Query 033030
Match_columns 129
No_of_seqs 105 out of 238
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 08:57:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033030.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033030hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd07978 TAF13 The TATA Binding 100.0 3.9E-40 8.4E-45 232.7 11.7 91 29-119 1-92 (92)
2 KOG3901 Transcription initiati 100.0 3.3E-38 7.2E-43 227.4 10.1 95 27-122 6-100 (109)
3 PF02269 TFIID-18kDa: Transcri 100.0 2.9E-39 6.2E-44 228.0 2.5 91 30-120 1-93 (93)
4 COG5248 TAF19 Transcription in 100.0 3.2E-31 6.9E-36 193.5 9.9 99 27-125 6-104 (126)
5 KOG3902 Histone acetyltransfer 99.9 1.1E-24 2.4E-29 181.2 12.4 111 1-117 1-114 (352)
6 cd07981 TAF12 TATA Binding Pro 97.4 0.0013 2.9E-08 44.1 7.4 48 47-94 18-67 (72)
7 PF03847 TFIID_20kDa: Transcri 97.3 0.00098 2.1E-08 44.8 5.9 59 36-94 5-65 (68)
8 smart00576 BTP Bromodomain tra 97.0 0.0046 9.9E-08 41.7 7.0 63 30-93 6-70 (77)
9 KOG1142 Transcription initiati 97.0 0.0022 4.7E-08 53.1 6.4 60 30-94 158-220 (258)
10 PF00808 CBFD_NFYB_HMF: Histon 96.8 0.0058 1.2E-07 39.6 6.1 57 35-91 7-65 (65)
11 PF07524 Bromo_TP: Bromodomain 96.2 0.031 6.7E-07 37.3 7.0 62 31-93 7-70 (77)
12 PLN00035 histone H4; Provision 96.1 0.036 7.9E-07 40.2 7.0 59 35-94 34-94 (103)
13 PF15630 CENP-S: Kinetochore c 96.0 0.021 4.6E-07 39.1 5.2 50 47-96 24-75 (76)
14 smart00803 TAF TATA box bindin 95.8 0.043 9.4E-07 36.3 6.0 56 36-92 8-65 (65)
15 cd00076 H4 Histone H4, one of 95.7 0.067 1.5E-06 37.5 6.9 60 34-94 17-78 (85)
16 PTZ00015 histone H4; Provision 95.4 0.063 1.4E-06 38.9 6.2 61 33-94 33-95 (102)
17 PF00125 Histone: Core histone 95.4 0.094 2E-06 34.3 6.5 64 31-94 10-75 (75)
18 cd07979 TAF9 TATA Binding Prot 95.0 0.15 3.3E-06 37.2 7.2 57 36-93 7-65 (117)
19 COG2036 HHT1 Histones H3 and H 93.7 0.24 5.3E-06 35.1 5.7 58 35-93 24-83 (91)
20 PF02969 TAF: TATA box binding 92.7 1 2.2E-05 30.1 7.2 46 47-92 19-66 (66)
21 smart00417 H4 Histone H4. 91.6 0.43 9.3E-06 32.6 4.5 56 34-90 17-74 (74)
22 KOG3902 Histone acetyltransfer 90.6 1.3 2.7E-05 38.1 7.3 78 36-117 81-161 (352)
23 PF02291 TFIID-31kDa: Transcri 90.3 1.2 2.6E-05 33.3 6.2 57 35-92 17-75 (129)
24 KOG0869 CCAAT-binding factor, 90.0 0.84 1.8E-05 35.7 5.3 63 31-93 33-98 (168)
25 smart00428 H3 Histone H3. 88.7 3.1 6.8E-05 30.2 7.2 64 29-92 32-99 (105)
26 PLN00158 histone H2B; Provisio 88.3 6.2 0.00013 29.3 8.6 87 7-93 4-92 (116)
27 cd08050 TAF6 TATA Binding Prot 83.3 4.5 9.7E-05 34.3 6.6 47 47-93 15-63 (343)
28 PF05236 TAF4: Transcription i 82.3 1.7 3.7E-05 35.2 3.6 82 32-114 49-131 (264)
29 PLN00121 histone H3; Provision 79.6 9.3 0.0002 29.0 6.5 61 32-92 68-130 (136)
30 KOG2549 Transcription initiati 78.4 5.6 0.00012 36.5 5.8 58 32-93 16-75 (576)
31 COG5247 BUR6 Class 2 transcrip 74.4 32 0.00069 25.3 8.1 83 25-108 17-102 (113)
32 PTZ00018 histone H3; Provision 74.2 15 0.00033 27.8 6.4 61 32-92 68-130 (136)
33 cd00074 H2A Histone 2A; H2A is 73.2 17 0.00036 26.7 6.2 42 55-96 45-88 (115)
34 PF09415 CENP-X: CENP-S associ 72.4 4 8.7E-05 27.6 2.6 44 45-88 16-62 (72)
35 cd08045 TAF4 TATA Binding Prot 70.2 27 0.00058 27.5 7.2 73 33-105 47-123 (212)
36 cd08048 TAF11 TATA Binding Pro 66.3 41 0.00088 23.3 6.9 58 35-93 21-83 (85)
37 PLN00160 histone H3; Provision 65.6 37 0.00081 24.3 6.5 64 29-92 24-90 (97)
38 PF02787 CPSase_L_D3: Carbamoy 64.9 24 0.00052 25.8 5.6 36 77-113 20-55 (123)
39 PLN00161 histone H3; Provision 63.9 42 0.00091 25.5 6.8 62 31-92 60-124 (135)
40 KOG3334 Transcription initiati 63.6 42 0.00091 25.9 6.8 59 33-92 16-76 (148)
41 KOG4336 TBP-associated transcr 62.4 37 0.00081 29.2 7.0 77 31-110 6-86 (323)
42 PTZ00463 histone H2B; Provisio 59.0 73 0.0016 23.7 9.1 44 49-92 47-92 (117)
43 KOG1659 Class 2 transcription 56.8 55 0.0012 26.9 6.8 83 24-107 6-91 (224)
44 TIGR03798 ocin_TIGR03798 bacte 54.4 25 0.00055 22.5 3.8 44 83-126 3-47 (64)
45 PF15290 Syntaphilin: Golgi-lo 51.6 57 0.0012 27.9 6.3 83 23-115 33-127 (305)
46 KOG2389 Predicted bromodomain 50.5 58 0.0013 28.4 6.3 57 36-93 35-93 (353)
47 PF07862 Nif11: Nitrogen fixat 49.1 35 0.00075 20.6 3.6 42 84-125 6-48 (49)
48 KOG0870 DNA polymerase epsilon 47.6 69 0.0015 25.3 5.8 47 47-93 29-77 (172)
49 smart00414 H2A Histone 2A. 47.2 50 0.0011 23.8 4.7 41 56-97 38-78 (106)
50 smart00427 H2B Histone H2B. 46.7 88 0.0019 22.1 5.8 45 49-93 20-66 (89)
51 KOG1744 Histone H2B [Chromatin 45.0 1.3E+02 0.0029 22.6 7.3 65 28-92 35-101 (127)
52 PRK07122 RNA polymerase sigma 44.2 1.6E+02 0.0034 23.8 7.7 51 35-87 20-70 (264)
53 KOG3467 Histone H4 [Chromatin 44.1 59 0.0013 23.4 4.5 68 26-97 17-97 (103)
54 COG5094 TAF9 Transcription ini 43.5 56 0.0012 24.9 4.6 38 56-93 39-81 (145)
55 COG3461 Uncharacterized conser 41.5 24 0.00052 25.5 2.2 32 84-115 64-95 (103)
56 PTZ00252 histone H2A; Provisio 37.8 79 0.0017 24.0 4.7 37 60-96 58-95 (134)
57 PF04433 SWIRM: SWIRM domain; 37.5 1.1E+02 0.0023 20.4 4.9 29 79-107 51-80 (86)
58 PHA00724 hypothetical protein 36.7 26 0.00056 24.3 1.7 35 39-73 1-35 (83)
59 PF04719 TAFII28: hTAFII28-lik 34.8 1.6E+02 0.0035 20.6 6.3 60 34-93 27-89 (90)
60 PTZ00017 histone H2A; Provisio 33.7 97 0.0021 23.5 4.6 39 57-96 57-95 (134)
61 KOG0871 Class 2 transcription 32.5 1.3E+02 0.0028 23.5 5.1 44 50-93 33-78 (156)
62 cd08047 TAF7 TATA Binding Prot 31.6 12 0.00027 28.4 -0.5 32 18-49 57-91 (162)
63 PF03540 TFIID_30kDa: Transcri 31.4 1.4E+02 0.0031 19.0 6.1 34 46-79 17-50 (51)
64 PLN00156 histone H2AX; Provisi 31.2 1.3E+02 0.0027 23.0 4.9 37 59-96 61-97 (139)
65 COG5095 TAF6 Transcription ini 30.8 1.2E+02 0.0025 26.9 5.1 46 48-93 22-69 (450)
66 PF09454 Vps23_core: Vps23 cor 30.6 1.6E+02 0.0035 19.3 6.1 45 49-93 7-51 (65)
67 PLN00157 histone H2A; Provisio 29.8 1.2E+02 0.0026 22.9 4.5 37 59-96 58-94 (132)
68 smart00540 LEM in nuclear memb 29.7 89 0.0019 19.2 3.2 33 33-65 8-41 (44)
69 PF12290 DUF3802: Protein of u 29.7 71 0.0015 23.7 3.2 33 41-73 22-55 (113)
70 PRK15067 ethanolamine ammonia 28.9 44 0.00095 30.1 2.3 34 28-61 170-206 (461)
71 PLN00153 histone H2A; Provisio 28.9 1.5E+02 0.0032 22.4 4.8 37 59-96 56-92 (129)
72 PF14164 YqzH: YqzH-like prote 28.7 53 0.0011 22.0 2.1 20 47-66 44-63 (64)
73 cd08813 DED_Caspase_8_repeat2 26.6 60 0.0013 22.5 2.2 35 83-117 19-55 (83)
74 PF11861 DUF3381: Domain of un 25.7 81 0.0018 24.1 3.0 74 42-116 13-95 (159)
75 PLN00154 histone H2A; Provisio 25.5 1.8E+02 0.0038 22.2 4.8 38 58-96 70-107 (136)
76 PF08318 COG4: COG4 transport 24.4 4.2E+02 0.0091 22.1 8.0 33 62-94 249-293 (331)
77 PRK00411 cdc6 cell division co 24.3 2.4E+02 0.0051 23.3 5.8 45 49-93 229-281 (394)
78 PTZ00361 26 proteosome regulat 24.0 72 0.0016 28.2 2.8 43 51-93 379-423 (438)
79 TIGR00764 lon_rel lon-related 22.8 5.4E+02 0.012 23.6 8.2 39 63-101 358-398 (608)
80 TIGR03015 pepcterm_ATPase puta 22.8 2.1E+02 0.0045 22.0 4.9 61 33-93 194-265 (269)
81 COG1931 Uncharacterized protei 21.9 1E+02 0.0022 23.7 2.8 24 95-118 48-71 (140)
82 PRK05481 lipoyl synthase; Prov 21.9 24 0.00053 29.0 -0.6 24 37-60 200-223 (289)
83 PRK00771 signal recognition pa 21.3 4.7E+02 0.01 23.1 7.3 65 32-107 278-344 (437)
84 TIGR02928 orc1/cdc6 family rep 20.6 3.2E+02 0.0068 22.2 5.8 43 50-92 222-272 (365)
85 COG1422 Predicted membrane pro 20.5 1.2E+02 0.0026 24.5 3.2 25 93-117 69-94 (201)
86 PRK12928 lipoyl synthase; Prov 20.4 27 0.00058 29.0 -0.6 22 38-59 209-230 (290)
87 PF06751 EutB: Ethanolamine am 20.4 53 0.0012 29.5 1.2 33 28-60 160-195 (444)
88 KOG2028 ATPase related to the 20.4 1.1E+02 0.0025 27.7 3.2 60 42-101 296-375 (554)
No 1
>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=3.9e-40 Score=232.69 Aligned_cols=91 Identities=58% Similarity=1.005 Sum_probs=88.0
Q ss_pred ccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh-cCCCCchhHHHHHHhhChhhHhHHHHHHHH
Q 033030 29 RGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGS-KGGKLSVEDFLYLIRKDLPKLNRCTELLSM 107 (129)
Q Consensus 29 k~~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~-~Rgkis~eDl~F~lR~D~~Kl~Rl~~lL~~ 107 (129)
++.|.+||++|||||||+++|++|||.+|||||++||++||++|+++|. ++|++++|||+|+|||||+||+|+++||+|
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 4689999999999999999999999999999999999999999999998 667899999999999999999999999999
Q ss_pred HHHHHHHHhhcc
Q 033030 108 QEELKQARKAFE 119 (129)
Q Consensus 108 k~~ik~Ark~fd 119 (129)
+++||+|||+||
T Consensus 81 k~~~k~ark~~d 92 (92)
T cd07978 81 KDELKKARKAFD 92 (92)
T ss_pred HHHHHHHHhccC
Confidence 999999999986
No 2
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=100.00 E-value=3.3e-38 Score=227.40 Aligned_cols=95 Identities=61% Similarity=1.014 Sum_probs=92.0
Q ss_pred ccccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChhhHhHHHHHHH
Q 033030 27 RKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLS 106 (129)
Q Consensus 27 ~kk~~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~Kl~Rl~~lL~ 106 (129)
+||++|++||++|||||||+++|+++||+++|+||++||.++|+.|+.++ +||++.+|||+|+||+||+||+|+++||.
T Consensus 6 ~rk~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g-~rgk~~veD~~f~lRkDpkK~~Rv~eLL~ 84 (109)
T KOG3901|consen 6 QRKHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG-KRGKVKVEDFKFLLRKDPKKLGRVKELLA 84 (109)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc-ccCceeHHHHHHHHHhChHHHhHHHHHHH
Confidence 47889999999999999999999999999999999999999999999998 89999999999999999999999999999
Q ss_pred HHHHHHHHHhhcccch
Q 033030 107 MQEELKQARKAFEVDE 122 (129)
Q Consensus 107 ~k~~ik~Ark~fd~de 122 (129)
|++++|+|||+|++.+
T Consensus 85 mneelk~ArKaF~~~~ 100 (109)
T KOG3901|consen 85 MNEELKKARKAFDETD 100 (109)
T ss_pred hHHHHHHHHhccchHh
Confidence 9999999999998765
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=2.9e-39 Score=228.02 Aligned_cols=91 Identities=54% Similarity=0.928 Sum_probs=38.9
Q ss_pred cccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCchhHHHHHHhhChhhHhHHHHHHHH
Q 033030 30 GVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKDLPKLNRCTELLSM 107 (129)
Q Consensus 30 ~~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg--kis~eDl~F~lR~D~~Kl~Rl~~lL~~ 107 (129)
++|++||++|||||||+++|++||+.+||+||++||+++|++|.++|++|| +|++|||+|+|||||.||+|+++||.|
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 479999999999999999999999999999999999999999999999885 599999999999999999999999999
Q ss_pred HHHHHHHHhhccc
Q 033030 108 QEELKQARKAFEV 120 (129)
Q Consensus 108 k~~ik~Ark~fd~ 120 (129)
++++++|+|.||+
T Consensus 81 k~~~~karK~~d~ 93 (93)
T PF02269_consen 81 KDEIKKARKDFDE 93 (93)
T ss_dssp -------------
T ss_pred HHHHHHHHHhhcC
Confidence 9999999999974
No 4
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=99.97 E-value=3.2e-31 Score=193.54 Aligned_cols=99 Identities=34% Similarity=0.607 Sum_probs=95.1
Q ss_pred ccccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChhhHhHHHHHHH
Q 033030 27 RKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLS 106 (129)
Q Consensus 27 ~kk~~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~Kl~Rl~~lL~ 106 (129)
||.++|.+||+.|||||||+.+|.++|++.+++||.+||.++|.+|..+|+.|||+++|||.|+||+||+||+|+++||.
T Consensus 6 rr~nLF~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rnK~k~eDfkfaLr~DpkKlgRveeLl~ 85 (126)
T COG5248 6 RRVNLFMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTKTEDFKFALRRDPKKLGRVEELLI 85 (126)
T ss_pred HHHHHHHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHhhChHHHhHHHHHHH
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhcccchhhh
Q 033030 107 MQEELKQARKAFEVDEEKL 125 (129)
Q Consensus 107 ~k~~ik~Ark~fd~de~~~ 125 (129)
.+++|+.|+|+|.+.+.++
T Consensus 86 tn~~i~~Akk~F~~~dsRy 104 (126)
T COG5248 86 TNEEIKLAKKAFEPKDSRY 104 (126)
T ss_pred hhHHHHHHhcccCchhHHH
Confidence 9999999999998876443
No 5
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=99.92 E-value=1.1e-24 Score=181.24 Aligned_cols=111 Identities=31% Similarity=0.445 Sum_probs=104.0
Q ss_pred CCCCCCCCCCCCcCCCCCCCCcccccccccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 033030 1 MSNPSTGQSSKSKAGSSQPYETTSFKRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG 80 (129)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~kk~~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg 80 (129)
|||++|+|+|++++.+-+..+ +-..|.-||++|||..|+.+.|++||++|+|++|..|+++++.+|.++|..||
T Consensus 1 ~n~~aasp~s~~st~~m~~tg------~~~ky~veiQqmmf~sGei~~P~pett~Lved~V~gqvie~l~qa~eia~lrg 74 (352)
T KOG3902|consen 1 SNDMAASPPSAPSTPQMQTTG------DIKKYRVEIQQMMFQSGEIPDPLPETTNLVEDNVRGQVIESLVQANEIADLRG 74 (352)
T ss_pred CCCccCCCCCCCCCccccccc------cchhHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhcC
Confidence 799999999999988888776 44579999999999999999999999999999999999999999999999999
Q ss_pred C--CchhHHHHHHhhChhhHhHHHHHHHHHHHH-HHHHhh
Q 033030 81 K--LSVEDFLYLIRKDLPKLNRCTELLSMQEEL-KQARKA 117 (129)
Q Consensus 81 k--is~eDl~F~lR~D~~Kl~Rl~~lL~~k~~i-k~Ark~ 117 (129)
. |+.||++|++|||++|+.||.+||.|++.+ |.|+..
T Consensus 75 sr~Itpedliflir~Drakv~rL~tyl~~kdlR~k~ak~q 114 (352)
T KOG3902|consen 75 SRSITPEDLIFLIRHDRAKVNRLVTYLSWKDLRGKFAKAQ 114 (352)
T ss_pred ccccChHHHHHHhhccHHHHHHHHHHHHHHHHHHhhhhhh
Confidence 6 999999999999999999999999999999 777754
No 6
>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=97.37 E-value=0.0013 Score=44.09 Aligned_cols=48 Identities=19% Similarity=0.333 Sum_probs=43.5
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhhC
Q 033030 47 PNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKD 94 (129)
Q Consensus 47 ~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~D 94 (129)
..-.++...++-+++-+|+.+++..|+.+|..||+ ++.+|+.+++.+.
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 56778888899999999999999999999998875 9999999999875
No 7
>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=97.28 E-value=0.00098 Score=44.80 Aligned_cols=59 Identities=17% Similarity=0.303 Sum_probs=43.7
Q ss_pred HHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhhC
Q 033030 36 LQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKD 94 (129)
Q Consensus 36 I~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~D 94 (129)
|+.|+--..-.....++...++-+|.-+||.+++..|+++|..||. +.+.|+.|.|.++
T Consensus 5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~ 65 (68)
T PF03847_consen 5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN 65 (68)
T ss_dssp HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence 4444444444556677778899999999999999999999999985 9999999999864
No 8
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=96.99 E-value=0.0046 Score=41.74 Aligned_cols=63 Identities=11% Similarity=0.237 Sum_probs=52.7
Q ss_pred cccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc--CCCCchhHHHHHHhh
Q 033030 30 GVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSK--GGKLSVEDFLYLIRK 93 (129)
Q Consensus 30 ~~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~--Rgkis~eDl~F~lR~ 93 (129)
.++..-|.+++...|= ..-.+.+.+.+-+++.+|+.+++..+.+.|.. |..+++.|+..+|.+
T Consensus 6 ~ll~~~Vaqil~~~Gf-~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 6 ALLRIAVAQILESAGF-DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 3566778999999983 24567799999999999999999999999965 445999999999875
No 9
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.99 E-value=0.0022 Score=53.13 Aligned_cols=60 Identities=15% Similarity=0.344 Sum_probs=47.9
Q ss_pred cccHHHHHHHHhhhCCCCCCcHH-HHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhhC
Q 033030 30 GVFQKDLQHMMYGFGDDPNPLPE-TVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKD 94 (129)
Q Consensus 30 ~~f~~EI~~mMy~fGD~~~P~~E-Tv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~D 94 (129)
+...+-++++ |...-+++ .-++|-||.-+||.++++.|+.+|..|++ |.+-||.|.|.++
T Consensus 158 ~kl~dLvqqI-----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~ 220 (258)
T KOG1142|consen 158 RKLDDLVQQI-----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERN 220 (258)
T ss_pred cchhHHHHhh-----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeecc
Confidence 3444445554 55555555 66699999999999999999999999885 9999999999874
No 10
>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=96.81 E-value=0.0058 Score=39.58 Aligned_cols=57 Identities=19% Similarity=0.279 Sum_probs=48.6
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHH
Q 033030 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLI 91 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~l 91 (129)
=|+.+|-.-.|...-..|++.+|-.....||..|+..|...|...|+ |+.+||..+|
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 47788888888888999999999999999999999999999986554 9999998765
No 11
>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=96.24 E-value=0.031 Score=37.32 Aligned_cols=62 Identities=15% Similarity=0.367 Sum_probs=50.8
Q ss_pred ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhh
Q 033030 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 93 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~ 93 (129)
....-|.+++...|= ..-.+.+.+.+-+|+..||.+|+..+...|...|+ +++.|+..+|..
T Consensus 7 ~l~~~va~il~~~GF-~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~ 70 (77)
T PF07524_consen 7 LLRRSVAQILKHAGF-DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEE 70 (77)
T ss_pred HHHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 455668888888883 23566779999999999999999999999976554 999999998864
No 12
>PLN00035 histone H4; Provisional
Probab=96.05 E-value=0.036 Score=40.22 Aligned_cols=59 Identities=7% Similarity=0.137 Sum_probs=48.5
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCchhHHHHHHhhC
Q 033030 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKD 94 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg--kis~eDl~F~lR~D 94 (129)
-|+.+.--.| +..-..+....+.+++.+|+.+++..|..+|...+ .|+.+|+.|+|++-
T Consensus 34 ~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 34 AIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred HHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence 3455566666 77888888889999999999999999999987544 49999999999864
No 13
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=95.97 E-value=0.021 Score=39.13 Aligned_cols=50 Identities=18% Similarity=0.407 Sum_probs=39.5
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhhChh
Q 033030 47 PNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKDLP 96 (129)
Q Consensus 47 ~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~D~~ 96 (129)
.+..++.+..|-|++-.|+.++...---.|...|+ |++||++.+.|++|.
T Consensus 24 ~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~ 75 (76)
T PF15630_consen 24 VEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPS 75 (76)
T ss_dssp SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HH
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCC
Confidence 35678999999999999999998877777765554 999999999999984
No 14
>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=95.79 E-value=0.043 Score=36.32 Aligned_cols=56 Identities=16% Similarity=0.186 Sum_probs=45.3
Q ss_pred HHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc--CCCCchhHHHHHHh
Q 033030 36 LQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSK--GGKLSVEDFLYLIR 92 (129)
Q Consensus 36 I~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~--Rgkis~eDl~F~lR 92 (129)
|+.+.=..|- ..-.++....+-+.|..++.++++.|.+++.. |..++++||-++||
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 57888899999999999999999999999864 55699999999886
No 15
>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=95.68 E-value=0.067 Score=37.46 Aligned_cols=60 Identities=12% Similarity=0.218 Sum_probs=47.8
Q ss_pred HHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCchhHHHHHHhhC
Q 033030 34 KDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKD 94 (129)
Q Consensus 34 ~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg--kis~eDl~F~lR~D 94 (129)
.-|+.+.--.| +..-..+...-+.+++.+|+.+++..|..+|...| .++.+|+.++|++-
T Consensus 17 ~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~ 78 (85)
T cd00076 17 PAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 78 (85)
T ss_pred HHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHC
Confidence 34555555556 67777778888889999999999999999987544 49999999999864
No 16
>PTZ00015 histone H4; Provisional
Probab=95.44 E-value=0.063 Score=38.89 Aligned_cols=61 Identities=7% Similarity=0.187 Sum_probs=46.8
Q ss_pred HHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCchhHHHHHHhhC
Q 033030 33 QKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKD 94 (129)
Q Consensus 33 ~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg--kis~eDl~F~lR~D 94 (129)
..-|+.|.--.|= ..-..+...-+-+++.+|+.+++..|..+|...+ .++.+|+.|++++-
T Consensus 33 k~~IrRLarr~Gv-kRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~ 95 (102)
T PTZ00015 33 KGAIRRLARRGGV-KRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95 (102)
T ss_pred HHHHHHHHHHcCC-ccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhc
Confidence 4456666665554 6666677778888888999999999998886544 49999999999753
No 17
>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=95.37 E-value=0.094 Score=34.31 Aligned_cols=64 Identities=11% Similarity=0.202 Sum_probs=50.4
Q ss_pred ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhhC
Q 033030 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKD 94 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~D 94 (129)
.|.+=++.+.=.++....-..++..+|..++-.++.+++..|..+|...++ |+..|+..++|.|
T Consensus 10 ~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 10 PFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred EEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 344444555544454456778999999999999999999999999976554 9999999999976
No 18
>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=94.96 E-value=0.15 Score=37.22 Aligned_cols=57 Identities=18% Similarity=0.339 Sum_probs=46.9
Q ss_pred HHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhh
Q 033030 36 LQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 93 (129)
Q Consensus 36 I~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~ 93 (129)
|..++--.|. .+=.+..+..+-|++..|..+++..|...|...|+ |+.||+.+++..
T Consensus 7 v~~iLk~~Gv-~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~ 65 (117)
T cd07979 7 IAAILKSMGI-TEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQS 65 (117)
T ss_pred HHHHHHHCCC-CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 5556666676 45678888899999999999999999999976554 999999999764
No 19
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=93.69 E-value=0.24 Score=35.15 Aligned_cols=58 Identities=12% Similarity=0.366 Sum_probs=49.2
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhh
Q 033030 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 93 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~ 93 (129)
-|+.+|--.|+. .-..+....+-+.|-+|+.++...|..+|...|+ |+.+|+..+++.
T Consensus 24 pv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~ 83 (91)
T COG2036 24 PVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKR 83 (91)
T ss_pred HHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHH
Confidence 356677777775 6777888899999999999999999999987665 999999998874
No 20
>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=92.67 E-value=1 Score=30.11 Aligned_cols=46 Identities=20% Similarity=0.193 Sum_probs=36.0
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCchhHHHHHHh
Q 033030 47 PNPLPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIR 92 (129)
Q Consensus 47 ~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~--~Rgkis~eDl~F~lR 92 (129)
.+-.+|....+.+=|.--|.++++.|.+... +|.+++++||=.+||
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 4577888899999999999999999999874 577899999998886
No 21
>smart00417 H4 Histone H4.
Probab=91.59 E-value=0.43 Score=32.65 Aligned_cols=56 Identities=7% Similarity=0.119 Sum_probs=37.5
Q ss_pred HHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCchhHHHHH
Q 033030 34 KDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYL 90 (129)
Q Consensus 34 ~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg--kis~eDl~F~ 90 (129)
.-|.-|.--.| ++.-..+...-+-+++.+|+.+++..|..++...| -++.+|+.|+
T Consensus 17 ~~IrRLaRr~G-vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 17 PAIRRLARRGG-VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred HHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 34444444444 35555555566666777788888888888886544 4999999874
No 22
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=90.62 E-value=1.3 Score=38.11 Aligned_cols=78 Identities=22% Similarity=0.133 Sum_probs=66.7
Q ss_pred HHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC---CchhHHHHHHhhChhhHhHHHHHHHHHHHHH
Q 033030 36 LQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK---LSVEDFLYLIRKDLPKLNRCTELLSMQEELK 112 (129)
Q Consensus 36 I~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk---is~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik 112 (129)
+.-+|.-+|| ....+.|++-+....+.....++...|.+|.. .+--|+.|+|++.+.|-+|.+..|++=.++|
T Consensus 81 edliflir~D----rakv~rL~tyl~~kdlR~k~ak~qdaa~~~~~~~~np~Ad~edlle~~~~k~~~~r~~~~~mri~k 156 (352)
T KOG3902|consen 81 EDLIFLIRHD----RAKVNRLVTYLSWKDLRGKFAKAQDAAMRRKQNPCNPQADFEDLLENHPSKIARMRKHLKDMRILK 156 (352)
T ss_pred HHHHHHhhcc----HHHHHHHHHHHHHHHHHHhhhhhhHHHHhhccCCCCCCccHHHHHHhCccchhhhhhhhhHHHHHH
Confidence 3446778888 67888899999999999888899888776543 6678999999999999999999999999999
Q ss_pred HHHhh
Q 033030 113 QARKA 117 (129)
Q Consensus 113 ~Ark~ 117 (129)
+|-|.
T Consensus 157 ~~~k~ 161 (352)
T KOG3902|consen 157 RALKI 161 (352)
T ss_pred HHhhc
Confidence 99765
No 23
>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=90.28 E-value=1.2 Score=33.33 Aligned_cols=57 Identities=18% Similarity=0.330 Sum_probs=42.6
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHh
Q 033030 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 92 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR 92 (129)
=|.+++-..|= .+=.+..+..+-|++..|+.+++..|..+|...|+ |..+|+..++.
T Consensus 17 ~i~~iL~~~Gv-~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~ 75 (129)
T PF02291_consen 17 VIHLILKSMGV-TEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQ 75 (129)
T ss_dssp HHHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHH
T ss_pred HHHHHHHHcCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHH
Confidence 35555555554 44577888899999999999999999999976654 99999999987
No 24
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=90.03 E-value=0.84 Score=35.74 Aligned_cols=63 Identities=11% Similarity=0.242 Sum_probs=48.6
Q ss_pred ccHHHHHHHHh-hhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc--CCCCchhHHHHHHhh
Q 033030 31 VFQKDLQHMMY-GFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSK--GGKLSVEDFLYLIRK 93 (129)
Q Consensus 31 ~f~~EI~~mMy-~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~--Rgkis~eDl~F~lR~ 93 (129)
+-..-|..+|- +.=-...-..+.-..|.|-|-+||.=++.+|.+...+ |.-|.-|||+++|-.
T Consensus 33 LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~t 98 (168)
T KOG0869|consen 33 LPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMST 98 (168)
T ss_pred ccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHH
Confidence 33555666663 3333445567788899999999999999999988764 666999999999986
No 25
>smart00428 H3 Histone H3.
Probab=88.71 E-value=3.1 Score=30.19 Aligned_cols=64 Identities=13% Similarity=0.218 Sum_probs=49.6
Q ss_pred ccccHHHHHHHHhhhCC--CCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHh
Q 033030 29 RGVFQKDLQHMMYGFGD--DPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 92 (129)
Q Consensus 29 k~~f~~EI~~mMy~fGD--~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR 92 (129)
|-.|..=++.++--|.+ .-.=..+....+.+..-.|++++...|..+|...++ |..+|+..+.|
T Consensus 32 k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 32 KAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred cccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 44566666666655543 446778899999999999999999999999987665 88899976644
No 26
>PLN00158 histone H2B; Provisional
Probab=88.26 E-value=6.2 Score=29.32 Aligned_cols=87 Identities=9% Similarity=0.157 Sum_probs=54.4
Q ss_pred CCCCCCcCCCCCCCCcccccccccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcC--CCCch
Q 033030 7 GQSSKSKAGSSQPYETTSFKRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKG--GKLSV 84 (129)
Q Consensus 7 ~~~~~~~~~~~~~~~~~~~~~kk~~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~R--gkis~ 84 (129)
+||.++-.-+..-.+....++++..|.-=|-..+-..-=..--...+..+|.-+|.+..-.|..+|..++... ..|+.
T Consensus 4 ~~~~k~~~~~~~~~~kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~Tlts 83 (116)
T PLN00158 4 TPSKKPAKKAAKGAKKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTS 83 (116)
T ss_pred CcchhhhhhccccccccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCH
Confidence 4555543333333332223334456655554444332222334677888999999999999999999998643 34999
Q ss_pred hHHHHHHhh
Q 033030 85 EDFLYLIRK 93 (129)
Q Consensus 85 eDl~F~lR~ 93 (129)
.+|--++|-
T Consensus 84 rEIqtAvrL 92 (116)
T PLN00158 84 REIQTAVRL 92 (116)
T ss_pred HHHHHHHHH
Confidence 999988874
No 27
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=83.29 E-value=4.5 Score=34.26 Aligned_cols=47 Identities=19% Similarity=0.164 Sum_probs=40.6
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCchhHHHHHHhh
Q 033030 47 PNPLPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIRK 93 (129)
Q Consensus 47 ~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~--~Rgkis~eDl~F~lR~ 93 (129)
..-.++.+..+-+-|..++.++++.|.+.+. +|.+++++||-.+||-
T Consensus 15 ~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~ 63 (343)
T cd08050 15 DSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRL 63 (343)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHH
Confidence 4667788888888999999999999999986 4667999999999984
No 28
>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=82.25 E-value=1.7 Score=35.24 Aligned_cols=82 Identities=23% Similarity=0.194 Sum_probs=31.0
Q ss_pred cHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChhhHh-HHHHHHHHHHH
Q 033030 32 FQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLN-RCTELLSMQEE 110 (129)
Q Consensus 32 f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~Kl~-Rl~~lL~~k~~ 110 (129)
+.+=|..++--+| ...+.++.+.||---+.++|.+|+..+..+|..|-...-+|..+.+++|..+-- .|.+.-...++
T Consensus 49 L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l~~~e~~~~e 127 (264)
T PF05236_consen 49 LQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFLEQLEKEEEE 127 (264)
T ss_dssp HHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH--------------------------------------
T ss_pred HHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHHHHHHHHHHH
Confidence 3444555555555 677999999999999999999999999999988877677888888899865443 34444444444
Q ss_pred HHHH
Q 033030 111 LKQA 114 (129)
Q Consensus 111 ik~A 114 (129)
++..
T Consensus 128 rr~~ 131 (264)
T PF05236_consen 128 RREE 131 (264)
T ss_dssp ----
T ss_pred HHHH
Confidence 4333
No 29
>PLN00121 histone H3; Provisional
Probab=79.65 E-value=9.3 Score=29.03 Aligned_cols=61 Identities=15% Similarity=0.205 Sum_probs=48.1
Q ss_pred cHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHh
Q 033030 32 FQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 92 (129)
Q Consensus 32 f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR 92 (129)
|..=++.++-.|++.-.=..+.+..+.+..-.||+++...+..+|...++ |...|+..+.|
T Consensus 68 F~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 68 FQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred HHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 44445555666676677888999999999999999999999999987776 66789876643
No 30
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=78.35 E-value=5.6 Score=36.54 Aligned_cols=58 Identities=26% Similarity=0.282 Sum_probs=46.6
Q ss_pred cHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhh--hcCCCCchhHHHHHHhh
Q 033030 32 FQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIG--SKGGKLSVEDFLYLIRK 93 (129)
Q Consensus 32 f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A--~~Rgkis~eDl~F~lR~ 93 (129)
+.+.+.+++ |- .+-.+|...++.+-|...|.++++.|.+.- +.|.+++++|+-.+||-
T Consensus 16 s~k~vAEsl---Gi-~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~ 75 (576)
T KOG2549|consen 16 SVKVVAESL---GI-TNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRS 75 (576)
T ss_pred HHHHHHHHh---Cc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhh
Confidence 444555544 33 567899999999999999999999998875 35778999999999984
No 31
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=74.42 E-value=32 Score=25.33 Aligned_cols=83 Identities=14% Similarity=0.122 Sum_probs=60.3
Q ss_pred cccccccc-HHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCchhHHHHHHhhChhhHhHH
Q 033030 25 FKRKRGVF-QKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKDLPKLNRC 101 (129)
Q Consensus 25 ~~~kk~~f-~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg--kis~eDl~F~lR~D~~Kl~Rl 101 (129)
.++++.-| ..-|..+|-.--|.-.-..-|--++-.-+--||+.|+...++.|...+ +++.|-|.-++-+|+ |+.-|
T Consensus 17 ~~~~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sde-kFdFL 95 (113)
T COG5247 17 QKKKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDE-KFDFL 95 (113)
T ss_pred hhhhhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhH-HHHHH
Confidence 34556556 788999998877765555555556666777788888888888875443 499999999988886 67777
Q ss_pred HHHHHHH
Q 033030 102 TELLSMQ 108 (129)
Q Consensus 102 ~~lL~~k 108 (129)
++.+..+
T Consensus 96 ~~~~~~~ 102 (113)
T COG5247 96 KNMEQFK 102 (113)
T ss_pred HHHHHhc
Confidence 7777643
No 32
>PTZ00018 histone H3; Provisional
Probab=74.24 E-value=15 Score=27.83 Aligned_cols=61 Identities=15% Similarity=0.205 Sum_probs=47.1
Q ss_pred cHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHh
Q 033030 32 FQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 92 (129)
Q Consensus 32 f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR 92 (129)
|..=++.+.--|+..-.=..+.+..+.+..-.||+++...+..+|...++ |...|+..+.|
T Consensus 68 F~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 68 FQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred HHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 44444555555666667788999999999999999999999999877666 66789876643
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=73.16 E-value=17 Score=26.71 Aligned_cols=42 Identities=10% Similarity=0.188 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhh--cCCCCchhHHHHHHhhChh
Q 033030 55 ALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIRKDLP 96 (129)
Q Consensus 55 ~l~EeIv~~~I~~l~~~A~~~A~--~Rgkis~eDl~F~lR~D~~ 96 (129)
-++-.++-....+++..|.+.|. .+.+|+.+||.-++|+|..
T Consensus 45 VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~E 88 (115)
T cd00074 45 VYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRNDEE 88 (115)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHH
Confidence 33333333333445555555554 2445999999999999975
No 34
>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=72.36 E-value=4 Score=27.55 Aligned_cols=44 Identities=18% Similarity=0.291 Sum_probs=34.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--C-CchhHHH
Q 033030 45 DDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--K-LSVEDFL 88 (129)
Q Consensus 45 D~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg--k-is~eDl~ 88 (129)
+...-..+++.++-+++.-|+.+-+.+|...|...| . +.+|||-
T Consensus 16 ~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LE 62 (72)
T PF09415_consen 16 DKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLE 62 (72)
T ss_dssp TT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHH
T ss_pred CCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence 444567889999999999999999999999887665 4 7888875
No 35
>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=70.20 E-value=27 Score=27.47 Aligned_cols=73 Identities=18% Similarity=0.163 Sum_probs=51.6
Q ss_pred HHHHHHHHhhhCCCC---CCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChhh-HhHHHHHH
Q 033030 33 QKDLQHMMYGFGDDP---NPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPK-LNRCTELL 105 (129)
Q Consensus 33 ~~EI~~mMy~fGD~~---~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~K-l~Rl~~lL 105 (129)
..-|...|..+|=.. ...++.+.+|-..+.++|.+|+..+..+|..|-...-+|..+.+++|..+ +..|.+.-
T Consensus 47 ~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~~~e 123 (212)
T cd08045 47 PSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLEQLE 123 (212)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHHHHH
Confidence 445555554433322 56899999999999999999999999999877554467777788888544 33344333
No 36
>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=66.31 E-value=41 Score=23.30 Aligned_cols=58 Identities=16% Similarity=0.277 Sum_probs=46.7
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc-----CCCCchhHHHHHHhh
Q 033030 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSK-----GGKLSVEDFLYLIRK 93 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~-----Rgkis~eDl~F~lR~ 93 (129)
-|+.+|=..-+ ..|.+..+.+|--+-..|+-+|+..|..+-.. +|.|..+.|.=+.|+
T Consensus 21 ~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr 83 (85)
T cd08048 21 AIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR 83 (85)
T ss_pred HHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence 35555655555 78999999999999999999999999998754 567888888777664
No 37
>PLN00160 histone H3; Provisional
Probab=65.61 E-value=37 Score=24.32 Aligned_cols=64 Identities=9% Similarity=0.105 Sum_probs=49.2
Q ss_pred ccccHHHHHHHHhhhC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHh
Q 033030 29 RGVFQKDLQHMMYGFG-DDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 92 (129)
Q Consensus 29 k~~f~~EI~~mMy~fG-D~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR 92 (129)
|-.|..=++.+.-.|. +.-.=..+....+.+..-.|++.+...|..+|...++ |...|+..+.|
T Consensus 24 k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 24 RLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred cccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 4567666666665553 4356678889999999999999999999999877676 66789876643
No 38
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=64.89 E-value=24 Score=25.81 Aligned_cols=36 Identities=31% Similarity=0.406 Sum_probs=27.6
Q ss_pred hcCCCCchhHHHHHHhhChhhHhHHHHHHHHHHHHHH
Q 033030 77 SKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQ 113 (129)
Q Consensus 77 ~~Rgkis~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik~ 113 (129)
-+|| +++|+|-=+-.=||--|.++++++.+.+.+++
T Consensus 20 lrrG-~sveeI~e~T~ID~wFL~~i~~Iv~~e~~L~~ 55 (123)
T PF02787_consen 20 LRRG-YSVEEIHELTKIDPWFLEQIKNIVDMEKELKE 55 (123)
T ss_dssp HHTT-B-HHHHHHHH---HHHHHHHHHHHHHHHHHHH
T ss_pred HHcC-CCHHHHHHHHCccHHHHHHHHHHHHHHHHHHH
Confidence 3566 79999999999999999999999999887777
No 39
>PLN00161 histone H3; Provisional
Probab=63.94 E-value=42 Score=25.51 Aligned_cols=62 Identities=8% Similarity=0.109 Sum_probs=45.4
Q ss_pred ccHHHHHHHHhhhC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHh
Q 033030 31 VFQKDLQHMMYGFG-DDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 92 (129)
Q Consensus 31 ~f~~EI~~mMy~fG-D~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR 92 (129)
-|..=+++++--|. +.-.=..+++..+.|..-.||+++...|.-+|...++ |-..|+..+.|
T Consensus 60 PF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 60 PFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 34444555555553 2245568889999999999999999999999877776 66788876644
No 40
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=63.60 E-value=42 Score=25.95 Aligned_cols=59 Identities=17% Similarity=0.274 Sum_probs=48.6
Q ss_pred HHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHh
Q 033030 33 QKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 92 (129)
Q Consensus 33 ~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR 92 (129)
.+-|.+|+...|= ++-.+--+.-|-|+...|.+.++..|.=.|...++ |.+||+.-+++
T Consensus 16 a~~i~~iL~s~GI-~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~ 76 (148)
T KOG3334|consen 16 ARVIASILKSLGI-QEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQ 76 (148)
T ss_pred HHHHHHHHHHcCc-cccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHH
Confidence 3457777777775 66777888888899999999999999988876555 99999998876
No 41
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=62.38 E-value=37 Score=29.24 Aligned_cols=77 Identities=12% Similarity=0.205 Sum_probs=59.7
Q ss_pred ccHHHHHHHHh--hhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhhChhhHhHHHHHHH
Q 033030 31 VFQKDLQHMMY--GFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKDLPKLNRCTELLS 106 (129)
Q Consensus 31 ~f~~EI~~mMy--~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~D~~Kl~Rl~~lL~ 106 (129)
....-|.+|++ ||++ -..-..+-+-++|+.||.++..++.......|+ ++.-|+.+.|++=--|++-|..++.
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 VLAPVVSNLLKTKGFDS---ISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIKVSSLYAYFQ 82 (323)
T ss_pred HHHHHHHHHHHHhCchH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCChhhhHHHHH
Confidence 55667788886 5555 334455567788999999999988887765554 9999999999999999999998887
Q ss_pred HHHH
Q 033030 107 MQEE 110 (129)
Q Consensus 107 ~k~~ 110 (129)
-+..
T Consensus 83 ~~~~ 86 (323)
T KOG4336|consen 83 KQEF 86 (323)
T ss_pred hccc
Confidence 5543
No 42
>PTZ00463 histone H2B; Provisional
Probab=58.96 E-value=73 Score=23.73 Aligned_cols=44 Identities=16% Similarity=0.231 Sum_probs=36.3
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCchhHHHHHHh
Q 033030 49 PLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIR 92 (129)
Q Consensus 49 P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg--kis~eDl~F~lR 92 (129)
-...+..+|.-+|.+-.-.+..+|..+|...+ -|+..||-.++|
T Consensus 47 IS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr 92 (117)
T PTZ00463 47 ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR 92 (117)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh
Confidence 46778888888888888889999999986443 499999988887
No 43
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=56.80 E-value=55 Score=26.87 Aligned_cols=83 Identities=17% Similarity=0.245 Sum_probs=60.0
Q ss_pred cccccccccH-HHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhhChhhHhH
Q 033030 24 SFKRKRGVFQ-KDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKDLPKLNR 100 (129)
Q Consensus 24 ~~~~kk~~f~-~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~D~~Kl~R 100 (129)
.+++.+..|- .-|+.+|-.=-|.-.-..-+=-++-.-+--||..||..+++++..||. ++.+-|.-++-+|+ |+.-
T Consensus 6 ~~~~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~-~FdF 84 (224)
T KOG1659|consen 6 SFKKYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDP-KFDF 84 (224)
T ss_pred hhhhhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccc-hhHH
Confidence 3455555664 778888877666544333333466677778999999999999988874 99999999998886 4666
Q ss_pred HHHHHHH
Q 033030 101 CTELLSM 107 (129)
Q Consensus 101 l~~lL~~ 107 (129)
|++++..
T Consensus 85 Lk~~v~~ 91 (224)
T KOG1659|consen 85 LKEVVEK 91 (224)
T ss_pred HHHHHHh
Confidence 6666543
No 44
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=54.37 E-value=25 Score=22.53 Aligned_cols=44 Identities=18% Similarity=0.285 Sum_probs=36.7
Q ss_pred chhHHHHHHhhChhhHhHHHHHHHHHHHHHHHHh-hcccchhhhh
Q 033030 83 SVEDFLYLIRKDLPKLNRCTELLSMQEELKQARK-AFEVDEEKLA 126 (129)
Q Consensus 83 s~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik~Ark-~fd~de~~~~ 126 (129)
++.+|+=.+++||.=..+|.......+.++-|+. .|+-+.+++.
T Consensus 3 ~l~~Fl~~~~~d~~L~~~l~~~~~~e~~~~lA~~~Gf~ft~~el~ 47 (64)
T TIGR03798 3 QLKAFLEKVKTDPDLREKLKAAEDPEDRVAIAKEAGFEFTGEDLK 47 (64)
T ss_pred HHHHHHHHHHcCHHHHHHHHHcCCHHHHHHHHHHcCCCCCHHHHH
Confidence 3578888899999999999998888999999986 7887777764
No 45
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=51.58 E-value=57 Score=27.92 Aligned_cols=83 Identities=16% Similarity=0.323 Sum_probs=41.3
Q ss_pred ccccccccccHHHHHHHHhhhCCCC---CCcHHHHH---HHHHHHHHHHHHHHHHHHHhhhcCCC-CchhHHHHH---Hh
Q 033030 23 TSFKRKRGVFQKDLQHMMYGFGDDP---NPLPETVA---LVEDIVVEYVTDLAHKAQDIGSKGGK-LSVEDFLYL---IR 92 (129)
Q Consensus 23 ~~~~~kk~~f~~EI~~mMy~fGD~~---~P~~ETv~---l~EeIv~~~I~~l~~~A~~~A~~Rgk-is~eDl~F~---lR 92 (129)
++..|+.+.|. .+||+. -|.||-.- ==-|+-+.++.--+....+.-. .+ .-++||.-+ ||
T Consensus 33 Sp~~rr~~rY~--------~C~dNHGikPP~PEQYLTPLQQKEV~iRHLkakLkes~~~l~--dRetEI~eLksQL~RMr 102 (305)
T PF15290_consen 33 SPTMRRSGRYM--------SCGDNHGIKPPNPEQYLTPLQQKEVCIRHLKAKLKESENRLH--DRETEIDELKSQLARMR 102 (305)
T ss_pred CCCCCCCCcee--------ecccCCCCCCCCHHHhcChHHHHHHHHHHHHHHHHHHHHHHH--hhHHHHHHHHHHHHHHH
Confidence 44455665553 588874 47776211 0122333333333333322111 12 446777554 45
Q ss_pred hC--hhhHhHHHHHHHHHHHHHHHH
Q 033030 93 KD--LPKLNRCTELLSMQEELKQAR 115 (129)
Q Consensus 93 ~D--~~Kl~Rl~~lL~~k~~ik~Ar 115 (129)
-| ..-.-||+--|-+|+-+|+.+
T Consensus 103 EDWIEEECHRVEAQLALKEARkEIk 127 (305)
T PF15290_consen 103 EDWIEEECHRVEAQLALKEARKEIK 127 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55 466777777777666555543
No 46
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=50.51 E-value=58 Score=28.44 Aligned_cols=57 Identities=12% Similarity=0.304 Sum_probs=45.3
Q ss_pred HHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhh
Q 033030 36 LQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 93 (129)
Q Consensus 36 I~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~ 93 (129)
+.|+.=+.|-...+.. .-.+++++++.||+++-..|..++-.-|+ ..+-|++-+|-.
T Consensus 35 vaQIcqslg~~~~~~s-ale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~d 93 (353)
T KOG2389|consen 35 VAQICQSLGYSSTQNS-ALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQD 93 (353)
T ss_pred HHHHHHhcCCcccccH-HHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHH
Confidence 5566667777666665 56799999999999999999999877676 778888887764
No 47
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=49.11 E-value=35 Score=20.55 Aligned_cols=42 Identities=21% Similarity=0.328 Sum_probs=34.5
Q ss_pred hhHHHHHHhhChhhHhHHHHHHHHHHHHHHHHh-hcccchhhh
Q 033030 84 VEDFLYLIRKDLPKLNRCTELLSMQEELKQARK-AFEVDEEKL 125 (129)
Q Consensus 84 ~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik~Ark-~fd~de~~~ 125 (129)
++.|+=.+++||.-..+|...-...+.++-|+. .|+-+.+++
T Consensus 6 l~~Fl~~~~~d~~l~~~l~~~~~~~e~~~lA~~~Gy~ft~~el 48 (49)
T PF07862_consen 6 LKAFLEKVKSDPELREQLKACQNPEEVVALAREAGYDFTEEEL 48 (49)
T ss_pred HHHHHHHHhcCHHHHHHHHhcCCHHHHHHHHHHcCCCCCHHHh
Confidence 567888888999999999998888899998886 677776665
No 48
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=47.63 E-value=69 Score=25.34 Aligned_cols=47 Identities=15% Similarity=0.176 Sum_probs=39.5
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc--CCCCchhHHHHHHhh
Q 033030 47 PNPLPETVALVEDIVVEYVTDLAHKAQDIGSK--GGKLSVEDFLYLIRK 93 (129)
Q Consensus 47 ~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~--Rgkis~eDl~F~lR~ 93 (129)
..-..|....|-.-..-|++.|+..|..+|.. |..|+.+|++-+|++
T Consensus 29 vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~E 77 (172)
T KOG0870|consen 29 VSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDE 77 (172)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHH
Confidence 34566777888888999999999999999963 455999999999996
No 49
>smart00414 H2A Histone 2A.
Probab=47.16 E-value=50 Score=23.79 Aligned_cols=41 Identities=22% Similarity=0.203 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChhh
Q 033030 56 LVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPK 97 (129)
Q Consensus 56 l~EeIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~K 97 (129)
.+=|++...|.++.-++..-. .+.+|+.+++.-++|+|..=
T Consensus 38 AvLEYLtaEILeLagn~a~~~-k~~rItp~hi~lAi~nD~EL 78 (106)
T smart00414 38 AVLEYLTAEVLELAGNAARDN-KKRRITPRHLQLAIRNDEEL 78 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHhc-CCCccchHHHhhhccCCHHH
Confidence 344555555666666655432 34469999999999999753
No 50
>smart00427 H2B Histone H2B.
Probab=46.74 E-value=88 Score=22.12 Aligned_cols=45 Identities=13% Similarity=0.219 Sum_probs=36.1
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCchhHHHHHHhh
Q 033030 49 PLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRK 93 (129)
Q Consensus 49 P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg--kis~eDl~F~lR~ 93 (129)
-..++..+|.-+|.+..-.+..+|.+++...+ .|+..+|--++|-
T Consensus 20 iS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl 66 (89)
T smart00427 20 ISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRL 66 (89)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 34567788888888888889999999986433 4999999988874
No 51
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=44.96 E-value=1.3e+02 Score=22.63 Aligned_cols=65 Identities=9% Similarity=0.206 Sum_probs=48.7
Q ss_pred cccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHh
Q 033030 28 KRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 92 (129)
Q Consensus 28 kk~~f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR 92 (129)
++..|..=+.+.+.+.-=.---..+...+|.-+|.+.+-.+..+|.++|..+++ |+-.++.-++|
T Consensus 35 ~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~r 101 (127)
T KOG1744|consen 35 RKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVR 101 (127)
T ss_pred ccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHH
Confidence 445666556666655443344778999999999999999999999999987776 77777766665
No 52
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=44.16 E-value=1.6e+02 Score=23.75 Aligned_cols=51 Identities=20% Similarity=0.221 Sum_probs=35.2
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhHH
Q 033030 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDF 87 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgkis~eDl 87 (129)
++..++-.+--......+.....+++|..|+--+.+-|.+... + .+..+||
T Consensus 20 ~~~~~~~~~~~~~~~~~~~~~~r~~Lv~~~l~LV~~iA~~y~~-~-g~~~~DL 70 (264)
T PRK07122 20 DVPEMFRELAGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDG-R-GEPRDDL 70 (264)
T ss_pred hHHHHHHHHHhccCCCHHHHHHHHHHHHHhHHHHHHHHHHHHh-C-CCCHHHH
Confidence 4455554443344466677778899999999988888888753 3 3778887
No 53
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=44.11 E-value=59 Score=23.40 Aligned_cols=68 Identities=18% Similarity=0.295 Sum_probs=38.6
Q ss_pred cccccccHHHHHHH-------HhhhCCCCCC----cHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCchhHHHHHHh
Q 033030 26 KRKRGVFQKDLQHM-------MYGFGDDPNP----LPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIR 92 (129)
Q Consensus 26 ~~kk~~f~~EI~~m-------My~fGD~~~P----~~ETv~l~EeIv~~~I~~l~~~A~~~A~--~Rgkis~eDl~F~lR 92 (129)
|+.+..++..|+.+ +---|.++.- ..||..+ ..+||.+.+.-|+-.+. .|..++.-|+++.|.
T Consensus 17 KrHRK~LsDnIqgitKpaIRRlARr~GVkRi~G~~yeE~~~~----~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LK 92 (103)
T KOG3467|consen 17 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGV----LKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALK 92 (103)
T ss_pred HHHHHHHHhhccccchHHHHHHHHhcCcchhchhhHHHHHHH----HHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHH
Confidence 34444666665522 2233444433 3455544 45555555555554443 456699999999998
Q ss_pred hChhh
Q 033030 93 KDLPK 97 (129)
Q Consensus 93 ~D~~K 97 (129)
+.-.+
T Consensus 93 R~G~~ 97 (103)
T KOG3467|consen 93 RQGRT 97 (103)
T ss_pred HcCce
Confidence 76544
No 54
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=43.47 E-value=56 Score=24.91 Aligned_cols=38 Identities=21% Similarity=0.293 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcC--CC---CchhHHHHHHhh
Q 033030 56 LVEDIVVEYVTDLAHKAQDIGSKG--GK---LSVEDFLYLIRK 93 (129)
Q Consensus 56 l~EeIv~~~I~~l~~~A~~~A~~R--gk---is~eDl~F~lR~ 93 (129)
-+-++.+.|-++++..|.-.|... |. +++||+..++-.
T Consensus 39 QLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 39 QLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 345688999999999999888754 43 888999998864
No 55
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=41.52 E-value=24 Score=25.53 Aligned_cols=32 Identities=19% Similarity=0.117 Sum_probs=26.9
Q ss_pred hhHHHHHHhhChhhHhHHHHHHHHHHHHHHHH
Q 033030 84 VEDFLYLIRKDLPKLNRCTELLSMQEELKQAR 115 (129)
Q Consensus 84 ~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik~Ar 115 (129)
.=+|-|+.||||.=-.-|+++|....-|+++-
T Consensus 64 ~mlLEwlrR~~p~wd~eL~eiLft~k~i~e~g 95 (103)
T COG3461 64 AMLLEWLRRHDPAWDAELHEILFTTKPIKELG 95 (103)
T ss_pred HHHHHHHHHcCchHHHHHHHHHhcCCcHhHHH
Confidence 34788999999999999999999888787663
No 56
>PTZ00252 histone H2A; Provisional
Probab=37.82 E-value=79 Score=24.04 Aligned_cols=37 Identities=19% Similarity=0.185 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHhh-hcCCCCchhHHHHHHhhChh
Q 033030 60 IVVEYVTDLAHKAQDIG-SKGGKLSVEDFLYLIRKDLP 96 (129)
Q Consensus 60 Iv~~~I~~l~~~A~~~A-~~Rgkis~eDl~F~lR~D~~ 96 (129)
+|...|.+|.-+|..-. ..+.+|+.+.|.-++|||..
T Consensus 58 YLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDeE 95 (134)
T PTZ00252 58 YLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDDD 95 (134)
T ss_pred HHHHHHHHHHHHHHHhccCCcccccHHHHHhhccChHH
Confidence 33333555554444321 22346999999999999964
No 57
>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=37.48 E-value=1.1e+02 Score=20.37 Aligned_cols=29 Identities=28% Similarity=0.328 Sum_probs=23.2
Q ss_pred CCCCchhHHHHHHh-hChhhHhHHHHHHHH
Q 033030 79 GGKLSVEDFLYLIR-KDLPKLNRCTELLSM 107 (129)
Q Consensus 79 Rgkis~eDl~F~lR-~D~~Kl~Rl~~lL~~ 107 (129)
.+.++.+|..=+++ -|..++.||.++|.-
T Consensus 51 ~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~ 80 (86)
T PF04433_consen 51 NKYLTKTDARKLIKGIDVNKIRRIYDFLER 80 (86)
T ss_dssp TS---HHHHHHHTTSSSHHHHHHHHHHHHH
T ss_pred CCcccHHHHHHHccccCHHHHHHHHHHHHH
Confidence 45699999999999 599999999999964
No 58
>PHA00724 hypothetical protein
Probab=36.72 E-value=26 Score=24.28 Aligned_cols=35 Identities=29% Similarity=0.283 Sum_probs=30.4
Q ss_pred HHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Q 033030 39 MMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQ 73 (129)
Q Consensus 39 mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~ 73 (129)
||-+.||+-+-.---+-++--|+++|+.++.--.+
T Consensus 1 mmsalgdviyilgil~p~lgli~rnyl~nlmgfvm 35 (83)
T PHA00724 1 MMSALGDVIYILGILIPLLGLIVRNYLVNLMGFVM 35 (83)
T ss_pred CcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78899999988888888999999999999976554
No 59
>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=34.76 E-value=1.6e+02 Score=20.65 Aligned_cols=60 Identities=15% Similarity=0.251 Sum_probs=42.1
Q ss_pred HHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC---CCchhHHHHHHhh
Q 033030 34 KDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG---KLSVEDFLYLIRK 93 (129)
Q Consensus 34 ~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rg---kis~eDl~F~lR~ 93 (129)
.-|+.+|=.+=....+.+..+-+|--+-.-|+-||+..|..+....+ .|....|.-+.|+
T Consensus 27 ~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rr 89 (90)
T PF04719_consen 27 AAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRR 89 (90)
T ss_dssp HHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHh
Confidence 35677765554447888888999999999999999999999986544 5888887766654
No 60
>PTZ00017 histone H2A; Provisional
Probab=33.75 E-value=97 Score=23.47 Aligned_cols=39 Identities=23% Similarity=0.239 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChh
Q 033030 57 VEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLP 96 (129)
Q Consensus 57 ~EeIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~ 96 (129)
+=|++...|.+|.-++..-. .+.+|+..+|.-++|+|..
T Consensus 57 VLEYLtaEILELAgNaa~d~-kk~RItPrHi~lAI~nDeE 95 (134)
T PTZ00017 57 VLEYLTAEVLELAGNAAKDN-KKKRITPRHIQLAIRNDEE 95 (134)
T ss_pred HHHHHHHHHHHHHHHHHHhc-CCCeecHHHHHhhccCcHH
Confidence 33444444666665554432 2345999999999999975
No 61
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=32.46 E-value=1.3e+02 Score=23.45 Aligned_cols=44 Identities=20% Similarity=0.357 Sum_probs=37.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhh
Q 033030 50 LPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 93 (129)
Q Consensus 50 ~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~ 93 (129)
..|+..++-+--++||.-+.+.|.+++....| |..|.++=+|-+
T Consensus 33 akeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~ 78 (156)
T KOG0871|consen 33 AKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALEN 78 (156)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHH
Confidence 45788899999999999999999999976543 998888887765
No 62
>cd08047 TAF7 TATA Binding Protein (TBP) Associated Factor 7 (TAF7) 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 7 (TAF7) 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 preinitiation 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
Probab=31.65 E-value=12 Score=28.42 Aligned_cols=32 Identities=22% Similarity=0.403 Sum_probs=22.8
Q ss_pred CCCCcccccc--ccccc-HHHHHHHHhhhCCCCCC
Q 033030 18 QPYETTSFKR--KRGVF-QKDLQHMMYGFGDDPNP 49 (129)
Q Consensus 18 ~~~~~~~~~~--kk~~f-~~EI~~mMy~fGD~~~P 49 (129)
.|.++..-|- ++.+| +.||.|||+.+++...+
T Consensus 57 LPtiiEs~KT~D~k~~yKtaDI~QMliv~~~~~~~ 91 (162)
T cd08047 57 LPTIIESHKTLDKKNLYKTADISQMLIVYEPDDSE 91 (162)
T ss_pred cCceeeeeeccccCceEEecChhhEEEEecCCCch
Confidence 3555533332 67788 99999999999996644
No 63
>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=31.35 E-value=1.4e+02 Score=18.98 Aligned_cols=34 Identities=18% Similarity=0.182 Sum_probs=29.4
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 033030 46 DPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKG 79 (129)
Q Consensus 46 ~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~R 79 (129)
..-..+-.+.||-=....||.+++..|++.+..|
T Consensus 17 ~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r 50 (51)
T PF03540_consen 17 FQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIR 50 (51)
T ss_pred CCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3557788899999999999999999999998655
No 64
>PLN00156 histone H2AX; Provisional
Probab=31.20 E-value=1.3e+02 Score=23.05 Aligned_cols=37 Identities=19% Similarity=0.223 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChh
Q 033030 59 DIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLP 96 (129)
Q Consensus 59 eIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~ 96 (129)
|+|...|.+|.-+|..-. .+.+|+.+.|.-++|+|..
T Consensus 61 EYLtaEVLELAgNaa~d~-kk~RItPrHi~lAIrnDeE 97 (139)
T PLN00156 61 EYLAAEVLELAGNAARDN-KKNRIVPRHIQLAVRNDEE 97 (139)
T ss_pred HHHHHHHHHHHHHHHHHc-CCCcCcHHHHHhhccCcHH
Confidence 444444666666654432 2446999999999999975
No 65
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=30.80 E-value=1.2e+02 Score=26.88 Aligned_cols=46 Identities=17% Similarity=0.234 Sum_probs=35.1
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHhh--hcCCCCchhHHHHHHhh
Q 033030 48 NPLPETVALVEDIVVEYVTDLAHKAQDIG--SKGGKLSVEDFLYLIRK 93 (129)
Q Consensus 48 ~P~~ETv~l~EeIv~~~I~~l~~~A~~~A--~~Rgkis~eDl~F~lR~ 93 (129)
+-.++....+--=+---|.++|++|.+.- +.|..++++|+-++||.
T Consensus 22 Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~ 69 (450)
T COG5095 22 NIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRS 69 (450)
T ss_pred ccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHh
Confidence 45566666665556667899999998764 35667999999999995
No 66
>PF09454 Vps23_core: Vps23 core domain; InterPro: IPR017916 The Endosomal Sorting Complex Required for Transport (ESCRT) complexes form the machinery driving protein sorting from endosomes to lysosomes. ESCRT complexes are central to receptor down-regulation, lysosome biogenesis, and budding of HIV. Yeast ESCRT-I consists of three protein subunits, VPS23, VPS28, and VPS37. In humans, ESCRT-I comprises TSG101, VPS28, and one of four potential human VPS37 homologues. The main role of ESCRT-I is to recognise ubiquitinated cargo via the UEV domain of the VPS23/TSG101 subunit. The assembly of the ESCRT-I complex is directed by the C-terminal steadiness box (SB) of VPS23, the N-terminal half of VPS28, and the C-terminal half of VPS37. The structure is primarily composed of three long, parallel helical hairpins, each corresponding to a different subunit. The additional domains and motifs extending beyond the core serve as gripping tools for ESCRT-I critical functions [, ]. This entry represents the Steadiness box domain.; PDB: 2CAZ_A 2F66_D 2F6M_A 2P22_A.
Probab=30.55 E-value=1.6e+02 Score=19.29 Aligned_cols=45 Identities=18% Similarity=0.189 Sum_probs=31.9
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhh
Q 033030 49 PLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRK 93 (129)
Q Consensus 49 P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~ 93 (129)
+.+-..+++|-..-++-++-+..+..-|-.+|+|+++.++=.+|.
T Consensus 7 ~~~l~~Ql~el~Aed~AieDtiy~L~~al~~g~I~~d~~lK~vR~ 51 (65)
T PF09454_consen 7 EDPLSNQLYELVAEDHAIEDTIYYLDRALQRGSIDLDTFLKQVRS 51 (65)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 455566777777777777777777777777899999988766653
No 67
>PLN00157 histone H2A; Provisional
Probab=29.79 E-value=1.2e+02 Score=22.92 Aligned_cols=37 Identities=19% Similarity=0.223 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChh
Q 033030 59 DIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLP 96 (129)
Q Consensus 59 eIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~ 96 (129)
|++..-|.+|.-++..-. .+.+|+.++|.-++|+|..
T Consensus 58 EYLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~nDeE 94 (132)
T PLN00157 58 EYLAAEVLELAGNAARDN-KKSRIVPRHIQLAVRNDEE 94 (132)
T ss_pred HHHHHHHHHHHHHHHHhc-CCccccHHHHhhcccCcHH
Confidence 333333556655554332 2346999999999999975
No 68
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=29.66 E-value=89 Score=19.24 Aligned_cols=33 Identities=21% Similarity=0.401 Sum_probs=26.6
Q ss_pred HHHHHHHHhhhCCCCCCcHHHHH-HHHHHHHHHH
Q 033030 33 QKDLQHMMYGFGDDPNPLPETVA-LVEDIVVEYV 65 (129)
Q Consensus 33 ~~EI~~mMy~fGD~~~P~~ETv~-l~EeIv~~~I 65 (129)
..||+..|-.+|-.+-|..+|.. ++|.=+..++
T Consensus 8 d~eL~~~L~~~G~~~gPIt~sTR~vy~kkL~~~~ 41 (44)
T smart00540 8 DAELRAELKQYGLPPGPITDTTRKLYEKKLRKLR 41 (44)
T ss_pred HHHHHHHHHHcCCCCCCcCcchHHHHHHHHHHHH
Confidence 57999999999999999988776 7776665554
No 69
>PF12290 DUF3802: Protein of unknown function (DUF3802); InterPro: IPR020979 This family of proteins is found in bacteria and are typically between 114 and 143 amino acids in length. There is a conserved KNLFD sequence motif. The annotation with this family suggests that it may be the B subunit of bacterial type IIA DNA topoisomerase but there is no evidence to support this annotation.
Probab=29.66 E-value=71 Score=23.66 Aligned_cols=33 Identities=15% Similarity=0.260 Sum_probs=24.7
Q ss_pred hhhCCCCCCcHHHHH-HHHHHHHHHHHHHHHHHH
Q 033030 41 YGFGDDPNPLPETVA-LVEDIVVEYVTDLAHKAQ 73 (129)
Q Consensus 41 y~fGD~~~P~~ETv~-l~EeIv~~~I~~l~~~A~ 73 (129)
|--+....+-.+|+. ++||.|-.+|+-+|.+=.
T Consensus 22 Fe~~~~~~~~~~Tv~d~vee~ia~~im~vc~Qnp 55 (113)
T PF12290_consen 22 FESSQSGDTGDETVEDVVEEQIASQIMAVCEQNP 55 (113)
T ss_pred hcCCCCCCcccchHHHHHHHHHHHHHHHHHccCC
Confidence 444455677788887 899999999998886543
No 70
>PRK15067 ethanolamine ammonia lyase large subunit; Provisional
Probab=28.93 E-value=44 Score=30.14 Aligned_cols=34 Identities=29% Similarity=0.522 Sum_probs=25.8
Q ss_pred cccccHHHHHHHHhhhCCC---CCCcHHHHHHHHHHH
Q 033030 28 KRGVFQKDLQHMMYGFGDD---PNPLPETVALVEDIV 61 (129)
Q Consensus 28 kk~~f~~EI~~mMy~fGD~---~~P~~ETv~l~EeIv 61 (129)
-++....-+..++||.||. -||-.+++.-+..++
T Consensus 170 ~~gI~asvldGL~yG~GDAVIGiNPa~Ds~~~~~~ll 206 (461)
T PRK15067 170 PDGIAASILDGLSYGVGDAVIGINPATDSVENVSRLL 206 (461)
T ss_pred HHHHHHHHHHHHhhcCCCeEEecCCCCCCHHHHHHHH
Confidence 5678888899999999997 478777766554443
No 71
>PLN00153 histone H2A; Provisional
Probab=28.87 E-value=1.5e+02 Score=22.36 Aligned_cols=37 Identities=22% Similarity=0.230 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChh
Q 033030 59 DIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLP 96 (129)
Q Consensus 59 eIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~ 96 (129)
|++...|.+|.-+|..-. .+.+|+.+.|.-++|+|..
T Consensus 56 EYLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~nDeE 92 (129)
T PLN00153 56 EYLTAEVLELAGNAARDN-KKNRIVPRHIQLAIRNDEE 92 (129)
T ss_pred HHHHHHHHHHHHHHHHhc-CCCccChHHHHhhccCcHH
Confidence 444444666665554432 2456999999999999964
No 72
>PF14164 YqzH: YqzH-like protein
Probab=28.68 E-value=53 Score=22.01 Aligned_cols=20 Identities=35% Similarity=0.649 Sum_probs=17.6
Q ss_pred CCCcHHHHHHHHHHHHHHHH
Q 033030 47 PNPLPETVALVEDIVVEYVT 66 (129)
Q Consensus 47 ~~P~~ETv~l~EeIv~~~I~ 66 (129)
.+|..+--.+|||+|-+||+
T Consensus 44 ~~~~~Dl~eiVeDvVY~yiT 63 (64)
T PF14164_consen 44 EEPDEDLHEIVEDVVYDYIT 63 (64)
T ss_pred cCCCchHHHHHHHHHHHHhc
Confidence 57888889999999999986
No 73
>cd08813 DED_Caspase_8_repeat2 Death Effector Domain, repeat 2, of Caspase-8. Death effector domain (DED) found in caspase-8 (CASP8, FLICE), repeat 2. Caspases are aspartate-specific cysteine proteases with functions in apoptosis and immune signaling. Initiator caspases are the first to be activated following death- or inflammation-inducing signals. Caspase-8 is an initiator of death receptor mediated apoptosis. Together with FADD, caspase-10, and the pseudo-caspase c-FLIP, it forms the death-inducing signaling complex (DISC), whose formation is triggered by the activation of type 1 tumor necrosis factor (TNF) receptors such as Fas, TNF receptor 1, and TRAIL receptor. Caspase-8 also plays many important non-apoptotic functions including roles in embryonic development, cell adhesion and motility, immune cell proliferation and differentiation, T-cell activation, and NFkappaB signaling. It contains two N-terminal DED domains and a C-terminal caspase domain. DEDs comprise a subfamily of the
Probab=26.60 E-value=60 Score=22.50 Aligned_cols=35 Identities=23% Similarity=0.405 Sum_probs=25.4
Q ss_pred chhHHHHHHhhC--hhhHhHHHHHHHHHHHHHHHHhh
Q 033030 83 SVEDFLYLIRKD--LPKLNRCTELLSMQEELKQARKA 117 (129)
Q Consensus 83 s~eDl~F~lR~D--~~Kl~Rl~~lL~~k~~ik~Ark~ 117 (129)
.++++.|+++.. +.|+.+++.+|.+=-++.+....
T Consensus 19 dL~s~kFLl~~~i~k~kle~~~s~Ldlf~eLEk~~~l 55 (83)
T cd08813 19 ELKSFKFLLQNELPKSKLDDETTLLDIFIEMEKKGIL 55 (83)
T ss_pred HHhhhHHHhhccccchHHhhhccHHHHHHHHHhhCCC
Confidence 356788999865 57888888888877666665543
No 74
>PF11861 DUF3381: Domain of unknown function (DUF3381); InterPro: IPR024576 This uncharacterised domain is found in eukaryotic rRNA methyltransferases like yeast Spb1 and mammalian homologue Ftsj3. Spb1 is required for proper assembly of pre-ribosomal particles during the biogenesis of the 60S ribosomal subunit [, ].
Probab=25.74 E-value=81 Score=24.10 Aligned_cols=74 Identities=22% Similarity=0.276 Sum_probs=47.2
Q ss_pred hhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc-------CCCCchhHHHHHHhhChhhHhH--HHHHHHHHHHHH
Q 033030 42 GFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSK-------GGKLSVEDFLYLIRKDLPKLNR--CTELLSMQEELK 112 (129)
Q Consensus 42 ~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~~-------Rgkis~eDl~F~lR~D~~Kl~R--l~~lL~~k~~ik 112 (129)
||+|...-+.-++.+.|=|-.+--++++..+..+... .-..++++|..++. |=+=|+| ++.||+|...+.
T Consensus 13 GY~egd~tl~~~~~~~dFi~s~dpi~~L~~~~~i~fdd~~~~i~~h~~TT~EIk~~c~-DLKVLGk~d~k~LLKWR~kir 91 (159)
T PF11861_consen 13 GYEEGDYTLYKTISASDFIKSEDPIDLLGSANEIVFDDASKEILKHPLTTEEIKECCK-DLKVLGKKDFKQLLKWRKKIR 91 (159)
T ss_pred CcCCCCceeeeeccHHHHhcCCcHHHHHHHcCeeeecchHHHHHcCCCCcHHHHHHHH-HHHhcCHHHHHHHHHHHHHHH
Confidence 5555555555566555555444455777777766542 12477777777764 5555666 889999987777
Q ss_pred HHHh
Q 033030 113 QARK 116 (129)
Q Consensus 113 ~Ark 116 (129)
+.-.
T Consensus 92 ~~~~ 95 (159)
T PF11861_consen 92 KELG 95 (159)
T ss_pred HHHh
Confidence 6643
No 75
>PLN00154 histone H2A; Provisional
Probab=25.46 E-value=1.8e+02 Score=22.19 Aligned_cols=38 Identities=21% Similarity=0.149 Sum_probs=25.2
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCCCchhHHHHHHhhChh
Q 033030 58 EDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLP 96 (129)
Q Consensus 58 EeIv~~~I~~l~~~A~~~A~~Rgkis~eDl~F~lR~D~~ 96 (129)
=|+|.-.|.+|.-+|..-. .+.+|+..+|.-++|+|..
T Consensus 70 LEYLtAEVLELAGNaA~d~-kk~RItPrHi~lAIrnDeE 107 (136)
T PLN00154 70 LEYLTAEVLELAGNASKDL-KVKRITPRHLQLAIRGDEE 107 (136)
T ss_pred HHHHHHHHHHHHHHHHHhh-CCceecHHHhhhhccCcHH
Confidence 3445544666665554432 2445999999999999964
No 76
>PF08318 COG4: COG4 transport protein; InterPro: IPR013167 This region is found in yeast oligomeric golgi complex component 4 which is involved in ER to Golgi and intra Golgi transport [].
Probab=24.35 E-value=4.2e+02 Score=22.09 Aligned_cols=33 Identities=21% Similarity=0.343 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHhhhc---------CCC-C--chhHHHHHHhhC
Q 033030 62 VEYVTDLAHKAQDIGSK---------GGK-L--SVEDFLYLIRKD 94 (129)
Q Consensus 62 ~~~I~~l~~~A~~~A~~---------Rgk-i--s~eDl~F~lR~D 94 (129)
..|+..-+.+|..+... .+. + -+||+.|++|+-
T Consensus 249 ~~y~~~Sv~KAi~lde~p~~~~~~~~~~~~~SS~vDDvffil~k~ 293 (331)
T PF08318_consen 249 EFYLRRSVEKAIQLDELPSLNSLLDSSSPPTSSVVDDVFFILRKV 293 (331)
T ss_pred HHHHHHHHHHHHHHHhcccccccccCCCcchhhHHHHHHHHHHHH
Confidence 34456667888887664 122 2 389999999975
No 77
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=24.34 E-value=2.4e+02 Score=23.26 Aligned_cols=45 Identities=24% Similarity=0.304 Sum_probs=34.5
Q ss_pred CcHHHHHHHHHHH------HHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhh
Q 033030 49 PLPETVALVEDIV------VEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 93 (129)
Q Consensus 49 P~~ETv~l~EeIv------~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~ 93 (129)
-.++.+.++-+++ ..++.++|..|...|..+|+ |+.+|+.=++..
T Consensus 229 ~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~ 281 (394)
T PRK00411 229 VDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEK 281 (394)
T ss_pred CCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHH
Confidence 4567777777777 66778999999988876654 999999766653
No 78
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=23.99 E-value=72 Score=28.17 Aligned_cols=43 Identities=12% Similarity=0.159 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CchhHHHHHHhh
Q 033030 51 PETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 93 (129)
Q Consensus 51 ~ETv~l~EeIv~~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~ 93 (129)
.+-+...+.+.-..|..+|..|...|.++++ |+.+||.-++++
T Consensus 379 ~~la~~t~g~sgAdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 379 EEFIMAKDELSGADIKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 3444555667777788999999998877664 999999888765
No 79
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=22.77 E-value=5.4e+02 Score=23.61 Aligned_cols=39 Identities=21% Similarity=0.208 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhhhcCCC--CchhHHHHHHhhChhhHhHH
Q 033030 63 EYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKDLPKLNRC 101 (129)
Q Consensus 63 ~~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~D~~Kl~Rl 101 (129)
..|.++|..|..+|..+|+ |+.+|+.=+++.-....+++
T Consensus 358 R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~~~~~~i 398 (608)
T TIGR00764 358 RELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAKTLEKQL 398 (608)
T ss_pred HHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHHHHHHHH
Confidence 5667777777666655553 77777776666544444444
No 80
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=22.76 E-value=2.1e+02 Score=22.05 Aligned_cols=61 Identities=10% Similarity=0.070 Sum_probs=39.0
Q ss_pred HHHHHHHH----hhhCC--CCCCcHHHHHHHHHHHHH---HHHHHHHHHHHhhhcCCC--CchhHHHHHHhh
Q 033030 33 QKDLQHMM----YGFGD--DPNPLPETVALVEDIVVE---YVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 93 (129)
Q Consensus 33 ~~EI~~mM----y~fGD--~~~P~~ETv~l~EeIv~~---~I~~l~~~A~~~A~~Rgk--is~eDl~F~lR~ 93 (129)
..|+..++ ...|. ...-.++.+..+-++..- +|..+|..|...|..+|+ |+.+++..+++.
T Consensus 194 ~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~ 265 (269)
T TIGR03015 194 REETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAE 265 (269)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 45665544 33342 223345666666666554 788888888888765553 999988887763
No 81
>COG1931 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.87 E-value=1e+02 Score=23.70 Aligned_cols=24 Identities=42% Similarity=0.474 Sum_probs=21.8
Q ss_pred hhhHhHHHHHHHHHHHHHHHHhhc
Q 033030 95 LPKLNRCTELLSMQEELKQARKAF 118 (129)
Q Consensus 95 ~~Kl~Rl~~lL~~k~~ik~Ark~f 118 (129)
.+-|.|++++|.-+..+..||+.|
T Consensus 48 ~~sL~~l~elLr~qrIlDtAR~~l 71 (140)
T COG1931 48 LKSLERLRELLRKQRILDTARMVL 71 (140)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHH
Confidence 477999999999999999999877
No 82
>PRK05481 lipoyl synthase; Provisional
Probab=21.86 E-value=24 Score=29.02 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=18.7
Q ss_pred HHHHhhhCCCCCCcHHHHHHHHHH
Q 033030 37 QHMMYGFGDDPNPLPETVALVEDI 60 (129)
Q Consensus 37 ~~mMy~fGD~~~P~~ETv~l~EeI 60 (129)
..||+|||++.+=..+|..+++++
T Consensus 200 t~~IvGfGET~ed~~~tl~~lrel 223 (289)
T PRK05481 200 SGLMVGLGETDEEVLEVMDDLRAA 223 (289)
T ss_pred eeeEEECCCCHHHHHHHHHHHHhc
Confidence 457899999887777777777765
No 83
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=21.26 E-value=4.7e+02 Score=23.09 Aligned_cols=65 Identities=18% Similarity=0.310 Sum_probs=41.5
Q ss_pred cHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCchhHHHHHHhhChhhHhHHHHHHHH
Q 033030 32 FQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIRKDLPKLNRCTELLSM 107 (129)
Q Consensus 32 f~~EI~~mMy~fGD~~~P~~ETv~l~EeIv~~~I~~l~~~A~~~A~--~Rgkis~eDl~F~lR~D~~Kl~Rl~~lL~~ 107 (129)
....+-..+.|.||. +.|+|.+-... + -.+|.+++. ..|+++++||+-+|+. =.|++=+..++.|
T Consensus 278 ~~~~~~~~ilgmgd~-------~~l~e~~~~~~--~-~~~~~~~~~~~~~~~f~l~d~~~q~~~-~~kmG~~~~~~~m 344 (437)
T PRK00771 278 DPDRFISRLLGMGDL-------ESLLEKVEEAL--D-EEEEEKDVEKMMKGKFTLKDMYKQLEA-MNKMGPLKQILQM 344 (437)
T ss_pred CHHHHHHHHhCCCCh-------HHHHHHHHHhh--h-HHHHHHHHHHHHcCCcCHHHHHHHHHH-HHhcCCHHHHHHh
Confidence 367788999999995 45555443211 1 122333322 3588999999999875 4567767777665
No 84
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=20.64 E-value=3.2e+02 Score=22.20 Aligned_cols=43 Identities=14% Similarity=0.202 Sum_probs=32.3
Q ss_pred cHHHHHHHHHHH------HHHHHHHHHHHHHhhhcCC--CCchhHHHHHHh
Q 033030 50 LPETVALVEDIV------VEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIR 92 (129)
Q Consensus 50 ~~ETv~l~EeIv------~~~I~~l~~~A~~~A~~Rg--kis~eDl~F~lR 92 (129)
.++.+.++.+++ ...+.++|..|...|..+| .|+.+|+.-++.
T Consensus 222 ~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~ 272 (365)
T TIGR02928 222 DDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQE 272 (365)
T ss_pred ChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 456677777776 3578889999998886655 499999886654
No 85
>COG1422 Predicted membrane protein [Function unknown]
Probab=20.53 E-value=1.2e+02 Score=24.51 Aligned_cols=25 Identities=20% Similarity=0.465 Sum_probs=18.4
Q ss_pred hChhhHhHHHHHHH-HHHHHHHHHhh
Q 033030 93 KDLPKLNRCTELLS-MQEELKQARKA 117 (129)
Q Consensus 93 ~D~~Kl~Rl~~lL~-~k~~ik~Ark~ 117 (129)
-|.+|++|+++.++ .|++.++|++.
T Consensus 69 iD~ekm~~~qk~m~efq~e~~eA~~~ 94 (201)
T COG1422 69 IDQEKMKELQKMMKEFQKEFREAQES 94 (201)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 47888888877664 57778888774
No 86
>PRK12928 lipoyl synthase; Provisional
Probab=20.41 E-value=27 Score=28.99 Aligned_cols=22 Identities=23% Similarity=0.443 Sum_probs=15.2
Q ss_pred HHHhhhCCCCCCcHHHHHHHHH
Q 033030 38 HMMYGFGDDPNPLPETVALVED 59 (129)
Q Consensus 38 ~mMy~fGD~~~P~~ETv~l~Ee 59 (129)
.||+|||++.+=..+|...+.+
T Consensus 209 ~iIvG~GET~ed~~etl~~Lre 230 (290)
T PRK12928 209 GLMLGLGETEDEVIETLRDLRA 230 (290)
T ss_pred cEEEeCCCCHHHHHHHHHHHHh
Confidence 6799999987655555555544
No 87
>PF06751 EutB: Ethanolamine ammonia lyase large subunit (EutB); InterPro: IPR010628 This family consists of several bacterial ethanolamine ammonia lyase large subunit (EutB) proteins. Ethanolamine ammonia-lyase is a bacterial enzyme that catalyses the adenosylcobalamin-dependent conversion of certain vicinal amino alcohols to oxo compounds and ammonia. The enzyme is a heterodimer composed of subunits of Mr approximately 55,000 (EutB) and 35,000 (EutC) [].; GO: 0008851 ethanolamine ammonia-lyase activity, 0006520 cellular amino acid metabolic process; PDB: 3ABQ_C 3ABS_C 3AO0_A 3ABR_A 3ABO_C 3ANY_A 2QEZ_B.
Probab=20.36 E-value=53 Score=29.47 Aligned_cols=33 Identities=30% Similarity=0.545 Sum_probs=19.4
Q ss_pred cccccHHHHHHHHhhhCCCC---CCcHHHHHHHHHH
Q 033030 28 KRGVFQKDLQHMMYGFGDDP---NPLPETVALVEDI 60 (129)
Q Consensus 28 kk~~f~~EI~~mMy~fGD~~---~P~~ETv~l~EeI 60 (129)
-++....-+..++||.||.. ||-.+++.-+..+
T Consensus 160 ~~gI~as~~dGl~yG~GDAVIGiNPa~ds~~~~~~l 195 (444)
T PF06751_consen 160 PEGIAASVLDGLSYGCGDAVIGINPASDSVESVARL 195 (444)
T ss_dssp HHHHHHHHHHHHHTT--SSEEEE--SS-SHHHHHHH
T ss_pred HHHHHHHHHHHHhhcCCceEeecCCCcCCHHHHHHH
Confidence 45677777888999999984 7776666544443
No 88
>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]
Probab=20.36 E-value=1.1e+02 Score=27.74 Aligned_cols=60 Identities=27% Similarity=0.542 Sum_probs=44.3
Q ss_pred hhCCCCC---CcHHHHHHHHHHHHHHHHHHH-------HHHHHhh-----hcCC-----CCchhHHHHHHhhChhhHhHH
Q 033030 42 GFGDDPN---PLPETVALVEDIVVEYVTDLA-------HKAQDIG-----SKGG-----KLSVEDFLYLIRKDLPKLNRC 101 (129)
Q Consensus 42 ~fGD~~~---P~~ETv~l~EeIv~~~I~~l~-------~~A~~~A-----~~Rg-----kis~eDl~F~lR~D~~Kl~Rl 101 (129)
-.||+.. |++.+.-.||+-+++||..++ -+|.+++ .+.| -+++||+.=.|.+...-+.|.
T Consensus 296 ~l~dser~~~~l~n~s~~ve~siidyla~lsdGDaR~aLN~Lems~~m~~tr~g~~~~~~lSidDvke~lq~s~~~YDr~ 375 (554)
T KOG2028|consen 296 SLGDSERPTDPLPNSSMFVEDSIIDYLAYLSDGDARAALNALEMSLSMFCTRSGQSSRVLLSIDDVKEGLQRSHILYDRA 375 (554)
T ss_pred hhccccccCCCCCCcchhhhHHHHHHHHHhcCchHHHHHHHHHHHHHHHHhhcCCcccceecHHHHHHHHhhccceeccc
Confidence 3569887 778877789999999999987 3444544 2335 399999998888876555553
Done!