_pred ccccCceeee-hhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCC-CcccHHHHHHHHHHhC-chHHh
Confidence 4445555433 4556666655545666666666665544444444444444333333 3488899999776554 47654
No 84
>PF09628 YvfG: YvfG protein; InterPro: IPR018590 Yvfg is a hypothetical protein of 71 residues expressed in some bacteria. The monomer consists of two parallel alpha helices, and the protein crystallises as a homo-dimer. ; PDB: 2GSV_A 2JS1_B.
Probab=20.26 E-value=3.6e+02 Score=20.17 Aligned_cols=39 Identities=23% Similarity=0.286 Sum_probs=28.6
Q ss_pred cHHHHHHHHHHHHHHHHHHH-----HHHHHHHhCcCCCCCchHHHHHHHHHHh
Q 028386 149 PMTIVVCGIAKMFVGELVET-----ARMVMTERNESGPIRPCHIREAYRRLKL 196 (210)
Q Consensus 149 nvvIavaGlaKvFVGELVEe-----Ar~Vq~E~~e~gPLqP~HIREA~RRL~~ 196 (210)
.-+.+|.+.-|+.||.||.- |.-+.. -.||.|||.+.+.
T Consensus 24 ~ki~AmNaYYr~Vv~tlvqDqltKNa~vl~R---------iqHLdEAY~KV~~ 67 (68)
T PF09628_consen 24 DKIHAMNAYYRSVVSTLVQDQLTKNAVVLKR---------IQHLDEAYQKVKR 67 (68)
T ss_dssp -CCHHHHHHHHHHHHHHHHHSSS-HHHHHHH---------HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHH---------HHHHHHHHHHHhc
Confidence 34688999999999999863 222222 4699999998875
No 85
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=20.25 E-value=4.5e+02 Score=20.88 Aligned_cols=63 Identities=11% Similarity=0.119 Sum_probs=49.3
Q ss_pred HHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCCCCCchHHHHHHHHHHh
Q 028386 132 NMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKL 196 (210)
Q Consensus 132 ~IKRLi~~vtgsqsVs~nvvIavaGlaKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~ 196 (210)
.|++|+.+. |-..+++.++..+.=++.-++.+|...|....+.- .+.-|....|+-|......
T Consensus 6 ~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA-~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 6 VIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHA-GKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHhc
Confidence 477777664 55578999999999999999999999999887654 3466777888877665543
Done!