Query 028537
Match_columns 207
No_of_seqs 124 out of 211
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 13:03:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028537.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028537hhsearch_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 8.4E-44 1.8E-48 303.2 11.9 109 96-205 81-190 (195)
2 PF04719 TAFII28: hTAFII28-lik 100.0 2.8E-43 6E-48 269.0 9.5 90 105-194 1-90 (90)
3 cd08048 TAF11 TATA Binding Pro 100.0 1.8E-38 3.9E-43 239.7 10.6 83 112-195 1-85 (85)
4 COG5251 TAF40 Transcription in 100.0 8.1E-32 1.7E-36 227.6 9.8 94 103-197 91-184 (199)
5 KOG3902 Histone acetyltransfer 99.3 2.4E-11 5.3E-16 110.8 10.3 99 98-197 191-330 (352)
6 PF00808 CBFD_NFYB_HMF: Histon 97.9 4E-05 8.6E-10 54.0 6.1 65 126-191 1-65 (65)
7 smart00803 TAF TATA box bindin 96.5 0.015 3.4E-07 42.0 7.0 64 127-192 2-65 (65)
8 cd07981 TAF12 TATA Binding Pro 96.0 0.058 1.3E-06 39.3 8.0 67 128-195 2-68 (72)
9 cd00074 H2A Histone 2A; H2A is 95.5 0.057 1.2E-06 43.3 6.9 66 127-193 20-85 (115)
10 PF00125 Histone: Core histone 95.2 0.067 1.5E-06 38.0 5.8 66 127-193 5-74 (75)
11 COG5262 HTA1 Histone H2A [Chro 94.4 0.1 2.2E-06 42.9 5.5 66 126-192 25-90 (132)
12 KOG0871 Class 2 transcription 94.3 0.24 5.1E-06 42.0 7.6 69 126-195 11-80 (156)
13 smart00414 H2A Histone 2A. 93.4 0.29 6.3E-06 38.7 6.3 66 127-193 9-74 (106)
14 COG2036 HHT1 Histones H3 and H 93.4 0.44 9.5E-06 37.0 7.1 80 115-196 7-86 (91)
15 PF02969 TAF: TATA box binding 93.3 0.46 1E-05 34.8 6.8 65 126-192 2-66 (66)
16 cd00076 H4 Histone H4, one of 93.1 0.68 1.5E-05 35.5 7.6 66 127-194 13-78 (85)
17 PTZ00017 histone H2A; Provisio 92.1 0.4 8.6E-06 39.8 5.6 65 128-193 28-92 (134)
18 PTZ00015 histone H4; Provision 91.8 1 2.3E-05 35.6 7.5 67 126-194 29-95 (102)
19 PLN00035 histone H4; Provision 91.4 1.2 2.6E-05 35.4 7.5 66 128-195 30-95 (103)
20 PLN00154 histone H2A; Provisio 90.4 1.1 2.3E-05 37.4 6.5 65 128-193 39-104 (136)
21 PLN00153 histone H2A; Provisio 90.1 0.91 2E-05 37.5 5.9 65 128-193 25-89 (129)
22 PLN00156 histone H2AX; Provisi 89.8 1 2.2E-05 37.7 6.0 65 128-193 30-94 (139)
23 PLN00157 histone H2A; Provisio 89.8 0.85 1.9E-05 37.7 5.5 65 128-193 27-91 (132)
24 PTZ00252 histone H2A; Provisio 89.0 1.5 3.1E-05 36.6 6.3 66 128-193 26-92 (134)
25 KOG1659 Class 2 transcription 88.5 1.4 3E-05 39.4 6.3 68 125-193 11-78 (224)
26 smart00417 H4 Histone H4. 88.1 1.7 3.8E-05 32.5 5.7 48 127-175 13-60 (74)
27 PF03847 TFIID_20kDa: Transcri 87.8 2.2 4.8E-05 31.2 6.0 64 129-193 1-64 (68)
28 PF09415 CENP-X: CENP-S associ 87.2 1.4 3.1E-05 32.6 4.7 65 129-193 1-67 (72)
29 smart00576 BTP Bromodomain tra 86.9 6.1 0.00013 28.8 7.9 64 130-195 9-72 (77)
30 cd08050 TAF6 TATA Binding Prot 85.2 4.2 9E-05 37.5 7.8 66 130-197 2-67 (343)
31 KOG1756 Histone 2A [Chromatin 83.4 4.2 9.1E-05 33.8 6.2 65 127-192 27-91 (131)
32 PTZ00463 histone H2B; Provisio 81.0 7.7 0.00017 31.7 6.8 67 133-201 34-100 (117)
33 COG5208 HAP5 CCAAT-binding fac 80.6 4.1 9E-05 37.0 5.7 75 118-193 100-174 (286)
34 PF07524 Bromo_TP: Bromodomain 80.4 17 0.00036 26.2 7.9 63 131-195 10-72 (77)
35 smart00427 H2B Histone H2B. 78.1 19 0.0004 28.1 7.9 67 133-201 7-73 (89)
36 PLN00158 histone H2B; Provisio 76.7 19 0.0004 29.5 7.8 66 133-200 33-98 (116)
37 COG5247 BUR6 Class 2 transcrip 76.0 9.8 0.00021 30.8 6.0 68 123-191 19-86 (113)
38 PRK07194 fliG flagellar motor 75.8 18 0.0004 33.2 8.6 89 105-200 216-323 (334)
39 COG5150 Class 2 transcription 75.1 16 0.00035 30.7 7.2 67 126-195 10-79 (148)
40 PF01706 FliG_C: FliG C-termin 71.1 9 0.00019 29.4 4.6 68 128-200 28-107 (110)
41 PF07526 POX: Associated with 65.0 57 0.0012 26.9 8.4 41 116-162 89-132 (140)
42 PRK13916 plasmid segregation p 61.2 6.1 0.00013 31.1 1.9 18 182-199 31-48 (97)
43 PRK05686 fliG flagellar motor 60.7 22 0.00047 32.6 5.7 69 127-200 249-329 (339)
44 KOG2140 Uncharacterized conser 60.6 40 0.00087 34.5 7.9 89 87-175 125-244 (739)
45 TIGR00207 fliG flagellar motor 59.9 24 0.00051 32.6 5.8 69 127-200 246-326 (338)
46 KOG0870 DNA polymerase epsilon 56.7 63 0.0014 28.1 7.5 49 127-175 10-60 (172)
47 KOG1142 Transcription initiati 55.3 20 0.00044 32.8 4.5 49 128-176 155-203 (258)
48 PF13443 HTH_26: Cro/C1-type H 51.2 5.3 0.00012 26.9 0.1 52 113-166 7-58 (63)
49 cd07978 TAF13 The TATA Binding 49.4 1.1E+02 0.0024 23.5 7.1 63 128-193 4-66 (92)
50 KOG1657 CCAAT-binding factor, 47.5 30 0.00066 30.9 4.3 71 122-193 69-139 (236)
51 smart00574 POX domain associat 47.1 1.1E+02 0.0025 25.7 7.4 42 115-162 88-132 (140)
52 PF04147 Nop14: Nop14-like fam 46.3 1.9E+02 0.0042 30.1 10.4 71 102-172 428-517 (840)
53 PF12174 RST: RCD1-SRO-TAF4 (R 44.9 67 0.0014 23.7 5.1 38 106-143 16-57 (70)
54 KOG1744 Histone H2B [Chromatin 43.6 76 0.0016 26.3 5.7 78 122-202 33-110 (127)
55 PF05236 TAF4: Transcription i 41.3 50 0.0011 29.1 4.7 51 128-178 44-97 (264)
56 KOG1757 Histone 2A [Chromatin 41.0 29 0.00063 28.6 2.9 64 128-192 31-95 (131)
57 KOG3871 Cell adhesion complex 39.4 1.2E+02 0.0026 29.7 7.2 48 155-202 145-204 (449)
58 PF03540 TFIID_30kDa: Transcri 39.1 1.4E+02 0.003 21.1 6.4 47 128-175 3-49 (51)
59 PF02269 TFIID-18kDa: Transcri 35.2 50 0.0011 25.2 3.3 59 133-193 7-66 (93)
60 PRK15398 aldehyde dehydrogenas 34.8 54 0.0012 31.4 4.2 46 131-177 8-53 (465)
61 COG3492 Uncharacterized protei 34.2 1.7E+02 0.0037 23.5 6.1 53 109-170 3-56 (104)
62 PF14911 MMS22L_C: S-phase gen 33.1 2.5E+02 0.0054 26.9 8.2 40 154-196 327-370 (373)
63 PF11521 TFIIE-A_C-term: C-ter 32.5 40 0.00086 26.0 2.4 21 105-125 58-78 (86)
64 PF13335 Mg_chelatase_2: Magne 30.6 2.4E+02 0.0052 21.4 6.4 27 165-192 68-94 (96)
65 COG5123 TOA2 Transcription ini 30.5 47 0.001 27.0 2.5 39 120-159 5-44 (113)
66 PRK14703 glutaminyl-tRNA synth 30.5 86 0.0019 32.7 5.0 92 106-202 586-681 (771)
67 cd08768 Cdc6_C Winged-helix do 30.2 2E+02 0.0043 20.3 6.3 39 161-200 24-62 (87)
68 KOG3467 Histone H4 [Chromatin 30.1 1.5E+02 0.0033 23.6 5.3 47 127-174 29-75 (103)
69 PF11011 DUF2849: Protein of u 29.8 33 0.00072 26.5 1.5 18 177-194 64-81 (90)
70 PF15510 CENP-W: Centromere ki 27.8 2.5E+02 0.0055 22.5 6.1 67 127-196 16-98 (102)
71 cd00923 Cyt_c_Oxidase_Va Cytoc 27.4 1.1E+02 0.0023 24.7 4.0 32 117-152 9-45 (103)
72 PF02978 SRP_SPB: Signal pepti 26.7 91 0.002 24.3 3.5 34 99-137 47-80 (104)
73 COG3937 Uncharacterized conser 26.4 89 0.0019 25.3 3.4 36 157-195 43-78 (108)
74 COG3763 Uncharacterized protei 26.2 2.8E+02 0.006 21.0 5.8 43 150-194 8-51 (71)
75 KOG3463 Transcription initiati 25.7 64 0.0014 26.2 2.5 33 119-152 3-35 (109)
76 cd03567 VHS_GGA VHS domain fam 25.1 94 0.002 25.4 3.5 34 166-200 104-137 (139)
77 cd07979 TAF9 TATA Binding Prot 25.0 3.5E+02 0.0076 21.4 7.9 63 132-196 6-68 (117)
78 cd04411 Ribosomal_P1_P2_L12p R 25.0 40 0.00087 26.6 1.2 12 78-89 92-103 (105)
79 PF02268 TFIIA_gamma_N: Transc 24.5 20 0.00043 25.1 -0.5 34 119-153 2-35 (49)
80 cd04404 RhoGAP-p50rhoGAP RhoGA 24.5 2.2E+02 0.0047 23.6 5.6 45 121-166 43-90 (195)
81 PF07462 MSP1_C: Merozoite sur 23.1 1.2E+02 0.0025 30.9 4.3 14 145-158 463-476 (574)
82 cd04378 RhoGAP_GMIP_PARG1 RhoG 22.9 1.5E+02 0.0032 25.0 4.4 45 122-167 37-84 (203)
83 cd04394 RhoGAP-ARHGAP11A RhoGA 22.0 2.5E+02 0.0054 23.8 5.6 46 120-166 38-84 (202)
84 PF08971 GlgS: Glycogen synthe 21.9 64 0.0014 24.1 1.7 23 104-126 29-55 (66)
85 PTZ00373 60S Acidic ribosomal 21.9 51 0.0011 26.5 1.3 12 78-89 98-109 (112)
86 KOG1991 Nuclear transport rece 20.5 83 0.0018 33.9 2.8 18 103-120 977-994 (1010)
87 PF02284 COX5A: Cytochrome c o 20.3 1.1E+02 0.0025 24.7 3.0 34 115-152 10-48 (108)
88 PF05823 Gp-FAR-1: Nematode fa 20.2 1.6E+02 0.0034 24.4 3.9 39 155-193 75-113 (154)
No 1
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=100.00 E-value=8.4e-44 Score=303.23 Aligned_cols=109 Identities=51% Similarity=0.845 Sum_probs=102.8
Q ss_pred CCcHHHHHHHHHHHhcCCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028537 96 SSDPAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 175 (207)
Q Consensus 96 ~~d~e~~~km~~Ll~~fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E 175 (207)
+.+.++.++|+.||++||+||++|||.||||+|+|+.|||||++|||. +|++|++|+|+||||||||||||+|++||++
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 345667779999999999999999999999999999999999999986 5999999999999999999999999999999
Q ss_pred hccCCCCCchHHHHHHHHHHhcCCCC-CCCC
Q 028537 176 RNESGPIRPCHIREAYRRLKLEGKVP-KRSV 205 (207)
Q Consensus 176 ~~e~gPLqP~HIREA~RRL~~~GklP-~rs~ 205 (207)
|++++||||+|||||||||+.+|++| ++.+
T Consensus 160 ~~e~~PLqP~HIREA~rrL~~qgk~~~~~~~ 190 (195)
T KOG3219|consen 160 WGESGPLQPKHIREAYRRLKLQGKLPNSRYK 190 (195)
T ss_pred hccCCCCCcHHHHHHHHHHHhcCCCCCCccc
Confidence 99999999999999999999999999 5544
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=2.8e-43 Score=268.98 Aligned_cols=90 Identities=51% Similarity=0.894 Sum_probs=68.4
Q ss_pred HHHHHhcCCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCc
Q 028537 105 MQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRP 184 (207)
Q Consensus 105 m~~Ll~~fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP 184 (207)
|+.|+++||+||++|||+||||+|+|++|||||++++|+|+||+|++|+|+||||+|||||||+|++||++|++++||+|
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 028537 185 CHIREAYRRL 194 (207)
Q Consensus 185 ~HIREA~RRL 194 (207)
+|||||||||
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=1.8e-38 Score=239.71 Aligned_cols=83 Identities=59% Similarity=0.965 Sum_probs=80.8
Q ss_pred CCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--CCCCCchHHHH
Q 028537 112 FTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNE--SGPIRPCHIRE 189 (207)
Q Consensus 112 fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e--~gPLqP~HIRE 189 (207)
||+|||+|||.||||+|+|++|||||++++| |+||+||+|+|+||||+|||||||+|++||++|++ ++||+|+||||
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 8999999999999999999999999999997 79999999999999999999999999999999999 89999999999
Q ss_pred HHHHHH
Q 028537 190 AYRRLK 195 (207)
Q Consensus 190 A~RRL~ 195 (207)
|||||+
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=8.1e-32 Score=227.59 Aligned_cols=94 Identities=36% Similarity=0.653 Sum_probs=89.8
Q ss_pred HHHHHHHhcCCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCC
Q 028537 103 AKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPI 182 (207)
Q Consensus 103 ~km~~Ll~~fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPL 182 (207)
+++..|+.+||+||+.|||.|||++|||..||||+++|++ |+|++|++|+|+||+|||||||||.|+.||.+|.++|||
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 5788899999999999999999999999999999999885 799999999999999999999999999999999999999
Q ss_pred CchHHHHHHHHHHhc
Q 028537 183 RPCHIREAYRRLKLE 197 (207)
Q Consensus 183 qP~HIREA~RRL~~~ 197 (207)
.|.|+|||||++..+
T Consensus 170 ~p~h~reayr~~~k~ 184 (199)
T COG5251 170 IPFHKREAYRYKLKK 184 (199)
T ss_pred ChHHHHHHHHHHHHh
Confidence 999999999988754
No 5
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=99.27 E-value=2.4e-11 Score=110.77 Aligned_cols=99 Identities=21% Similarity=0.278 Sum_probs=80.3
Q ss_pred cHHHHHHHHH---HHhcCCHHHHHHHHHHHhcCCChhHHHHHHHHhcC----CCCCCccHHHHHHHHHHHHHHHHHHHHH
Q 028537 98 DPAKMAKMQA---ILNQFTEDQMNRYESFRRSALQKSNMRRLLVSITG----SQKISLPMTIVVCGIAKMFVGELVETAR 170 (207)
Q Consensus 98 d~e~~~km~~---Ll~~fteEQldRYE~fRRS~F~K~~IKRLi~~vtg----sqsVs~nvvIavaGlAKvFVGELVEeAr 170 (207)
|+..+++|.. .-..||.+||..|..||+++|.+.+-||+ ..+++ ..+++.++.-+++.||...|+-||+.|+
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 4444444433 56899999999999999999999999986 44443 2257888999999999999999999999
Q ss_pred HHHHHh----------------------------------ccCCCCCchHHHHHHHHHHhc
Q 028537 171 MVMTER----------------------------------NESGPIRPCHIREAYRRLKLE 197 (207)
Q Consensus 171 ~Vq~E~----------------------------------~e~gPLqP~HIREA~RRL~~~ 197 (207)
.|+... ....||+|+||+||||||+-.
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 136899999999999999954
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=97.89 E-value=4e-05 Score=53.96 Aligned_cols=65 Identities=15% Similarity=0.210 Sum_probs=53.7
Q ss_pred cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHH
Q 028537 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY 191 (207)
Q Consensus 126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~ 191 (207)
+.||.+.|||||...-+...||.+...+|+-.+-+||.+|..+|.++... +.+.=|+|.||..|+
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 36999999999998755557999999999999999999999999998774 456789999999885
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=96.49 E-value=0.015 Score=41.96 Aligned_cols=64 Identities=19% Similarity=0.207 Sum_probs=55.1
Q ss_pred CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (207)
.|++..||+|..+ .|-..+|+.+.-.++...+.|+-+|+..|.+++..-+ +.-|.+.+|.-|++
T Consensus 2 ~~p~~~i~ria~~-~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hak-Rktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAES-LGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSK-RTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHH-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCeecHHHHHHHhC
Confidence 5899999999876 5656799999999999999999999999999988653 44588999988864
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=96.01 E-value=0.058 Score=39.30 Aligned_cols=67 Identities=21% Similarity=0.279 Sum_probs=60.3
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (207)
++|.++..|+..+.++..+++++..++.-++=-||-.+++.|..+...++.. -|.++.|.-+++|..
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 6789999999999988889999999999999999999999999999887544 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=95.54 E-value=0.057 Score=43.30 Aligned_cols=66 Identities=15% Similarity=0.260 Sum_probs=57.0
Q ss_pred CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
.||-+.|.|+|..-.+...|+....+.++++--.++.||.|.|-...... ...-|.|.||..|++-
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 47888899999875556789999999999999999999999999887654 4578999999999875
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=95.24 E-value=0.067 Score=37.96 Aligned_cols=66 Identities=23% Similarity=0.262 Sum_probs=52.9
Q ss_pred CCChhHHHHHHHHhcCC----CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 127 ALQKSNMRRLLVSITGS----QKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgs----qsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
..++.-++|++..+... .+++.....+|..+...|+.+|.+.|..+....+ ..=|.|.||.-|.|.
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 34566677776666543 4789999999999999999999999999987654 445999999999873
No 11
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=94.40 E-value=0.1 Score=42.94 Aligned_cols=66 Identities=18% Similarity=0.255 Sum_probs=56.4
Q ss_pred cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (207)
Q Consensus 126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (207)
+-|+=..||||+..-...+.|+....+.++++--.++.||.|.|-.+.... ...-|-|+||+.|.|
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 458888999999866667789999999999999999999999999886643 355789999999987
No 12
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=94.26 E-value=0.24 Score=42.05 Aligned_cols=69 Identities=13% Similarity=0.249 Sum_probs=53.4
Q ss_pred cCCChhHHHHHHHHhcC-CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537 126 SALQKSNMRRLLVSITG-SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (207)
Q Consensus 126 S~F~K~~IKRLi~~vtg-sqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (207)
.+|||++|-|+|..++. .-.|....--++---+=.||--|..+|-+|+.+. ...-|-|.|+-.|+..|-
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 47999999999999886 4445555444444445589999999999999876 456799999999998773
No 13
>smart00414 H2A Histone 2A.
Probab=93.39 E-value=0.29 Score=38.72 Aligned_cols=66 Identities=18% Similarity=0.293 Sum_probs=54.3
Q ss_pred CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
.|+=..|.|++..-.-...|+....+-++++--.++.||.|.|-...... ...-|.|.||.-|.+-
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 46777799999876556689999999999999999999999998775543 4567999999987653
No 14
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=93.38 E-value=0.44 Score=37.03 Aligned_cols=80 Identities=19% Similarity=0.274 Sum_probs=68.4
Q ss_pred HHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537 115 DQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL 194 (207)
Q Consensus 115 EQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL 194 (207)
.+..||..+=...|++..|+|||.++.. ..||....-.+.-....|+=+|.+.|-.+...- .+.-+++..|.-|++++
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 4567888888889999999999998664 489999999999999999999999999887654 56789999999999887
Q ss_pred Hh
Q 028537 195 KL 196 (207)
Q Consensus 195 ~~ 196 (207)
..
T Consensus 85 ~~ 86 (91)
T COG2036 85 GR 86 (91)
T ss_pred cc
Confidence 54
No 15
>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=93.35 E-value=0.46 Score=34.80 Aligned_cols=65 Identities=15% Similarity=0.194 Sum_probs=47.4
Q ss_pred cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (207)
Q Consensus 126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (207)
+-|++..||-+..+ +|-.+++++++..++-=.-.-+.+||+.|.++|..- .+.-|.+.+|..|+|
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 35888999987554 665679999999999999999999999999998864 456799999999876
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=93.05 E-value=0.68 Score=35.45 Aligned_cols=66 Identities=18% Similarity=0.247 Sum_probs=55.4
Q ss_pred CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL 194 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL 194 (207)
.++|+.|+||+.. .|-..||..+...+..+.+.|+-+|+..|....+.- .+.-+....|.-|++|.
T Consensus 13 gi~k~~I~RLarr-~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha-~RKTVt~~DV~~alkr~ 78 (85)
T cd00076 13 GITKPAIRRLARR-GGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHA-KRKTVTAMDVVYALKRQ 78 (85)
T ss_pred cCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcCcHHHHHHHHHHC
Confidence 6999999999876 455689999999999999999999999999887643 44558888898887764
No 17
>PTZ00017 histone H2A; Provisional
Probab=92.10 E-value=0.4 Score=39.75 Aligned_cols=65 Identities=17% Similarity=0.269 Sum_probs=52.8
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
|+=..|.|++..-.-...|+....+.++++--.++.||.|.|-...... ...-|.|.||.-|+|-
T Consensus 28 FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~-kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 28 FPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDN-KKKRITPRHIQLAIRN 92 (134)
T ss_pred cchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhc-CCCeecHHHHHhhccC
Confidence 6667788888764334578888999999999999999999998876644 3568999999988874
No 18
>PTZ00015 histone H4; Provisional
Probab=91.82 E-value=1 Score=35.65 Aligned_cols=67 Identities=21% Similarity=0.275 Sum_probs=56.6
Q ss_pred cCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHH
Q 028537 126 SALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRL 194 (207)
Q Consensus 126 S~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL 194 (207)
..++|+.|+||+.. .|-..||..+...+..+.+.|+-+|+..|..+.+.- .+.-+....|.-|++|.
T Consensus 29 ~gI~k~~IrRLarr-~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA-~RKTVt~~DV~~AlKr~ 95 (102)
T PTZ00015 29 RGITKGAIRRLARR-GGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYA-RRKTVTAMDVVYALKRQ 95 (102)
T ss_pred cCCCHHHHHHHHHH-cCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcccHHHHHHHHHhc
Confidence 47999999999876 566689999999999999999999999999886644 45568899998887664
No 19
>PLN00035 histone H4; Provisional
Probab=91.38 E-value=1.2 Score=35.39 Aligned_cols=66 Identities=20% Similarity=0.275 Sum_probs=56.5
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (207)
|+++.|+||+.. .|-..||..+...+..+.+.|+-+|+..|....+.. .+.-+....|.-|++|+.
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 999999999876 455689999999999999999999999999887654 455688999999987754
No 20
>PLN00154 histone H2A; Provisional
Probab=90.42 E-value=1.1 Score=37.44 Aligned_cols=65 Identities=17% Similarity=0.253 Sum_probs=51.9
Q ss_pred CChhHHHHHHHHhc-CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 128 LQKSNMRRLLVSIT-GSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 128 F~K~~IKRLi~~vt-gsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
|+=.-|.|++..-+ -.+.|+....+.++++--.++.||.|.|-...... ...-|.|.||.-|+|-
T Consensus 39 FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~-kk~RItPrHi~lAIrn 104 (136)
T PLN00154 39 FPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDL-KVKRITPRHLQLAIRG 104 (136)
T ss_pred CchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhh-CCceecHHHhhhhccC
Confidence 66667888887643 24578999999999999999999999998775544 3466999999988764
No 21
>PLN00153 histone H2A; Provisional
Probab=90.14 E-value=0.91 Score=37.46 Aligned_cols=65 Identities=18% Similarity=0.271 Sum_probs=51.5
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
|+=.-|.|++..-.-...|+....+-++++--.++.||.|.|-...... ...-|.|.||.-|+|-
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 5556688887653334578888889999999999999999998876544 4679999999988764
No 22
>PLN00156 histone H2AX; Provisional
Probab=89.85 E-value=1 Score=37.66 Aligned_cols=65 Identities=17% Similarity=0.279 Sum_probs=51.8
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
|+=.-|.|++..-.-...|+....+.++++--.++.||.|.|-...... ....|.|.||.-|+|-
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 5666678887654334578888889999999999999999998876554 3579999999988764
No 23
>PLN00157 histone H2A; Provisional
Probab=89.82 E-value=0.85 Score=37.74 Aligned_cols=65 Identities=17% Similarity=0.262 Sum_probs=52.2
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
|+=.-|.|++..-.-...|+....+.++++--.++.||.|.|-...... ...-|.|.||.-|+|-
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 5556688888764434578888889999999999999999998876544 3579999999988764
No 24
>PTZ00252 histone H2A; Provisional
Probab=89.04 E-value=1.5 Score=36.56 Aligned_cols=66 Identities=14% Similarity=0.213 Sum_probs=52.4
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHh-ccCCCCCchHHHHHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTER-NESGPIRPCHIREAYRR 193 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~-~e~gPLqP~HIREA~RR 193 (207)
|+=.-|.|++..-.-...|+....+-++++--.++.||.|.|-...... +...-|.|.||.-|+|-
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 5555677887654434578888889999999999999999999987543 45689999999988764
No 25
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=88.54 E-value=1.4 Score=39.41 Aligned_cols=68 Identities=10% Similarity=0.345 Sum_probs=51.8
Q ss_pred hcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 125 RSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 125 RS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
-+.|+-+.|||||+.--.-.+|.+.|=++|+=---+|+-.||-+++++-..++ ..-|.|.||+.|+..
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 46799999999997532222566666566666667999999999999977663 567899999988754
No 26
>smart00417 H4 Histone H4.
Probab=88.12 E-value=1.7 Score=32.52 Aligned_cols=48 Identities=23% Similarity=0.259 Sum_probs=42.6
Q ss_pred CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028537 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 175 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E 175 (207)
.++|+.|+||+.. .|-..||..+...+..+.|.|+-+|+..|....+.
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 6999999999876 56668999999999999999999999999888653
No 27
>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=87.77 E-value=2.2 Score=31.23 Aligned_cols=64 Identities=17% Similarity=0.273 Sum_probs=47.9
Q ss_pred ChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 129 QKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 129 ~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
.|.++..||.+|-++..+.+.+.-++.=||=-||-.+|+.|..+.+.|+. .-|.+..|.-.+.|
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 47889999999988888999999999999999999999999999988753 35666766666655
No 28
>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=87.19 E-value=1.4 Score=32.60 Aligned_cols=65 Identities=20% Similarity=0.195 Sum_probs=46.0
Q ss_pred ChhHHHHHHHHhcC--CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 129 QKSNMRRLLVSITG--SQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 129 ~K~~IKRLi~~vtg--sqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
|+..|.||+..... ..+|+.+.+.+++-+-++||-|-|-.|.......+..+=|.+.||..-.=.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 46678888764332 235888899999999999999999999887666555555899999765433
No 29
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=86.86 E-value=6.1 Score=28.80 Aligned_cols=64 Identities=17% Similarity=0.166 Sum_probs=51.4
Q ss_pred hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537 130 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (207)
Q Consensus 130 K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (207)
|..|.+++.. .|..++++...-.+.-+.--|+.+|...++..++--+.+.|. +..|..|+..+.
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 4456666544 677789999999999999999999999999999766666665 899999988764
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=85.23 E-value=4.2 Score=37.45 Aligned_cols=66 Identities=14% Similarity=0.215 Sum_probs=56.1
Q ss_pred hhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhc
Q 028537 130 KSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLE 197 (207)
Q Consensus 130 K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~ 197 (207)
+..||-++.+ +|-..+++.++..++-....++.+|+++|.+.|..- .+.=|.+.||..|+|.+.-+
T Consensus 2 ~~~i~~ia~~-~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hs-kR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 2 QESIKLIAES-LGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHS-KRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred hhHHHHHHHH-cCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHh-CCCcCCHHHHHHHHHHhCCC
Confidence 4667777665 454589999999999999999999999999998865 45789999999999988765
No 31
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=83.38 E-value=4.2 Score=33.81 Aligned_cols=65 Identities=18% Similarity=0.293 Sum_probs=49.6
Q ss_pred CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (207)
-|+=..|.|++..--.-+.|+..-.+.|+++--.+..||.|.|-....+. ...-|.|+||+-|++
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 35566678887652223467777778888999999999999998876653 356789999999988
No 32
>PTZ00463 histone H2B; Provisional
Probab=80.99 E-value=7.7 Score=31.70 Aligned_cols=67 Identities=15% Similarity=0.168 Sum_probs=45.6
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcCCCC
Q 028537 133 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201 (207)
Q Consensus 133 IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~GklP 201 (207)
|.|++.+|-....||....-+|.+|..=++-.|..+|-.+..- +...-|.+.+|+.|+| |.+.|.|.
T Consensus 34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~-nkr~TltsrEIQtAvr-LlLpGELa 100 (117)
T PTZ00463 34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKY-TRRDTLSSREIQTAIR-LVLPGELA 100 (117)
T ss_pred HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCcCCHHHHHHHHh-hcccHHHH
Confidence 8888888877777777766666654444444444455555432 4677899999999987 55556654
No 33
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=80.60 E-value=4.1 Score=36.98 Aligned_cols=75 Identities=17% Similarity=0.302 Sum_probs=56.0
Q ss_pred HHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 118 NRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 118 dRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
+|-..+.--+|+-+.|||+|..--+---|+..+-++.+-++-+||.||+-.|--+. +++.+.-||-..|.+|+.+
T Consensus 100 ~~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~a-e~NkRRtLQksDia~Av~k 174 (286)
T COG5208 100 ERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINA-EENKRRTLQKSDIAAAVKK 174 (286)
T ss_pred hHHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHH-hHhhhhHHHHHHHHHHHHH
Confidence 33366777789999999998643332236666667778889999999999886654 4456677888889988875
No 34
>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=80.38 E-value=17 Score=26.18 Aligned_cols=63 Identities=16% Similarity=0.201 Sum_probs=50.0
Q ss_pred hHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537 131 SNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (207)
Q Consensus 131 ~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (207)
..|.+++.+ .|..++++...-++.-++.-|+.+|...++..++.-+.+.|. +.+|..|+..+-
T Consensus 10 ~~va~il~~-~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~-~~Dv~~al~~~g 72 (77)
T PF07524_consen 10 RSVAQILKH-AGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPN-LQDVEQALEEMG 72 (77)
T ss_pred HHHHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCC-HHHHHHHHHHhC
Confidence 334444433 676778899999999999999999999999998777777777 888988887653
No 35
>smart00427 H2B Histone H2B.
Probab=78.13 E-value=19 Score=28.09 Aligned_cols=67 Identities=15% Similarity=0.229 Sum_probs=49.0
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcCCCC
Q 028537 133 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201 (207)
Q Consensus 133 IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~GklP 201 (207)
|.|++.++-....++....-+|.+|..=+.-.|..+|-.+..- +...-|.+.+|+.|+|-+ +-|.|.
T Consensus 7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~-nkr~TltsreIqtAvrl~-LpgeLa 73 (89)
T smart00427 7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARY-NKKSTLSSREIQTAVRLI-LPGELA 73 (89)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCCcCCHHHHHHHHHHH-ccHHHH
Confidence 8888888887777887777777777666666666677666543 356789999999998854 445543
No 36
>PLN00158 histone H2B; Provisional
Probab=76.70 E-value=19 Score=29.46 Aligned_cols=66 Identities=15% Similarity=0.217 Sum_probs=46.3
Q ss_pred HHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcCCC
Q 028537 133 MRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKV 200 (207)
Q Consensus 133 IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkl 200 (207)
|.|++.+|-....||....-+|.+|..=++-.|..+|-.+..- +...-|.+.+|+.|+|-+ +-|.|
T Consensus 33 I~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~-nkr~TltsrEIqtAvrLv-LpgEL 98 (116)
T PLN00158 33 IYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARY-NKKPTVTSREIQTAVRLI-LPGEL 98 (116)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhc-cCCCcCCHHHHHHHHHHh-ccHHH
Confidence 8899888877777877766667766555555555566555442 467789999999998854 34543
No 37
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=75.98 E-value=9.8 Score=30.82 Aligned_cols=68 Identities=10% Similarity=0.207 Sum_probs=44.2
Q ss_pred HHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHH
Q 028537 123 FRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAY 191 (207)
Q Consensus 123 fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~ 191 (207)
|-.++|+-+.|||||+---.-.+|++.+-++++----+|+.+||-+.++..... .+.-+.-.||..|.
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 667889999999998743221256666555555556789999988776654322 23445566666554
No 38
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=75.84 E-value=18 Score=33.21 Aligned_cols=89 Identities=13% Similarity=0.297 Sum_probs=59.4
Q ss_pred HHHHHhcCCHHHHHH-------HHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHH----HHHH-HH
Q 028537 105 MQAILNQFTEDQMNR-------YESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELV----ETAR-MV 172 (207)
Q Consensus 105 m~~Ll~~fteEQldR-------YE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELV----EeAr-~V 172 (207)
+..-|..++++.... |+... ++....|..|+..+. ++.++.+++|+..-+.-+|+ ..|. .+
T Consensus 216 il~~L~~~dp~~a~~Ir~~mF~FedL~--~~~~qtia~iL~~v~-----~~~la~aLkg~~~e~r~~il~nmS~Raa~~l 288 (334)
T PRK07194 216 LMEMLKEHDEEVVNEIEDNMYDFFILS--RQSEETLQRLMDEVP-----MELWAVALKGTEPALRQAILRVMPKRQAQAL 288 (334)
T ss_pred HHHHHHhhCHHHHHHHHHhcCCHHHHh--cCCHHHHHHHHHhCC-----HHHHHHHHccCCHHHHHHHHHHccHHHHHHH
Confidence 444556667777666 44443 366666777766542 35688889888765555544 4444 45
Q ss_pred HHHhccCCCCCchHHHHH-------HHHHHhcCCC
Q 028537 173 MTERNESGPIRPCHIREA-------YRRLKLEGKV 200 (207)
Q Consensus 173 q~E~~e~gPLqP~HIREA-------~RRL~~~Gkl 200 (207)
++++...||++...+.+| .|+|-.+|+|
T Consensus 289 ~eele~~gpV~~sdvE~Aq~~Iv~~~r~L~~~G~I 323 (334)
T PRK07194 289 EAQIERLGPVPLSRVEQARKEIMALVRELAEAGEI 323 (334)
T ss_pred HHHHHhcCCCcHHHHHHHHHHHHHHHHHHHHCCCE
Confidence 667777999999988876 5677778865
No 39
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=75.06 E-value=16 Score=30.67 Aligned_cols=67 Identities=19% Similarity=0.258 Sum_probs=47.6
Q ss_pred cCCChhHHHHHHHHhcCCC-CCCccH--HHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537 126 SALQKSNMRRLLVSITGSQ-KISLPM--TIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (207)
Q Consensus 126 S~F~K~~IKRLi~~vtgsq-sVs~nv--vIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (207)
-+|||++|.|.|..++.-- .++... +++=+|| .|+--|..+|-++|++. ...-|-|.|+-.|+.-|-
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 3699999999998887532 123332 2333444 68888889999998865 345799999999987653
No 40
>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=71.15 E-value=9 Score=29.43 Aligned_cols=68 Identities=26% Similarity=0.482 Sum_probs=39.8
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHH----HHHH-HHHHHHHHhccCCCCCchHHHHH-------HHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVG----ELVE-TARMVMTERNESGPIRPCHIREA-------YRRLK 195 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVG----ELVE-eAr~Vq~E~~e~gPLqP~HIREA-------~RRL~ 195 (207)
++...+.+|+.++. ++.+++++.|-..-|.- .|-. .|..|+++....||+.+..+.+| .|+|.
T Consensus 28 l~~~~l~~ll~~v~-----~~~la~ALkga~~e~~~~il~nms~r~a~~l~~e~~~~g~v~~~di~~Aq~~iv~~~r~l~ 102 (110)
T PF01706_consen 28 LDDRDLQKLLREVD-----PDDLALALKGASEELREKILSNMSKRAAEMLREEMEALGPVRLSDIEEAQREIVEIVRRLE 102 (110)
T ss_dssp S-HHHHHHHHTTS------HHHHHHHHCTS-HHHHHHHHTTS-HHHHHHHHHHHHHH-S--HHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHCC-----HhHHHHHHccCCHHHHHHHHHHcCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHH
Confidence 55566666665432 34688888776655444 4444 34566777778899999988876 45666
Q ss_pred hcCCC
Q 028537 196 LEGKV 200 (207)
Q Consensus 196 ~~Gkl 200 (207)
.+|+|
T Consensus 103 ~~G~I 107 (110)
T PF01706_consen 103 EEGEI 107 (110)
T ss_dssp HTTSS
T ss_pred HCcCE
Confidence 77765
No 41
>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=64.98 E-value=57 Score=26.89 Aligned_cols=41 Identities=12% Similarity=0.301 Sum_probs=28.0
Q ss_pred HHHHHHHHHhcCCChhHHHHHHH---HhcCCCCCCccHHHHHHHHHHHHH
Q 028537 116 QMNRYESFRRSALQKSNMRRLLV---SITGSQKISLPMTIVVCGIAKMFV 162 (207)
Q Consensus 116 QldRYE~fRRS~F~K~~IKRLi~---~vtgsqsVs~nvvIavaGlAKvFV 162 (207)
=-.||..|+ ..|.-++. .++|...-..-...++..|+|.|=
T Consensus 89 Vd~RY~qY~------~Qmq~VvssFe~vaG~gaA~~YtalAlqamSrhFR 132 (140)
T PF07526_consen 89 VDRRYRQYY------DQMQAVVSSFEAVAGLGAAAPYTALALQAMSRHFR 132 (140)
T ss_pred HHHHHHHHH------HHHHHHHHHHHHHhcCCcchhhHHHHHHHHHHHHH
Confidence 346999994 45666644 456644444567889999999884
No 42
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=61.18 E-value=6.1 Score=31.13 Aligned_cols=18 Identities=44% Similarity=0.481 Sum_probs=15.8
Q ss_pred CCchHHHHHHHHHHhcCC
Q 028537 182 IRPCHIREAYRRLKLEGK 199 (207)
Q Consensus 182 LqP~HIREA~RRL~~~Gk 199 (207)
-.|.|||+|+|||..+|-
T Consensus 31 T~~~~iR~~L~rYI~~~G 48 (97)
T PRK13916 31 TKTAHIREALRRYIEEIG 48 (97)
T ss_pred CccHHHHHHHHHHHHhcC
Confidence 458999999999999874
No 43
>PRK05686 fliG flagellar motor switch protein G; Validated
Probab=60.72 E-value=22 Score=32.61 Aligned_cols=69 Identities=25% Similarity=0.476 Sum_probs=49.3
Q ss_pred CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHH----HHHHHHHHHHH-HHHHHhccCCCCCchHHHHHH-------HHH
Q 028537 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAK----MFVGELVETAR-MVMTERNESGPIRPCHIREAY-------RRL 194 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAK----vFVGELVEeAr-~Vq~E~~e~gPLqP~HIREA~-------RRL 194 (207)
+++...+.+|+..|. ++.+++++.|-.. .|+.-|-..+. .+++++...||++...+.+|- |+|
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 377777888877653 3578899987554 55566666554 556677789999999988764 577
Q ss_pred HhcCCC
Q 028537 195 KLEGKV 200 (207)
Q Consensus 195 ~~~Gkl 200 (207)
-.+|+|
T Consensus 324 ~~~G~I 329 (339)
T PRK05686 324 AEAGEI 329 (339)
T ss_pred HHCCCE
Confidence 777874
No 44
>KOG2140 consensus Uncharacterized conserved protein [General function prediction only]
Probab=60.58 E-value=40 Score=34.50 Aligned_cols=89 Identities=22% Similarity=0.335 Sum_probs=58.5
Q ss_pred cccccCCCCC-CcHHHHHHHHHHHhcCCHHHHHH--HHHHHhc------CCChhHHHHHHH----------------Hhc
Q 028537 87 DVELGKFPSS-SDPAKMAKMQAILNQFTEDQMNR--YESFRRS------ALQKSNMRRLLV----------------SIT 141 (207)
Q Consensus 87 ~~~l~~~~~~-~d~e~~~km~~Ll~~fteEQldR--YE~fRRS------~F~K~~IKRLi~----------------~vt 141 (207)
++..+....+ -.|.+...|+.-+..=+..+|.| ||+.|.+ ++|..+|+-+|. +|.
T Consensus 125 ~l~~trtGG~YIPPaKL~~mq~qi~Dk~s~~yQRmnWEalkksInglInkvn~sNi~~ii~eLfqeNiirgRgl~crsv~ 204 (739)
T KOG2140|consen 125 DLLRTRTGGAYIPPAKLRMMQAQITDKNSIEYQRMNWEALKKSINGLINKVNASNIQEIIRELFQENIIRGRGLLCRSVM 204 (739)
T ss_pred HHhhccCCCeecCHHHHHHHHHHhcccchHHHHHHHHHHHHHHhHHHHhhhhHHHHHHHHHHHHHHHHHhccchhHHHHH
Confidence 3444444333 25677677777776666566665 8998876 677777766632 233
Q ss_pred CCCCCCccHHHHHHHHHHHH------HHHHHHHHHHHHHH
Q 028537 142 GSQKISLPMTIVVCGIAKMF------VGELVETARMVMTE 175 (207)
Q Consensus 142 gsqsVs~nvvIavaGlAKvF------VGELVEeAr~Vq~E 175 (207)
-.|.-+++.+-|.++|+-|. ||||+-+-+-||..
T Consensus 205 ~aq~asp~ft~vyaALvAviNskfP~IgElLlkrLilqf~ 244 (739)
T KOG2140|consen 205 QAQAASPGFTPVYAALVAVINSKFPQIGELLLKRLILQFK 244 (739)
T ss_pred HHHhcCCCCcHHHHHHHHHHccCCchHHHHHHHHHHHHHH
Confidence 33455667777777777765 89999888888764
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=59.89 E-value=24 Score=32.62 Aligned_cols=69 Identities=22% Similarity=0.409 Sum_probs=49.7
Q ss_pred CCChhHHHHHHHHhcCCCCCCccHHHHHHHH----HHHHHHHHHHHHHH-HHHHhccCCCCCchHHHHH-------HHHH
Q 028537 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGI----AKMFVGELVETARM-VMTERNESGPIRPCHIREA-------YRRL 194 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGl----AKvFVGELVEeAr~-Vq~E~~e~gPLqP~HIREA-------~RRL 194 (207)
.++...|.+|+..|. ++.+++++.|- -.-|..-+-..+.+ ++++....||++...+.+| .|+|
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 377777888777653 35788888774 44566666665554 4667777999999988866 5677
Q ss_pred HhcCCC
Q 028537 195 KLEGKV 200 (207)
Q Consensus 195 ~~~Gkl 200 (207)
-.+|.|
T Consensus 321 ~~~G~I 326 (338)
T TIGR00207 321 EETGEI 326 (338)
T ss_pred HHCCCE
Confidence 888875
No 46
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=56.73 E-value=63 Score=28.07 Aligned_cols=49 Identities=18% Similarity=0.241 Sum_probs=41.5
Q ss_pred CCChhHHHHHHHHhcCC--CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028537 127 ALQKSNMRRLLVSITGS--QKISLPMTIVVCGIAKMFVGELVETARMVMTE 175 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgs--qsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E 175 (207)
.||++.|.|||..+..- .+|+.....+|+=-|-|||--|...|..++..
T Consensus 10 ~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~ 60 (172)
T KOG0870|consen 10 NLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKD 60 (172)
T ss_pred hccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 59999999999888752 25777788889999999999999999999774
No 47
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=55.28 E-value=20 Score=32.80 Aligned_cols=49 Identities=22% Similarity=0.358 Sum_probs=43.0
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTER 176 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~ 176 (207)
+.|.+|..|+..|.+...+-++|-.+|.=||==||-.||..|..+.+.|
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 5678888888888888778889999999999999999999998887765
No 48
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=51.24 E-value=5.3 Score=26.90 Aligned_cols=52 Identities=17% Similarity=0.207 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHH
Q 028537 113 TEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELV 166 (207)
Q Consensus 113 teEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELV 166 (207)
.+-.+..++..|+++++++.|.++++.-. .+++-..+..|+-+-.+=++||+
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 49
>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=49.41 E-value=1.1e+02 Score=23.48 Aligned_cols=63 Identities=17% Similarity=0.213 Sum_probs=46.5
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
|.+. |+.+|=..-..+.+.+..+.+|--|.--||-+|+-+|..+.. | ..+.+.+++|.=++|+
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 777774433334556678888999999999999999999977 4 3455699999888775
No 50
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=47.55 E-value=30 Score=30.94 Aligned_cols=71 Identities=18% Similarity=0.319 Sum_probs=51.3
Q ss_pred HHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 122 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 122 ~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
.|....|+.+.|||+|..=-.-++|+....++++-.+-+||-||...+- +..+.+.+..|+=.||-.|..+
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 3556679999999998754444478888899999999999999988742 2233345566666777666543
No 51
>smart00574 POX domain associated with HOX domains.
Probab=47.11 E-value=1.1e+02 Score=25.68 Aligned_cols=42 Identities=14% Similarity=0.269 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhcCCChhHHHHHHH---HhcCCCCCCccHHHHHHHHHHHHH
Q 028537 115 DQMNRYESFRRSALQKSNMRRLLV---SITGSQKISLPMTIVVCGIAKMFV 162 (207)
Q Consensus 115 EQldRYE~fRRS~F~K~~IKRLi~---~vtgsqsVs~nvvIavaGlAKvFV 162 (207)
|=-.||..|+ ..|.-++. .++|...-..-...++..|++.|=
T Consensus 88 eVd~RY~qY~------~qmq~v~ssFe~vaG~g~a~~yt~lAl~a~SrhFr 132 (140)
T smart00574 88 EVDRRYKHYY------EQMQTVVSSFDQAAGLGAAKPYTALALKTISRHFR 132 (140)
T ss_pred HHHHHHHHHH------HHHHHHHHHHHHHhcCCchHHHHHHHHHHHHHHHH
Confidence 3457999994 45666654 345543333446778888888884
No 52
>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=46.29 E-value=1.9e+02 Score=30.13 Aligned_cols=71 Identities=17% Similarity=0.280 Sum_probs=46.1
Q ss_pred HHHHHHHHhcCCHHH----HHHHHHHHhcCC---ChhHHHHHHH----Hh--cCCCCCCc------cHHHHHHHHHHHHH
Q 028537 102 MAKMQAILNQFTEDQ----MNRYESFRRSAL---QKSNMRRLLV----SI--TGSQKISL------PMTIVVCGIAKMFV 162 (207)
Q Consensus 102 ~~km~~Ll~~fteEQ----ldRYE~fRRS~F---~K~~IKRLi~----~v--tgsqsVs~------nvvIavaGlAKvFV 162 (207)
.+.+..||...+.++ ..|.-.|...+| ||.++.+|+. .+ ..++.-+. .++-.|-.||+.|.
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 367777777887 6777776632 11 12222022 34555778888888
Q ss_pred HHHHHHHHHH
Q 028537 163 GELVETARMV 172 (207)
Q Consensus 163 GELVEeAr~V 172 (207)
-.+.+..+.+
T Consensus 508 ~~~a~~~r~~ 517 (840)
T PF04147_consen 508 EEAAECFREV 517 (840)
T ss_pred HHHHHHHHHH
Confidence 8877777766
No 53
>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=44.94 E-value=67 Score=23.66 Aligned_cols=38 Identities=24% Similarity=0.545 Sum_probs=30.1
Q ss_pred HHHHhcCCHHHHH----HHHHHHhcCCChhHHHHHHHHhcCC
Q 028537 106 QAILNQFTEDQMN----RYESFRRSALQKSNMRRLLVSITGS 143 (207)
Q Consensus 106 ~~Ll~~fteEQld----RYE~fRRS~F~K~~IKRLi~~vtgs 143 (207)
..|...+++.+++ .|+.||+..++|...=|.+..++|.
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 6999999999999977777888885
No 54
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=43.55 E-value=76 Score=26.34 Aligned_cols=78 Identities=18% Similarity=0.208 Sum_probs=45.1
Q ss_pred HHHhcCCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcCCCC
Q 028537 122 SFRRSALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKVP 201 (207)
Q Consensus 122 ~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~GklP 201 (207)
.+|..+|..- |.|++.+|-.+..++..-..||.+|--.|+-.|.-+|=....-.+. .-|.-.||+-|+| |.+-|++.
T Consensus 33 ~~~~e~~s~y-v~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~kr-stisSreiqta~r-LllPgel~ 109 (127)
T KOG1744|consen 33 TRRKESYSEY-VYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKR-STISSREIQTAVR-LLLPGELA 109 (127)
T ss_pred ccccCceeee-hhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCC-CcccHHHHHHHHH-HhCchHHh
Confidence 3444455333 4456666655445666666666665544455555555444443333 3488999999887 55557765
Q ss_pred C
Q 028537 202 K 202 (207)
Q Consensus 202 ~ 202 (207)
.
T Consensus 110 k 110 (127)
T KOG1744|consen 110 K 110 (127)
T ss_pred h
Confidence 4
No 55
>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=41.35 E-value=50 Score=29.12 Aligned_cols=51 Identities=16% Similarity=0.247 Sum_probs=34.1
Q ss_pred CChhHHHHHHHHhc---CCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Q 028537 128 LQKSNMRRLLVSIT---GSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNE 178 (207)
Q Consensus 128 F~K~~IKRLi~~vt---gsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e 178 (207)
|+...+.+.|..+. |...+..+++-.|+--++.++-.|||.+..+...|-+
T Consensus 44 L~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~ 97 (264)
T PF05236_consen 44 LNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRD 97 (264)
T ss_dssp S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH--------
T ss_pred cCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 77877877777765 4345888999999999999999999999999776643
No 56
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=41.00 E-value=29 Score=28.64 Aligned_cols=64 Identities=19% Similarity=0.275 Sum_probs=44.5
Q ss_pred CChhHHHHHHHHh-cCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537 128 LQKSNMRRLLVSI-TGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYR 192 (207)
Q Consensus 128 F~K~~IKRLi~~v-tgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (207)
|+=.-|.|.+.+- +...+|...-++-+++|-..+-.|+.|.|=..-+.. .-.-|.|.||+-|.|
T Consensus 31 FpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdL-KvKRitprHlqLAiR 95 (131)
T KOG1757|consen 31 FPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDL-KVKRITPRHLQLAIR 95 (131)
T ss_pred cchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccc-eeeeccchhheeeec
Confidence 5556677776543 444467778888889999999999999874332211 123588999998876
No 57
>KOG3871 consensus Cell adhesion complex protein bystin [Extracellular structures]
Probab=39.45 E-value=1.2e+02 Score=29.69 Aligned_cols=48 Identities=25% Similarity=0.335 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhc------cCCCCCchHHHHHHHHHH------hcCCCCC
Q 028537 155 CGIAKMFVGELVETARMVMTERN------ESGPIRPCHIREAYRRLK------LEGKVPK 202 (207)
Q Consensus 155 aGlAKvFVGELVEeAr~Vq~E~~------e~gPLqP~HIREA~RRL~------~~GklP~ 202 (207)
..|+++...-|-|+--+|..+.- -..|=.|-.+-|.|+... ..||||+
T Consensus 145 ~tL~diIm~ki~ekead~~~~~~~~~~~e~~~~~ldpkV~e~Y~~Vg~~lskyrsGKlPK 204 (449)
T KOG3871|consen 145 YTLADIIMAKIREKEADVETEQSDPDENEFPMPALDPKVIEMYEGVGSVLSKYRSGKLPK 204 (449)
T ss_pred ccHHHHHHHHHHHHHhhHHhhhcccccccCCCCCCCHHHHHHHHHHHHHHHHhhcCCCch
Confidence 55667777777775545544321 123334445666766432 4599885
No 58
>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=39.08 E-value=1.4e+02 Score=21.10 Aligned_cols=47 Identities=15% Similarity=0.129 Sum_probs=36.7
Q ss_pred CChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028537 128 LQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTE 175 (207)
Q Consensus 128 F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E 175 (207)
+|...+..+++. .|.+.....++=.|+=.+-=||-+|+..|+..++-
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 566777777755 67665556788889999999999999999887653
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=35.18 E-value=50 Score=25.20 Aligned_cols=59 Identities=20% Similarity=0.233 Sum_probs=27.8
Q ss_pred HHHHHHHhcCC-CCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 133 MRRLLVSITGS-QKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 133 IKRLi~~vtgs-qsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
|+.+|=. .|. ..+.+..+.+|--|...||-+|+-.|..+...+ .++-|.+++|.=++|+
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 IRQMMYG-FGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRR-GSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHHC-TTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------------
T ss_pred HHHHHHH-cCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhcc-ccCcCcHHHHHHHHhc
Confidence 5666533 343 456667888899999999999999999986554 4778899999888875
No 60
>PRK15398 aldehyde dehydrogenase EutE; Provisional
Probab=34.82 E-value=54 Score=31.41 Aligned_cols=46 Identities=20% Similarity=0.303 Sum_probs=36.4
Q ss_pred hHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 028537 131 SNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERN 177 (207)
Q Consensus 131 ~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~ 177 (207)
..||++|.+...||+||++.+.-+-|..+- |-+.|+.|+.-+.+|.
T Consensus 8 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d-v~~av~~A~~A~~~w~ 53 (465)
T PRK15398 8 QVVKAVLAEMLSSQTVSPPAAVGEMGVFAS-VDDAVAAAKVAQQRYQ 53 (465)
T ss_pred HHHHHHHHHhhcccccccccccccccHHHH-HHHHHHHHHHHHHHHH
Confidence 357888888888899999887777777766 5678888888888774
No 61
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.15 E-value=1.7e+02 Score=23.48 Aligned_cols=53 Identities=17% Similarity=0.333 Sum_probs=35.1
Q ss_pred HhcCCHHHHHHHHHHHhcCCChhHHHHHHHHhcCCCCCCccH-HHHHHHHHHHHHHHHHHHHH
Q 028537 109 LNQFTEDQMNRYESFRRSALQKSNMRRLLVSITGSQKISLPM-TIVVCGIAKMFVGELVETAR 170 (207)
Q Consensus 109 l~~fteEQldRYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nv-vIavaGlAKvFVGELVEeAr 170 (207)
+.+||++|.+|+++ +..|||+.+.--. +=-+|| .+.++||+.--++.-+.+|-
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 46789999999986 3566776654322 222344 45678998888877766653
No 62
>PF14911 MMS22L_C: S-phase genomic integrity recombination mediator, C-terminal
Probab=33.15 E-value=2.5e+02 Score=26.94 Aligned_cols=40 Identities=23% Similarity=0.199 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHH----HHHHHHHHHHhccCCCCCchHHHHHHHHHHh
Q 028537 154 VCGIAKMFVGEL----VETARMVMTERNESGPIRPCHIREAYRRLKL 196 (207)
Q Consensus 154 vaGlAKvFVGEL----VEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~ 196 (207)
|+-+.+-+|--| .+.++++=..|+ .=+-.+||+||.||..
T Consensus 327 vA~l~p~lV~~Lip~i~q~l~~~E~kRG---~G~d~~lR~~~~rL~~ 370 (373)
T PF14911_consen 327 VAELDPQLVISLIPTIRQSLKDSERKRG---LGRDVALRKALSRLLS 370 (373)
T ss_pred HHHhCHHHHHHHHHHHHHHHHHHHHHhc---CCcCHHHHHHHHHHHH
Confidence 344444444444 445555544553 3456899999999974
No 63
>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=32.55 E-value=40 Score=25.98 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=15.2
Q ss_pred HHHHHhcCCHHHHHHHHHHHh
Q 028537 105 MQAILNQFTEDQMNRYESFRR 125 (207)
Q Consensus 105 m~~Ll~~fteEQldRYE~fRR 125 (207)
.-.|+..||+++.+.|-.--+
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 357899999999999965443
No 64
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=30.60 E-value=2.4e+02 Score=21.43 Aligned_cols=27 Identities=30% Similarity=0.332 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhccCCCCCchHHHHHHH
Q 028537 165 LVETARMVMTERNESGPIRPCHIREAYR 192 (207)
Q Consensus 165 LVEeAr~Vq~E~~e~gPLqP~HIREA~R 192 (207)
|+-.|++|.+- .+..-|.+.||.||+.
T Consensus 68 ilrvARTIADL-~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 68 ILRVARTIADL-EGSERITREHIAEALS 94 (96)
T ss_pred HHHHHHHHHhH-cCCCCCCHHHHHHHHh
Confidence 45668888663 4677899999999974
No 65
>COG5123 TOA2 Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=30.53 E-value=47 Score=26.95 Aligned_cols=39 Identities=31% Similarity=0.314 Sum_probs=22.4
Q ss_pred HHHHHhcCCChhHHHHHHHHhcCCCCCCccHHH-HHHHHHH
Q 028537 120 YESFRRSALQKSNMRRLLVSITGSQKISLPMTI-VVCGIAK 159 (207)
Q Consensus 120 YE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvI-avaGlAK 159 (207)
||.|||+.+-|.-.+-|=.-|.. ..++++.+. ++-.|-|
T Consensus 5 YElYRrs~ig~~L~dalD~lis~-g~isp~lam~vLetFDk 44 (113)
T COG5123 5 YELYRRSMIGKVLEDALDELISA-GVISPNLAMHVLETFDK 44 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc-CCcCHHHHHHHHHHhhh
Confidence 99999998876655444222222 257777554 2344444
No 66
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=30.51 E-value=86 Score=32.65 Aligned_cols=92 Identities=16% Similarity=0.196 Sum_probs=58.5
Q ss_pred HHHHhcCCHHHHHHHHHHHhc-CCChhHHHHHHHHhcCCCCCCccHHH---HHHHHHHHHHHHHHHHHHHHHHHhccCCC
Q 028537 106 QAILNQFTEDQMNRYESFRRS-ALQKSNMRRLLVSITGSQKISLPMTI---VVCGIAKMFVGELVETARMVMTERNESGP 181 (207)
Q Consensus 106 ~~Ll~~fteEQldRYE~fRRS-~F~K~~IKRLi~~vtgsqsVs~nvvI---avaGlAKvFVGELVEeAr~Vq~E~~e~gP 181 (207)
+.=+..||++|-.|.+-|... +|+..-.+-|+++..... .-..++- --..+|..+++||.....+- . -..-|
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 335678999999999999865 888887766643221000 0001110 01246788888888776653 1 24568
Q ss_pred CCchHHHHHHHHHHhcCCCCC
Q 028537 182 IRPCHIREAYRRLKLEGKVPK 202 (207)
Q Consensus 182 LqP~HIREA~RRL~~~GklP~ 202 (207)
|.|.||-+-++ |..+|+|-.
T Consensus 662 l~pe~LaeLv~-lV~~g~IS~ 681 (771)
T PRK14703 662 FTPAALARLVA-LVDAGRIST 681 (771)
T ss_pred CCHHHHHHHHH-HHHcCCccH
Confidence 99999999874 666787754
No 67
>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=30.22 E-value=2e+02 Score=20.29 Aligned_cols=39 Identities=21% Similarity=0.294 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHhcCCC
Q 028537 161 FVGELVETARMVMTERNESGPIRPCHIREAYRRLKLEGKV 200 (207)
Q Consensus 161 FVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkl 200 (207)
=.|+|.+.=..+++.. ...||....+++-+..|...|-|
T Consensus 24 ~~~~vy~~Y~~~c~~~-~~~~l~~~~~~~~l~~L~~~gli 62 (87)
T cd08768 24 TTGEVYEVYEELCEEI-GVDPLTQRRISDLLSELEMLGLL 62 (87)
T ss_pred cHHHHHHHHHHHHHHc-CCCCCcHHHHHHHHHHHHHcCCe
Confidence 3588888888888765 78899999999999999988865
No 68
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=30.10 E-value=1.5e+02 Score=23.55 Aligned_cols=47 Identities=23% Similarity=0.332 Sum_probs=34.9
Q ss_pred CCChhHHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028537 127 ALQKSNMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMT 174 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~ 174 (207)
.++|..||||... .|-..|+--+---..+++|+|+-.++.-|..-..
T Consensus 29 gitKpaIRRlARr-~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~ 75 (103)
T KOG3467|consen 29 GITKPAIRRLARR-GGVKRISGLIYEETRGVLKVFLENVIRDAVTYTE 75 (103)
T ss_pred ccchHHHHHHHHh-cCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5779999998654 3433455556666789999999999998876543
No 69
>PF11011 DUF2849: Protein of unknown function (DUF2849); InterPro: IPR021270 This bacterial family of proteins has no known function.
Probab=29.78 E-value=33 Score=26.49 Aligned_cols=18 Identities=39% Similarity=0.630 Sum_probs=15.1
Q ss_pred ccCCCCCchHHHHHHHHH
Q 028537 177 NESGPIRPCHIREAYRRL 194 (207)
Q Consensus 177 ~e~gPLqP~HIREA~RRL 194 (207)
...|.++|.|+||.+|..
T Consensus 64 ~~dG~~~P~~~RE~iRa~ 81 (90)
T PF11011_consen 64 GADGRPRPVHLRERIRAR 81 (90)
T ss_pred cCCCCccchhHHHhhhcc
Confidence 357889999999999864
No 70
>PF15510 CENP-W: Centromere kinetochore component W
Probab=27.80 E-value=2.5e+02 Score=22.46 Aligned_cols=67 Identities=21% Similarity=0.270 Sum_probs=43.0
Q ss_pred CCChhHHHHHHHHhcCCCCC--CccHH--------------HHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHH
Q 028537 127 ALQKSNMRRLLVSITGSQKI--SLPMT--------------IVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREA 190 (207)
Q Consensus 127 ~F~K~~IKRLi~~vtgsqsV--s~nvv--------------IavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA 190 (207)
+-|+..+||++...-....+ +-++. +=+.+ =+||-.|-|+||.=.-| +..+-|.++|+..|
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 46889999999998
Q ss_pred HHHHHh
Q 028537 191 YRRLKL 196 (207)
Q Consensus 191 ~RRL~~ 196 (207)
...+..
T Consensus 93 aKviLK 98 (102)
T PF15510_consen 93 AKVILK 98 (102)
T ss_pred HHHHHH
Confidence 876653
No 71
>cd00923 Cyt_c_Oxidase_Va Cytochrome c oxidase subunit Va. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Va is one of three mammalian subunits that lacks a transmembrane region. Subunit Va is located on the matrix side of the membrane and binds thyroid hormone T2, releasing allosteric inhibition caused by the binding of ATP to subunit IV and allowing high turnover at elevated intramitochondrial ATP/ADP ratios.
Probab=27.37 E-value=1.1e+02 Score=24.73 Aligned_cols=32 Identities=28% Similarity=0.552 Sum_probs=25.0
Q ss_pred HHHHHHHHhcCCChhH-----HHHHHHHhcCCCCCCccHHH
Q 028537 117 MNRYESFRRSALQKSN-----MRRLLVSITGSQKISLPMTI 152 (207)
Q Consensus 117 ldRYE~fRRS~F~K~~-----IKRLi~~vtgsqsVs~nvvI 152 (207)
-.||+.| |++.. +||-||+..+---||.+-+|
T Consensus 9 ~aRye~~----F~~~~iD~we~rr~mN~l~~~DlVP~P~ii 45 (103)
T cd00923 9 DARYETY----FNRPDIDGWELRRGLNNLFGYDLVPEPKVI 45 (103)
T ss_pred HHHHHHH----hCCcCccHHHHHHHHHHHhccccCCCcHHH
Confidence 4699999 88885 89999999887667776443
No 72
>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=26.68 E-value=91 Score=24.29 Aligned_cols=34 Identities=24% Similarity=0.435 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHhcCCChhHHHHHH
Q 028537 99 PAKMAKMQAILNQFTEDQMNRYESFRRSALQKSNMRRLL 137 (207)
Q Consensus 99 ~e~~~km~~Ll~~fteEQldRYE~fRRS~F~K~~IKRLi 137 (207)
+.+..++..++++||+++++--..+.. +-++||.
T Consensus 47 ~~~lk~~~~Ii~SMT~~Er~~p~ll~~-----sR~~RIA 80 (104)
T PF02978_consen 47 EKKLKRMEAIIDSMTPEERDNPKLLNE-----SRRRRIA 80 (104)
T ss_dssp HHHHHHHHHHHTTSBHHHHHCGGGHHH-----HHHHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHhCccccch-----HHHHHHH
Confidence 445588999999999999977777633 5677764
No 73
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=26.41 E-value=89 Score=25.34 Aligned_cols=36 Identities=33% Similarity=0.402 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHH
Q 028537 157 IAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLK 195 (207)
Q Consensus 157 lAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~ 195 (207)
=||-||-+|+..++.-+.+|.+. .|..|++....|-
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 47889999999999777777655 6777877766554
No 74
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.23 E-value=2.8e+02 Score=21.03 Aligned_cols=43 Identities=23% Similarity=0.343 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH-HHHHhccCCCCCchHHHHHHHHH
Q 028537 150 MTIVVCGIAKMFVGELVETARM-VMTERNESGPIRPCHIREAYRRL 194 (207)
Q Consensus 150 vvIavaGlAKvFVGELVEeAr~-Vq~E~~e~gPLqP~HIREA~RRL 194 (207)
+.|+++-++-+|.|-.| ||+ ++++..+..||-++-||.=+-.+
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 56777888888888666 444 45567899999999888766544
No 75
>KOG3463 consensus Transcription initiation factor IIA, gamma subunit [Transcription]
Probab=25.70 E-value=64 Score=26.21 Aligned_cols=33 Identities=21% Similarity=0.352 Sum_probs=22.2
Q ss_pred HHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHH
Q 028537 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTI 152 (207)
Q Consensus 119 RYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvI 152 (207)
-|+.|||+.+-+.-.+-| -.....+.++++++.
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 599999999977654444 333344567877654
No 76
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=25.13 E-value=94 Score=25.36 Aligned_cols=34 Identities=26% Similarity=0.309 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhccCCCCCchHHHHHHHHHHhcCCC
Q 028537 166 VETARMVMTERNESGPIRPCHIREAYRRLKLEGKV 200 (207)
Q Consensus 166 VEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~~Gkl 200 (207)
-++.+.+-..|.+.=+=.|. +.++|..|+.+|-+
T Consensus 104 k~kil~li~~W~~~f~~~p~-~~~~Y~~Lk~~G~i 137 (139)
T cd03567 104 KTKIIELLYSWTLELPHEPK-IKEAYDMLKKQGII 137 (139)
T ss_pred HHHHHHHHHHHHHHhcccch-HHHHHHHHHHCCCc
Confidence 33444445568665444566 99999999999965
No 77
>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=25.00 E-value=3.5e+02 Score=21.43 Aligned_cols=63 Identities=11% Similarity=0.119 Sum_probs=49.9
Q ss_pred HHHHHHHHhcCCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHHHHh
Q 028537 132 NMRRLLVSITGSQKISLPMTIVVCGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRRLKL 196 (207)
Q Consensus 132 ~IKRLi~~vtgsqsVs~nvvIavaGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RRL~~ 196 (207)
.|++|+.+. |-..+++.++..+.=|+.-|+.+|...|....+.- .+.-|....|+-|......
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 467777653 54578999999999999999999999999987654 4567888888888776543
No 78
>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=24.98 E-value=40 Score=26.59 Aligned_cols=12 Identities=33% Similarity=0.554 Sum_probs=5.8
Q ss_pred CCcccccccccc
Q 028537 78 YDEEDDENVDVE 89 (207)
Q Consensus 78 ~dee~ed~~~~~ 89 (207)
+++|+||+|-+.
T Consensus 92 e~eE~dddmgf~ 103 (105)
T cd04411 92 EEEEEDEDFGFG 103 (105)
T ss_pred cccccccccCcc
Confidence 334445555543
No 79
>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=24.53 E-value=20 Score=25.08 Aligned_cols=34 Identities=26% Similarity=0.342 Sum_probs=19.4
Q ss_pred HHHHHHhcCCChhHHHHHHHHhcCCCCCCccHHHH
Q 028537 119 RYESFRRSALQKSNMRRLLVSITGSQKISLPMTIV 153 (207)
Q Consensus 119 RYE~fRRS~F~K~~IKRLi~~vtgsqsVs~nvvIa 153 (207)
.|+.||++++-.+=..-| .....++.+++.++.-
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 489999998866544443 3333345788876543
No 80
>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=24.45 E-value=2.2e+02 Score=23.63 Aligned_cols=45 Identities=22% Similarity=0.256 Sum_probs=29.1
Q ss_pred HHHHhcCCChhHHHHHHHHhcCCCCCCcc---HHHHHHHHHHHHHHHHH
Q 028537 121 ESFRRSALQKSNMRRLLVSITGSQKISLP---MTIVVCGIAKMFVGELV 166 (207)
Q Consensus 121 E~fRRS~F~K~~IKRLi~~vtgsqsVs~n---vvIavaGlAKvFVGELV 166 (207)
..||.+. +...|+++...+.-+..++-+ -+.+++++-|.|+-+|-
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 4688775 566678877665432222211 35678999999998874
No 81
>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=23.10 E-value=1.2e+02 Score=30.86 Aligned_cols=14 Identities=21% Similarity=0.259 Sum_probs=8.1
Q ss_pred CCCccHHHHHHHHH
Q 028537 145 KISLPMTIVVCGIA 158 (207)
Q Consensus 145 sVs~nvvIavaGlA 158 (207)
+|..+|+++=-||+
T Consensus 463 SIdkDi~tAnDGl~ 476 (574)
T PF07462_consen 463 SIDKDIATANDGLA 476 (574)
T ss_pred HHhhhHHHhhhHHH
Confidence 46666766644443
No 82
>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=22.94 E-value=1.5e+02 Score=25.00 Aligned_cols=45 Identities=20% Similarity=0.330 Sum_probs=29.6
Q ss_pred HHHhcCCChhHHHHHHHHhcCCCC---CCccHHHHHHHHHHHHHHHHHH
Q 028537 122 SFRRSALQKSNMRRLLVSITGSQK---ISLPMTIVVCGIAKMFVGELVE 167 (207)
Q Consensus 122 ~fRRS~F~K~~IKRLi~~vtgsqs---Vs~nvvIavaGlAKvFVGELVE 167 (207)
.||.++ ++..|++|...+--+.. .++.-+..++++-|.|+-+|-+
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 588888 57788888665532211 1222356789999999887644
No 83
>cd04394 RhoGAP-ARHGAP11A RhoGAP-ARHGAP11A: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP11A-like proteins. The mouse homolog of human ArhGAP11A has been detected as a gene exclusively expressed in immature ganglion cells, potentially playing a role in retinal development. The exact function of ArhGAP11A is unknown. 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=22.03 E-value=2.5e+02 Score=23.76 Aligned_cols=46 Identities=24% Similarity=0.325 Sum_probs=29.6
Q ss_pred HHHHHhcCCChhHHHHHHHHhcCCCCCC-ccHHHHHHHHHHHHHHHHH
Q 028537 120 YESFRRSALQKSNMRRLLVSITGSQKIS-LPMTIVVCGIAKMFVGELV 166 (207)
Q Consensus 120 YE~fRRS~F~K~~IKRLi~~vtgsqsVs-~nvvIavaGlAKvFVGELV 166 (207)
=..||.++ ++..|+.|...+-.+..+. ..-...++++-|.|+-||-
T Consensus 38 EGIFR~sG-~~~~i~~l~~~~d~~~~~~~~~~~~~vaslLK~flReLP 84 (202)
T cd04394 38 EGLFRKSG-SVVRQKELKAKLEGGEACLSSALPCDVAGLLKQFFRELP 84 (202)
T ss_pred CCeeeCCC-CHHHHHHHHHHHcCCCCCccccCHHHHHHHHHHHHhcCC
Confidence 35788888 5777888876654322211 1123558999999987764
No 84
>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=21.93 E-value=64 Score=24.06 Aligned_cols=23 Identities=30% Similarity=0.642 Sum_probs=16.1
Q ss_pred HHHHHHhcCCHHHH----HHHHHHHhc
Q 028537 104 KMQAILNQFTEDQM----NRYESFRRS 126 (207)
Q Consensus 104 km~~Ll~~fteEQl----dRYE~fRRS 126 (207)
.+..+-.+||++|. +||+.||+-
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 35567899999995 699999984
No 85
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=21.90 E-value=51 Score=26.53 Aligned_cols=12 Identities=17% Similarity=0.548 Sum_probs=5.7
Q ss_pred CCcccccccccc
Q 028537 78 YDEEDDENVDVE 89 (207)
Q Consensus 78 ~dee~ed~~~~~ 89 (207)
+.+|+||+|-+.
T Consensus 98 e~ee~ddDmgf~ 109 (112)
T PTZ00373 98 EEEEEEDDLGFS 109 (112)
T ss_pred cccccccccccc
Confidence 334445555543
No 86
>KOG1991 consensus Nuclear transport receptor RANBP7/RANBP8 (importin beta superfamily) [Nuclear structure; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.52 E-value=83 Score=33.87 Aligned_cols=18 Identities=17% Similarity=0.405 Sum_probs=13.0
Q ss_pred HHHHHHHhcCCHHHHHHH
Q 028537 103 AKMQAILNQFTEDQMNRY 120 (207)
Q Consensus 103 ~km~~Ll~~fteEQldRY 120 (207)
.+.+.|+++||++|.+-.
T Consensus 977 ~~yq~l~~~L~~~q~~~l 994 (1010)
T KOG1991|consen 977 VRYQKLISTLTPEQQDSL 994 (1010)
T ss_pred HHHHHHHhcCCHHHHHHH
Confidence 467778888888876543
No 87
>PF02284 COX5A: Cytochrome c oxidase subunit Va; InterPro: IPR003204 Cytochrome c oxidase (1.9.3.1 from EC) is an oligomeric enzymatic complex which is a component of the respiratory chain complex and is involved in the transfer of electrons from cytochrome c to oxygen []. In eukaryotes this enzyme complex is located in the mitochondrial inner membrane; in aerobic prokaryotes it is found in the plasma membrane. In eukaryotes, in addition to the three large subunits, I, II and III, that form the catalytic centre of the enzyme complex, there are a variable number of small polypeptidic subunits. One of these subunits is known as Va.; GO: 0004129 cytochrome-c oxidase activity; PDB: 2DYR_R 3AG1_E 3ABL_E 1V54_R 2EIJ_R 1OCR_E 2DYS_E 2EIM_E 2OCC_E 3ASN_R ....
Probab=20.32 E-value=1.1e+02 Score=24.74 Aligned_cols=34 Identities=26% Similarity=0.488 Sum_probs=21.7
Q ss_pred HHHHHHHHHHhcCCChh-----HHHHHHHHhcCCCCCCccHHH
Q 028537 115 DQMNRYESFRRSALQKS-----NMRRLLVSITGSQKISLPMTI 152 (207)
Q Consensus 115 EQldRYE~fRRS~F~K~-----~IKRLi~~vtgsqsVs~nvvI 152 (207)
+=..||+.| |++. -+||-||+..+--.||.+.+|
T Consensus 10 eF~ary~~~----F~~~~iD~we~rrglN~l~~~DlVP~P~ii 48 (108)
T PF02284_consen 10 EFDARYEKY----FNRPDIDGWELRRGLNNLFGYDLVPEPKII 48 (108)
T ss_dssp HHHHHHHHH----HH-TT--HHHHHHHHHHHTTSSB---HHHH
T ss_pred HHHHHHHHH----hCCccccHHHHHHHHHHHhccccCCChHHH
Confidence 335699998 6554 588999998887667766443
No 88
>PF05823 Gp-FAR-1: Nematode fatty acid retinoid binding protein (Gp-FAR-1); InterPro: IPR008632 Parasitic nematodes produce at least two structurally novel classes of small helix-rich retinol- and fatty-acid-binding proteins that have no counterparts in their plant or animal hosts and thus represent potential targets for new nematicides. Gp-FAR-1 is a member of the nematode-specific fatty-acid- and retinol-binding (FAR) family of proteins but localises to the surface of the organism, placing it in a strategic position for interaction with the host. Gp-FAR-1 functions as a broad-spectrum retinol- and fatty-acid-binding protein, and it is thought that it is involved in the evasion of primary host plant defence systems [].; GO: 0008289 lipid binding; PDB: 2W9Y_A.
Probab=20.16 E-value=1.6e+02 Score=24.44 Aligned_cols=39 Identities=21% Similarity=0.257 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCCCchHHHHHHHH
Q 028537 155 CGIAKMFVGELVETARMVMTERNESGPIRPCHIREAYRR 193 (207)
Q Consensus 155 aGlAKvFVGELVEeAr~Vq~E~~e~gPLqP~HIREA~RR 193 (207)
.-=||-||-+|+..++.+....-...++.++||..-.+.
T Consensus 75 ~peak~Fv~~li~~~~~l~~~~~~G~~~~~~~lk~~~k~ 113 (154)
T PF05823_consen 75 SPEAKAFVKELIAKARSLYAQYSAGEKPDLEELKQLAKK 113 (154)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHT----THHHHHHH--
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHhh
Confidence 444789999999999998776544556677888655443
Done!