Query psy7662
Match_columns 220
No_of_seqs 218 out of 384
Neff 4.8
Searched_HMMs 46136
Date Sat Aug 17 00:13:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7662.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7662hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3901|consensus 100.0 2.7E-37 5.9E-42 241.0 8.6 100 119-218 4-103 (109)
2 cd07978 TAF13 The TATA Binding 100.0 1.7E-36 3.8E-41 232.9 10.7 90 123-212 1-92 (92)
3 PF02269 TFIID-18kDa: Transcri 100.0 7.4E-35 1.6E-39 223.8 2.8 90 124-213 1-93 (93)
4 COG5248 TAF19 Transcription in 99.9 1.7E-27 3.6E-32 188.1 8.0 97 119-215 4-101 (126)
5 KOG3901|consensus 99.9 1.9E-25 4.1E-30 174.6 2.3 83 30-112 3-89 (109)
6 cd07978 TAF13 The TATA Binding 99.9 2.3E-22 5E-27 154.7 3.8 72 35-106 1-78 (92)
7 PF02269 TFIID-18kDa: Transcri 99.8 6.3E-22 1.4E-26 152.1 3.1 75 36-110 1-82 (93)
8 COG5248 TAF19 Transcription in 99.8 1E-19 2.2E-24 144.1 2.1 82 31-112 4-90 (126)
9 KOG3902|consensus 99.8 3.7E-18 8.1E-23 154.5 10.5 93 120-212 20-116 (352)
10 KOG3902|consensus 99.2 2.1E-11 4.6E-16 111.0 5.2 130 33-210 21-161 (352)
11 smart00576 BTP Bromodomain tra 94.9 0.059 1.3E-06 39.7 4.9 61 124-186 6-70 (77)
12 PF03847 TFIID_20kDa: Transcri 94.2 0.09 1.9E-06 38.5 4.4 57 130-186 5-64 (68)
13 PF00808 CBFD_NFYB_HMF: Histon 94.0 0.13 2.8E-06 36.3 4.8 56 129-184 7-65 (65)
14 cd07981 TAF12 TATA Binding Pro 93.9 0.22 4.8E-06 36.4 6.0 47 141-187 18-67 (72)
15 smart00803 TAF TATA box bindin 93.4 0.24 5.2E-06 35.8 5.3 55 130-185 8-65 (65)
16 PF07524 Bromo_TP: Bromodomain 93.3 0.22 4.7E-06 36.4 5.1 59 125-185 7-69 (77)
17 PF15630 CENP-S: Kinetochore c 92.1 0.29 6.2E-06 36.7 4.4 48 142-189 25-75 (76)
18 PLN00035 histone H4; Provision 91.7 0.54 1.2E-05 37.3 5.8 60 127-187 32-94 (103)
19 smart00576 BTP Bromodomain tra 91.5 0.3 6.5E-06 35.9 3.9 57 37-95 7-67 (77)
20 cd00076 H4 Histone H4, one of 89.5 1.5 3.3E-05 33.5 6.4 62 125-187 14-78 (85)
21 PTZ00015 histone H4; Provision 88.6 1 2.2E-05 35.6 5.0 62 125-187 31-95 (102)
22 PF07524 Bromo_TP: Bromodomain 88.2 0.73 1.6E-05 33.6 3.7 54 39-94 9-66 (77)
23 PF03847 TFIID_20kDa: Transcri 87.8 1.4 3E-05 32.3 4.9 46 42-87 5-51 (68)
24 PF00125 Histone: Core histone 87.4 1 2.2E-05 32.2 4.1 58 130-187 15-75 (75)
25 PF02969 TAF: TATA box binding 87.0 1.5 3.3E-05 32.0 4.8 45 141-185 19-66 (66)
26 cd07981 TAF12 TATA Binding Pro 85.8 2.4 5.2E-05 30.9 5.3 46 53-98 18-66 (72)
27 KOG0869|consensus 84.9 1.4 3.1E-05 37.6 4.2 82 123-204 31-118 (168)
28 KOG1142|consensus 84.1 2.5 5.3E-05 38.6 5.6 60 123-187 157-220 (258)
29 cd07979 TAF9 TATA Binding Prot 82.2 4.8 0.0001 32.2 6.1 55 130-185 7-64 (117)
30 COG2036 HHT1 Histones H3 and H 79.0 3.9 8.5E-05 31.7 4.4 56 130-186 25-83 (91)
31 smart00417 H4 Histone H4. 74.5 6.3 0.00014 29.4 4.3 58 125-183 14-74 (74)
32 KOG2549|consensus 73.6 5.6 0.00012 39.9 4.9 46 141-186 27-75 (576)
33 cd00074 H2A Histone 2A; H2A is 71.0 7.5 0.00016 31.2 4.3 42 147-189 47-88 (115)
34 KOG1142|consensus 69.7 13 0.00029 33.9 6.0 68 35-107 157-230 (258)
35 PF00808 CBFD_NFYB_HMF: Histon 66.9 14 0.00031 25.7 4.6 41 42-82 8-48 (65)
36 cd08050 TAF6 TATA Binding Prot 63.7 12 0.00026 34.8 4.7 45 141-185 15-62 (343)
37 smart00803 TAF TATA box bindin 61.1 15 0.00032 26.5 3.8 53 42-95 8-63 (65)
38 TIGR00207 fliG flagellar motor 52.3 19 0.00041 33.5 4.0 98 40-154 157-259 (338)
39 PF02291 TFIID-31kDa: Transcri 43.1 64 0.0014 26.4 5.3 55 130-185 18-75 (129)
40 PF05236 TAF4: Transcription i 41.3 33 0.00071 30.6 3.6 68 125-193 48-116 (264)
41 smart00414 H2A Histone 2A. 40.8 44 0.00096 26.4 3.9 37 154-190 42-78 (106)
42 smart00428 H3 Histone H3. 37.6 1.7E+02 0.0038 23.2 6.8 62 123-184 32-98 (105)
43 PF09415 CENP-X: CENP-S associ 37.2 36 0.00077 25.1 2.7 41 141-181 18-62 (72)
44 cd07979 TAF9 TATA Binding Prot 36.6 55 0.0012 26.1 3.9 57 43-100 8-67 (117)
45 PLN00157 histone H2A; Provisio 35.7 69 0.0015 26.6 4.4 41 148-189 54-94 (132)
46 PRK07194 fliG flagellar motor 34.1 40 0.00087 31.3 3.1 96 39-151 153-252 (334)
47 PTZ00017 histone H2A; Provisio 34.1 73 0.0016 26.5 4.3 39 150-189 57-95 (134)
48 PF00125 Histone: Core histone 34.1 78 0.0017 22.3 4.0 41 43-83 16-56 (75)
49 PLN00156 histone H2AX; Provisi 32.8 86 0.0019 26.2 4.5 41 148-189 57-97 (139)
50 cd08048 TAF11 TATA Binding Pro 32.8 1.9E+02 0.004 21.9 6.1 56 130-186 22-83 (85)
51 PLN00035 histone H4; Provision 30.9 76 0.0016 25.2 3.7 59 39-98 32-93 (103)
52 cd08045 TAF4 TATA Binding Prot 30.7 2.8E+02 0.006 23.9 7.6 53 142-194 65-118 (212)
53 PTZ00015 histone H4; Provision 29.4 50 0.0011 26.2 2.5 61 37-98 31-94 (102)
54 PLN00153 histone H2A; Provisio 29.3 1.1E+02 0.0024 25.3 4.6 40 149-189 53-92 (129)
55 COG2036 HHT1 Histones H3 and H 27.8 1E+02 0.0022 23.9 3.9 52 43-95 26-80 (91)
56 PHA00724 hypothetical protein 27.2 44 0.00096 25.2 1.7 36 45-80 1-36 (83)
57 KOG4336|consensus 26.0 1.3E+02 0.0027 28.5 4.8 77 125-204 6-87 (323)
58 PF02969 TAF: TATA box binding 23.6 1E+02 0.0022 22.4 3.1 41 54-94 20-63 (66)
59 PRK07122 RNA polymerase sigma 23.5 2.4E+02 0.0052 25.0 6.1 72 129-201 20-100 (264)
60 cd00076 H4 Histone H4, one of 23.4 1.7E+02 0.0036 22.4 4.3 59 38-97 15-76 (85)
61 PF04433 SWIRM: SWIRM domain; 22.3 1.8E+02 0.0039 21.2 4.3 31 171-201 50-81 (86)
62 PLN00154 histone H2A; Provisio 22.1 1.7E+02 0.0037 24.4 4.5 36 154-189 72-107 (136)
63 smart00417 H4 Histone H4. 21.7 1.9E+02 0.0041 21.5 4.3 33 62-94 38-73 (74)
64 COG3461 Uncharacterized conser 21.6 68 0.0015 25.3 1.9 32 178-209 65-96 (103)
65 KOG3467|consensus 20.5 1.3E+02 0.0029 23.6 3.3 43 144-190 52-97 (103)
No 1
>KOG3901|consensus
Probab=100.00 E-value=2.7e-37 Score=241.00 Aligned_cols=100 Identities=61% Similarity=1.049 Sum_probs=96.7
Q ss_pred CCCcccccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchhHhhhccChhHHHHHHHHH
Q psy7662 119 PSGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGRTGRVQVEDIVFLVRKDNRKYARVKDLL 198 (220)
Q Consensus 119 ~~~rk~~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~arrgki~~eDl~FllRkD~~Kl~Rv~~lL 198 (220)
+..|+++|++||++|||||||+++|+++||+++|+||++||.++|+.|+.+++||++++|||+|+||+||+|++|+++||
T Consensus 4 ~~~rk~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g~rgk~~veD~~f~lRkDpkK~~Rv~eLL 83 (109)
T KOG3901|consen 4 PEQRKHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIGKRGKVKVEDFKFLLRKDPKKLGRVKELL 83 (109)
T ss_pred HHHHHHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhcccCceeHHHHHHHHHhChHHHhHHHHHH
Confidence 34489999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhccccccccc
Q psy7662 199 TMNEELKKARKAFDEVKFVT 218 (220)
Q Consensus 199 ~~k~~ik~Ark~fd~~~~~~ 218 (220)
.|+++||+|||+||+.+|..
T Consensus 84 ~mneelk~ArKaF~~~~y~~ 103 (109)
T KOG3901|consen 84 AMNEELKKARKAFDETDYEL 103 (109)
T ss_pred HhHHHHHHHHhccchHhHHh
Confidence 99999999999999999864
No 2
>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=100.00 E-value=1.7e-36 Score=232.88 Aligned_cols=90 Identities=58% Similarity=1.050 Sum_probs=87.4
Q ss_pred ccccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc--CCCCCCcchhHhhhccChhHHHHHHHHHHH
Q psy7662 123 KRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG--RTGRVQVEDIVFLVRKDNRKYARVKDLLTM 200 (220)
Q Consensus 123 k~~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a--rrgki~~eDl~FllRkD~~Kl~Rv~~lL~~ 200 (220)
+++|++||++|||||||+++|++|||++||+||++||++||++|.++| +++++++|||+|+|||||+||+|+++||+|
T Consensus 1 ~~~f~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL~~ 80 (92)
T cd07978 1 KRLFTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGKVKVEDLIFLLRKDPKKLARLRELLSM 80 (92)
T ss_pred CCccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 478999999999999999999999999999999999999999999998 678999999999999999999999999999
Q ss_pred HHHHHHHHhccc
Q psy7662 201 NEELKKARKAFD 212 (220)
Q Consensus 201 k~~ik~Ark~fd 212 (220)
+++||+|||+||
T Consensus 81 k~~~k~ark~~d 92 (92)
T cd07978 81 KDELKKARKAFD 92 (92)
T ss_pred HHHHHHHHhccC
Confidence 999999999997
No 3
>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=100.00 E-value=7.4e-35 Score=223.78 Aligned_cols=90 Identities=52% Similarity=0.963 Sum_probs=38.8
Q ss_pred cccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc-CC--CCCCcchhHhhhccChhHHHHHHHHHHH
Q psy7662 124 RMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RT--GRVQVEDIVFLVRKDNRKYARVKDLLTM 200 (220)
Q Consensus 124 ~~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a-rr--gki~~eDl~FllRkD~~Kl~Rv~~lL~~ 200 (220)
++|++||++|||||||+++|++|||.+||+||++||+++|++|..+| +| ++|++|||+|+|||||+|++|+++||+|
T Consensus 1 ~~f~~eI~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~Kl~Rl~~~L~~ 80 (93)
T PF02269_consen 1 HLFSKEIRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKKLARLRELLSM 80 (93)
T ss_dssp ---CCCCHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-----------------------------------
T ss_pred CchHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999998 34 5999999999999999999999999999
Q ss_pred HHHHHHHHhcccc
Q psy7662 201 NEELKKARKAFDE 213 (220)
Q Consensus 201 k~~ik~Ark~fd~ 213 (220)
++++++|||.||+
T Consensus 81 k~~~~karK~~d~ 93 (93)
T PF02269_consen 81 KDEIKKARKDFDE 93 (93)
T ss_dssp -------------
T ss_pred HHHHHHHHHhhcC
Confidence 9999999999985
No 4
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=99.94 E-value=1.7e-27 Score=188.13 Aligned_cols=97 Identities=32% Similarity=0.605 Sum_probs=93.2
Q ss_pred CCCcccccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCCCCcchhHhhhccChhHHHHHHHH
Q psy7662 119 PSGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTGRVQVEDIVFLVRKDNRKYARVKDL 197 (220)
Q Consensus 119 ~~~rk~~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a-rrgki~~eDl~FllRkD~~Kl~Rv~~l 197 (220)
+..|.++|.++|++|||||||+.+|.++|+++++++|.+||.++|.+|..+| .||++++|||.|+||+||+||+|+++|
T Consensus 4 ~~rr~nLF~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rnK~k~eDfkfaLr~DpkKlgRveeL 83 (126)
T COG5248 4 EARRVNLFMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTKTEDFKFALRRDPKKLGRVEEL 83 (126)
T ss_pred hhHHHHHHHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHhhChHHHhHHHHH
Confidence 3457899999999999999999999999999999999999999999999999 589999999999999999999999999
Q ss_pred HHHHHHHHHHHhcccccc
Q psy7662 198 LTMNEELKKARKAFDEVK 215 (220)
Q Consensus 198 L~~k~~ik~Ark~fd~~~ 215 (220)
|..+++|+-|+++|.+.+
T Consensus 84 l~tn~~i~~Akk~F~~~d 101 (126)
T COG5248 84 LITNEEIKLAKKAFEPKD 101 (126)
T ss_pred HHhhHHHHHHhcccCchh
Confidence 999999999999999876
No 5
>KOG3901|consensus
Probab=99.91 E-value=1.9e-25 Score=174.61 Aligned_cols=83 Identities=45% Similarity=0.727 Sum_probs=74.9
Q ss_pred CCccccccchHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhcCCCCceeec----cccccCCceeeecc
Q psy7662 30 LPSGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGRTGPTFLSL----LKFKSNKNVCVFSF 105 (220)
Q Consensus 30 ~~~~rk~~f~kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~arrgk~~l~d----lrfd~~K~~~~~~f 105 (220)
.|..||++|+|||++|||||||++||+|+||++||+||++||++|||.|+.++++||.+++| +|.|++|+-+|.+.
T Consensus 3 ~~~~rk~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g~rgk~~veD~~f~lRkDpkK~~Rv~eL 82 (109)
T KOG3901|consen 3 EPEQRKHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIGKRGKVKVEDFKFLLRKDPKKLGRVKEL 82 (109)
T ss_pred cHHHHHHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhcccCceeHHHHHHHHHhChHHHhHHHHH
Confidence 35679999999999999999999999999999999999999999999999999999876666 78889999999888
Q ss_pred ccccccc
Q psy7662 106 QFEEEEQ 112 (220)
Q Consensus 106 q~~~~~~ 112 (220)
..-+++.
T Consensus 83 L~mneel 89 (109)
T KOG3901|consen 83 LAMNEEL 89 (109)
T ss_pred HHhHHHH
Confidence 8777653
No 6
>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=99.85 E-value=2.3e-22 Score=154.66 Aligned_cols=72 Identities=42% Similarity=0.768 Sum_probs=62.4
Q ss_pred cccchHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc--CCCCc----eeeccccccCCceeeeccc
Q psy7662 35 KRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG--RTGPT----FLSLLKFKSNKNVCVFSFQ 106 (220)
Q Consensus 35 k~~f~kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a--rrgk~----~l~dlrfd~~K~~~~~~fq 106 (220)
+++|++||++|||||||+++|+||||.+||+||++||++||++|+++| ++|++ .+|.+|+|++|+-++..|.
T Consensus 1 ~~~f~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL 78 (92)
T cd07978 1 KRLFTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGKVKVEDLIFLLRKDPKKLARLRELL 78 (92)
T ss_pred CCccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCHHHHHHHHHHH
Confidence 578999999999999999999999999999999999999999999999 56764 5555788888876654443
No 7
>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=99.84 E-value=6.3e-22 Score=152.12 Aligned_cols=75 Identities=39% Similarity=0.678 Sum_probs=38.9
Q ss_pred ccchHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCC------CceeeccccccCCceeeeccccc
Q psy7662 36 RMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTG------PTFLSLLKFKSNKNVCVFSFQFE 108 (220)
Q Consensus 36 ~~f~kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrg------k~~l~dlrfd~~K~~~~~~fq~~ 108 (220)
++|++||++|||||||+++|+||||.+||+||++||++||++|.++| ++| .+.+|.+|+|+.|+-++..|.-.
T Consensus 1 ~~f~~eI~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~Kl~Rl~~~L~~ 80 (93)
T PF02269_consen 1 HLFSKEIRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKKLARLRELLSM 80 (93)
T ss_dssp ---CCCCHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-----------------------------------
T ss_pred CchHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 57999999999999999999999999999999999999999999999 554 36777789999999888777665
Q ss_pred cc
Q psy7662 109 EE 110 (220)
Q Consensus 109 ~~ 110 (220)
.+
T Consensus 81 k~ 82 (93)
T PF02269_consen 81 KD 82 (93)
T ss_dssp --
T ss_pred HH
Confidence 55
No 8
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=99.77 E-value=1e-19 Score=144.10 Aligned_cols=82 Identities=23% Similarity=0.349 Sum_probs=73.0
Q ss_pred CccccccchHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCCCceeeccc----cccCCceeeecc
Q psy7662 31 PSGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTGPTFLSLLK----FKSNKNVCVFSF 105 (220)
Q Consensus 31 ~~~rk~~f~kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrgk~~l~dlr----fd~~K~~~~~~f 105 (220)
+.+|.++|.|||.+|||||||+++|.++|+++|++||.+||.++|.+|.++| -|||.+++||+ .|++|+-+|-+.
T Consensus 4 ~~rr~nLF~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rnK~k~eDfkfaLr~DpkKlgRveeL 83 (126)
T COG5248 4 EARRVNLFMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTKTEDFKFALRRDPKKLGRVEEL 83 (126)
T ss_pred hhHHHHHHHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHhhChHHHhHHHHH
Confidence 4578899999999999999999999999999999999999999999999999 78988888855 567778888888
Q ss_pred ccccccc
Q psy7662 106 QFEEEEQ 112 (220)
Q Consensus 106 q~~~~~~ 112 (220)
...++..
T Consensus 84 l~tn~~i 90 (126)
T COG5248 84 LITNEEI 90 (126)
T ss_pred HHhhHHH
Confidence 7777764
No 9
>KOG3902|consensus
Probab=99.75 E-value=3.7e-18 Score=154.52 Aligned_cols=93 Identities=26% Similarity=0.441 Sum_probs=86.8
Q ss_pred CCcccccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc-CCC--CCCcchhHhhhccChhHHHHHHH
Q psy7662 120 SGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTG--RVQVEDIVFLVRKDNRKYARVKD 196 (220)
Q Consensus 120 ~~rk~~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a-rrg--ki~~eDl~FllRkD~~Kl~Rv~~ 196 (220)
.|+-..|.-||++|||..|+.+.|++||++|+|++|..|+++++.+|.++| .|| .|+.||++|++|||++|+.||.+
T Consensus 20 tg~~~ky~veiQqmmf~sGei~~P~pett~Lved~V~gqvie~l~qa~eia~lrgsr~Itpedliflir~Drakv~rL~t 99 (352)
T KOG3902|consen 20 TGDIKKYRVEIQQMMFQSGEIPDPLPETTNLVEDNVRGQVIESLVQANEIADLRGSRSITPEDLIFLIRHDRAKVNRLVT 99 (352)
T ss_pred cccchhHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccccChHHHHHHhhccHHHHHHHHH
Confidence 445678999999999999999999999999999999999999999999998 455 79999999999999999999999
Q ss_pred HHHHHHHH-HHHHhccc
Q psy7662 197 LLTMNEEL-KKARKAFD 212 (220)
Q Consensus 197 lL~~k~~i-k~Ark~fd 212 (220)
||.|++.+ |.|+.+..
T Consensus 100 yl~~kdlR~k~ak~qda 116 (352)
T KOG3902|consen 100 YLSWKDLRGKFAKAQDA 116 (352)
T ss_pred HHHHHHHHHhhhhhhHH
Confidence 99999999 88887764
No 10
>KOG3902|consensus
Probab=99.18 E-value=2.1e-11 Score=110.96 Aligned_cols=130 Identities=22% Similarity=0.280 Sum_probs=106.0
Q ss_pred cccccchHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCC------CceeeccccccCCceeeecc
Q psy7662 33 GRKRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTG------PTFLSLLKFKSNKNVCVFSF 105 (220)
Q Consensus 33 ~rk~~f~kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrg------k~~l~dlrfd~~K~~~~~~f 105 (220)
++-.-|.-||++|||..|+.+.|+|||++|+|++|.-++++++..|.++| .|| .+.+|++|||++|
T Consensus 21 g~~~ky~veiQqmmf~sGei~~P~pett~Lved~V~gqvie~l~qa~eia~lrgsr~Itpedliflir~Drak------- 93 (352)
T KOG3902|consen 21 GDIKKYRVEIQQMMFQSGEIPDPLPETTNLVEDNVRGQVIESLVQANEIADLRGSRSITPEDLIFLIRHDRAK------- 93 (352)
T ss_pred ccchhHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccccChHHHHHHhhccHHH-------
Confidence 34468999999999999999999999999999999999999999999999 777 4677888887544
Q ss_pred ccccccccCCCCCCCCcccccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc-CC--C-CCCcchhH
Q psy7662 106 QFEEEEQDTPVNLPSGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RT--G-RVQVEDIV 181 (220)
Q Consensus 106 q~~~~~~~~~~~~~~~rk~~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a-rr--g-ki~~eDl~ 181 (220)
.+.|++-|....+.....++...| ++ | ..+--|+-
T Consensus 94 -----------------------------------------v~rL~tyl~~kdlR~k~ak~qdaa~~~~~~~~np~Ad~e 132 (352)
T KOG3902|consen 94 -----------------------------------------VNRLVTYLSWKDLRGKFAKAQDAAMRRKQNPCNPQADFE 132 (352)
T ss_pred -----------------------------------------HHHHHHHHHHHHHHHhhhhhhHHHHhhccCCCCCCccHH
Confidence 344555555555555555665554 22 3 45668999
Q ss_pred hhhccChhHHHHHHHHHHHHHHHHHHHhc
Q psy7662 182 FLVRKDNRKYARVKDLLTMNEELKKARKA 210 (220)
Q Consensus 182 FllRkD~~Kl~Rv~~lL~~k~~ik~Ark~ 210 (220)
++|++.+.|-+|.+.-|++-..+|+|-+.
T Consensus 133 dlle~~~~k~~~~r~~~~~mri~k~~~k~ 161 (352)
T KOG3902|consen 133 DLLENHPSKIARMRKHLKDMRILKRALKI 161 (352)
T ss_pred HHHHhCccchhhhhhhhhHHHHHHHHhhc
Confidence 99999999999999999999999999876
No 11
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=94.93 E-value=0.059 Score=39.73 Aligned_cols=61 Identities=11% Similarity=0.264 Sum_probs=49.9
Q ss_pred cccHHHHHHhhhhcC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhhcc
Q psy7662 124 RMFSKELRCMMYGFG-DDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLVRK 186 (220)
Q Consensus 124 ~~f~kEI~~MMygfG-D~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~FllRk 186 (220)
.+...-|.+++...| |. -.+.+.+.+=+++.+|+.++.+.|.+.+ +|..+++.|+..++.+
T Consensus 6 ~ll~~~Vaqil~~~Gf~~--~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 6 ALLRIAVAQILESAGFDS--FQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHHHHHHHcCccc--cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 345667889999998 54 4456889999999999999999998875 5778999999988764
No 12
>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=94.18 E-value=0.09 Score=38.52 Aligned_cols=57 Identities=14% Similarity=0.274 Sum_probs=41.2
Q ss_pred HHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhcC-CC--CCCcchhHhhhcc
Q psy7662 130 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGR-TG--RVQVEDIVFLVRK 186 (220)
Q Consensus 130 I~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~ar-rg--ki~~eDl~FllRk 186 (220)
|+.|+--..-.....++...++=+|.-+||.+++..|+.+|+ || .+.+.|+.|.|.+
T Consensus 5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 444554444445566777889999999999999999999993 43 7999999999875
No 13
>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=93.97 E-value=0.13 Score=36.29 Aligned_cols=56 Identities=20% Similarity=0.277 Sum_probs=46.7
Q ss_pred HHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhh
Q psy7662 129 ELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLV 184 (220)
Q Consensus 129 EI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~Fll 184 (220)
=|+.+|-.-.|...-..|++.+|-.....||..|+..|...+ +|..|+.+|+..+|
T Consensus 7 ~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 7 RVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 367788888888888999999999999999999999999987 45689999998764
No 14
>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=93.92 E-value=0.22 Score=36.40 Aligned_cols=47 Identities=15% Similarity=0.362 Sum_probs=40.3
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCCCCcchhHhhhccC
Q psy7662 141 RNPYTESVDILEDAVIDFLVDMTQKAMEMGR---TGRVQVEDIVFLVRKD 187 (220)
Q Consensus 141 ~~P~~ETv~l~EdIV~e~I~~l~~~A~~~ar---rgki~~eDl~FllRkD 187 (220)
..-.++...++-+++-+|+.+++..|..+|+ |+.++.+|+.+.+.+.
T Consensus 18 ~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 18 EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 4566778889999999999999999999982 4579999999998764
No 15
>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=93.35 E-value=0.24 Score=35.82 Aligned_cols=55 Identities=18% Similarity=0.266 Sum_probs=43.9
Q ss_pred HHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCCcchhHhhhc
Q psy7662 130 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEM---GRTGRVQVEDIVFLVR 185 (220)
Q Consensus 130 I~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~---arrgki~~eDl~FllR 185 (220)
|+.+.=..|- ..-.++....+-+.|..++.++++.|.+. |+|..++++|+-+++|
T Consensus 8 i~ria~~~Gi-~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 8 IKDVAESLGI-GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred HHHHHHHCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 4444444555 46777888899999999999999999877 4688999999998876
No 16
>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=93.29 E-value=0.22 Score=36.37 Aligned_cols=59 Identities=14% Similarity=0.284 Sum_probs=47.1
Q ss_pred ccHHHHHHhhhhcC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhhc
Q psy7662 125 MFSKELRCMMYGFG-DDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLVR 185 (220)
Q Consensus 125 ~f~kEI~~MMygfG-D~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~FllR 185 (220)
....=+.+++...| |.. .+.+.+.+-+|+..||.++.+.+...+ +|..+++.|+..+|.
T Consensus 7 ~l~~~va~il~~~GF~~~--~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~ 69 (77)
T PF07524_consen 7 LLRRSVAQILKHAGFDSA--SPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALE 69 (77)
T ss_pred HHHHHHHHHHHHcCcccc--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 34555778888877 654 456799999999999999999988775 566899999998775
No 17
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=92.08 E-value=0.29 Score=36.68 Aligned_cols=48 Identities=13% Similarity=0.272 Sum_probs=36.7
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHH---HhcCCCCCCcchhHhhhccChh
Q psy7662 142 NPYTESVDILEDAVIDFLVDMTQKAM---EMGRTGRVQVEDIVFLVRKDNR 189 (220)
Q Consensus 142 ~P~~ETv~l~EdIV~e~I~~l~~~A~---~~arrgki~~eDl~FllRkD~~ 189 (220)
+..++.+..|-|++..|+.++...-- ++|+|..|+++|++.+.||+|.
T Consensus 25 ~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~ 75 (76)
T PF15630_consen 25 EVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPS 75 (76)
T ss_dssp EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HH
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCC
Confidence 46788999999999999998765543 3467889999999999999984
No 18
>PLN00035 histone H4; Provisional
Probab=91.71 E-value=0.54 Score=37.28 Aligned_cols=60 Identities=15% Similarity=0.201 Sum_probs=47.0
Q ss_pred HHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCCcchhHhhhccC
Q psy7662 127 SKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEM---GRTGRVQVEDIVFLVRKD 187 (220)
Q Consensus 127 ~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~---arrgki~~eDl~FllRkD 187 (220)
..-|+.+.--.| +.--+.+...-+.+++.+|+.+++..|... |.|..|+.+|+.+++++-
T Consensus 32 k~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 32 KPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred HHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence 344666666667 566677777788888888999998888776 467899999999999864
No 19
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=91.50 E-value=0.3 Score=35.93 Aligned_cols=57 Identities=12% Similarity=0.234 Sum_probs=45.0
Q ss_pred cchHHHHHhhhhcC-CCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCC--Cceeeccccc
Q psy7662 37 MFSKELRCMMYGFG-DDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTG--PTFLSLLKFK 95 (220)
Q Consensus 37 ~f~kel~~mmygfG-D~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrg--k~~l~dlrfd 95 (220)
+...=+.+++...| |.. .|.+++.|=+++..||.++++.|..+| ..| .+.++|+..+
T Consensus 7 ll~~~Vaqil~~~Gf~~~--~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~A 67 (77)
T smart00576 7 LLRIAVAQILESAGFDSF--QESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLA 67 (77)
T ss_pred HHHHHHHHHHHHcCcccc--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHH
Confidence 34556788999888 544 466999999999999999999999999 445 4567777654
No 20
>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=89.50 E-value=1.5 Score=33.48 Aligned_cols=62 Identities=15% Similarity=0.266 Sum_probs=46.5
Q ss_pred ccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCCcchhHhhhccC
Q psy7662 125 MFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEM---GRTGRVQVEDIVFLVRKD 187 (220)
Q Consensus 125 ~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~---arrgki~~eDl~FllRkD 187 (220)
+-..-|+.+.--.| +.--+.+...-+.+++.+|+.++++.|... |+|..++.+|+.+++++.
T Consensus 14 i~k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~ 78 (85)
T cd00076 14 ITKPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 78 (85)
T ss_pred CCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHC
Confidence 44455666766666 555666666777778888888888888766 467899999999999864
No 21
>PTZ00015 histone H4; Provisional
Probab=88.60 E-value=1 Score=35.62 Aligned_cols=62 Identities=13% Similarity=0.244 Sum_probs=43.6
Q ss_pred ccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCCcchhHhhhccC
Q psy7662 125 MFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEM---GRTGRVQVEDIVFLVRKD 187 (220)
Q Consensus 125 ~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~---arrgki~~eDl~FllRkD 187 (220)
+-..-|+.|.--.|= .--+.+...-+-+++.+|+.+++..|... |+|..++.+|+.+++++-
T Consensus 31 I~k~~IrRLarr~Gv-kRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~ 95 (102)
T PTZ00015 31 ITKGAIRRLARRGGV-KRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95 (102)
T ss_pred CCHHHHHHHHHHcCC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhc
Confidence 445566777766664 44444455666677777777888887665 568899999999998753
No 22
>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=88.23 E-value=0.73 Score=33.59 Aligned_cols=54 Identities=17% Similarity=0.278 Sum_probs=41.1
Q ss_pred hHHHHHhhhhcC-CCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCCC--ceeecccc
Q psy7662 39 SKELRCMMYGFG-DDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTGP--TFLSLLKF 94 (220)
Q Consensus 39 ~kel~~mmygfG-D~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrgk--~~l~dlrf 94 (220)
..=+.+++...| |.. .+.+++.|-+|+..||.+++..+..+| ..|| +.+.|+..
T Consensus 9 ~~~va~il~~~GF~~~--~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~ 66 (77)
T PF07524_consen 9 RRSVAQILKHAGFDSA--SPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQ 66 (77)
T ss_pred HHHHHHHHHHcCcccc--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHH
Confidence 344667777777 544 466799999999999999999999999 4454 55666654
No 23
>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=1.4 Score=32.28 Aligned_cols=46 Identities=13% Similarity=0.198 Sum_probs=32.0
Q ss_pred HHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCCCc
Q psy7662 42 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTGPT 87 (220)
Q Consensus 42 l~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrgk~ 87 (220)
|..|+=-..-.....|+.-.+|=+|.-+||.+++..|+.+| +||..
T Consensus 5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~ 51 (68)
T PF03847_consen 5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSS 51 (68)
T ss_dssp HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-S
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCC
Confidence 34444444445566788999999999999999999999999 56644
No 24
>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=87.44 E-value=1 Score=32.17 Aligned_cols=58 Identities=21% Similarity=0.235 Sum_probs=43.8
Q ss_pred HHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhhccC
Q psy7662 130 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLVRKD 187 (220)
Q Consensus 130 I~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~FllRkD 187 (220)
++.+.=..+....=..++..+|-.++-.++.+++..|..++ +|..|+..|+..++|.|
T Consensus 15 ~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 15 LREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred eehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 33333333333445678889999999999999999998886 46789999999999865
No 25
>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=87.04 E-value=1.5 Score=31.96 Aligned_cols=45 Identities=22% Similarity=0.309 Sum_probs=34.6
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCCcchhHhhhc
Q psy7662 141 RNPYTESVDILEDAVIDFLVDMTQKAMEM---GRTGRVQVEDIVFLVR 185 (220)
Q Consensus 141 ~~P~~ETv~l~EdIV~e~I~~l~~~A~~~---arrgki~~eDl~FllR 185 (220)
.+-.+|....+-+=|.--|.++++.|.+. ++|.+++++|+=.+||
T Consensus 19 ~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 19 SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp --B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 34677888899999999999999999887 4788999999988876
No 26
>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=85.82 E-value=2.4 Score=30.91 Aligned_cols=46 Identities=11% Similarity=0.182 Sum_probs=37.0
Q ss_pred CCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCCC--ceeeccccccCC
Q psy7662 53 RNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTGP--TFLSLLKFKSNK 98 (220)
Q Consensus 53 ~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrgk--~~l~dlrfd~~K 98 (220)
..-.++...+|-+++-+|+.+++..|..+| +||+ +...|+.+.-.+
T Consensus 18 ~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 18 EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 456788999999999999999999999999 4663 567777665433
No 27
>KOG0869|consensus
Probab=84.91 E-value=1.4 Score=37.58 Aligned_cols=82 Identities=13% Similarity=0.184 Sum_probs=55.9
Q ss_pred ccccHHHHHHhhh-hcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhhccC--hhHHHHHHH
Q psy7662 123 KRMFSKELRCMMY-GFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLVRKD--NRKYARVKD 196 (220)
Q Consensus 123 k~~f~kEI~~MMy-gfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~FllRkD--~~Kl~Rv~~ 196 (220)
+.+=..-|..+|- +.=-...-..+....|.+.|-+||.=++.+|.... +|+.|+-|||+++|-.= .-...=|+-
T Consensus 31 r~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~Y~eplki 110 (168)
T KOG0869|consen 31 RFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFENYAEPLKI 110 (168)
T ss_pred hhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHhHHHHHHH
Confidence 4455566666773 22223334567788999999999999999999875 47899999999999743 333344444
Q ss_pred HHHHHHHH
Q psy7662 197 LLTMNEEL 204 (220)
Q Consensus 197 lL~~k~~i 204 (220)
||..-.++
T Consensus 111 yL~kYRe~ 118 (168)
T KOG0869|consen 111 YLQKYREL 118 (168)
T ss_pred HHHHHHHH
Confidence 44444444
No 28
>KOG1142|consensus
Probab=84.07 E-value=2.5 Score=38.56 Aligned_cols=60 Identities=18% Similarity=0.393 Sum_probs=46.0
Q ss_pred ccccHHHHHHhhhhcCCCCCCcHH-HHHHHHHHHHHHHHHHHHHHHHhcC-C--CCCCcchhHhhhccC
Q psy7662 123 KRMFSKELRCMMYGFGDDRNPYTE-SVDILEDAVIDFLVDMTQKAMEMGR-T--GRVQVEDIVFLVRKD 187 (220)
Q Consensus 123 k~~f~kEI~~MMygfGD~~~P~~E-Tv~l~EdIV~e~I~~l~~~A~~~ar-r--gki~~eDl~FllRkD 187 (220)
|+....-++++ |...-+++ .-++|=+|.-+||.++++.|+.+|+ | .+|.+-||.|.|-++
T Consensus 157 k~kl~dLvqqI-----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~ 220 (258)
T KOG1142|consen 157 KRKLDDLVQQI-----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERN 220 (258)
T ss_pred ccchhHHHHhh-----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeecc
Confidence 44445555555 66666655 5569999999999999999999993 4 479999999999665
No 29
>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=82.25 E-value=4.8 Score=32.16 Aligned_cols=55 Identities=9% Similarity=0.225 Sum_probs=43.4
Q ss_pred HHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhhc
Q psy7662 130 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLVR 185 (220)
Q Consensus 130 I~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~FllR 185 (220)
|..++--.|. ..=.+..+..+=|++..|+.+++..|...| .|..|+.||+..++.
T Consensus 7 v~~iLk~~Gv-~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~ 64 (117)
T cd07979 7 IAAILKSMGI-TEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQ 64 (117)
T ss_pred HHHHHHHCCC-CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3455555565 355677888889999999999999998775 577999999999874
No 30
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=78.97 E-value=3.9 Score=31.72 Aligned_cols=56 Identities=20% Similarity=0.474 Sum_probs=45.7
Q ss_pred HHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhhcc
Q psy7662 130 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLVRK 186 (220)
Q Consensus 130 I~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~FllRk 186 (220)
++.+|--.|+. .-..+.+..+-+.|-+|+.++...|..+| .|..|+.+|+..+++.
T Consensus 25 v~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~ 83 (91)
T COG2036 25 VRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKR 83 (91)
T ss_pred HHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHH
Confidence 45666667764 56667888999999999999999998886 5779999999988763
No 31
>smart00417 H4 Histone H4.
Probab=74.48 E-value=6.3 Score=29.43 Aligned_cols=58 Identities=17% Similarity=0.202 Sum_probs=33.0
Q ss_pred ccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCCcchhHhh
Q psy7662 125 MFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEM---GRTGRVQVEDIVFL 183 (220)
Q Consensus 125 ~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~---arrgki~~eDl~Fl 183 (220)
+-..-|+.|.--.|=- --+.+...-+-+++.+|+.++++.|... |+|..++.+|+.|+
T Consensus 14 I~k~~IrRLaRr~Gvk-RIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 14 ITKPAIRRLARRGGVK-RISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CCHHHHHHHHHHcCcc-hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 3444555555555542 2222233334444445555666666554 56789999999874
No 32
>KOG2549|consensus
Probab=73.60 E-value=5.6 Score=39.90 Aligned_cols=46 Identities=20% Similarity=0.338 Sum_probs=41.1
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCCcchhHhhhcc
Q psy7662 141 RNPYTESVDILEDAVIDFLVDMTQKAMEM---GRTGRVQVEDIVFLVRK 186 (220)
Q Consensus 141 ~~P~~ETv~l~EdIV~e~I~~l~~~A~~~---arrgki~~eDl~FllRk 186 (220)
.+-.+|+..++.+-|...|.++++.|.+. ++|.+++++|+-.+||-
T Consensus 27 ~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~ 75 (576)
T KOG2549|consen 27 TNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRS 75 (576)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhh
Confidence 46788999999999999999999999887 56789999999999973
No 33
>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=71.05 E-value=7.5 Score=31.24 Aligned_cols=42 Identities=17% Similarity=0.325 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchhHhhhccChh
Q psy7662 147 SVDILEDAVIDFLVDMTQKAMEMGRTGRVQVEDIVFLVRKDNR 189 (220)
Q Consensus 147 Tv~l~EdIV~e~I~~l~~~A~~~arrgki~~eDl~FllRkD~~ 189 (220)
.+.+||.+..+ |.++.-++...+++.+|+.+||.-++|+|..
T Consensus 47 LaAvLEYL~aE-IlelA~n~ak~~k~krItp~hi~lAi~nD~E 88 (115)
T cd00074 47 LAAVLEYLTAE-VLELAGNAARDNKKKRITPRHLQLAVRNDEE 88 (115)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHcCCCeEcHHHHHHHHhccHH
Confidence 34455555544 5555555555556779999999999999975
No 34
>KOG1142|consensus
Probab=69.68 E-value=13 Score=33.91 Aligned_cols=68 Identities=13% Similarity=0.270 Sum_probs=47.0
Q ss_pred cccchHHHHHhhhhcCCCCCCchh-HHHHHHHHHHHHHHHHHHHHHHhc-CCCCce--eeccccccCCc--eeeecccc
Q psy7662 35 KRMFSKELRCMMYGFGDDRNPYTE-SVDILEDAVIDFLVDMTQKAMEMG-RTGPTF--LSLLKFKSNKN--VCVFSFQF 107 (220)
Q Consensus 35 k~~f~kel~~mmygfGD~~~P~~e-Tv~llEeIv~~yI~~l~~~A~~~a-rrgk~~--l~dlrfd~~K~--~~~~~fq~ 107 (220)
|+.....++++ |...-+++ .-++|=+|.-+|+.++++.|+.+| .|+.++ +-|+.|.-.|+ +..-.|..
T Consensus 157 k~kl~dLvqqI-----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf~s 230 (258)
T KOG1142|consen 157 KRKLDDLVQQI-----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGFSS 230 (258)
T ss_pred ccchhHHHHhh-----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCccc
Confidence 44455555555 66555544 778999999999999999999999 566554 44777776663 44344433
No 35
>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=66.87 E-value=14 Score=25.74 Aligned_cols=41 Identities=20% Similarity=0.264 Sum_probs=35.0
Q ss_pred HHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc
Q psy7662 42 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG 82 (220)
Q Consensus 42 l~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a 82 (220)
|+.+|=.-.|...-..|++.+|-.....||..|+..|...|
T Consensus 8 vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a 48 (65)
T PF00808_consen 8 VKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIA 48 (65)
T ss_dssp HHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55666666777778899999999999999999999999999
No 36
>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=63.71 E-value=12 Score=34.83 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=38.3
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhhc
Q psy7662 141 RNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLVR 185 (220)
Q Consensus 141 ~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~FllR 185 (220)
..-.++.+..+-+-|...+.++++.|.+.+ +|.+++++|+-.++|
T Consensus 15 ~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~ 62 (343)
T cd08050 15 DSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALR 62 (343)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence 456677778888888999999999998875 678999999999886
No 37
>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=61.13 E-value=15 Score=26.47 Aligned_cols=53 Identities=15% Similarity=0.155 Sum_probs=38.9
Q ss_pred HHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc---CCCCceeeccccc
Q psy7662 42 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGPTFLSLLKFK 95 (220)
Q Consensus 42 l~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a---rrgk~~l~dlrfd 95 (220)
|+.+.=..|-. .-.++....|-+.+..++.++++.|..++ +|...+.+|+.++
T Consensus 8 i~ria~~~Gi~-ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~A 63 (65)
T smart00803 8 IKDVAESLGIG-NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSA 63 (65)
T ss_pred HHHHHHHCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHH
Confidence 44444445554 56677889999999999999999999998 3445677777654
No 38
>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=52.34 E-value=19 Score=33.53 Aligned_cols=98 Identities=16% Similarity=0.159 Sum_probs=65.9
Q ss_pred HHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhcCCC----CceeeccccccCCceeeeccccccccccCC
Q psy7662 40 KELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGRTG----PTFLSLLKFKSNKNVCVFSFQFEEEEQDTP 115 (220)
Q Consensus 40 kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~arrg----k~~l~dlrfd~~K~~~~~~fq~~~~~~~~~ 115 (220)
.+...++|-...-....|+.+.-+|+++.+++..+.. ......| ...+.-+..+..+.+ +..+.+
T Consensus 157 ~~~~ei~~ria~l~~vs~~~i~~ie~~L~~~~~~~~~--~~~~~gG~~~~a~ILN~~~~~~~~~i----l~~L~~----- 225 (338)
T TIGR00207 157 EVQAEVARRIATMGRTSPEVVAEVERVLEGKLDSLNS--DYTKMGGVRAVAEIINLMDRKTEKTI----ITSLEE----- 225 (338)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHhhcc--ccccCChHHHHHHHHHhCCchHHHHH----HHHHHH-----
Confidence 4556778888889999999999999999999877643 1111234 245555555555444 222222
Q ss_pred CCCCCCcccccHHHHHHhhhhcCCCCCCcHHHHH-HHHHH
Q psy7662 116 VNLPSGRKRMFSKELRCMMYGFGDDRNPYTESVD-ILEDA 154 (220)
Q Consensus 116 ~~~~~~rk~~f~kEI~~MMygfGD~~~P~~ETv~-l~EdI 154 (220)
..+-+..+|+..||.|-|-..-.+.++. ++.++
T Consensus 226 ------~dp~la~~Ir~~mF~Fedl~~ld~~~l~~llrev 259 (338)
T TIGR00207 226 ------FDPELAEEIKKEMFVFEDIVDLDDRSIQRVLREV 259 (338)
T ss_pred ------hCHHHHHHHHHHccCHHHHhcCCHHHHHHHHHhC
Confidence 2345889999999999998776666555 44444
No 39
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 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 []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=43.12 E-value=64 Score=26.41 Aligned_cols=55 Identities=11% Similarity=0.222 Sum_probs=38.8
Q ss_pred HHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhhc
Q psy7662 130 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLVR 185 (220)
Q Consensus 130 I~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~FllR 185 (220)
|.+++-..|= .+=.+..+..+=|++..|+.+++..|...| .+..|+.+|+..++.
T Consensus 18 i~~iL~~~Gv-~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~ 75 (129)
T PF02291_consen 18 IHLILKSMGV-TEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQ 75 (129)
T ss_dssp HHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHH
T ss_pred HHHHHHHcCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHH
Confidence 3444444543 344667888888999999999999998775 567999999999885
No 40
>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=41.32 E-value=33 Score=30.60 Aligned_cols=68 Identities=21% Similarity=0.267 Sum_probs=31.9
Q ss_pred ccHHHHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCCcchhHhhhccChhHHHH
Q psy7662 125 MFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGR-TGRVQVEDIVFLVRKDNRKYAR 193 (220)
Q Consensus 125 ~f~kEI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~ar-rgki~~eDl~FllRkD~~Kl~R 193 (220)
.+.+=|+.++=-+| ...+.++.+.||---+.++|.+|+.++..+|+ |...+-++..+.+++|..+--|
T Consensus 48 ~L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr 116 (264)
T PF05236_consen 48 PLQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLR 116 (264)
T ss_dssp HHHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH---------------------------
T ss_pred HHHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHH
Confidence 34444556665556 67899999999999999999999999999983 4444557777778888544333
No 41
>smart00414 H2A Histone 2A.
Probab=40.80 E-value=44 Score=26.43 Aligned_cols=37 Identities=11% Similarity=0.245 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCcchhHhhhccChhH
Q psy7662 154 AVIDFLVDMTQKAMEMGRTGRVQVEDIVFLVRKDNRK 190 (220)
Q Consensus 154 IV~e~I~~l~~~A~~~arrgki~~eDl~FllRkD~~K 190 (220)
+++..|.++.-++..-.++.+|+.+++.-++|+|..=
T Consensus 42 YLtaEILeLagn~a~~~k~~rItp~hi~lAi~nD~EL 78 (106)
T smart00414 42 YLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEEL 78 (106)
T ss_pred HHHHHHHHHHHHHHHhcCCCccchHHHhhhccCCHHH
Confidence 3444466666665554456689999999999999753
No 42
>smart00428 H3 Histone H3.
Probab=37.60 E-value=1.7e+02 Score=23.15 Aligned_cols=62 Identities=18% Similarity=0.237 Sum_probs=44.3
Q ss_pred ccccHHHHHHhhhhcCC--CCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc---CCCCCCcchhHhhh
Q psy7662 123 KRMFSKELRCMMYGFGD--DRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGRVQVEDIVFLV 184 (220)
Q Consensus 123 k~~f~kEI~~MMygfGD--~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a---rrgki~~eDl~Fll 184 (220)
|--|..=++.++=-|.+ .-.=..++...+.+..-.|++.+...|..+| +|..|...|+..+.
T Consensus 32 k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ 98 (105)
T smart00428 32 KAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLAR 98 (105)
T ss_pred cccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHH
Confidence 44455555555544433 3455678889999999999999999887775 56788899996654
No 43
>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=37.19 E-value=36 Score=25.13 Aligned_cols=41 Identities=15% Similarity=0.269 Sum_probs=31.5
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhcC-CC--C-CCcchhH
Q psy7662 141 RNPYTESVDILEDAVIDFLVDMTQKAMEMGR-TG--R-VQVEDIV 181 (220)
Q Consensus 141 ~~P~~ETv~l~EdIV~e~I~~l~~~A~~~ar-rg--k-i~~eDl~ 181 (220)
..-..+++.++-+++.-|+.+.+.+|...++ .| . +.++||-
T Consensus 18 tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LE 62 (72)
T PF09415_consen 18 TKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLE 62 (72)
T ss_dssp -EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHH
T ss_pred CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence 3445689999999999999999999999873 23 5 8888874
No 44
>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=36.57 E-value=55 Score=26.09 Aligned_cols=57 Identities=12% Similarity=0.134 Sum_probs=43.1
Q ss_pred HHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCC--CceeeccccccCCce
Q psy7662 43 RCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTG--PTFLSLLKFKSNKNV 100 (220)
Q Consensus 43 ~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrg--k~~l~dlrfd~~K~~ 100 (220)
..++-..|.. .=.|..+..|=|.+-.|..+++..|..+| ..| .+..+|++.+-...+
T Consensus 8 ~~iLk~~Gv~-~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~ 67 (117)
T cd07979 8 AAILKSMGIT-EYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRV 67 (117)
T ss_pred HHHHHHCCCC-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHh
Confidence 3445555653 44678889999999999999999999999 334 578899998755544
No 45
>PLN00157 histone H2A; Provisional
Probab=35.66 E-value=69 Score=26.56 Aligned_cols=41 Identities=20% Similarity=0.361 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchhHhhhccChh
Q psy7662 148 VDILEDAVIDFLVDMTQKAMEMGRTGRVQVEDIVFLVRKDNR 189 (220)
Q Consensus 148 v~l~EdIV~e~I~~l~~~A~~~arrgki~~eDl~FllRkD~~ 189 (220)
+.+||-++-| |.++.-+|..-.++.+|+...|.-++|+|..
T Consensus 54 AAVLEYLtaE-VLELAgnaa~d~kk~RItPrHi~lAI~nDeE 94 (132)
T PLN00157 54 AAVLEYLAAE-VLELAGNAARDNKKSRIVPRHIQLAVRNDEE 94 (132)
T ss_pred HHHHHHHHHH-HHHHHHHHHHhcCCccccHHHHhhcccCcHH
Confidence 3345444444 5666655555445669999999999999975
No 46
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=34.11 E-value=40 Score=31.30 Aligned_cols=96 Identities=14% Similarity=0.167 Sum_probs=60.5
Q ss_pred hHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhcCCCC----ceeeccccccCCceeeeccccccccccC
Q psy7662 39 SKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGRTGP----TFLSLLKFKSNKNVCVFSFQFEEEEQDT 114 (220)
Q Consensus 39 ~kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~arrgk----~~l~dlrfd~~K~~~~~~fq~~~~~~~~ 114 (220)
-.+...+++....-....|+++.-+++.+..++..+..... ...-|. ..+..+..+. +. .|..+.+
T Consensus 153 e~~~~~v~~ria~l~~Vs~e~~~~V~e~l~~~~~~~~~~~~-~~~~G~~~aa~ILn~l~~~~-~~----il~~L~~---- 222 (334)
T PRK07194 153 EDRQDDILYRIAQLDDVDRDVVDELDELIERCLAVLSEQSH-TKVIGVKQAADIINRFPGDR-QQ----LMEMLKE---- 222 (334)
T ss_pred HHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHhhhhccc-ccCCCHHHHHHHHHhCchhH-HH----HHHHHHh----
Confidence 35677888999999999999999888777777665332110 112242 2222232111 11 1222222
Q ss_pred CCCCCCCcccccHHHHHHhhhhcCCCCCCcHHHHHHH
Q psy7662 115 PVNLPSGRKRMFSKELRCMMYGFGDDRNPYTESVDIL 151 (220)
Q Consensus 115 ~~~~~~~rk~~f~kEI~~MMygfGD~~~P~~ETv~l~ 151 (220)
...-+..+|+..||.|-|-.+=.+.|+.++
T Consensus 223 -------~dp~~a~~Ir~~mF~FedL~~~~~qtia~i 252 (334)
T PRK07194 223 -------HDEEVVNEIEDNMYDFFILSRQSEETLQRL 252 (334)
T ss_pred -------hCHHHHHHHHHhcCCHHHHhcCCHHHHHHH
Confidence 245678899999999999988888888844
No 47
>PTZ00017 histone H2A; Provisional
Probab=34.08 E-value=73 Score=26.46 Aligned_cols=39 Identities=18% Similarity=0.384 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhcCCCCCCcchhHhhhccChh
Q psy7662 150 ILEDAVIDFLVDMTQKAMEMGRTGRVQVEDIVFLVRKDNR 189 (220)
Q Consensus 150 l~EdIV~e~I~~l~~~A~~~arrgki~~eDl~FllRkD~~ 189 (220)
+||-+.-| |.++.-++..-.++.+|+..+|.-++|+|..
T Consensus 57 VLEYLtaE-ILELAgNaa~d~kk~RItPrHi~lAI~nDeE 95 (134)
T PTZ00017 57 VLEYLTAE-VLELAGNAAKDNKKKRITPRHIQLAIRNDEE 95 (134)
T ss_pred HHHHHHHH-HHHHHHHHHHhcCCCeecHHHHHhhccCcHH
Confidence 44433333 5566655555445568999999999999975
No 48
>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=34.07 E-value=78 Score=22.26 Aligned_cols=41 Identities=17% Similarity=0.162 Sum_probs=31.0
Q ss_pred HHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhcC
Q psy7662 43 RCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGR 83 (220)
Q Consensus 43 ~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~ar 83 (220)
+.+.=..+...--..+++.+|..++-+++.+++..|..+|.
T Consensus 16 r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~ 56 (75)
T PF00125_consen 16 REIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLAR 56 (75)
T ss_dssp HHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHh
Confidence 33333333334456789999999999999999999999983
No 49
>PLN00156 histone H2AX; Provisional
Probab=32.82 E-value=86 Score=26.23 Aligned_cols=41 Identities=20% Similarity=0.352 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchhHhhhccChh
Q psy7662 148 VDILEDAVIDFLVDMTQKAMEMGRTGRVQVEDIVFLVRKDNR 189 (220)
Q Consensus 148 v~l~EdIV~e~I~~l~~~A~~~arrgki~~eDl~FllRkD~~ 189 (220)
+.+||-++-| |.++.-+|..-.++.+|+.+.|.-++|+|..
T Consensus 57 AAVLEYLtaE-VLELAgNaa~d~kk~RItPrHi~lAIrnDeE 97 (139)
T PLN00156 57 SAVLEYLAAE-VLELAGNAARDNKKNRIVPRHIQLAVRNDEE 97 (139)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHcCCCcCcHHHHHhhccCcHH
Confidence 3344444433 6666666655555669999999999999965
No 50
>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=32.78 E-value=1.9e+02 Score=21.95 Aligned_cols=56 Identities=13% Similarity=0.191 Sum_probs=45.2
Q ss_pred HHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhc----C--CCCCCcchhHhhhcc
Q psy7662 130 LRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG----R--TGRVQVEDIVFLVRK 186 (220)
Q Consensus 130 I~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~a----r--rgki~~eDl~FllRk 186 (220)
|+.+|=..-+ ..|.+.++.+|--+-..|+-+|+..|..+. . +|.|..+.|.=+.|+
T Consensus 22 iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr 83 (85)
T cd08048 22 IKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR 83 (85)
T ss_pred HHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence 5556655555 788999999999999999999999999984 2 578888888766654
No 51
>PLN00035 histone H4; Provisional
Probab=30.87 E-value=76 Score=25.21 Aligned_cols=59 Identities=8% Similarity=0.026 Sum_probs=42.3
Q ss_pred hHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCC--CceeeccccccCC
Q psy7662 39 SKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTG--PTFLSLLKFKSNK 98 (220)
Q Consensus 39 ~kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrg--k~~l~dlrfd~~K 98 (220)
..-|+-|.=-.| +.--..+....|.+++.+|+.++++.|..+| +.| .++.+|+.++-++
T Consensus 32 k~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr 93 (103)
T PLN00035 32 KPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
T ss_pred HHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 344556666666 5555666778888899999999999999998 333 4778888775443
No 52
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) 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 4 (TAF4) 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 eukaryote. 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 hypotheses are
Probab=30.75 E-value=2.8e+02 Score=23.91 Aligned_cols=53 Identities=21% Similarity=0.263 Sum_probs=41.9
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCCcchhHhhhccChhHHHHH
Q psy7662 142 NPYTESVDILEDAVIDFLVDMTQKAMEMGR-TGRVQVEDIVFLVRKDNRKYARV 194 (220)
Q Consensus 142 ~P~~ETv~l~EdIV~e~I~~l~~~A~~~ar-rgki~~eDl~FllRkD~~Kl~Rv 194 (220)
...++.+.+|-..+.++|.+|+.++..+++ |....-+|..+.++.|+.+--|.
T Consensus 65 ~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~ 118 (212)
T cd08045 65 EVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRF 118 (212)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHH
Confidence 568999999999999999999999999983 43333678888889885544333
No 53
>PTZ00015 histone H4; Provisional
Probab=29.37 E-value=50 Score=26.15 Aligned_cols=61 Identities=10% Similarity=0.104 Sum_probs=38.1
Q ss_pred cchHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc---CCCCceeeccccccCC
Q psy7662 37 MFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGPTFLSLLKFKSNK 98 (220)
Q Consensus 37 ~f~kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a---rrgk~~l~dlrfd~~K 98 (220)
+-..-|+.|.=-.|=-. -..+-...+-+++.+|+.++++.|..+| +|..++.+|+.++.++
T Consensus 31 I~k~~IrRLarr~GvkR-IS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr 94 (102)
T PTZ00015 31 ITKGAIRRLARRGGVKR-ISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKR 94 (102)
T ss_pred CCHHHHHHHHHHcCCcc-chHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHh
Confidence 33345555555555332 2233445666677778888999998888 3445788888776443
No 54
>PLN00153 histone H2A; Provisional
Probab=29.29 E-value=1.1e+02 Score=25.25 Aligned_cols=40 Identities=18% Similarity=0.366 Sum_probs=27.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCCCcchhHhhhccChh
Q psy7662 149 DILEDAVIDFLVDMTQKAMEMGRTGRVQVEDIVFLVRKDNR 189 (220)
Q Consensus 149 ~l~EdIV~e~I~~l~~~A~~~arrgki~~eDl~FllRkD~~ 189 (220)
.+||-++-| |.++.-+|..-.++.+|+...|.-++|+|..
T Consensus 53 AVLEYLtaE-VLELAgnaa~d~kk~RItPrHi~lAI~nDeE 92 (129)
T PLN00153 53 AVLEYLTAE-VLELAGNAARDNKKNRIVPRHIQLAIRNDEE 92 (129)
T ss_pred HHHHHHHHH-HHHHHHHHHHhcCCCccChHHHHhhccCcHH
Confidence 344444433 6666666555445679999999999999964
No 55
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=27.81 E-value=1e+02 Score=23.89 Aligned_cols=52 Identities=15% Similarity=0.330 Sum_probs=37.2
Q ss_pred HHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCCC--ceeeccccc
Q psy7662 43 RCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTGP--TFLSLLKFK 95 (220)
Q Consensus 43 ~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrgk--~~l~dlrfd 95 (220)
+-+|=-.|+. .-..+.+..|.+.+-+|+.++...|..+| +.|+ ++-+|+..+
T Consensus 26 ~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la 80 (91)
T COG2036 26 RRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLA 80 (91)
T ss_pred HHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHH
Confidence 3444444444 44566788999999999999999999999 4454 566665543
No 56
>PHA00724 hypothetical protein
Probab=27.16 E-value=44 Score=25.21 Aligned_cols=36 Identities=25% Similarity=0.264 Sum_probs=31.2
Q ss_pred hhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHH
Q psy7662 45 MMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAME 80 (220)
Q Consensus 45 mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~ 80 (220)
||-+.||+.+-+-=-+-++-=|++.|+.++.--.+-
T Consensus 1 mmsalgdviyilgil~p~lgli~rnyl~nlmgfvmg 36 (83)
T PHA00724 1 MMSALGDVIYILGILIPLLGLIVRNYLVNLMGFVMG 36 (83)
T ss_pred CcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 788999999988888899999999999998765553
No 57
>KOG4336|consensus
Probab=26.00 E-value=1.3e+02 Score=28.52 Aligned_cols=77 Identities=9% Similarity=0.154 Sum_probs=57.0
Q ss_pred ccHHHHHHhhh--hcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh---cCCCCCCcchhHhhhccChhHHHHHHHHHH
Q psy7662 125 MFSKELRCMMY--GFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEM---GRTGRVQVEDIVFLVRKDNRKYARVKDLLT 199 (220)
Q Consensus 125 ~f~kEI~~MMy--gfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~---arrgki~~eDl~FllRkD~~Kl~Rv~~lL~ 199 (220)
....=|..|++ ||++.. .-+.+-|=++|..||.++-.+++.. ++|-.++.-|+.+.|+.=--|++-|..++.
T Consensus 6 vl~~VV~~Ll~~~gfd~is---~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~v~sL~~~~q 82 (323)
T KOG4336|consen 6 VLAPVVSNLLKTKGFDSIS---NAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIKVSSLYAYFQ 82 (323)
T ss_pred HHHHHHHHHHHHhCchHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCChhhhHHHHH
Confidence 44555677775 555532 3344456678899999998777654 677899999999999999999999998887
Q ss_pred HHHHH
Q psy7662 200 MNEEL 204 (220)
Q Consensus 200 ~k~~i 204 (220)
.....
T Consensus 83 ~~~~s 87 (323)
T KOG4336|consen 83 KQEFS 87 (323)
T ss_pred hccch
Confidence 65543
No 58
>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=23.56 E-value=1e+02 Score=22.40 Aligned_cols=41 Identities=17% Similarity=0.112 Sum_probs=30.0
Q ss_pred CCchhHHHHHHHHHHHHHHHHHHHHHHhc---CCCCceeecccc
Q psy7662 54 NPYTESVDILEDAVIDFLVDMTQKAMEMG---RTGPTFLSLLKF 94 (220)
Q Consensus 54 ~P~~eTv~llEeIv~~yI~~l~~~A~~~a---rrgk~~l~dlrf 94 (220)
+-.++....|-+-|.--|.++++.|.++. +|.+....|+-.
T Consensus 20 ~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ 63 (66)
T PF02969_consen 20 NLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINS 63 (66)
T ss_dssp -B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHH
Confidence 45678889999999999999999999987 455666666543
No 59
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=23.46 E-value=2.4e+02 Score=24.99 Aligned_cols=72 Identities=17% Similarity=0.081 Sum_probs=46.7
Q ss_pred HHHHhhhhcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcchhH----h-hh----ccChhHHHHHHHHHH
Q psy7662 129 ELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGRTGRVQVEDIV----F-LV----RKDNRKYARVKDLLT 199 (220)
Q Consensus 129 EI~~MMygfGD~~~P~~ETv~l~EdIV~e~I~~l~~~A~~~arrgki~~eDl~----F-ll----RkD~~Kl~Rv~~lL~ 199 (220)
++..++-.+=-......+.....+.+|..++.-+.+-|.....+| +..+||+ . || |-||.|=-|+.+|-.
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~r~~Lv~~~l~LV~~iA~~y~~~g-~~~~DLiQeG~iGLi~AierFDp~~G~~FsTYA~ 98 (264)
T PRK07122 20 DVPEMFRELAGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDGRG-EPRDDLVQVARVGLVNAVNRFDVETGSDFVSFAV 98 (264)
T ss_pred hHHHHHHHHHhccCCCHHHHHHHHHHHHHhHHHHHHHHHHHHhCC-CCHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHH
Confidence 556665544334445667777889999999998888888876554 7888883 2 22 345655555555554
Q ss_pred HH
Q psy7662 200 MN 201 (220)
Q Consensus 200 ~k 201 (220)
|.
T Consensus 99 ~~ 100 (264)
T PRK07122 99 PT 100 (264)
T ss_pred HH
Confidence 43
No 60
>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=23.35 E-value=1.7e+02 Score=22.36 Aligned_cols=59 Identities=10% Similarity=0.081 Sum_probs=40.6
Q ss_pred chHHHHHhhhhcCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHhc-CCC--CceeeccccccC
Q psy7662 38 FSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG-RTG--PTFLSLLKFKSN 97 (220)
Q Consensus 38 f~kel~~mmygfGD~~~P~~eTv~llEeIv~~yI~~l~~~A~~~a-rrg--k~~l~dlrfd~~ 97 (220)
-..-|+.|.=-.| +.--..+...-+.+++.+|+.++++.|..+| ..| .++.+|+.++-+
T Consensus 15 ~k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alk 76 (85)
T cd00076 15 TKPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALK 76 (85)
T ss_pred CHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHH
Confidence 3445555555556 4445556677788888899999999999998 333 467778766543
No 61
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=22.26 E-value=1.8e+02 Score=21.22 Aligned_cols=31 Identities=23% Similarity=0.203 Sum_probs=24.3
Q ss_pred CCCCCCcchhHhhhc-cChhHHHHHHHHHHHH
Q psy7662 171 RTGRVQVEDIVFLVR-KDNRKYARVKDLLTMN 201 (220)
Q Consensus 171 rrgki~~eDl~FllR-kD~~Kl~Rv~~lL~~k 201 (220)
..+.++..|..=+++ -|..++.||.++|.-.
T Consensus 50 ~~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~ 81 (86)
T PF04433_consen 50 PNKYLTKTDARKLIKGIDVNKIRRIYDFLERW 81 (86)
T ss_dssp TTS---HHHHHHHTTSSSHHHHHHHHHHHHHT
T ss_pred CCCcccHHHHHHHccccCHHHHHHHHHHHHHc
Confidence 346899999999999 5999999999999754
No 62
>PLN00154 histone H2A; Provisional
Probab=22.11 E-value=1.7e+02 Score=24.38 Aligned_cols=36 Identities=11% Similarity=0.208 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCCcchhHhhhccChh
Q psy7662 154 AVIDFLVDMTQKAMEMGRTGRVQVEDIVFLVRKDNR 189 (220)
Q Consensus 154 IV~e~I~~l~~~A~~~arrgki~~eDl~FllRkD~~ 189 (220)
+++--|.+|.-+|..-.++.+|+...+.-++|+|..
T Consensus 72 YLtAEVLELAGNaA~d~kk~RItPrHi~lAIrnDeE 107 (136)
T PLN00154 72 YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEE 107 (136)
T ss_pred HHHHHHHHHHHHHHHhhCCceecHHHhhhhccCcHH
Confidence 333335566555555445668999999999999964
No 63
>smart00417 H4 Histone H4.
Probab=21.65 E-value=1.9e+02 Score=21.51 Aligned_cols=33 Identities=9% Similarity=0.133 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHhc-CC--CCceeecccc
Q psy7662 62 ILEDAVIDFLVDMTQKAMEMG-RT--GPTFLSLLKF 94 (220)
Q Consensus 62 llEeIv~~yI~~l~~~A~~~a-rr--gk~~l~dlrf 94 (220)
-+-+++.+|+.++.+.|..+| .. .-++.+|+.|
T Consensus 38 elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 38 ETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 344445566677788888877 33 3467777665
No 64
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=21.61 E-value=68 Score=25.32 Aligned_cols=32 Identities=19% Similarity=0.231 Sum_probs=27.3
Q ss_pred chhHhhhccChhHHHHHHHHHHHHHHHHHHHh
Q psy7662 178 EDIVFLVRKDNRKYARVKDLLTMNEELKKARK 209 (220)
Q Consensus 178 eDl~FllRkD~~Kl~Rv~~lL~~k~~ik~Ark 209 (220)
=+|-|+.||||.=-+-++++|....-|+++-.
T Consensus 65 mlLEwlrR~~p~wd~eL~eiLft~k~i~e~ge 96 (103)
T COG3461 65 MLLEWLRRHDPAWDAELHEILFTTKPIKELGE 96 (103)
T ss_pred HHHHHHHHcCchHHHHHHHHHhcCCcHhHHHh
Confidence 46889999999999999999999888887643
No 65
>KOG3467|consensus
Probab=20.46 E-value=1.3e+02 Score=23.56 Aligned_cols=43 Identities=26% Similarity=0.532 Sum_probs=27.2
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHH---HhcCCCCCCcchhHhhhccChhH
Q psy7662 144 YTESVDILEDAVIDFLVDMTQKAM---EMGRTGRVQVEDIVFLVRKDNRK 190 (220)
Q Consensus 144 ~~ETv~l~EdIV~e~I~~l~~~A~---~~arrgki~~eDl~FllRkD~~K 190 (220)
..||-.+.. .||.+.+.-|. +.|+|+.++.-|+++.|.+.-.+
T Consensus 52 yeE~~~~~k----~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 52 YEETRGVLK----VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred HHHHHHHHH----HHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 345555444 44555554443 34678899999999998765433
Done!