Query 033020
Match_columns 129
No_of_seqs 104 out of 236
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 08:49:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033020.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033020hhsearch_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 8.5E-45 232.7 11.5 91 29-119 1-92 (92)
2 KOG3901 Transcription initiati 100.0 2.1E-38 4.6E-43 228.4 10.1 97 27-124 6-102 (109)
3 PF02269 TFIID-18kDa: Transcri 100.0 4.1E-39 8.8E-44 227.2 2.2 91 30-120 1-93 (93)
4 COG5248 TAF19 Transcription in 100.0 2.7E-31 5.8E-36 193.9 9.7 99 27-125 6-104 (126)
5 KOG3902 Histone acetyltransfer 99.9 2.8E-25 6E-30 184.8 12.3 111 1-117 1-114 (352)
6 cd07981 TAF12 TATA Binding Pro 97.3 0.0015 3.2E-08 43.9 7.2 48 47-94 18-67 (72)
7 PF03847 TFIID_20kDa: Transcri 97.2 0.001 2.2E-08 44.7 5.5 59 36-94 5-65 (68)
8 smart00576 BTP Bromodomain tra 96.9 0.0062 1.3E-07 41.1 6.9 64 29-93 5-70 (77)
9 PF00808 CBFD_NFYB_HMF: Histon 96.8 0.0058 1.2E-07 39.6 6.0 58 34-91 6-65 (65)
10 KOG1142 Transcription initiati 96.7 0.0054 1.2E-07 50.8 6.9 60 30-94 158-220 (258)
11 PF07524 Bromo_TP: Bromodomain 96.1 0.035 7.6E-07 37.1 6.9 62 30-93 6-70 (77)
12 PLN00035 histone H4; Provision 96.0 0.036 7.8E-07 40.3 6.8 69 26-95 17-95 (103)
13 cd00076 H4 Histone H4, one of 95.7 0.063 1.4E-06 37.6 6.7 62 33-95 16-79 (85)
14 smart00803 TAF TATA box bindin 95.6 0.051 1.1E-06 36.0 5.9 56 36-92 8-65 (65)
15 PF15630 CENP-S: Kinetochore c 95.6 0.036 7.7E-07 38.0 5.1 49 48-96 25-75 (76)
16 PTZ00015 histone H4; Provision 95.2 0.073 1.6E-06 38.6 6.0 63 31-94 31-95 (102)
17 PF00125 Histone: Core histone 95.1 0.12 2.5E-06 33.9 6.3 65 30-94 9-75 (75)
18 cd07979 TAF9 TATA Binding Prot 94.6 0.21 4.5E-06 36.5 7.1 57 36-93 7-65 (117)
19 COG2036 HHT1 Histones H3 and H 93.7 0.23 5E-06 35.3 5.6 57 36-93 25-83 (91)
20 PF02969 TAF: TATA box binding 92.0 1.2 2.7E-05 29.7 7.0 46 47-92 19-66 (66)
21 smart00417 H4 Histone H4. 91.1 0.48 1E-05 32.4 4.4 59 31-90 14-74 (74)
22 PF02291 TFIID-31kDa: Transcri 89.5 1.5 3.3E-05 32.8 6.2 57 35-92 17-75 (129)
23 KOG3902 Histone acetyltransfer 89.1 2 4.3E-05 37.0 7.3 79 35-117 80-161 (352)
24 KOG0869 CCAAT-binding factor, 88.5 1.2 2.6E-05 34.9 5.2 65 29-93 31-98 (168)
25 smart00428 H3 Histone H3. 87.6 4 8.7E-05 29.6 7.2 65 28-92 31-99 (105)
26 PF05236 TAF4: Transcription i 84.1 1.2 2.5E-05 36.2 3.3 83 31-114 48-131 (264)
27 cd08050 TAF6 TATA Binding Prot 82.0 4.9 0.00011 34.0 6.4 46 47-92 15-62 (343)
28 cd08045 TAF4 TATA Binding Prot 80.2 10 0.00022 29.8 7.2 58 48-105 65-123 (212)
29 PLN00121 histone H3; Provision 77.6 12 0.00026 28.4 6.6 61 31-91 67-129 (136)
30 KOG2549 Transcription initiati 77.2 5.9 0.00013 36.4 5.6 58 32-93 16-75 (576)
31 PTZ00018 histone H3; Provision 71.5 20 0.00043 27.2 6.4 61 31-91 67-129 (136)
32 PF09415 CENP-X: CENP-S associ 71.1 5.1 0.00011 27.1 2.9 44 45-88 16-62 (72)
33 cd08048 TAF11 TATA Binding Pro 70.8 31 0.00067 23.9 6.8 58 35-93 21-83 (85)
34 cd00074 H2A Histone 2A; H2A is 69.8 21 0.00046 26.1 6.1 44 53-96 43-88 (115)
35 PF02787 CPSase_L_D3: Carbamoy 68.0 18 0.0004 26.4 5.5 35 78-113 21-55 (123)
36 PLN00158 histone H2B; Provisio 67.0 50 0.0011 24.5 8.5 64 29-92 26-91 (116)
37 PRK07122 RNA polymerase sigma 62.5 51 0.0011 26.6 7.6 66 13-87 5-70 (264)
38 PLN00160 histone H3; Provision 62.0 49 0.0011 23.7 6.6 65 28-92 23-90 (97)
39 PLN00161 histone H3; Provision 61.3 51 0.0011 25.1 6.9 62 31-92 60-124 (135)
40 KOG4336 TBP-associated transcr 59.0 43 0.00094 28.8 6.8 78 31-111 6-87 (323)
41 KOG3334 Transcription initiati 58.4 56 0.0012 25.3 6.7 59 33-92 16-76 (148)
42 KOG1659 Class 2 transcription 57.8 49 0.0011 27.2 6.6 82 25-107 7-91 (224)
43 KOG2389 Predicted bromodomain 51.3 54 0.0012 28.6 6.2 57 35-92 34-92 (353)
44 KOG1744 Histone H2B [Chromatin 49.4 1.1E+02 0.0024 23.0 7.1 65 28-92 35-101 (127)
45 PF15290 Syntaphilin: Golgi-lo 46.8 66 0.0014 27.5 5.9 94 12-115 22-127 (305)
46 KOG0870 DNA polymerase epsilon 45.2 69 0.0015 25.3 5.5 47 47-93 29-77 (172)
47 smart00414 H2A Histone 2A. 44.9 47 0.001 23.9 4.2 39 57-96 39-77 (106)
48 TIGR03798 ocin_TIGR03798 bacte 44.5 39 0.00085 21.6 3.5 44 83-126 3-47 (64)
49 smart00427 H2B Histone H2B. 43.0 1E+02 0.0022 21.8 5.6 44 49-92 20-65 (89)
50 KOG3467 Histone H4 [Chromatin 42.3 60 0.0013 23.3 4.4 73 26-98 17-98 (103)
51 COG5094 TAF9 Transcription ini 41.1 62 0.0013 24.7 4.5 37 56-92 39-80 (145)
52 COG3461 Uncharacterized conser 41.0 24 0.00052 25.5 2.2 32 84-115 64-95 (103)
53 PF04433 SWIRM: SWIRM domain; 38.9 93 0.002 20.7 4.8 29 79-107 51-80 (86)
54 KOG0871 Class 2 transcription 36.9 96 0.0021 24.2 5.1 43 50-92 33-77 (156)
55 PLN00157 histone H2A; Provisio 36.3 77 0.0017 24.0 4.4 31 65-96 64-94 (132)
56 cd08813 DED_Caspase_8_repeat2 35.8 38 0.00081 23.5 2.5 35 83-117 19-55 (83)
57 PHA00724 hypothetical protein 35.7 26 0.00056 24.3 1.6 35 39-73 1-35 (83)
58 PF04719 TAFII28: hTAFII28-lik 34.9 1.6E+02 0.0035 20.7 6.1 59 35-93 28-89 (90)
59 PF07862 Nif11: Nitrogen fixat 34.8 65 0.0014 19.3 3.2 42 84-125 6-48 (49)
60 PF03540 TFIID_30kDa: Transcri 33.0 1.3E+02 0.0029 19.1 6.1 34 46-79 17-50 (51)
61 PTZ00252 histone H2A; Provisio 32.9 86 0.0019 23.8 4.2 18 79-96 78-95 (134)
62 PRK12333 nucleoside triphospha 32.7 2.7E+02 0.0057 22.5 7.2 57 61-117 51-120 (204)
63 PF14164 YqzH: YqzH-like prote 31.6 44 0.00096 22.4 2.2 20 47-66 44-63 (64)
64 PTZ00017 histone H2A; Provisio 30.5 98 0.0021 23.5 4.1 37 59-96 59-95 (134)
65 smart00540 LEM in nuclear memb 29.2 97 0.0021 19.1 3.3 34 32-65 7-41 (44)
66 PLN00156 histone H2AX; Provisi 28.4 1.2E+02 0.0027 23.1 4.4 37 59-96 61-97 (139)
67 COG3956 Protein containing tet 28.3 2.2E+02 0.0048 25.5 6.4 60 60-119 283-355 (488)
68 COG5095 TAF6 Transcription ini 27.6 1.3E+02 0.0029 26.5 4.9 46 48-93 22-69 (450)
69 PRK09562 mazG nucleoside triph 27.6 3.5E+02 0.0075 22.2 7.6 57 61-117 60-129 (262)
70 PF12290 DUF3802: Protein of u 27.5 82 0.0018 23.3 3.2 34 41-74 22-56 (113)
71 PLN00153 histone H2A; Provisio 26.7 1.4E+02 0.003 22.5 4.4 36 60-96 57-92 (129)
72 TIGR00444 mazG MazG family pro 26.5 3.6E+02 0.0079 22.1 7.4 57 61-117 46-115 (248)
73 PF01795 Methyltransf_5: MraW 26.4 1.1E+02 0.0024 26.0 4.2 53 31-83 142-200 (310)
74 COG1422 Predicted membrane pro 26.3 80 0.0017 25.5 3.2 25 93-117 69-94 (201)
75 COG5247 BUR6 Class 2 transcrip 25.8 2.8E+02 0.006 20.5 7.8 78 30-108 23-102 (113)
76 PF04157 EAP30: EAP30/Vps36 fa 24.9 2.1E+02 0.0046 22.4 5.4 81 30-116 57-144 (223)
77 KOG2076 RNA polymerase III tra 24.4 1.1E+02 0.0023 29.9 4.1 33 26-62 129-167 (895)
78 PF09454 Vps23_core: Vps23 cor 24.0 2.2E+02 0.0047 18.6 5.8 44 49-92 7-50 (65)
79 KOG2028 ATPase related to the 23.4 93 0.002 28.2 3.3 60 42-101 296-375 (554)
80 COG1013 PorB Pyruvate:ferredox 23.3 44 0.00095 28.0 1.2 61 6-75 132-193 (294)
81 PRK15067 ethanolamine ammonia 23.1 57 0.0012 29.4 1.9 34 28-61 170-206 (461)
82 KOG0027 Calmodulin and related 22.9 1.3E+02 0.0028 21.7 3.6 74 31-122 25-98 (151)
83 PF01885 PTS_2-RNA: RNA 2'-pho 22.3 85 0.0018 24.4 2.6 15 80-94 31-45 (186)
84 PRK00411 cdc6 cell division co 22.1 2.6E+02 0.0055 23.1 5.6 44 49-92 229-280 (394)
85 PF11861 DUF3381: Domain of un 22.0 1.1E+02 0.0024 23.4 3.1 73 42-115 13-94 (159)
86 PF08318 COG4: COG4 transport 21.9 4.7E+02 0.01 21.8 7.5 33 62-94 249-293 (331)
87 TIGR00764 lon_rel lon-related 21.6 5.1E+02 0.011 23.8 7.8 39 63-101 358-398 (608)
88 PLN00154 histone H2A; Provisio 20.8 2.4E+02 0.0051 21.5 4.6 37 59-96 71-107 (136)
89 PRK05481 lipoyl synthase; Prov 20.7 25 0.00055 28.9 -0.7 24 37-60 200-223 (289)
90 PTZ00361 26 proteosome regulat 20.2 88 0.0019 27.6 2.5 42 52-93 380-423 (438)
91 TIGR03285 methan_mark_14 putat 20.1 55 0.0012 29.2 1.2 33 58-94 62-94 (445)
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=232.66 Aligned_cols=91 Identities=60% Similarity=1.053 Sum_probs=88.1
Q ss_pred ccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh-ccCCCChhHHHHHhhcChhhHhHHHHHHHH
Q 033020 29 RGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGS-KRGKLSVEDFLYLIRKDPPKLNRCTELLSM 107 (129)
Q Consensus 29 k~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~-~Rgkis~eDl~FllR~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 HHHHHHHHhccc
Q 033020 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=2.1e-38 Score=228.40 Aligned_cols=97 Identities=60% Similarity=1.034 Sum_probs=93.2
Q ss_pred ccccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChhhHhHHHHHHH
Q 033020 27 RKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPPKLNRCTELLS 106 (129)
Q Consensus 27 ~~k~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~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 47899999999999999999999999999999999999999999999998 89999999999999999999999999999
Q ss_pred HHHHHHHHHhccccChhh
Q 033020 107 MQEELKQARKAFEVDEEK 124 (129)
Q Consensus 107 ~k~~ik~Ark~fd~~~~~ 124 (129)
|+++||+|||+|++.+-.
T Consensus 85 mneelk~ArKaF~~~~y~ 102 (109)
T KOG3901|consen 85 MNEELKKARKAFDETDYE 102 (109)
T ss_pred hHHHHHHHHhccchHhHH
Confidence 999999999999987633
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=4.1e-39 Score=227.23 Aligned_cols=91 Identities=56% Similarity=0.976 Sum_probs=38.8
Q ss_pred cccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC--CCChhHHHHHhhcChhhHhHHHHHHHH
Q 033020 30 GVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG--KLSVEDFLYLIRKDPPKLNRCTELLSM 107 (129)
Q Consensus 30 ~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rg--kis~eDl~FllR~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 HHHHHHHHhcccc
Q 033020 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 9999999999985
No 4
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=99.97 E-value=2.7e-31 Score=193.89 Aligned_cols=99 Identities=37% Similarity=0.663 Sum_probs=95.6
Q ss_pred ccccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChhhHhHHHHHHH
Q 033020 27 RKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPPKLNRCTELLS 106 (129)
Q Consensus 27 ~~k~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~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 67789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhccccChhhh
Q 033020 107 MQEELKQARKAFEVDEEKL 125 (129)
Q Consensus 107 ~k~~ik~Ark~fd~~~~~~ 125 (129)
.+++|+.|+|+|++.+..+
T Consensus 86 tn~~i~~Akk~F~~~dsRy 104 (126)
T COG5248 86 TNEEIKLAKKAFEPKDSRY 104 (126)
T ss_pred hhHHHHHHhcccCchhHHH
Confidence 9999999999999987543
No 5
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=99.93 E-value=2.8e-25 Score=184.75 Aligned_cols=111 Identities=32% Similarity=0.468 Sum_probs=102.7
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCccccccccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC
Q 033020 1 MSNPSAGQSSKSKAGSSQPCETTSFKRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG 80 (129)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~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 799999999987777777665 34579999999999999999999999999999999999999999999999999
Q ss_pred C--CChhHHHHHhhcChhhHhHHHHHHHHHHHH-HHHHhc
Q 033020 81 K--LSVEDFLYLIRKDPPKLNRCTELLSMQEEL-KQARKA 117 (129)
Q Consensus 81 k--is~eDl~FllR~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 5 999999999999999999999999999999 888764
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=97.32 E-value=0.0015 Score=43.87 Aligned_cols=48 Identities=23% Similarity=0.385 Sum_probs=43.4
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhcC
Q 033020 47 PNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRKD 94 (129)
Q Consensus 47 ~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~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 56778888899999999999999999999998885 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=97.23 E-value=0.001 Score=44.75 Aligned_cols=59 Identities=20% Similarity=0.344 Sum_probs=44.2
Q ss_pred HHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhcC
Q 033020 36 LQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRKD 94 (129)
Q Consensus 36 I~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~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 4455555555556677778899999999999999999999999985 9999999999764
No 8
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=96.88 E-value=0.0062 Score=41.08 Aligned_cols=64 Identities=13% Similarity=0.263 Sum_probs=53.2
Q ss_pred ccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC--CCChhHHHHHhhc
Q 033020 29 RGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG--KLSVEDFLYLIRK 93 (129)
Q Consensus 29 k~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rg--kis~eDl~FllR~ 93 (129)
+.++..-|.+++...|= ..-.+.+.+.+=+++..|+.+|++.+.+.|...| .+++.|+..+|.+
T Consensus 5 ~~ll~~~Vaqil~~~Gf-~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 5 FALLRIAVAQILESAGF-DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHHHHHHHHcCc-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 34677789999999983 2356679999999999999999999999996544 5999999998865
No 9
>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=96.79 E-value=0.0058 Score=39.57 Aligned_cols=58 Identities=17% Similarity=0.264 Sum_probs=48.9
Q ss_pred HHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHh
Q 033020 34 KDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLI 91 (129)
Q Consensus 34 ~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~Fll 91 (129)
.=|+.+|-.-.|...-..|++.+|-.....||..|+..|...|...|+ |+.+||..+|
T Consensus 6 a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 6 ARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 347788888888888999999999999999999999999999986554 9999998764
No 10
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.75 E-value=0.0054 Score=50.80 Aligned_cols=60 Identities=20% Similarity=0.386 Sum_probs=48.0
Q ss_pred cccHHHHHHHHhhhCCCCCCcHH-HHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhcC
Q 033020 30 GVFQKDLQHMMYGFGDDPNPLPE-TVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRKD 94 (129)
Q Consensus 30 ~~f~~EI~~mMy~fGD~~~P~~e-Tv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~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 3444445555 66655555 55699999999999999999999999885 9999999999865
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=96.14 E-value=0.035 Score=37.06 Aligned_cols=62 Identities=16% Similarity=0.419 Sum_probs=51.7
Q ss_pred cccHHHHHHHHhhhC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhc
Q 033020 30 GVFQKDLQHMMYGFG-DDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRK 93 (129)
Q Consensus 30 ~~f~~EI~~mMy~fG-D~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~ 93 (129)
.....-|.+++...| |. -.+.+.+.+-+|+..||.+|.+.+...|...|+ +++.|+...|..
T Consensus 6 ~~l~~~va~il~~~GF~~--~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~ 70 (77)
T PF07524_consen 6 SLLRRSVAQILKHAGFDS--ASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEE 70 (77)
T ss_pred HHHHHHHHHHHHHcCccc--cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 356677889998888 44 556779999999999999999999999976565 899999988864
No 12
>PLN00035 histone H4; Provisional
Probab=96.01 E-value=0.036 Score=40.26 Aligned_cols=69 Identities=12% Similarity=0.215 Sum_probs=53.2
Q ss_pred cccccccHHHH--------HHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC--CCChhHHHHHhhcCh
Q 033020 26 KRKRGVFQKDL--------QHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG--KLSVEDFLYLIRKDP 95 (129)
Q Consensus 26 ~~~k~~f~~EI--------~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rg--kis~eDl~FllR~D~ 95 (129)
|+++..+...| +-+.-..| +..-..+....+.+++.+|+.+++..|..++...+ .|+.+|+.|+|++--
T Consensus 17 kr~~k~~~d~i~~ipk~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g 95 (103)
T PLN00035 17 KRHRKVLRDNIQGITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
T ss_pred hHHHHHHHhhhccCCHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcC
Confidence 45554554444 45556666 77788888889999999999999999999987544 499999999998653
No 13
>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=95.66 E-value=0.063 Score=37.60 Aligned_cols=62 Identities=11% Similarity=0.210 Sum_probs=49.5
Q ss_pred HHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC--CCChhHHHHHhhcCh
Q 033020 33 QKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG--KLSVEDFLYLIRKDP 95 (129)
Q Consensus 33 ~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rg--kis~eDl~FllR~D~ 95 (129)
..-|+.+.--.| +..-..+...-+.+++.+|+.+++..|..++...| .++.+|+.++|++.-
T Consensus 16 k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g 79 (85)
T cd00076 16 KPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 79 (85)
T ss_pred HHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCC
Confidence 345566666666 67777778888889999999999999999987544 499999999998753
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=95.65 E-value=0.051 Score=35.96 Aligned_cols=56 Identities=18% Similarity=0.226 Sum_probs=45.0
Q ss_pred HHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc--cCCCChhHHHHHhh
Q 033020 36 LQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSK--RGKLSVEDFLYLIR 92 (129)
Q Consensus 36 I~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~--Rgkis~eDl~FllR 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 56788888999999999999999999999864 55699999999886
No 15
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=95.59 E-value=0.036 Score=38.02 Aligned_cols=49 Identities=20% Similarity=0.478 Sum_probs=38.9
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC--CCChhHHHHHhhcChh
Q 033020 48 NPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG--KLSVEDFLYLIRKDPP 96 (129)
Q Consensus 48 ~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rg--kis~eDl~FllR~D~~ 96 (129)
+..++.+..|-|++-.|+..+...---.|+..| .|+.||++.+.|++|.
T Consensus 25 ~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~ 75 (76)
T PF15630_consen 25 EVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPS 75 (76)
T ss_dssp EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HH
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCC
Confidence 467889999999999999988877777776545 4999999999999974
No 16
>PTZ00015 histone H4; Provisional
Probab=95.23 E-value=0.073 Score=38.56 Aligned_cols=63 Identities=6% Similarity=0.186 Sum_probs=47.4
Q ss_pred ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC--CCChhHHHHHhhcC
Q 033020 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG--KLSVEDFLYLIRKD 94 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rg--kis~eDl~FllR~D 94 (129)
+-..-|+.|.--.| ++.-..+...-+-+++.+|+.+++..|..++...+ .++.+|+.|++++-
T Consensus 31 I~k~~IrRLarr~G-vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~ 95 (102)
T PTZ00015 31 ITKGAIRRLARRGG-VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95 (102)
T ss_pred CCHHHHHHHHHHcC-CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhc
Confidence 33455666666555 45666667778888888999999999998886544 49999999999764
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=95.10 E-value=0.12 Score=33.87 Aligned_cols=65 Identities=12% Similarity=0.168 Sum_probs=51.4
Q ss_pred cccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhcC
Q 033020 30 GVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRKD 94 (129)
Q Consensus 30 ~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~D 94 (129)
..|.+=++++.=.++..-.-..++..+|-.++-.++.+++..|..+|...++ |+.+|+..++|.|
T Consensus 9 ~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 9 FPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred eEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 3455555555555555456778999999999999999999999999975554 9999999999876
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=94.59 E-value=0.21 Score=36.54 Aligned_cols=57 Identities=16% Similarity=0.330 Sum_probs=46.6
Q ss_pred HHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhc
Q 033020 36 LQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRK 93 (129)
Q Consensus 36 I~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~ 93 (129)
|..++-..|.. +=.+..+..+-|++..|+.+++..|...|...|+ |+.||+..++..
T Consensus 7 v~~iLk~~Gv~-~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~ 65 (117)
T cd07979 7 IAAILKSMGIT-EYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQS 65 (117)
T ss_pred HHHHHHHCCCC-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 55666666764 5677888899999999999999999999976554 999999998763
No 19
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=93.69 E-value=0.23 Score=35.27 Aligned_cols=57 Identities=14% Similarity=0.378 Sum_probs=48.3
Q ss_pred HHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhc
Q 033020 36 LQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRK 93 (129)
Q Consensus 36 I~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~ 93 (129)
|+.+|--.|+. .-..+.+..+-+.|-+|+.++...|..+|...|+ |+.+|+..+++.
T Consensus 25 v~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~ 83 (91)
T COG2036 25 VRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKR 83 (91)
T ss_pred HHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHH
Confidence 56677777775 6677888899999999999999999999987665 999999998864
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=92.04 E-value=1.2 Score=29.68 Aligned_cols=46 Identities=22% Similarity=0.242 Sum_probs=35.9
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--ccCCCChhHHHHHhh
Q 033020 47 PNPLPETVALVEDIVVEYVSDLAHKAQDLGS--KRGKLSVEDFLYLIR 92 (129)
Q Consensus 47 ~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~--~Rgkis~eDl~FllR 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 4567888889999999999999999999884 577899999998886
No 21
>smart00417 H4 Histone H4.
Probab=91.14 E-value=0.48 Score=32.39 Aligned_cols=59 Identities=7% Similarity=0.126 Sum_probs=38.9
Q ss_pred ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC--CCChhHHHHH
Q 033020 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG--KLSVEDFLYL 90 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rg--kis~eDl~Fl 90 (129)
+-..-|+-|.--.| ++.-..+...-+-+++.+|+.+++..|..++...| .++.+|+.|+
T Consensus 14 I~k~~IrRLaRr~G-vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 14 ITKPAIRRLARRGG-VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 33444555555444 34455555556666777788888888888886544 4999999874
No 22
>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=89.46 E-value=1.5 Score=32.77 Aligned_cols=57 Identities=19% Similarity=0.332 Sum_probs=42.6
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhh
Q 033020 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIR 92 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR 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 35555655554 44577888889999999999999999999976664 99999999887
No 23
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=89.06 E-value=2 Score=36.96 Aligned_cols=79 Identities=24% Similarity=0.192 Sum_probs=67.3
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC---CChhHHHHHhhcChhhHhHHHHHHHHHHHH
Q 033020 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK---LSVEDFLYLIRKDPPKLNRCTELLSMQEEL 111 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk---is~eDl~FllR~D~~Kl~Rl~~lL~~k~~i 111 (129)
++.-+|.-+|| ....+.|++-+....+.....++...|.+|.. .+--|+-|+|++.+.|-+|.+.-|++-..+
T Consensus 80 pedliflir~D----rakv~rL~tyl~~kdlR~k~ak~qdaa~~~~~~~~np~Ad~edlle~~~~k~~~~r~~~~~mri~ 155 (352)
T KOG3902|consen 80 PEDLIFLIRHD----RAKVNRLVTYLSWKDLRGKFAKAQDAAMRRKQNPCNPQADFEDLLENHPSKIARMRKHLKDMRIL 155 (352)
T ss_pred hHHHHHHhhcc----HHHHHHHHHHHHHHHHHHhhhhhhHHHHhhccCCCCCCccHHHHHHhCccchhhhhhhhhHHHHH
Confidence 34556788888 67888899999999999899899888876543 566899999999999999999999999999
Q ss_pred HHHHhc
Q 033020 112 KQARKA 117 (129)
Q Consensus 112 k~Ark~ 117 (129)
|+|-|.
T Consensus 156 k~~~k~ 161 (352)
T KOG3902|consen 156 KRALKI 161 (352)
T ss_pred HHHhhc
Confidence 999765
No 24
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=88.51 E-value=1.2 Score=34.86 Aligned_cols=65 Identities=15% Similarity=0.265 Sum_probs=49.7
Q ss_pred ccccHHHHHHHHh-hhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc--cCCCChhHHHHHhhc
Q 033020 29 RGVFQKDLQHMMY-GFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSK--RGKLSVEDFLYLIRK 93 (129)
Q Consensus 29 k~~f~~EI~~mMy-~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~--Rgkis~eDl~FllR~ 93 (129)
|.+-..-|..+|- +.=-..--..+.-..|.+-|-+||.=++.+|.+..++ |..|.-|||+++|-.
T Consensus 31 r~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~t 98 (168)
T KOG0869|consen 31 RFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMST 98 (168)
T ss_pred hhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHH
Confidence 3455566667773 3333344566788899999999999999999998864 666999999999974
No 25
>smart00428 H3 Histone H3.
Probab=87.59 E-value=4 Score=29.61 Aligned_cols=65 Identities=14% Similarity=0.224 Sum_probs=50.6
Q ss_pred cccccHHHHHHHHhhhCC--CCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhh
Q 033020 28 KRGVFQKDLQHMMYGFGD--DPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIR 92 (129)
Q Consensus 28 ~k~~f~~EI~~mMy~fGD--~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR 92 (129)
.|-.|..=++.++--|.+ .-.=..++...+.+..-.|++++...|..+|...++ |..+|+..+.|
T Consensus 31 ~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 31 RKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred ccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 345677777777766654 446678899999999999999999999999977665 77899976643
No 26
>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=84.06 E-value=1.2 Score=36.23 Aligned_cols=83 Identities=27% Similarity=0.233 Sum_probs=32.0
Q ss_pred ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChhh-HhHHHHHHHHHH
Q 033020 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPPK-LNRCTELLSMQE 109 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~D~~K-l~Rl~~lL~~k~ 109 (129)
.+.+=|+.++--+| ...+.++.+.||---+.++|.+|+..+..+|..|-....+|..+.+++|..+ |..|.++-...+
T Consensus 48 ~L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l~~~e~~~~ 126 (264)
T PF05236_consen 48 PLQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFLEQLEKEEE 126 (264)
T ss_dssp HHHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH-------------------------------------
T ss_pred HHHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHHHHHHHHHH
Confidence 34444555565556 6789999999999999999999999999999888777778888888988654 444544444444
Q ss_pred HHHHH
Q 033020 110 ELKQA 114 (129)
Q Consensus 110 ~ik~A 114 (129)
+++..
T Consensus 127 err~~ 131 (264)
T PF05236_consen 127 ERREE 131 (264)
T ss_dssp -----
T ss_pred HHHHH
Confidence 44433
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=81.97 E-value=4.9 Score=33.99 Aligned_cols=46 Identities=22% Similarity=0.231 Sum_probs=39.8
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--ccCCCChhHHHHHhh
Q 033020 47 PNPLPETVALVEDIVVEYVSDLAHKAQDLGS--KRGKLSVEDFLYLIR 92 (129)
Q Consensus 47 ~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~--~Rgkis~eDl~FllR 92 (129)
..-.++.+..+-+-|..++.++++.|.+.+. +|.+++++||-.++|
T Consensus 15 ~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~ 62 (343)
T cd08050 15 DSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALR 62 (343)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence 4567788888888899999999999999986 466799999999988
No 28
>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=80.18 E-value=10 Score=29.84 Aligned_cols=58 Identities=22% Similarity=0.190 Sum_probs=45.5
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChhh-HhHHHHHH
Q 033020 48 NPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPPK-LNRCTELL 105 (129)
Q Consensus 48 ~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~D~~K-l~Rl~~lL 105 (129)
...++.+.+|-..+.++|.+|+..+..+|..|-...-+|..+.+++|..+ +..|.++-
T Consensus 65 ~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~~~e 123 (212)
T cd08045 65 EVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLEQLE 123 (212)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHHHHH
Confidence 56899999999999999999999999999877555567778888888544 44444433
No 29
>PLN00121 histone H3; Provisional
Probab=77.60 E-value=12 Score=28.44 Aligned_cols=61 Identities=13% Similarity=0.156 Sum_probs=48.7
Q ss_pred ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHh
Q 033020 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLI 91 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~Fll 91 (129)
.|..=|+.++-.|++.-.=..++...+.+..-.||+++...+.-+|...++ |...|+..+.
T Consensus 67 pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 67 PFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 455555666666776667788999999999999999999999999977676 6678987654
No 30
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=77.25 E-value=5.9 Score=36.42 Aligned_cols=58 Identities=26% Similarity=0.302 Sum_probs=46.2
Q ss_pred cHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--ccCCCChhHHHHHhhc
Q 033020 32 FQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGS--KRGKLSVEDFLYLIRK 93 (129)
Q Consensus 32 f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~--~Rgkis~eDl~FllR~ 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 344444443 33 5678999999999999999999999998753 5778999999999983
No 31
>PTZ00018 histone H3; Provisional
Probab=71.54 E-value=20 Score=27.24 Aligned_cols=61 Identities=13% Similarity=0.156 Sum_probs=47.8
Q ss_pred ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHh
Q 033020 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLI 91 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~Fll 91 (129)
.|..=|+.+.-.|+..-.=..+++..+.+..-.||+++...+..+|...++ |...|+..+.
T Consensus 67 pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 67 PFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 455555666666666667788999999999999999999999999877666 6678987653
No 32
>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=71.06 E-value=5.1 Score=27.06 Aligned_cols=44 Identities=18% Similarity=0.302 Sum_probs=34.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC--C-CChhHHH
Q 033020 45 DDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG--K-LSVEDFL 88 (129)
Q Consensus 45 D~~~P~~eTv~liEdIV~~~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 444567789999999999999999999999887666 4 7888874
No 33
>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=70.79 E-value=31 Score=23.91 Aligned_cols=58 Identities=16% Similarity=0.284 Sum_probs=47.0
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc-----cCCCChhHHHHHhhc
Q 033020 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSK-----RGKLSVEDFLYLIRK 93 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~-----Rgkis~eDl~FllR~ 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 78899999999999999999999999999764 567888888777664
No 34
>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=69.79 E-value=21 Score=26.11 Aligned_cols=44 Identities=9% Similarity=0.217 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh--ccCCCChhHHHHHhhcChh
Q 033020 53 TVALVEDIVVEYVSDLAHKAQDLGS--KRGKLSVEDFLYLIRKDPP 96 (129)
Q Consensus 53 Tv~liEdIV~~~i~~l~~~A~~~A~--~Rgkis~eDl~FllR~D~~ 96 (129)
+.-++=.++-....+++..|.+.|. .+.+|+.+||.-++|+|..
T Consensus 43 A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~E 88 (115)
T cd00074 43 APVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRNDEE 88 (115)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHH
Confidence 3334333443444455555555554 2445999999999999974
No 35
>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=68.01 E-value=18 Score=26.44 Aligned_cols=35 Identities=37% Similarity=0.585 Sum_probs=27.4
Q ss_pred ccCCCChhHHHHHhhcChhhHhHHHHHHHHHHHHHH
Q 033020 78 KRGKLSVEDFLYLIRKDPPKLNRCTELLSMQEELKQ 113 (129)
Q Consensus 78 ~Rgkis~eDl~FllR~D~~Kl~Rl~~lL~~k~~ik~ 113 (129)
+|| .++|+|-=+-.=||--|.+++++..+.+.+++
T Consensus 21 rrG-~sveeI~e~T~ID~wFL~~i~~Iv~~e~~L~~ 55 (123)
T PF02787_consen 21 RRG-YSVEEIHELTKIDPWFLEQIKNIVDMEKELKE 55 (123)
T ss_dssp HTT-B-HHHHHHHH---HHHHHHHHHHHHHHHHHHH
T ss_pred HcC-CCHHHHHHHHCccHHHHHHHHHHHHHHHHHHH
Confidence 566 79999999999999999999999999888777
No 36
>PLN00158 histone H2B; Provisional
Probab=66.96 E-value=50 Score=24.54 Aligned_cols=64 Identities=8% Similarity=0.190 Sum_probs=44.9
Q ss_pred ccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcc--CCCChhHHHHHhh
Q 033020 29 RGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKR--GKLSVEDFLYLIR 92 (129)
Q Consensus 29 k~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~R--gkis~eDl~FllR 92 (129)
+..|.-=|-..+-..-=..--...+..+|.-+|.+..-.|..+|.+++... ..|+..+|--++|
T Consensus 26 ~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvr 91 (116)
T PLN00158 26 TETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVR 91 (116)
T ss_pred cccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 355555544444332222234677888999999999999999999998643 3499999988777
No 37
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=62.49 E-value=51 Score=26.58 Aligned_cols=66 Identities=26% Similarity=0.364 Sum_probs=43.4
Q ss_pred CCCCCCCCCCccccccccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCChhHH
Q 033020 13 KAGSSQPCETTSFKRKRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGKLSVEDF 87 (129)
Q Consensus 13 ~~~~~~~~~~~~~~~~k~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgkis~eDl 87 (129)
.+|+++|..++.. +. ++..++-.+--......+.....+.+|..|+--+.+-|.+... +| +..+||
T Consensus 5 ~~~~~~~~~~~~~------~~-~~~~~~~~~~~~~~~~~~~~~~r~~Lv~~~l~LV~~iA~~y~~-~g-~~~~DL 70 (264)
T PRK07122 5 AAGGSRPRASTDE------YA-DVPEMFRELAGLPAGSPEFQRQRDRIVTRCLPLADHIARRFDG-RG-EPRDDL 70 (264)
T ss_pred cCCCCCCCCchhh------hh-hHHHHHHHHHhccCCCHHHHHHHHHHHHHhHHHHHHHHHHHHh-CC-CCHHHH
Confidence 3566677653221 11 5555555443345566777778999999999988888888763 33 777887
No 38
>PLN00160 histone H3; Provisional
Probab=61.97 E-value=49 Score=23.73 Aligned_cols=65 Identities=8% Similarity=0.072 Sum_probs=49.8
Q ss_pred cccccHHHHHHHHhhhC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhh
Q 033020 28 KRGVFQKDLQHMMYGFG-DDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIR 92 (129)
Q Consensus 28 ~k~~f~~EI~~mMy~fG-D~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR 92 (129)
.|-.|..=++.+.-.|. +.-.=..++...+.+..-.|++.+...+.-+|...++ |...|+..+.|
T Consensus 23 ~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 23 RRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred ccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 34567777777776663 4345678888999999999999999999988877666 66789876543
No 39
>PLN00161 histone H3; Provisional
Probab=61.31 E-value=51 Score=25.08 Aligned_cols=62 Identities=8% Similarity=0.079 Sum_probs=46.4
Q ss_pred ccHHHHHHHHhhhCC-CCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhh
Q 033020 31 VFQKDLQHMMYGFGD-DPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIR 92 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD-~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR 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 456666666655532 234568888999999999999999999999877776 66688876643
No 40
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=59.03 E-value=43 Score=28.84 Aligned_cols=78 Identities=12% Similarity=0.201 Sum_probs=60.8
Q ss_pred ccHHHHHHHHh--hhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhcChhhHhHHHHHHH
Q 033020 31 VFQKDLQHMMY--GFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRKDPPKLNRCTELLS 106 (129)
Q Consensus 31 ~f~~EI~~mMy--~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~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 56667788886 4555 334455567788999999999998888766565 9999999999999999999999887
Q ss_pred HHHHH
Q 033020 107 MQEEL 111 (129)
Q Consensus 107 ~k~~i 111 (129)
-....
T Consensus 83 ~~~~s 87 (323)
T KOG4336|consen 83 KQEFS 87 (323)
T ss_pred hccch
Confidence 55443
No 41
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=58.40 E-value=56 Score=25.26 Aligned_cols=59 Identities=15% Similarity=0.267 Sum_probs=48.2
Q ss_pred HHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhh
Q 033020 33 QKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIR 92 (129)
Q Consensus 33 ~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR 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 3456777888774 66777788888899999999999999988876554 99999998876
No 42
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=57.83 E-value=49 Score=27.18 Aligned_cols=82 Identities=17% Similarity=0.299 Sum_probs=58.9
Q ss_pred ccccccccH-HHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhcChhhHhHH
Q 033020 25 FKRKRGVFQ-KDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRKDPPKLNRC 101 (129)
Q Consensus 25 ~~~~k~~f~-~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~D~~Kl~Rl 101 (129)
+++++..|- .-|+.+|-.=-|.-.-..-+=-+|-.-+--||..||..+++++..||. ++.+-|.-++-+++ |+.-|
T Consensus 7 ~~~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~-~FdFL 85 (224)
T KOG1659|consen 7 FKKYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDP-KFDFL 85 (224)
T ss_pred hhhhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccc-hhHHH
Confidence 344445555 678888876655543333333466677778999999999999988873 99999999999886 56777
Q ss_pred HHHHHH
Q 033020 102 TELLSM 107 (129)
Q Consensus 102 ~~lL~~ 107 (129)
++++..
T Consensus 86 k~~v~~ 91 (224)
T KOG1659|consen 86 KEVVEK 91 (224)
T ss_pred HHHHHh
Confidence 776543
No 43
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=51.32 E-value=54 Score=28.64 Aligned_cols=57 Identities=12% Similarity=0.298 Sum_probs=44.9
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhh
Q 033020 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIR 92 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR 92 (129)
-+.|+.=+.|-...+.. .-.+++++++.||+++-..|..++-.-|+ ..+.|++-+|-
T Consensus 34 avaQIcqslg~~~~~~s-ale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~ 92 (353)
T KOG2389|consen 34 AVAQICQSLGYSSTQNS-ALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQ 92 (353)
T ss_pred HHHHHHHhcCCcccccH-HHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHH
Confidence 35566666777665555 56799999999999999999999877776 77788887765
No 44
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=49.41 E-value=1.1e+02 Score=23.03 Aligned_cols=65 Identities=11% Similarity=0.214 Sum_probs=47.3
Q ss_pred cccccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhh
Q 033020 28 KRGVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIR 92 (129)
Q Consensus 28 ~k~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR 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 345555555556655433344778899999999999999999999999987776 66666665555
No 45
>PF15290 Syntaphilin: Golgi-localised syntaxin-1-binding clamp
Probab=46.81 E-value=66 Score=27.54 Aligned_cols=94 Identities=17% Similarity=0.355 Sum_probs=44.0
Q ss_pred CCCCCCCCCCCccccccccccHHHHHHHHhhhCCCC---CCcHHHHH---HHHHHHHHHHHHHHHHHHHhhhccCC-CCh
Q 033020 12 SKAGSSQPCETTSFKRKRGVFQKDLQHMMYGFGDDP---NPLPETVA---LVEDIVVEYVSDLAHKAQDLGSKRGK-LSV 84 (129)
Q Consensus 12 ~~~~~~~~~~~~~~~~~k~~f~~EI~~mMy~fGD~~---~P~~eTv~---liEdIV~~~i~~l~~~A~~~A~~Rgk-is~ 84 (129)
|.+|+---+++++.+++.+.|. .+||+. .|.||-.- ==-++-+.++.--+....+.-. .+ .-+
T Consensus 22 snSgS~KgSd~Sp~~rr~~rY~--------~C~dNHGikPP~PEQYLTPLQQKEV~iRHLkakLkes~~~l~--dRetEI 91 (305)
T PF15290_consen 22 SNSGSCKGSDSSPTMRRSGRYM--------SCGDNHGIKPPNPEQYLTPLQQKEVCIRHLKAKLKESENRLH--DRETEI 91 (305)
T ss_pred CCCccccCCCCCCCCCCCCcee--------ecccCCCCCCCCHHHhcChHHHHHHHHHHHHHHHHHHHHHHH--hhHHHH
Confidence 3344444445555556666553 588865 47776211 0112222222222222222111 11 345
Q ss_pred hHHHHH---hhcC--hhhHhHHHHHHHHHHHHHHHH
Q 033020 85 EDFLYL---IRKD--PPKLNRCTELLSMQEELKQAR 115 (129)
Q Consensus 85 eDl~Fl---lR~D--~~Kl~Rl~~lL~~k~~ik~Ar 115 (129)
+||.-. ||-| ..-.-||+--|-+|+-+|+.+
T Consensus 92 ~eLksQL~RMrEDWIEEECHRVEAQLALKEARkEIk 127 (305)
T PF15290_consen 92 DELKSQLARMREDWIEEECHRVEAQLALKEARKEIK 127 (305)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666544 4444 355667777776665555543
No 46
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=45.19 E-value=69 Score=25.32 Aligned_cols=47 Identities=17% Similarity=0.218 Sum_probs=39.0
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--ccCCCChhHHHHHhhc
Q 033020 47 PNPLPETVALVEDIVVEYVSDLAHKAQDLGS--KRGKLSVEDFLYLIRK 93 (129)
Q Consensus 47 ~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~--~Rgkis~eDl~FllR~ 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 3455677778888889999999999999996 3445999999999995
No 47
>smart00414 H2A Histone 2A.
Probab=44.91 E-value=47 Score=23.95 Aligned_cols=39 Identities=23% Similarity=0.284 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChh
Q 033020 57 VEDIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPP 96 (129)
Q Consensus 57 iEdIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~D~~ 96 (129)
+=|++...|.++.-++.... .+.+|+.+++.-++|+|..
T Consensus 39 vLEYLtaEILeLagn~a~~~-k~~rItp~hi~lAi~nD~E 77 (106)
T smart00414 39 VLEYLTAEVLELAGNAARDN-KKRRITPRHLQLAIRNDEE 77 (106)
T ss_pred HHHHHHHHHHHHHHHHHHhc-CCCccchHHHhhhccCCHH
Confidence 34444444666665554432 2446999999999999975
No 48
>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=44.54 E-value=39 Score=21.62 Aligned_cols=44 Identities=20% Similarity=0.360 Sum_probs=35.6
Q ss_pred ChhHHHHHhhcChhhHhHHHHHHHHHHHHHHHHh-ccccChhhhh
Q 033020 83 SVEDFLYLIRKDPPKLNRCTELLSMQEELKQARK-AFEVDEEKLA 126 (129)
Q Consensus 83 s~eDl~FllR~D~~Kl~Rl~~lL~~k~~ik~Ark-~fd~~~~~~~ 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 3577888899999888888888888899998886 6777776664
No 49
>smart00427 H2B Histone H2B.
Probab=43.02 E-value=1e+02 Score=21.84 Aligned_cols=44 Identities=16% Similarity=0.262 Sum_probs=35.4
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhhcc--CCCChhHHHHHhh
Q 033020 49 PLPETVALVEDIVVEYVSDLAHKAQDLGSKR--GKLSVEDFLYLIR 92 (129)
Q Consensus 49 P~~eTv~liEdIV~~~i~~l~~~A~~~A~~R--gkis~eDl~FllR 92 (129)
-..++..+|.-+|.+..-.+..+|.+++... ..|+..+|--++|
T Consensus 20 iS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvr 65 (89)
T smart00427 20 ISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVR 65 (89)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 3456778888888888889999999998643 3499999988877
No 50
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=42.35 E-value=60 Score=23.35 Aligned_cols=73 Identities=16% Similarity=0.276 Sum_probs=40.8
Q ss_pred cccccccHHHHHHH-------HhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--ccCCCChhHHHHHhhcChh
Q 033020 26 KRKRGVFQKDLQHM-------MYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGS--KRGKLSVEDFLYLIRKDPP 96 (129)
Q Consensus 26 ~~~k~~f~~EI~~m-------My~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~--~Rgkis~eDl~FllR~D~~ 96 (129)
|+.+..++..|+.+ +---|.++.-.--.-.-+.....+||.+.+.-|+-.+. .|..++.-|+++.|.+.-.
T Consensus 17 KrHRK~LsDnIqgitKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 17 KRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred HHHHHHHHhhccccchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 44555666666522 22334444433222223333455555566655555443 4666999999999987655
Q ss_pred hH
Q 033020 97 KL 98 (129)
Q Consensus 97 Kl 98 (129)
+|
T Consensus 97 ~~ 98 (103)
T KOG3467|consen 97 TL 98 (103)
T ss_pred ee
Confidence 43
No 51
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=41.11 E-value=62 Score=24.70 Aligned_cols=37 Identities=22% Similarity=0.316 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhccC--C---CChhHHHHHhh
Q 033020 56 LVEDIVVEYVSDLAHKAQDLGSKRG--K---LSVEDFLYLIR 92 (129)
Q Consensus 56 liEdIV~~~i~~l~~~A~~~A~~Rg--k---is~eDl~FllR 92 (129)
-+-++.+.|-++++..|.-.|...| . +++||+..++-
T Consensus 39 QLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~a 80 (145)
T COG5094 39 QLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALA 80 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHH
Confidence 3456889999999999998887544 3 78899999886
No 52
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=40.97 E-value=24 Score=25.53 Aligned_cols=32 Identities=22% Similarity=0.220 Sum_probs=27.0
Q ss_pred hhHHHHHhhcChhhHhHHHHHHHHHHHHHHHH
Q 033020 84 VEDFLYLIRKDPPKLNRCTELLSMQEELKQAR 115 (129)
Q Consensus 84 ~eDl~FllR~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 34788999999999999999999888887763
No 53
>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=38.89 E-value=93 Score=20.70 Aligned_cols=29 Identities=28% Similarity=0.285 Sum_probs=23.2
Q ss_pred cCCCChhHHHHHhh-cChhhHhHHHHHHHH
Q 033020 79 RGKLSVEDFLYLIR-KDPPKLNRCTELLSM 107 (129)
Q Consensus 79 Rgkis~eDl~FllR-~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 599999999999974
No 54
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=36.90 E-value=96 Score=24.16 Aligned_cols=43 Identities=19% Similarity=0.363 Sum_probs=36.4
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhh
Q 033020 50 LPETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIR 92 (129)
Q Consensus 50 ~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR 92 (129)
..|+.+++-+--++||.-|.+.|.+++....| |..|.++-+|-
T Consensus 33 akeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe 77 (156)
T KOG0871|consen 33 AKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALE 77 (156)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHH
Confidence 46788899999999999999999999976543 99888887776
No 55
>PLN00157 histone H2A; Provisional
Probab=36.29 E-value=77 Score=23.97 Aligned_cols=31 Identities=23% Similarity=0.307 Sum_probs=21.2
Q ss_pred HHHHHHHHHHhhhccCCCChhHHHHHhhcChh
Q 033020 65 VSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPP 96 (129)
Q Consensus 65 i~~l~~~A~~~A~~Rgkis~eDl~FllR~D~~ 96 (129)
|.+|.-++..-. .+.+|+.++|.-++|+|..
T Consensus 64 VLELAgnaa~d~-kk~RItPrHi~lAI~nDeE 94 (132)
T PLN00157 64 VLELAGNAARDN-KKSRIVPRHIQLAVRNDEE 94 (132)
T ss_pred HHHHHHHHHHhc-CCccccHHHHhhcccCcHH
Confidence 555554444322 2346999999999999974
No 56
>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=35.75 E-value=38 Score=23.54 Aligned_cols=35 Identities=23% Similarity=0.419 Sum_probs=27.0
Q ss_pred ChhHHHHHhhcC--hhhHhHHHHHHHHHHHHHHHHhc
Q 033020 83 SVEDFLYLIRKD--PPKLNRCTELLSMQEELKQARKA 117 (129)
Q Consensus 83 s~eDl~FllR~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 356789999865 67888899999887777776554
No 57
>PHA00724 hypothetical protein
Probab=35.73 E-value=26 Score=24.29 Aligned_cols=35 Identities=29% Similarity=0.274 Sum_probs=30.0
Q ss_pred HHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Q 033020 39 MMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQ 73 (129)
Q Consensus 39 mMy~fGD~~~P~~eTv~liEdIV~~~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 68899999988888888999999999999875544
No 58
>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=34.87 E-value=1.6e+02 Score=20.66 Aligned_cols=59 Identities=15% Similarity=0.272 Sum_probs=41.6
Q ss_pred HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC---CCChhHHHHHhhc
Q 033020 35 DLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG---KLSVEDFLYLIRK 93 (129)
Q Consensus 35 EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rg---kis~eDl~FllR~ 93 (129)
-|+.+|=.+=....+.+..+-+|-.+-.-|+-||+..|..+....+ .|.+..|.-+.|+
T Consensus 28 ~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rr 89 (90)
T PF04719_consen 28 AIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRR 89 (90)
T ss_dssp HHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHh
Confidence 5667765554447788888899999999999999999999987544 4888877766653
No 59
>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=34.82 E-value=65 Score=19.32 Aligned_cols=42 Identities=24% Similarity=0.406 Sum_probs=33.0
Q ss_pred hhHHHHHhhcChhhHhHHHHHHHHHHHHHHHHh-ccccChhhh
Q 033020 84 VEDFLYLIRKDPPKLNRCTELLSMQEELKQARK-AFEVDEEKL 125 (129)
Q Consensus 84 ~eDl~FllR~D~~Kl~Rl~~lL~~k~~ik~Ark-~fd~~~~~~ 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 567788888999888888888888888888886 666665544
No 60
>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=33.04 E-value=1.3e+02 Score=19.12 Aligned_cols=34 Identities=24% Similarity=0.252 Sum_probs=29.5
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 033020 46 DPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKR 79 (129)
Q Consensus 46 ~~~P~~eTv~liEdIV~~~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 4557788889999999999999999999998655
No 61
>PTZ00252 histone H2A; Provisional
Probab=32.90 E-value=86 Score=23.84 Aligned_cols=18 Identities=17% Similarity=0.263 Sum_probs=15.4
Q ss_pred cCCCChhHHHHHhhcChh
Q 033020 79 RGKLSVEDFLYLIRKDPP 96 (129)
Q Consensus 79 Rgkis~eDl~FllR~D~~ 96 (129)
+.+|+++.|.-++|+|..
T Consensus 78 k~RItPrHi~lAIrNDeE 95 (134)
T PTZ00252 78 PKRLTPRTVTLAVRHDDD 95 (134)
T ss_pred cccccHHHHHhhccChHH
Confidence 346999999999999964
No 62
>PRK12333 nucleoside triphosphate pyrophosphohydrolase; Reviewed
Probab=32.73 E-value=2.7e+02 Score=22.51 Aligned_cols=57 Identities=19% Similarity=0.331 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHHHHh---hhccCCCChhHHHH-----HhhcChh-----hHhHHHHHHHHHHHHHHHHhc
Q 033020 61 VVEYVSDLAHKAQDL---GSKRGKLSVEDFLY-----LIRKDPP-----KLNRCTELLSMQEELKQARKA 117 (129)
Q Consensus 61 V~~~i~~l~~~A~~~---A~~Rgkis~eDl~F-----llR~D~~-----Kl~Rl~~lL~~k~~ik~Ark~ 117 (129)
+.+-+-+++.+..-+ |.-+|.++++|++- ++|+.|. +..=..+.+..++.||++.|.
T Consensus 51 l~EELGDlLlqVvfha~iaee~g~F~~~DV~~~i~~KlirRHPHVFg~~~~~~~~ev~~~We~iK~~Ek~ 120 (204)
T PRK12333 51 LAEELGDVLLQVAFHSVIAEEEGRFTYPDVERGIVEKLIRRHPHVFGDVQVSGPEEVVANWQAIKAAERG 120 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccCCccCCCCCCCCHHHHHHHHHHHHHHHHh
Confidence 344455555555444 34578999999985 5677773 333457888888999988773
No 63
>PF14164 YqzH: YqzH-like protein
Probab=31.60 E-value=44 Score=22.37 Aligned_cols=20 Identities=30% Similarity=0.632 Sum_probs=17.7
Q ss_pred CCCcHHHHHHHHHHHHHHHH
Q 033020 47 PNPLPETVALVEDIVVEYVS 66 (129)
Q Consensus 47 ~~P~~eTv~liEdIV~~~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 64
>PTZ00017 histone H2A; Provisional
Probab=30.46 E-value=98 Score=23.45 Aligned_cols=37 Identities=22% Similarity=0.292 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChh
Q 033020 59 DIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPP 96 (129)
Q Consensus 59 dIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~D~~ 96 (129)
|++...|.+|.-++..-. .+.+|+.++|.-++|+|..
T Consensus 59 EYLtaEILELAgNaa~d~-kk~RItPrHi~lAI~nDeE 95 (134)
T PTZ00017 59 EYLTAEVLELAGNAAKDN-KKKRITPRHIQLAIRNDEE 95 (134)
T ss_pred HHHHHHHHHHHHHHHHhc-CCCeecHHHHHhhccCcHH
Confidence 334433555555544322 2345999999999999974
No 65
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=29.23 E-value=97 Score=19.05 Aligned_cols=34 Identities=21% Similarity=0.362 Sum_probs=27.0
Q ss_pred cHHHHHHHHhhhCCCCCCcHHHHH-HHHHHHHHHH
Q 033020 32 FQKDLQHMMYGFGDDPNPLPETVA-LVEDIVVEYV 65 (129)
Q Consensus 32 f~~EI~~mMy~fGD~~~P~~eTv~-liEdIV~~~i 65 (129)
=..||+..|-.||-..-|..+|.. ++|.=+..++
T Consensus 7 Sd~eL~~~L~~~G~~~gPIt~sTR~vy~kkL~~~~ 41 (44)
T smart00540 7 SDAELRAELKQYGLPPGPITDTTRKLYEKKLRKLR 41 (44)
T ss_pred CHHHHHHHHHHcCCCCCCcCcchHHHHHHHHHHHH
Confidence 357999999999999999988776 6666665544
No 66
>PLN00156 histone H2AX; Provisional
Probab=28.38 E-value=1.2e+02 Score=23.11 Aligned_cols=37 Identities=19% Similarity=0.268 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChh
Q 033020 59 DIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPP 96 (129)
Q Consensus 59 dIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~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 333333555555554332 2346999999999999964
No 67
>COG3956 Protein containing tetrapyrrole methyltransferase domain and MazG-like (predicted pyrophosphatase) domain [General function prediction only]
Probab=28.33 E-value=2.2e+02 Score=25.52 Aligned_cols=60 Identities=23% Similarity=0.421 Sum_probs=44.6
Q ss_pred HHHHHHHHHHHHHHHhhhc---cCCCChhHHHH-----HhhcCh-----hhHhHHHHHHHHHHHHHHHHhccc
Q 033020 60 IVVEYVSDLAHKAQDLGSK---RGKLSVEDFLY-----LIRKDP-----PKLNRCTELLSMQEELKQARKAFE 119 (129)
Q Consensus 60 IV~~~i~~l~~~A~~~A~~---Rgkis~eDl~F-----llR~D~-----~Kl~Rl~~lL~~k~~ik~Ark~fd 119 (129)
.+++.+-+++.+..-.|+. -|-+.++|++- .+|+.| .++.-..++|..++++|+|.+...
T Consensus 283 hmvEELGDvLlQVllHaqIGkdeGyf~I~dVI~~i~~KMIrRHPHvF~d~qve~~~dv~e~WdeiKkae~~~q 355 (488)
T COG3956 283 HMVEELGDVLLQVLLHAQIGKDEGYFNINDVISGISEKMIRRHPHVFKDEQVEDSTDVLEKWDEIKKAEKDLQ 355 (488)
T ss_pred hHHHHHHHHHHHHHHHHhhcccCCeeeHHHHHHHHHHHHHHhCcccccccccccHHHHHHHHHHHHHHhcCCC
Confidence 3667777777777777754 34599999985 467776 456667899999999999988633
No 68
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=27.61 E-value=1.3e+02 Score=26.52 Aligned_cols=46 Identities=20% Similarity=0.283 Sum_probs=34.6
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHhh--hccCCCChhHHHHHhhc
Q 033020 48 NPLPETVALVEDIVVEYVSDLAHKAQDLG--SKRGKLSVEDFLYLIRK 93 (129)
Q Consensus 48 ~P~~eTv~liEdIV~~~i~~l~~~A~~~A--~~Rgkis~eDl~FllR~ 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 45566666655556666889999999865 35667999999999993
No 69
>PRK09562 mazG nucleoside triphosphate pyrophosphohydrolase; Reviewed
Probab=27.60 E-value=3.5e+02 Score=22.25 Aligned_cols=57 Identities=19% Similarity=0.271 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHhhh---ccCCCChhHHH------HHhhcChh----hHhHHHHHHHHHHHHHHHHhc
Q 033020 61 VVEYVSDLAHKAQDLGS---KRGKLSVEDFL------YLIRKDPP----KLNRCTELLSMQEELKQARKA 117 (129)
Q Consensus 61 V~~~i~~l~~~A~~~A~---~Rgkis~eDl~------FllR~D~~----Kl~Rl~~lL~~k~~ik~Ark~ 117 (129)
+.+-|-+++.....+|. .+|.+.++|.+ |.-||-.. ...-+.++...++.+|+..|.
T Consensus 60 l~eElGDvL~~vv~~a~~~~e~~~~d~e~vl~~~~~K~~~R~p~vf~~~~~~s~~e~~~~We~~K~~ek~ 129 (262)
T PRK09562 60 LREELGDLLLQVVFHAQMAEEQGAFDFADVVEAISDKLIRRHPHVFGDVEAESSEEVLANWEQIKAEERA 129 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHhhhchhhccCCCCCCHHHHHHHHHHHHHHHHh
Confidence 45566677776666654 46789999988 55454422 233467888888888888764
No 70
>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=27.51 E-value=82 Score=23.33 Aligned_cols=34 Identities=15% Similarity=0.271 Sum_probs=24.5
Q ss_pred hhhCCCCCCcHHHHH-HHHHHHHHHHHHHHHHHHH
Q 033020 41 YGFGDDPNPLPETVA-LVEDIVVEYVSDLAHKAQD 74 (129)
Q Consensus 41 y~fGD~~~P~~eTv~-liEdIV~~~i~~l~~~A~~ 74 (129)
|--+....+-.+||. ++|+.|-.+|+-+|.+=.+
T Consensus 22 Fe~~~~~~~~~~Tv~d~vee~ia~~im~vc~Qnp~ 56 (113)
T PF12290_consen 22 FESSQSGDTGDETVEDVVEEQIASQIMAVCEQNPE 56 (113)
T ss_pred hcCCCCCCcccchHHHHHHHHHHHHHHHHHccCCC
Confidence 443455667778876 8888888888888865443
No 71
>PLN00153 histone H2A; Provisional
Probab=26.75 E-value=1.4e+02 Score=22.50 Aligned_cols=36 Identities=22% Similarity=0.258 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChh
Q 033020 60 IVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPP 96 (129)
Q Consensus 60 IV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~D~~ 96 (129)
++.-.|.+|.-+|..-. .+.+|+++.|.-++|+|..
T Consensus 57 YLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~nDeE 92 (129)
T PLN00153 57 YLTAEVLELAGNAARDN-KKNRIVPRHIQLAIRNDEE 92 (129)
T ss_pred HHHHHHHHHHHHHHHhc-CCCccChHHHHhhccCcHH
Confidence 33333555555544332 2446999999999999964
No 72
>TIGR00444 mazG MazG family protein. This family of prokaryotic proteins has no known function. It includes the uncharacterized protein MazG in E. coli.
Probab=26.45 E-value=3.6e+02 Score=22.08 Aligned_cols=57 Identities=26% Similarity=0.370 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHhh---hccCCCChhHHHH-----HhhcChh-----hHhHHHHHHHHHHHHHHHHhc
Q 033020 61 VVEYVSDLAHKAQDLG---SKRGKLSVEDFLY-----LIRKDPP-----KLNRCTELLSMQEELKQARKA 117 (129)
Q Consensus 61 V~~~i~~l~~~A~~~A---~~Rgkis~eDl~F-----llR~D~~-----Kl~Rl~~lL~~k~~ik~Ark~ 117 (129)
+.+-+-+|+.....+| ...|.++++|++- ++|+.|. +..=+.++....+.+|+..|.
T Consensus 46 l~eELGDlL~qvv~~a~iar~~g~f~~edvl~~~~~K~irRhphVf~~~~~~s~~e~~~~We~~K~~Ek~ 115 (248)
T TIGR00444 46 LREELGDLLLQVVFYAQMAQEEGYFDFDDVCAGISEKLVRRHPHVFADVKAEDESEVLARWEQIKAEEKA 115 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhchhhhhccccCCHHHHHHHHHHHHHHHHh
Confidence 4556777777777775 5678899999973 2344332 222367888888889988764
No 73
>PF01795 Methyltransf_5: MraW methylase family; InterPro: IPR002903 This is a family of S-adenosyl-L-methionine-dependent methyltransferases, which are found primarily, though not exclusively, in bacteria. The Escherichia coli protein is essential and has been linked to peptidoglycan biosynthesis [, ].; GO: 0008168 methyltransferase activity; PDB: 1N2X_A 1M6Y_A 1WG8_A 3TKA_A.
Probab=26.42 E-value=1.1e+02 Score=26.03 Aligned_cols=53 Identities=17% Similarity=0.268 Sum_probs=32.9
Q ss_pred ccHHHHHHHHhhhCCCCCCcHHHHHHHHHH------HHHHHHHHHHHHHHhhhccCCCC
Q 033020 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDI------VVEYVSDLAHKAQDLGSKRGKLS 83 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD~~~P~~eTv~liEdI------V~~~i~~l~~~A~~~A~~Rgkis 83 (129)
+=..||..++|-|||.++...-...+++.- -+.++.+++..|.....+++++.
T Consensus 142 ~se~~L~~I~~~yGee~~a~~IA~~Iv~~R~~~pi~tT~~L~~iI~~~~~~~~~~~~~h 200 (310)
T PF01795_consen 142 YSEEELARIFREYGEEKFARRIARAIVEARKKKPITTTKELAEIIEKAVPKKRRRRKIH 200 (310)
T ss_dssp S-HHHHHHHHHHHH--TTHHHHHHHHHHHHHHSS--BHHHHHHHHHHHS-HHHCC-SS-
T ss_pred cCHHHHHHHHHhcCchhHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCcccccccCC
Confidence 345799999999999887666666666654 25667777777776554444443
No 74
>COG1422 Predicted membrane protein [Function unknown]
Probab=26.27 E-value=80 Score=25.52 Aligned_cols=25 Identities=20% Similarity=0.484 Sum_probs=18.4
Q ss_pred cChhhHhHHHHHHH-HHHHHHHHHhc
Q 033020 93 KDPPKLNRCTELLS-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 47788888877654 57788888774
No 75
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=25.79 E-value=2.8e+02 Score=20.48 Aligned_cols=78 Identities=10% Similarity=0.075 Sum_probs=56.7
Q ss_pred cccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccC--CCChhHHHHHhhcChhhHhHHHHHHHH
Q 033020 30 GVFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRG--KLSVEDFLYLIRKDPPKLNRCTELLSM 107 (129)
Q Consensus 30 ~~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rg--kis~eDl~FllR~D~~Kl~Rl~~lL~~ 107 (129)
+.-..-|+.+|-.--|.-.-..-|--++-.-+--||++|+...++.|...+ +++.|-|.-++-+|+ |+.-|++++..
T Consensus 23 rFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sde-kFdFL~~~~~~ 101 (113)
T COG5247 23 RFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDE-KFDFLKNMEQF 101 (113)
T ss_pred cCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhH-HHHHHHHHHHh
Confidence 455677888998776665544455556666677788888888888875444 499999999998885 67777777754
Q ss_pred H
Q 033020 108 Q 108 (129)
Q Consensus 108 k 108 (129)
+
T Consensus 102 ~ 102 (113)
T COG5247 102 K 102 (113)
T ss_pred c
Confidence 3
No 76
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=24.90 E-value=2.1e+02 Score=22.42 Aligned_cols=81 Identities=16% Similarity=0.231 Sum_probs=48.6
Q ss_pred cccHHHHHHHHhhhCCCCCCcH-------HHHHHHHHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChhhHhHHH
Q 033020 30 GVFQKDLQHMMYGFGDDPNPLP-------ETVALVEDIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPPKLNRCT 102 (129)
Q Consensus 30 ~~f~~EI~~mMy~fGD~~~P~~-------eTv~liEdIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~D~~Kl~Rl~ 102 (129)
.-|+.++++|+-..|=.+--.. .+...-..=|-.+|.++|..... ...|-|++.|+.-.+.+.+.. .
T Consensus 57 ~~~r~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c~~~~~--~~GGii~L~dl~~~~nr~R~g----~ 130 (223)
T PF04157_consen 57 PEFRSQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVCLATRS--KNGGIISLSDLYCRYNRARGG----S 130 (223)
T ss_dssp HHHHHHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHHHHHCC--TTTSEEEHHHHHHHHHHCTTT----S
T ss_pred chHHHHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHHHHHHh--cCCCEEEHHHHHHHHHHhccc----C
Confidence 5788899999998885432111 24443333345577777773332 223459999999888874422 3
Q ss_pred HHHHHHHHHHHHHh
Q 033020 103 ELLSMQEELKQARK 116 (129)
Q Consensus 103 ~lL~~k~~ik~Ark 116 (129)
++++-+|.++.++.
T Consensus 131 ~lISp~Di~~A~~~ 144 (223)
T PF04157_consen 131 ELISPEDILRACKL 144 (223)
T ss_dssp ST--HHHHHHHHHH
T ss_pred CCcCHHHHHHHHHH
Confidence 37787887776665
No 77
>KOG2076 consensus RNA polymerase III transcription factor TFIIIC [Transcription]
Probab=24.37 E-value=1.1e+02 Score=29.93 Aligned_cols=33 Identities=15% Similarity=0.431 Sum_probs=25.2
Q ss_pred cccccccHHHHHHHH------hhhCCCCCCcHHHHHHHHHHHH
Q 033020 26 KRKRGVFQKDLQHMM------YGFGDDPNPLPETVALVEDIVV 62 (129)
Q Consensus 26 ~~~k~~f~~EI~~mM------y~fGD~~~P~~eTv~liEdIV~ 62 (129)
.+.+.....||++|| |+.||- .+...+..|||.
T Consensus 129 ~r~~~~l~~~l~~ll~eAN~lfarg~~----eeA~~i~~EvIk 167 (895)
T KOG2076|consen 129 SRGKSKLAPELRQLLGEANNLFARGDL----EEAEEILMEVIK 167 (895)
T ss_pred CCcccccCHHHHHHHHHHHHHHHhCCH----HHHHHHHHHHHH
Confidence 356778999999998 999984 566667777665
No 78
>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=23.97 E-value=2.2e+02 Score=18.64 Aligned_cols=44 Identities=20% Similarity=0.228 Sum_probs=28.8
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhh
Q 033020 49 PLPETVALVEDIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIR 92 (129)
Q Consensus 49 P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR 92 (129)
+.+-..+++|-+.-++-++-+-.+..-|-.+|+|+++.++=.+|
T Consensus 7 ~~~l~~Ql~el~Aed~AieDtiy~L~~al~~g~I~~d~~lK~vR 50 (65)
T PF09454_consen 7 EDPLSNQLYELVAEDHAIEDTIYYLDRALQRGSIDLDTFLKQVR 50 (65)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 34455566666666666666666666666789999988876555
No 79
>KOG2028 consensus ATPase related to the helicase subunit of the Holliday junction resolvase [Replication, recombination and repair]
Probab=23.43 E-value=93 Score=28.25 Aligned_cols=60 Identities=27% Similarity=0.548 Sum_probs=45.3
Q ss_pred hhCCCCC---CcHHHHHHHHHHHHHHHHHHH-------HHHHHhh-----hccC-----CCChhHHHHHhhcChhhHhHH
Q 033020 42 GFGDDPN---PLPETVALVEDIVVEYVSDLA-------HKAQDLG-----SKRG-----KLSVEDFLYLIRKDPPKLNRC 101 (129)
Q Consensus 42 ~fGD~~~---P~~eTv~liEdIV~~~i~~l~-------~~A~~~A-----~~Rg-----kis~eDl~FllR~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 3569888 788877889999999999987 3455554 2344 399999999888877666664
No 80
>COG1013 PorB Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit [Energy production and conversion]
Probab=23.33 E-value=44 Score=27.98 Aligned_cols=61 Identities=18% Similarity=0.164 Sum_probs=36.3
Q ss_pred CCCCCCCCCCCCCCCCCccccccccccHH-HHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHh
Q 033020 6 AGQSSKSKAGSSQPCETTSFKRKRGVFQK-DLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDL 75 (129)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~k~~f~~-EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~ 75 (129)
-+|.|+|++-...+.-+...|+ .+.+ ++-.||-++|- |...++.+-. ..+++..+.+|.+.
T Consensus 132 ggQ~S~tTp~G~~t~t~p~Gk~---~~~k~d~~~la~a~G~---~yVAr~~~~~---~~~l~~~i~kA~~~ 193 (294)
T COG1013 132 GGQASPTTPKGAKTKTTPYGKR---SEKKKDPGLLAMAAGA---TYVARASVGD---PKDLTEKIKKAAEH 193 (294)
T ss_pred CCccCCCCCCCceeeecCCCCC---cCCCCCHHHHHHHCCC---CeEEEecccC---HHHHHHHHHHHHhc
Confidence 3566666665555443333222 1144 78888988883 6666666555 55666666666654
No 81
>PRK15067 ethanolamine ammonia lyase large subunit; Provisional
Probab=23.06 E-value=57 Score=29.44 Aligned_cols=34 Identities=29% Similarity=0.530 Sum_probs=26.9
Q ss_pred cccccHHHHHHHHhhhCCCC---CCcHHHHHHHHHHH
Q 033020 28 KRGVFQKDLQHMMYGFGDDP---NPLPETVALVEDIV 61 (129)
Q Consensus 28 ~k~~f~~EI~~mMy~fGD~~---~P~~eTv~liEdIV 61 (129)
-++....-+.-++||.||.- ||-.+++.-+..++
T Consensus 170 ~~gI~asvldGL~yG~GDAVIGiNPa~Ds~~~~~~ll 206 (461)
T PRK15067 170 PDGIAASILDGLSYGVGDAVIGINPATDSVENVSRLL 206 (461)
T ss_pred HHHHHHHHHHHHhhcCCCeEEecCCCCCCHHHHHHHH
Confidence 56888999999999999974 88887776555444
No 82
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=22.92 E-value=1.3e+02 Score=21.74 Aligned_cols=74 Identities=26% Similarity=0.395 Sum_probs=44.7
Q ss_pred ccHHHHHHHHhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChhhHhHHHHHHHHHHH
Q 033020 31 VFQKDLQHMMYGFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPPKLNRCTELLSMQEE 110 (129)
Q Consensus 31 ~f~~EI~~mMy~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~D~~Kl~Rl~~lL~~k~~ 110 (129)
.-..|+...|-.+|-. |..+ .+.++..+.-. ..-|.|+.++|+-++.+......-.. .-.++
T Consensus 25 i~~~el~~~lr~lg~~--~t~~-----------el~~~~~~~D~--dg~g~I~~~eF~~l~~~~~~~~~~~~---~~~~e 86 (151)
T KOG0027|consen 25 ISVEELGAVLRSLGQN--PTEE-----------ELRDLIKEIDL--DGDGTIDFEEFLDLMEKLGEEKTDEE---ASSEE 86 (151)
T ss_pred ccHHHHHHHHHHcCCC--CCHH-----------HHHHHHHHhCC--CCCCeEcHHHHHHHHHhhhccccccc---ccHHH
Confidence 5578999999999975 2221 11222222111 13567999999998875533211111 34558
Q ss_pred HHHHHhccccCh
Q 033020 111 LKQARKAFEVDE 122 (129)
Q Consensus 111 ik~Ark~fd~~~ 122 (129)
+++|-+.||.|.
T Consensus 87 l~eaF~~fD~d~ 98 (151)
T KOG0027|consen 87 LKEAFRVFDKDG 98 (151)
T ss_pred HHHHHHHHccCC
Confidence 899999998874
No 83
>PF01885 PTS_2-RNA: RNA 2'-phosphotransferase, Tpt1 / KptA family; InterPro: IPR002745 The final step of tRNA splicing in Saccharomyces cerevisiae (Baker's yeast) requires 2'-phosphotransferase (Tpt1) to transfer the 2'-phosphate from ligated tRNA to NAD, producing mature tRNA and ADP ribose-1' '-2' '-cyclic phosphate. Yeast and Mus musculus (Mouse) Tpt1 protein and bacterial KptA protein can catalyze the conversion of the generated intermediate to both product and the original substrate, these enzymes likely use the same reaction mechanism. Step 1 of this reaction is strikingly similar to the ADP-ribosylation of proteins catalyzed by a number of bacterial toxins. KptA, a functional Tpt1 protein homologue from Escherichia coli is strikingly similar to yeast Tpt1 in its kinetic parameters, although E. coli is not known to have a 2'-phosphorylated RNA substrate [,].; GO: 0016772 transferase activity, transferring phosphorus-containing groups, 0006388 tRNA splicing, via endonucleolytic cleavage and ligation; PDB: 1WFX_A.
Probab=22.25 E-value=85 Score=24.45 Aligned_cols=15 Identities=40% Similarity=0.570 Sum_probs=7.7
Q ss_pred CCCChhHHHHHhhcC
Q 033020 80 GKLSVEDFLYLIRKD 94 (129)
Q Consensus 80 gkis~eDl~FllR~D 94 (129)
|-++++||+=.++..
T Consensus 31 G~v~v~dLL~~~~~~ 45 (186)
T PF01885_consen 31 GWVSVDDLLRALRFK 45 (186)
T ss_dssp --EEHHHHHHHHHHT
T ss_pred CCEeHHHHHHHHHHc
Confidence 346666666555553
No 84
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=22.14 E-value=2.6e+02 Score=23.07 Aligned_cols=44 Identities=20% Similarity=0.277 Sum_probs=34.0
Q ss_pred CcHHHHHHHHHHH------HHHHHHHHHHHHHhhhccCC--CChhHHHHHhh
Q 033020 49 PLPETVALVEDIV------VEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIR 92 (129)
Q Consensus 49 P~~eTv~liEdIV------~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR 92 (129)
-.++.+.++-+++ ..++.++|..|...|..+|. |+.+|+.=++.
T Consensus 229 ~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~ 280 (394)
T PRK00411 229 VDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYE 280 (394)
T ss_pred CCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHH
Confidence 4567777777777 66778999999998876664 89999976665
No 85
>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=21.95 E-value=1.1e+02 Score=23.40 Aligned_cols=73 Identities=19% Similarity=0.262 Sum_probs=44.6
Q ss_pred hhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc-------cCCCChhHHHHHhhcChhhHhH--HHHHHHHHHHHH
Q 033020 42 GFGDDPNPLPETVALVEDIVVEYVSDLAHKAQDLGSK-------RGKLSVEDFLYLIRKDPPKLNR--CTELLSMQEELK 112 (129)
Q Consensus 42 ~fGD~~~P~~eTv~liEdIV~~~i~~l~~~A~~~A~~-------Rgkis~eDl~FllR~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 5555555555555555544444445777777766542 23477777776664 4444566 788899877776
Q ss_pred HHH
Q 033020 113 QAR 115 (129)
Q Consensus 113 ~Ar 115 (129)
+.-
T Consensus 92 ~~~ 94 (159)
T PF11861_consen 92 KEL 94 (159)
T ss_pred HHH
Confidence 654
No 86
>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=21.95 E-value=4.7e+02 Score=21.79 Aligned_cols=33 Identities=24% Similarity=0.349 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHhhhc---------cCC-C--ChhHHHHHhhcC
Q 033020 62 VEYVSDLAHKAQDLGSK---------RGK-L--SVEDFLYLIRKD 94 (129)
Q Consensus 62 ~~~i~~l~~~A~~~A~~---------Rgk-i--s~eDl~FllR~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 34456667888887764 122 2 279999999965
No 87
>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=21.64 E-value=5.1e+02 Score=23.77 Aligned_cols=39 Identities=18% Similarity=0.218 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHhhhccCC--CChhHHHHHhhcChhhHhHH
Q 033020 63 EYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRKDPPKLNRC 101 (129)
Q Consensus 63 ~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~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 77777776665444433443
No 88
>PLN00154 histone H2A; Provisional
Probab=20.76 E-value=2.4e+02 Score=21.52 Aligned_cols=37 Identities=22% Similarity=0.202 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcChh
Q 033020 59 DIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKDPP 96 (129)
Q Consensus 59 dIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~D~~ 96 (129)
|+|.-.|.+|.-+|.+-. .+.+|+..+|.-++|+|..
T Consensus 71 EYLtAEVLELAGNaA~d~-kk~RItPrHi~lAIrnDeE 107 (136)
T PLN00154 71 EYLTAEVLELAGNASKDL-KVKRITPRHLQLAIRGDEE 107 (136)
T ss_pred HHHHHHHHHHHHHHHHhh-CCceecHHHhhhhccCcHH
Confidence 334433455554444332 2345999999999999964
No 89
>PRK05481 lipoyl synthase; Provisional
Probab=20.71 E-value=25 Score=28.92 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=19.0
Q ss_pred HHHHhhhCCCCCCcHHHHHHHHHH
Q 033020 37 QHMMYGFGDDPNPLPETVALVEDI 60 (129)
Q Consensus 37 ~~mMy~fGD~~~P~~eTv~liEdI 60 (129)
..||+|||++.+=..+|..+++++
T Consensus 200 t~~IvGfGET~ed~~~tl~~lrel 223 (289)
T PRK05481 200 SGLMVGLGETDEEVLEVMDDLRAA 223 (289)
T ss_pred eeeEEECCCCHHHHHHHHHHHHhc
Confidence 458899999887777777777765
No 90
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=20.21 E-value=88 Score=27.65 Aligned_cols=42 Identities=14% Similarity=0.186 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhccCC--CChhHHHHHhhc
Q 033020 52 ETVALVEDIVVEYVSDLAHKAQDLGSKRGK--LSVEDFLYLIRK 93 (129)
Q Consensus 52 eTv~liEdIV~~~i~~l~~~A~~~A~~Rgk--is~eDl~FllR~ 93 (129)
+-+...+.+.--.|..+|..|...|.++++ |+.+||.-++++
T Consensus 380 ~la~~t~g~sgAdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 380 EFIMAKDELSGADIKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 344455666677788899999998877664 999999887765
No 91
>TIGR03285 methan_mark_14 putative methanogenesis marker protein 14. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it.
Probab=20.10 E-value=55 Score=29.21 Aligned_cols=33 Identities=21% Similarity=0.415 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHhhhccCCCChhHHHHHhhcC
Q 033020 58 EDIVVEYVSDLAHKAQDLGSKRGKLSVEDFLYLIRKD 94 (129)
Q Consensus 58 EdIV~~~i~~l~~~A~~~A~~Rgkis~eDl~FllR~D 94 (129)
.|-|.+-+.+.+.++++-| .++++||-|++|.-
T Consensus 62 resV~elV~dtl~e~~k~A----~l~i~DL~FVVRST 94 (445)
T TIGR03285 62 RESVAELVKDTLKESLKKA----GLDIDDLDFVVRST 94 (445)
T ss_pred HHHHHHHHHHHHHHHHHHc----CCChhhccEEEecc
Confidence 3333444444555555544 48888999999953
Done!