Query 033783
Match_columns 111
No_of_seqs 103 out of 221
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 06:14:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033783.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033783hhsearch_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 1.3E-40 2.7E-45 228.3 11.5 90 12-101 2-92 (92)
2 PF02269 TFIID-18kDa: Transcri 100.0 3.8E-40 8.3E-45 225.7 2.2 91 12-102 1-93 (93)
3 KOG3901 Transcription initiati 100.0 6.8E-38 1.5E-42 219.0 11.1 93 11-104 8-100 (109)
4 COG5248 TAF19 Transcription in 100.0 8.2E-31 1.8E-35 185.6 10.8 96 10-105 7-102 (126)
5 KOG3902 Histone acetyltransfer 99.8 6.7E-21 1.5E-25 153.8 10.7 88 12-99 24-114 (352)
6 smart00576 BTP Bromodomain tra 97.3 0.0016 3.5E-08 42.6 7.2 62 12-75 6-70 (77)
7 cd07981 TAF12 TATA Binding Pro 97.2 0.0032 7E-08 40.9 7.8 59 18-76 7-67 (72)
8 PF03847 TFIID_20kDa: Transcri 97.2 0.0022 4.8E-08 41.7 6.5 60 17-76 4-65 (68)
9 PF07524 Bromo_TP: Bromodomain 96.9 0.0067 1.5E-07 39.3 7.0 62 12-75 6-70 (77)
10 PF00808 CBFD_NFYB_HMF: Histon 96.8 0.0078 1.7E-07 37.8 6.2 57 17-73 7-65 (65)
11 PF15630 CENP-S: Kinetochore c 96.1 0.02 4.3E-07 38.1 5.5 50 29-78 24-75 (76)
12 smart00803 TAF TATA box bindin 96.1 0.031 6.8E-07 35.9 6.1 56 18-74 8-65 (65)
13 PLN00035 histone H4; Provision 96.0 0.05 1.1E-06 38.3 7.4 63 13-76 30-94 (103)
14 cd00076 H4 Histone H4, one of 95.7 0.091 2E-06 35.7 7.2 64 12-76 13-78 (85)
15 PF00125 Histone: Core histone 95.4 0.07 1.5E-06 33.9 5.7 48 29-76 26-75 (75)
16 PTZ00015 histone H4; Provision 95.2 0.088 1.9E-06 36.9 6.2 63 13-76 31-95 (102)
17 PF02969 TAF: TATA box binding 94.7 0.3 6.6E-06 31.6 7.2 46 29-74 19-66 (66)
18 cd07979 TAF9 TATA Binding Prot 94.1 0.36 7.9E-06 34.2 7.2 56 19-75 8-65 (117)
19 COG2036 HHT1 Histones H3 and H 92.9 0.42 9E-06 32.9 5.7 58 17-75 24-83 (91)
20 KOG1142 Transcription initiati 92.9 0.2 4.3E-06 40.4 4.6 60 16-76 158-220 (258)
21 KOG0869 CCAAT-binding factor, 92.2 0.43 9.3E-06 36.2 5.4 49 27-75 48-98 (168)
22 smart00417 H4 Histone H4. 91.2 0.49 1.1E-05 31.4 4.3 59 13-72 14-74 (74)
23 KOG3902 Histone acetyltransfer 91.1 1.1 2.3E-05 37.4 7.1 79 17-99 80-161 (352)
24 PF02291 TFIID-31kDa: Transcri 89.3 1.8 3.9E-05 31.4 6.3 54 20-74 20-75 (129)
25 cd08050 TAF6 TATA Binding Prot 86.7 2.7 5.8E-05 34.5 6.5 48 28-75 14-63 (343)
26 KOG2549 Transcription initiati 81.0 4.4 9.5E-05 36.1 5.8 47 29-75 27-75 (576)
27 cd08045 TAF4 TATA Binding Prot 80.7 7.7 0.00017 29.6 6.5 67 16-82 48-117 (212)
28 PF05236 TAF4: Transcription i 79.9 2.8 6.1E-05 32.9 3.9 76 18-94 53-129 (264)
29 smart00428 H3 Histone H3. 79.7 16 0.00034 25.7 7.3 47 28-74 51-99 (105)
30 cd08048 TAF11 TATA Binding Pro 73.9 24 0.00052 23.7 7.4 62 13-75 17-83 (85)
31 PF09415 CENP-X: CENP-S associ 73.0 4.2 9.1E-05 26.6 2.7 44 27-70 16-62 (72)
32 KOG4336 TBP-associated transcr 70.8 14 0.0003 30.8 5.8 74 15-91 8-85 (323)
33 PF02787 CPSase_L_D3: Carbamoy 67.2 26 0.00057 24.8 6.0 37 58-95 19-55 (123)
34 cd00074 H2A Histone 2A; H2A is 65.9 21 0.00047 25.3 5.3 31 48-78 56-88 (115)
35 KOG2389 Predicted bromodomain 63.8 37 0.0008 28.7 7.0 67 8-75 20-93 (353)
36 PLN00121 histone H3; Provision 62.1 44 0.00096 24.5 6.5 57 18-74 72-130 (136)
37 KOG3334 Transcription initiati 57.0 70 0.0015 23.9 6.8 56 18-74 19-76 (148)
38 KOG0870 DNA polymerase epsilon 56.7 43 0.00093 25.6 5.8 70 29-98 29-106 (172)
39 PTZ00018 histone H3; Provision 52.6 78 0.0017 23.3 6.4 56 18-73 72-129 (136)
40 smart00427 H2B Histone H2B. 50.3 77 0.0017 21.7 5.7 45 31-75 20-66 (89)
41 PF04719 TAFII28: hTAFII28-lik 47.0 90 0.002 21.2 6.9 63 13-75 24-89 (90)
42 TIGR03798 ocin_TIGR03798 bacte 46.6 47 0.001 20.5 4.0 44 65-108 3-47 (64)
43 smart00540 LEM in nuclear memb 45.9 43 0.00093 20.0 3.5 38 10-47 3-41 (44)
44 COG3461 Uncharacterized conser 45.6 20 0.00043 25.1 2.3 32 66-97 64-95 (103)
45 KOG0871 Class 2 transcription 44.5 71 0.0015 24.1 5.2 44 32-75 33-78 (156)
46 COG5094 TAF9 Transcription ini 42.3 64 0.0014 23.8 4.6 37 39-75 40-81 (145)
47 PF04433 SWIRM: SWIRM domain; 42.1 90 0.002 20.1 5.0 29 61-89 51-80 (86)
48 smart00414 H2A Histone 2A. 40.5 78 0.0017 22.1 4.7 40 39-79 39-78 (106)
49 PLN00158 histone H2B; Provisio 39.8 1.2E+02 0.0026 21.8 5.6 44 32-75 47-92 (116)
50 KOG3467 Histone H4 [Chromatin 37.8 87 0.0019 21.8 4.5 69 6-79 23-97 (103)
51 COG4008 Predicted metal-bindin 36.8 46 0.00099 24.7 3.1 38 1-41 86-123 (153)
52 PF13499 EF-hand_7: EF-hand do 36.5 91 0.002 18.3 4.6 53 10-73 14-66 (66)
53 PHA00724 hypothetical protein 36.3 28 0.00061 23.3 1.8 35 21-55 1-35 (83)
54 PF07862 Nif11: Nitrogen fixat 36.0 82 0.0018 18.2 3.7 42 65-106 5-47 (49)
55 PTZ00463 histone H2B; Provisio 35.6 1.6E+02 0.0035 21.2 5.7 43 32-74 48-92 (117)
56 PLN00161 histone H3; Provision 35.3 1.8E+02 0.0039 21.4 6.8 57 18-74 65-124 (135)
57 KOG1659 Class 2 transcription 34.9 1.3E+02 0.0028 24.0 5.6 50 38-88 39-90 (224)
58 TIGR03015 pepcterm_ATPase puta 33.5 1.7E+02 0.0038 21.8 6.0 45 31-75 216-265 (269)
59 PTZ00252 histone H2A; Provisio 32.8 1E+02 0.0023 22.6 4.5 37 42-78 58-95 (134)
60 PLN00157 histone H2A; Provisio 32.4 1.1E+02 0.0023 22.4 4.5 36 42-78 59-94 (132)
61 COG5095 TAF6 Transcription ini 32.1 1.1E+02 0.0025 26.1 5.1 46 30-75 22-69 (450)
62 PF01795 Methyltransf_5: MraW 31.5 90 0.002 25.7 4.4 52 12-63 141-198 (310)
63 PF14164 YqzH: YqzH-like prote 31.1 47 0.001 21.5 2.1 20 29-48 44-63 (64)
64 KOG1744 Histone H2B [Chromatin 30.9 2E+02 0.0042 21.0 5.6 44 31-74 56-101 (127)
65 PTZ00361 26 proteosome regulat 30.6 48 0.0011 28.3 2.8 43 33-75 379-423 (438)
66 PLN00160 histone H3; Provision 30.4 1.9E+02 0.004 20.0 6.6 57 18-74 31-90 (97)
67 KOG3423 Transcription initiati 30.2 2.4E+02 0.0052 21.7 6.2 38 25-62 98-135 (176)
68 PRK00771 signal recognition pa 29.8 2.6E+02 0.0057 23.9 7.1 69 10-89 274-344 (437)
69 PF03540 TFIID_30kDa: Transcri 29.5 1.4E+02 0.0031 18.4 6.1 35 27-61 16-50 (51)
70 PF11861 DUF3381: Domain of un 27.6 78 0.0017 23.4 3.1 74 24-98 13-95 (159)
71 PF09454 Vps23_core: Vps23 cor 27.2 1.7E+02 0.0037 18.5 6.1 44 31-74 7-50 (65)
72 PF12290 DUF3802: Protein of u 27.1 87 0.0019 22.4 3.2 33 23-55 22-55 (113)
73 COG1422 Predicted membrane pro 25.7 95 0.002 24.3 3.4 27 75-101 69-96 (201)
74 PTZ00017 histone H2A; Provisio 25.1 1.8E+02 0.0039 21.3 4.6 38 40-78 58-95 (134)
75 PRK05481 lipoyl synthase; Prov 25.0 19 0.00042 28.7 -0.5 24 19-42 200-223 (289)
76 PRK00411 cdc6 cell division co 24.9 3.6E+02 0.0078 21.5 8.3 45 31-75 229-281 (394)
77 COG1004 Ugd Predicted UDP-gluc 24.8 94 0.002 26.8 3.5 46 11-56 260-307 (414)
78 cd08813 DED_Caspase_8_repeat2 24.4 83 0.0018 21.1 2.5 35 65-99 19-55 (83)
79 COG5247 BUR6 Class 2 transcrip 24.0 2.7E+02 0.0059 19.8 6.3 72 17-89 28-101 (113)
80 PF07887 Calmodulin_bind: Calm 23.7 1.4E+02 0.0029 24.7 4.1 36 61-99 183-225 (299)
81 TIGR02928 orc1/cdc6 family rep 23.6 2.7E+02 0.0059 21.9 5.8 43 32-74 222-272 (365)
82 PF09778 Guanylate_cyc_2: Guan 23.5 48 0.001 26.0 1.4 16 91-106 193-208 (212)
83 PRK12928 lipoyl synthase; Prov 23.4 21 0.00046 28.6 -0.6 22 20-41 209-230 (290)
84 COG1067 LonB Predicted ATP-dep 22.6 1.3E+02 0.0029 27.2 4.1 57 46-104 367-425 (647)
85 PLN00156 histone H2AX; Provisi 22.5 2.4E+02 0.0052 20.8 4.8 37 41-78 61-97 (139)
86 PRK07194 fliG flagellar motor 22.4 1.7E+02 0.0038 23.8 4.5 23 17-39 230-252 (334)
87 COG0091 RplV Ribosomal protein 22.3 3E+02 0.0065 19.7 5.4 53 52-107 23-77 (120)
88 KOG0034 Ca2+/calmodulin-depend 22.1 3.4E+02 0.0074 20.5 5.8 34 45-78 143-178 (187)
89 PF06769 Plasmid_Txe: Plasmid 21.9 1.2E+02 0.0026 20.1 2.9 23 66-88 6-28 (80)
90 TIGR00764 lon_rel lon-related 21.7 5.7E+02 0.012 22.7 8.3 40 45-84 358-399 (608)
91 PTZ00454 26S protease regulato 21.6 92 0.002 26.1 2.8 42 35-76 343-386 (398)
92 PLN00153 histone H2A; Provisio 21.4 2.6E+02 0.0057 20.3 4.8 37 41-78 56-92 (129)
93 KOG0027 Calmodulin and related 21.3 1.7E+02 0.0037 20.4 3.8 76 11-104 23-98 (151)
94 PF09432 THP2: Tho complex sub 20.8 89 0.0019 23.0 2.2 19 17-37 103-121 (132)
95 TIGR01242 26Sp45 26S proteasom 20.1 1E+02 0.0023 24.8 2.8 44 32-75 317-362 (364)
96 PF01885 PTS_2-RNA: RNA 2'-pho 20.0 80 0.0017 23.8 2.0 15 62-76 31-45 (186)
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=1.3e-40 Score=228.26 Aligned_cols=90 Identities=58% Similarity=0.940 Sum_probs=87.0
Q ss_pred hhhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh-cCCCCcHHHHHHHHhhChhHHhHHHHHHHHH
Q 033783 12 SFKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGS-KGGKLSVEDFLYLIRKDLPKLNRCTELLSMQ 90 (111)
Q Consensus 12 ~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~-~Rgki~~eDl~F~lR~D~~Kl~Rl~~lL~~k 90 (111)
.+|++||++|||||||+++|++|||++||+||++||++||++|.++|+ ++|++++|||+|+|||||+||+|+++||+|+
T Consensus 2 ~~f~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL~~k 81 (92)
T cd07978 2 RLFTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGKVKVEDLIFLLRKDPKKLARLRELLSMK 81 (92)
T ss_pred CccHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 468999999999999999999999999999999999999999999998 6778999999999999999999999999999
Q ss_pred HHHHHHHhhcC
Q 033783 91 EELKQARKAFE 101 (111)
Q Consensus 91 ~~ik~ark~fd 101 (111)
+++|+|||+||
T Consensus 82 ~~~k~ark~~d 92 (92)
T cd07978 82 DELKKARKAFD 92 (92)
T ss_pred HHHHHHHhccC
Confidence 99999999986
No 2
>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=3.8e-40 Score=225.67 Aligned_cols=91 Identities=53% Similarity=0.863 Sum_probs=38.7
Q ss_pred hhhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCcHHHHHHHHhhChhHHhHHHHHHHH
Q 033783 12 SFKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKDLPKLNRCTELLSM 89 (111)
Q Consensus 12 ~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg--ki~~eDl~F~lR~D~~Kl~Rl~~lL~~ 89 (111)
+.|.+||++|||||||+++|++|||.+||+||++||+++|++|.++|++|| +|++|||+|+|||||.|++|+++||+|
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 368899999999999999999999999999999999999999999999885 599999999999999999999999999
Q ss_pred HHHHHHHHhhcCc
Q 033783 90 QEELKQARKAFEV 102 (111)
Q Consensus 90 k~~ik~ark~fd~ 102 (111)
++++++|||.||+
T Consensus 81 k~~~~karK~~d~ 93 (93)
T PF02269_consen 81 KDEIKKARKDFDE 93 (93)
T ss_dssp -------------
T ss_pred HHHHHHHHHhhcC
Confidence 9999999999984
No 3
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=100.00 E-value=6.8e-38 Score=218.99 Aligned_cols=93 Identities=58% Similarity=0.933 Sum_probs=90.0
Q ss_pred hhhhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChhHHhHHHHHHHHH
Q 033783 11 ESFKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQ 90 (111)
Q Consensus 11 ~~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~Kl~Rl~~lL~~k 90 (111)
..+|++||++|||||||+++|+++||+++|+||++||+++|+.|+.++ +||++.+|||.|+||+||+|++|+++||.|+
T Consensus 8 k~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g-~rgk~~veD~~f~lRkDpkK~~Rv~eLL~mn 86 (109)
T KOG3901|consen 8 KHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG-KRGKVKVEDFKFLLRKDPKKLGRVKELLAMN 86 (109)
T ss_pred HHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc-ccCceeHHHHHHHHHhChHHHhHHHHHHHhH
Confidence 468999999999999999999999999999999999999999999988 8999999999999999999999999999999
Q ss_pred HHHHHHHhhcCcch
Q 033783 91 EELKQARKAFEVDE 104 (111)
Q Consensus 91 ~~ik~ark~fd~d~ 104 (111)
+++|+|||+|++.+
T Consensus 87 eelk~ArKaF~~~~ 100 (109)
T KOG3901|consen 87 EELKKARKAFDETD 100 (109)
T ss_pred HHHHHHHhccchHh
Confidence 99999999999765
No 4
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=99.97 E-value=8.2e-31 Score=185.63 Aligned_cols=96 Identities=32% Similarity=0.517 Sum_probs=92.7
Q ss_pred hhhhhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChhHHhHHHHHHHH
Q 033783 10 EESFKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLSM 89 (111)
Q Consensus 10 ~~~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~Kl~Rl~~lL~~ 89 (111)
-.++|.+||++|||||||+.+|.++|+++++++|.+||.++|.+|..+|+.|||+++|||.|+||+||+||+|+++||..
T Consensus 7 r~nLF~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rnK~k~eDfkfaLr~DpkKlgRveeLl~t 86 (126)
T COG5248 7 RVNLFMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTKTEDFKFALRRDPKKLGRVEELLIT 86 (126)
T ss_pred HHHHHHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhcccchHHHHHHHHhhChHHHhHHHHHHHh
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhcCcchh
Q 033783 90 QEELKQARKAFEVDEE 105 (111)
Q Consensus 90 k~~ik~ark~fd~d~~ 105 (111)
+++|+.|+|+|...+.
T Consensus 87 n~~i~~Akk~F~~~ds 102 (126)
T COG5248 87 NEEIKLAKKAFEPKDS 102 (126)
T ss_pred hHHHHHHhcccCchhH
Confidence 9999999999987663
No 5
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=99.85 E-value=6.7e-21 Score=153.84 Aligned_cols=88 Identities=38% Similarity=0.542 Sum_probs=83.0
Q ss_pred hhhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhChhHHhHHHHHHHH
Q 033783 12 SFKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKDLPKLNRCTELLSM 89 (111)
Q Consensus 12 ~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D~~Kl~Rl~~lL~~ 89 (111)
.-|+-||++|||..|+.+.|++||++|+|++|+.|+++++.+|.++|..||. |+.||++|++|||++|+.||.+||.|
T Consensus 24 ~ky~veiQqmmf~sGei~~P~pett~Lved~V~gqvie~l~qa~eia~lrgsr~Itpedliflir~Drakv~rL~tyl~~ 103 (352)
T KOG3902|consen 24 KKYRVEIQQMMFQSGEIPDPLPETTNLVEDNVRGQVIESLVQANEIADLRGSRSITPEDLIFLIRHDRAKVNRLVTYLSW 103 (352)
T ss_pred hhHHHHHHHHHHHhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccccChHHHHHHhhccHHHHHHHHHHHHH
Confidence 3477799999999999999999999999999999999999999999999996 99999999999999999999999999
Q ss_pred HHHH-HHHHhh
Q 033783 90 QEEL-KQARKA 99 (111)
Q Consensus 90 k~~i-k~ark~ 99 (111)
++.+ |.|+.+
T Consensus 104 kdlR~k~ak~q 114 (352)
T KOG3902|consen 104 KDLRGKFAKAQ 114 (352)
T ss_pred HHHHHhhhhhh
Confidence 9999 777653
No 6
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.32 E-value=0.0016 Score=42.61 Aligned_cols=62 Identities=15% Similarity=0.322 Sum_probs=52.2
Q ss_pred hhhHHHHHHhhhhhC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc--CCCCcHHHHHHHHhh
Q 033783 12 SFKKIVIQHMMYGFG-DDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSK--GGKLSVEDFLYLIRK 75 (111)
Q Consensus 12 ~~~~~EI~~mMy~fG-D~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~--Rgki~~eDl~F~lR~ 75 (111)
++.+.-|.+++...| |. -.+.+.+.+=+++..|+.++++.|.+.|.. |..+++.|+..++.+
T Consensus 6 ~ll~~~Vaqil~~~Gf~~--~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 6 ALLRIAVAQILESAGFDS--FQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHHHHHHHcCccc--cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 456778999999998 54 455689999999999999999999999965 445999999999875
No 7
>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=97.22 E-value=0.0032 Score=40.92 Aligned_cols=59 Identities=17% Similarity=0.321 Sum_probs=47.4
Q ss_pred HHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhC
Q 033783 18 IQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKD 76 (111)
Q Consensus 18 I~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D 76 (111)
|..|+=..--...-.++...++-+++-+|+.+++..|+.+|..||+ ++.+|+.+.+++.
T Consensus 7 l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 7 LQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred HHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 3444433322356788888999999999999999999999997775 9999999999875
No 8
>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=97.17 E-value=0.0022 Score=41.74 Aligned_cols=60 Identities=15% Similarity=0.282 Sum_probs=44.8
Q ss_pred HHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhC
Q 033783 17 VIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKD 76 (111)
Q Consensus 17 EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D 76 (111)
-|+.++--..-.....++...++-++.-+||.+++..|+.+|..||. +.+.|+.|.|.++
T Consensus 4 ~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~ 65 (68)
T PF03847_consen 4 KLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN 65 (68)
T ss_dssp HHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence 34555555555566778888899999999999999999999998886 9999999999764
No 9
>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=96.91 E-value=0.0067 Score=39.34 Aligned_cols=62 Identities=18% Similarity=0.387 Sum_probs=51.5
Q ss_pred hhhHHHHHHhhhhhC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhh
Q 033783 12 SFKKIVIQHMMYGFG-DDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 75 (111)
Q Consensus 12 ~~~~~EI~~mMy~fG-D~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~ 75 (111)
.+.+.-|.+++...| |.. .+.+.+.+-+++..||.++++.+...|...|+ +++.|+..+|..
T Consensus 6 ~~l~~~va~il~~~GF~~~--~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~ 70 (77)
T PF07524_consen 6 SLLRRSVAQILKHAGFDSA--SPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEE 70 (77)
T ss_pred HHHHHHHHHHHHHcCcccc--CHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 456677888998888 544 55679999999999999999999999975555 999999988864
No 10
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=96.76 E-value=0.0078 Score=37.78 Aligned_cols=57 Identities=19% Similarity=0.277 Sum_probs=48.0
Q ss_pred HHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHH
Q 033783 17 VIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLI 73 (111)
Q Consensus 17 EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~l 73 (111)
=|+.+|=.-.|...-..|++.+|-.....|+..|+..|...|...|+ |+.+|+..+|
T Consensus 7 ~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 7 RVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 46777777788888899999999999999999999999999986665 9999998765
No 11
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=96.13 E-value=0.02 Score=38.08 Aligned_cols=50 Identities=18% Similarity=0.389 Sum_probs=39.6
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCcHHHHHHHHhhChh
Q 033783 29 PNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKDLP 78 (111)
Q Consensus 29 ~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg--ki~~eDl~F~lR~D~~ 78 (111)
.+..|+.+..|-|++..|+.++...--..|.-.| .|++||++.+.|++|.
T Consensus 24 ~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~ 75 (76)
T PF15630_consen 24 VEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPS 75 (76)
T ss_dssp SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HH
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCC
Confidence 3567899999999999999999887777776444 4999999999999984
No 12
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=96.08 E-value=0.031 Score=35.85 Aligned_cols=56 Identities=20% Similarity=0.209 Sum_probs=44.7
Q ss_pred HHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCcHHHHHHHHh
Q 033783 18 IQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIR 74 (111)
Q Consensus 18 I~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~--~Rgki~~eDl~F~lR 74 (111)
|+.+.=..|- ..-.++....+-+.+..++.++++.|.+++. .|..++++|+-+++|
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 4444444454 4678888899999999999999999999886 455699999999886
No 13
>PLN00035 histone H4; Provisional
Probab=96.02 E-value=0.05 Score=38.27 Aligned_cols=63 Identities=10% Similarity=0.145 Sum_probs=51.2
Q ss_pred hhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCcHHHHHHHHhhC
Q 033783 13 FKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKD 76 (111)
Q Consensus 13 ~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg--ki~~eDl~F~lR~D 76 (111)
+-...|+.+.--.| +..-..+....+.+++.+|+.+++..|..+|...| .++.+|+.|++++-
T Consensus 30 ipk~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 30 ITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred CCHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence 44556777777777 77778888889999999999999999999987444 49999999999864
No 14
>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=95.65 E-value=0.091 Score=35.65 Aligned_cols=64 Identities=14% Similarity=0.227 Sum_probs=51.3
Q ss_pred hhhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCcHHHHHHHHhhC
Q 033783 12 SFKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKD 76 (111)
Q Consensus 12 ~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg--ki~~eDl~F~lR~D 76 (111)
.+...-|+.+.--.| +..-..+...-+.+++.+|+.+++..|..+|...| .++.+|+.+++++-
T Consensus 13 gi~k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~ 78 (85)
T cd00076 13 GITKPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 78 (85)
T ss_pred cCCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHC
Confidence 344556777777777 67777778888889999999999999999987444 49999999999864
No 15
>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=95.36 E-value=0.07 Score=33.88 Aligned_cols=48 Identities=10% Similarity=0.248 Sum_probs=42.2
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhC
Q 033783 29 PNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKD 76 (111)
Q Consensus 29 ~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D 76 (111)
..-..++..+|-.++-.++.+++..|..+|...++ |+..|+..++|.|
T Consensus 26 ~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 26 YRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp SEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred cccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 45678999999999999999999999999975554 9999999999976
No 16
>PTZ00015 histone H4; Provisional
Probab=95.23 E-value=0.088 Score=36.94 Aligned_cols=63 Identities=10% Similarity=0.178 Sum_probs=46.3
Q ss_pred hhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc--CCCCcHHHHHHHHhhC
Q 033783 13 FKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSK--GGKLSVEDFLYLIRKD 76 (111)
Q Consensus 13 ~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~--Rgki~~eDl~F~lR~D 76 (111)
.....|+.+.--.| +..-..+...-+-+++.+|+.+++..|..+|.. |..++.+|+.|++++-
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 34456666666555 345556666778888888999999999988864 4449999999999753
No 17
>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=94.66 E-value=0.3 Score=31.61 Aligned_cols=46 Identities=20% Similarity=0.193 Sum_probs=36.0
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCcHHHHHHHHh
Q 033783 29 PNPLPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIR 74 (111)
Q Consensus 29 ~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~--~Rgki~~eDl~F~lR 74 (111)
.+-.+|....+-+=|.--|.++++.|.+... +|.+++++|+=.+||
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 4567888889999999999999999999875 677899999998887
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=94.08 E-value=0.36 Score=34.15 Aligned_cols=56 Identities=16% Similarity=0.313 Sum_probs=44.4
Q ss_pred HHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCcHHHHHHHHhh
Q 033783 19 QHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRK 75 (111)
Q Consensus 19 ~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg--ki~~eDl~F~lR~ 75 (111)
..++-..|.. .=.+..+..+-|++..|..+++..|..+|.-.| .|+.||+..++..
T Consensus 8 ~~iLk~~Gv~-~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~ 65 (117)
T cd07979 8 AAILKSMGIT-EYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQS 65 (117)
T ss_pred HHHHHHCCCC-ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 3444455654 456788889999999999999999999997544 4999999999763
No 19
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=92.94 E-value=0.42 Score=32.87 Aligned_cols=58 Identities=12% Similarity=0.367 Sum_probs=47.8
Q ss_pred HHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhh
Q 033783 17 VIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 75 (111)
Q Consensus 17 EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~ 75 (111)
-++.+|=-.|+. .-..+....+-+.+-+|+.++...|..+|...|+ |+.+|+..+++.
T Consensus 24 pv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~ 83 (91)
T COG2036 24 PVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKR 83 (91)
T ss_pred HHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHH
Confidence 455666666665 5667788899999999999999999999986665 999999998874
No 20
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.87 E-value=0.2 Score=40.39 Aligned_cols=60 Identities=13% Similarity=0.331 Sum_probs=46.5
Q ss_pred HHHHHhhhhhCCCCCCcH-HHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhC
Q 033783 16 IVIQHMMYGFGDDPNPLP-ETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKD 76 (111)
Q Consensus 16 ~EI~~mMy~fGD~~~P~~-eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D 76 (111)
..|..+|--. |...-++ |.-++|-+|.-+||.++++.|+.+|..|++ |.+-||.|.|.++
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 3444444333 5544444 466799999999999999999999998875 9999999999874
No 21
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=92.20 E-value=0.43 Score=36.17 Aligned_cols=49 Identities=14% Similarity=0.272 Sum_probs=41.2
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCcHHHHHHHHhh
Q 033783 27 DDPNPLPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIRK 75 (111)
Q Consensus 27 D~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~--~Rgki~~eDl~F~lR~ 75 (111)
-...-..++-..|.+.|-+||.=++.+|.+... .|..|+-|||+++|-.
T Consensus 48 ~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~t 98 (168)
T KOG0869|consen 48 ANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMST 98 (168)
T ss_pred cccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHH
Confidence 334456678889999999999999999998876 4666999999999985
No 22
>smart00417 H4 Histone H4.
Probab=91.21 E-value=0.49 Score=31.35 Aligned_cols=59 Identities=10% Similarity=0.135 Sum_probs=37.8
Q ss_pred hhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCcHHHHHHH
Q 033783 13 FKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYL 72 (111)
Q Consensus 13 ~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg--ki~~eDl~F~ 72 (111)
+...-|+-|.--.|= +.-..+...-+-+++.+|+.+++..|..+|...| .++.+|+.|+
T Consensus 14 I~k~~IrRLaRr~Gv-kRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 14 ITKPAIRRLARRGGV-KRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred CCHHHHHHHHHHcCc-chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 334455555554443 4444445555666666777888888888886444 4999999874
No 23
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=91.12 E-value=1.1 Score=37.36 Aligned_cols=79 Identities=22% Similarity=0.124 Sum_probs=66.9
Q ss_pred HHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC---CcHHHHHHHHhhChhHHhHHHHHHHHHHHH
Q 033783 17 VIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK---LSVEDFLYLIRKDLPKLNRCTELLSMQEEL 93 (111)
Q Consensus 17 EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk---i~~eDl~F~lR~D~~Kl~Rl~~lL~~k~~i 93 (111)
++.-+|.-+|| -...+.|++-+...++.....++...|.+|.. .+--|+-|+|++.+.|-+|.+.-|++-..+
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 34457778888 67788899999999999888888888765532 666899999999999999999999999999
Q ss_pred HHHHhh
Q 033783 94 KQARKA 99 (111)
Q Consensus 94 k~ark~ 99 (111)
|+|-|.
T Consensus 156 k~~~k~ 161 (352)
T KOG3902|consen 156 KRALKI 161 (352)
T ss_pred HHHhhc
Confidence 999765
No 24
>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=89.33 E-value=1.8 Score=31.37 Aligned_cols=54 Identities=19% Similarity=0.342 Sum_probs=39.4
Q ss_pred HhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHh
Q 033783 20 HMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 74 (111)
Q Consensus 20 ~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR 74 (111)
+++=..| +.+=.+..+..+=|+...|+.+++..|..+|.-.|+ |+.+|+..++.
T Consensus 20 ~iL~~~G-v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~ 75 (129)
T PF02291_consen 20 LILKSMG-VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQ 75 (129)
T ss_dssp HHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHH
T ss_pred HHHHHcC-CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHH
Confidence 3333344 334577888899999999999999999999975554 99999999987
No 25
>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=86.68 E-value=2.7 Score=34.47 Aligned_cols=48 Identities=19% Similarity=0.135 Sum_probs=40.6
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCcHHHHHHHHhh
Q 033783 28 DPNPLPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIRK 75 (111)
Q Consensus 28 ~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~--~Rgki~~eDl~F~lR~ 75 (111)
...-.++.+..+-+-+..++.++++.|.+.+. +|.+++++|+-.++|-
T Consensus 14 i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~ 63 (343)
T cd08050 14 IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRL 63 (343)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHH
Confidence 34567778888888899999999999999986 5667999999999884
No 26
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=81.03 E-value=4.4 Score=36.06 Aligned_cols=47 Identities=28% Similarity=0.331 Sum_probs=41.2
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhh--hcCCCCcHHHHHHHHhh
Q 033783 29 PNPLPETVALVEDIVVEYVTDLAHKAQDIG--SKGGKLSVEDFLYLIRK 75 (111)
Q Consensus 29 ~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a--~~Rgki~~eDl~F~lR~ 75 (111)
.+-.+|+..++.+-|.-.|.++++.|.+.- +.|.+++++|+-++||-
T Consensus 27 ~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~ 75 (576)
T KOG2549|consen 27 TNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRS 75 (576)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhh
Confidence 457889999999999999999999998874 35778999999999984
No 27
>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=80.72 E-value=7.7 Score=29.58 Aligned_cols=67 Identities=16% Similarity=0.146 Sum_probs=49.2
Q ss_pred HHHHHhhhhhCCCC---CCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChhHHhH
Q 033783 16 IVIQHMMYGFGDDP---NPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNR 82 (111)
Q Consensus 16 ~EI~~mMy~fGD~~---~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~Kl~R 82 (111)
.-|...|..+|=.. ...++.+.+|-..+.++|.+|+..+..+|..|-...-+|..+.+++|+.+--|
T Consensus 48 ~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~ 117 (212)
T cd08045 48 SPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLR 117 (212)
T ss_pred HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHH
Confidence 35666664444332 56899999999999999999999999999866544466777777877644333
No 28
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=79.90 E-value=2.8 Score=32.95 Aligned_cols=76 Identities=25% Similarity=0.208 Sum_probs=28.4
Q ss_pred HHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChhHHhH-HHHHHHHHHHHH
Q 033783 18 IQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNR-CTELLSMQEELK 94 (111)
Q Consensus 18 I~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~Kl~R-l~~lL~~k~~ik 94 (111)
|+.++=-+| ...+.++.+.||---+.++|.+|+..+..+|..|-..+-+|..+.+++|..+--| |.+.-...++++
T Consensus 53 i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l~~~e~~~~err 129 (264)
T PF05236_consen 53 IQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFLEQLEKEEEERR 129 (264)
T ss_dssp HHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH----------------------------------------
T ss_pred HHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHHHHHHHHHHHHH
Confidence 344443445 6779999999999999999999999999999877666668888888888655444 444433333333
No 29
>smart00428 H3 Histone H3.
Probab=79.65 E-value=16 Score=25.67 Aligned_cols=47 Identities=11% Similarity=0.166 Sum_probs=39.3
Q ss_pred CCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHh
Q 033783 28 DPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 74 (111)
Q Consensus 28 ~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR 74 (111)
.-.=.+++...+.+..-.|++++...|..+|...++ +...|+..+.|
T Consensus 51 ~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 51 DLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred CceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 446678899999999999999999999999976665 78899976644
No 30
>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=73.88 E-value=24 Score=23.67 Aligned_cols=62 Identities=19% Similarity=0.315 Sum_probs=50.3
Q ss_pred hhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc-----CCCCcHHHHHHHHhh
Q 033783 13 FKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSK-----GGKLSVEDFLYLIRK 75 (111)
Q Consensus 13 ~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~-----Rgki~~eDl~F~lR~ 75 (111)
|...-|+.+|=..-+ ..|.+..+.+|--+...|+-+|+..|..+-.. +|.|..+.|.=+.|+
T Consensus 17 f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr 83 (85)
T cd08048 17 FPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR 83 (85)
T ss_pred ccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence 445567777766666 78889999999999999999999999998764 567888888777664
No 31
>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=73.00 E-value=4.2 Score=26.59 Aligned_cols=44 Identities=18% Similarity=0.291 Sum_probs=34.8
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--C-CcHHHHH
Q 033783 27 DDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--K-LSVEDFL 70 (111)
Q Consensus 27 D~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg--k-i~~eDl~ 70 (111)
+...-..+++.++-+++.-|+.+-+.+|...|...| . +.++||-
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 445567889999999999999999999999887665 4 8888875
No 32
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=70.80 E-value=14 Score=30.78 Aligned_cols=74 Identities=12% Similarity=0.231 Sum_probs=56.2
Q ss_pred HHHHHHhhh--hhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhChhHHhHHHHHHHHH
Q 033783 15 KIVIQHMMY--GFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKDLPKLNRCTELLSMQ 90 (111)
Q Consensus 15 ~~EI~~mMy--~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D~~Kl~Rl~~lL~~k 90 (111)
..=|.+|++ ||++ -..-+..-+=++|+.||.++..++.......|+ ++.-|+.++|++=--|++-|..++.-+
T Consensus 8 ~~VV~~Ll~~~gfd~---is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~v~sL~~~~q~~ 84 (323)
T KOG4336|consen 8 APVVSNLLKTKGFDS---ISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIKVSSLYAYFQKQ 84 (323)
T ss_pred HHHHHHHHHHhCchH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCChhhhHHHHHhc
Confidence 344666775 5555 333445566788999999999998887765555 999999999999999999999888754
Q ss_pred H
Q 033783 91 E 91 (111)
Q Consensus 91 ~ 91 (111)
.
T Consensus 85 ~ 85 (323)
T KOG4336|consen 85 E 85 (323)
T ss_pred c
Confidence 4
No 33
>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=67.16 E-value=26 Score=24.80 Aligned_cols=37 Identities=30% Similarity=0.399 Sum_probs=28.0
Q ss_pred hhcCCCCcHHHHHHHHhhChhHHhHHHHHHHHHHHHHH
Q 033783 58 GSKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQEELKQ 95 (111)
Q Consensus 58 a~~Rgki~~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik~ 95 (111)
|-+|| .++|+|-=+-.=||--|.+++++..+.+.+++
T Consensus 19 AlrrG-~sveeI~e~T~ID~wFL~~i~~Iv~~e~~L~~ 55 (123)
T PF02787_consen 19 ALRRG-YSVEEIHELTKIDPWFLEQIKNIVDMEKELKE 55 (123)
T ss_dssp HHHTT-B-HHHHHHHH---HHHHHHHHHHHHHHHHHHH
T ss_pred HHHcC-CCHHHHHHHHCccHHHHHHHHHHHHHHHHHHH
Confidence 34566 79999999999999999999999999887777
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=65.87 E-value=21 Score=25.27 Aligned_cols=31 Identities=13% Similarity=0.233 Sum_probs=21.9
Q ss_pred HHHHHHHHHhhh--cCCCCcHHHHHHHHhhChh
Q 033783 48 TDLAHKAQDIGS--KGGKLSVEDFLYLIRKDLP 78 (111)
Q Consensus 48 ~~l~~~A~~~a~--~Rgki~~eDl~F~lR~D~~ 78 (111)
.+++..|.+.|. .+.+|+.+|+.-++|+|..
T Consensus 56 aEIlelA~n~ak~~k~krItp~hi~lAi~nD~E 88 (115)
T cd00074 56 AEVLELAGNAARDNKKKRITPRHLQLAVRNDEE 88 (115)
T ss_pred HHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHH
Confidence 444555555544 3456999999999999975
No 35
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=63.75 E-value=37 Score=28.70 Aligned_cols=67 Identities=15% Similarity=0.291 Sum_probs=50.9
Q ss_pred cchhhhhHH-----HHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhh
Q 033783 8 ASEESFKKI-----VIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 75 (111)
Q Consensus 8 ~~~~~~~~~-----EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~ 75 (111)
++++.-|.. -+.|+.=+.|-...|.. .-..++++++.||+++-..|..++..-|+ ..+-|++-++-.
T Consensus 20 ~~~~~~ya~sla~~avaQIcqslg~~~~~~s-ale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~d 93 (353)
T KOG2389|consen 20 ESEEAEYAFSLARVAVAQICQSLGYSSTQNS-ALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQD 93 (353)
T ss_pred chhHHHHHHHHHHHHHHHHHHhcCCcccccH-HHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHH
Confidence 444444444 45666667787776666 56789999999999999999999987777 777888877754
No 36
>PLN00121 histone H3; Provisional
Probab=62.06 E-value=44 Score=24.53 Aligned_cols=57 Identities=12% Similarity=0.178 Sum_probs=44.6
Q ss_pred HHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHh
Q 033783 18 IQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 74 (111)
Q Consensus 18 I~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR 74 (111)
++.+.-.|+..-.=..++...+.+..-.|++++...|.-+|...++ |...|+..+.|
T Consensus 72 VREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 72 VREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred HHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 3444445566667888999999999999999999999999876666 66789876643
No 37
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=57.04 E-value=70 Score=23.93 Aligned_cols=56 Identities=20% Similarity=0.299 Sum_probs=42.9
Q ss_pred HHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHh
Q 033783 18 IQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 74 (111)
Q Consensus 18 I~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR 74 (111)
|.+|+-..| .++=.|--+.-|-|....|.+.++..|.-+|+-.|+ |.+||+.-+++
T Consensus 19 i~~iL~s~G-I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~ 76 (148)
T KOG3334|consen 19 IASILKSLG-IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQ 76 (148)
T ss_pred HHHHHHHcC-ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHH
Confidence 444555555 345566677788889999999999999988875444 99999998876
No 38
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=56.74 E-value=43 Score=25.62 Aligned_cols=70 Identities=16% Similarity=0.120 Sum_probs=49.3
Q ss_pred CCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCcHHHHHHHHhhC--hhHHh----HHHHHHHHHHHHHHHHh
Q 033783 29 PNPLPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIRKD--LPKLN----RCTELLSMQEELKQARK 98 (111)
Q Consensus 29 ~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~--~Rgki~~eDl~F~lR~D--~~Kl~----Rl~~lL~~k~~ik~ark 98 (111)
..-..|....|-.-..-|++.|+..|..+|. .|..++.+|++-+|++= +.-+. -+..|-...+..|.++.
T Consensus 29 vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~plk~~Le~yk~~~k~Kk~~~~ 106 (172)
T KOG0870|consen 29 VSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVNPLKSALEAYKKAVKQKKLAKA 106 (172)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhhHHHHHHHHHHHHHHHHHHhcc
Confidence 4456778888889999999999999999997 34559999999999952 22222 24444444455555554
No 39
>PTZ00018 histone H3; Provisional
Probab=52.56 E-value=78 Score=23.26 Aligned_cols=56 Identities=11% Similarity=0.153 Sum_probs=43.1
Q ss_pred HHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHH
Q 033783 18 IQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLI 73 (111)
Q Consensus 18 I~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~l 73 (111)
++.+.-.|+..-.=..++...+.+..-.|++++...+.-+|...++ |...|+..+.
T Consensus 72 VREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 72 VREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred HHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 3334444555557788999999999999999999999998876665 6678986664
No 40
>smart00427 H2B Histone H2B.
Probab=50.34 E-value=77 Score=21.69 Aligned_cols=45 Identities=13% Similarity=0.219 Sum_probs=36.2
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhhc--CCCCcHHHHHHHHhh
Q 033783 31 PLPETVALVEDIVVEYVTDLAHKAQDIGSK--GGKLSVEDFLYLIRK 75 (111)
Q Consensus 31 P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~--Rgki~~eDl~F~lR~ 75 (111)
-..++..+|.-++.+-.-.+..+|.+++.. |..|+..++--++|-
T Consensus 20 iS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl 66 (89)
T smart00427 20 ISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRL 66 (89)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 345677888888988888999999999874 444999999988883
No 41
>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=46.95 E-value=90 Score=21.23 Aligned_cols=63 Identities=19% Similarity=0.303 Sum_probs=43.1
Q ss_pred hhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC---CCcHHHHHHHHhh
Q 033783 13 FKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG---KLSVEDFLYLIRK 75 (111)
Q Consensus 13 ~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg---ki~~eDl~F~lR~ 75 (111)
|-..-|+.+|=.+=....+.+..+-+|--+-.-|+-+|+..|..+....+ .|....+.-+.|+
T Consensus 24 ~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rr 89 (90)
T PF04719_consen 24 FNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRR 89 (90)
T ss_dssp --HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHh
Confidence 33446777776555557788888899999999999999999999987544 4888877766653
No 42
>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=46.64 E-value=47 Score=20.54 Aligned_cols=44 Identities=18% Similarity=0.285 Sum_probs=35.3
Q ss_pred cHHHHHHHHhhChhHHhHHHHHHHHHHHHHHHHh-hcCcchhhhh
Q 033783 65 SVEDFLYLIRKDLPKLNRCTELLSMQEELKQARK-AFEVDEEKLA 108 (111)
Q Consensus 65 ~~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik~ark-~fd~d~~~~~ 108 (111)
++.+|+=.+++||.=..+|+......+.++-|+. .|+-+.+++.
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 3577888899999988899998888899998886 6776666653
No 43
>smart00540 LEM in nuclear membrane-associated proteins. LEM, domain in nuclear membrane-associated proteins, including lamino-associated polypeptide 2 and emerin.
Probab=45.88 E-value=43 Score=19.97 Aligned_cols=38 Identities=16% Similarity=0.315 Sum_probs=29.8
Q ss_pred hhhhhHHHHHHhhhhhCCCCCCcHHHHH-HHHHHHHHHH
Q 033783 10 EESFKKIVIQHMMYGFGDDPNPLPETVA-LVEDIVVEYV 47 (111)
Q Consensus 10 ~~~~~~~EI~~mMy~fGD~~~P~~eTv~-l~Ediv~~~i 47 (111)
...+...||+..|-.+|-.+-|..+|.. +.|.=+...+
T Consensus 3 ~~~LSd~eL~~~L~~~G~~~gPIt~sTR~vy~kkL~~~~ 41 (44)
T smart00540 3 VDRLSDAELRAELKQYGLPPGPITDTTRKLYEKKLRKLR 41 (44)
T ss_pred hhHcCHHHHHHHHHHcCCCCCCcCcchHHHHHHHHHHHH
Confidence 3466778999999999999999988776 6666555444
No 44
>COG3461 Uncharacterized conserved protein [Function unknown]
Probab=45.61 E-value=20 Score=25.10 Aligned_cols=32 Identities=19% Similarity=0.117 Sum_probs=27.4
Q ss_pred HHHHHHHHhhChhHHhHHHHHHHHHHHHHHHH
Q 033783 66 VEDFLYLIRKDLPKLNRCTELLSMQEELKQAR 97 (111)
Q Consensus 66 ~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik~ar 97 (111)
.=+|-|+.||||.=-+-++++|...+-|+++-
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 45788999999999999999999888887763
No 45
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=44.53 E-value=71 Score=24.07 Aligned_cols=44 Identities=20% Similarity=0.357 Sum_probs=36.9
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhh
Q 033783 32 LPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 75 (111)
Q Consensus 32 ~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~ 75 (111)
..|+..++-+.-++||.-+.+.|.+++....| |..|.++-+|-+
T Consensus 33 akeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~ 78 (156)
T KOG0871|consen 33 AKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALEN 78 (156)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHH
Confidence 46888899999999999999999999986543 888888777764
No 46
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=42.31 E-value=64 Score=23.81 Aligned_cols=37 Identities=22% Similarity=0.316 Sum_probs=29.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhc--CCC---CcHHHHHHHHhh
Q 033783 39 VEDIVVEYVTDLAHKAQDIGSK--GGK---LSVEDFLYLIRK 75 (111)
Q Consensus 39 ~Ediv~~~i~~l~~~A~~~a~~--Rgk---i~~eDl~F~lR~ 75 (111)
+-+..+.|-++++..|.-.|.- ||. +++||+..++-.
T Consensus 40 Ll~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 40 LLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 4467889999999999888864 443 888999998864
No 47
>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=42.12 E-value=90 Score=20.08 Aligned_cols=29 Identities=28% Similarity=0.328 Sum_probs=23.2
Q ss_pred CCCCcHHHHHHHHh-hChhHHhHHHHHHHH
Q 033783 61 GGKLSVEDFLYLIR-KDLPKLNRCTELLSM 89 (111)
Q Consensus 61 Rgki~~eDl~F~lR-~D~~Kl~Rl~~lL~~ 89 (111)
.+.++.+|..=+++ -|..++.|+.++|.-
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 45599999999999 599999999999974
No 48
>smart00414 H2A Histone 2A.
Probab=40.49 E-value=78 Score=22.06 Aligned_cols=40 Identities=23% Similarity=0.218 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChhH
Q 033783 39 VEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPK 79 (111)
Q Consensus 39 ~Ediv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~K 79 (111)
+=|++...|.++.-++..-. ++.+|+.+++.-++|+|..=
T Consensus 39 vLEYLtaEILeLagn~a~~~-k~~rItp~hi~lAi~nD~EL 78 (106)
T smart00414 39 VLEYLTAEVLELAGNAARDN-KKRRITPRHLQLAIRNDEEL 78 (106)
T ss_pred HHHHHHHHHHHHHHHHHHhc-CCCccchHHHhhhccCCHHH
Confidence 44445555666665554422 34469999999999999753
No 49
>PLN00158 histone H2B; Provisional
Probab=39.81 E-value=1.2e+02 Score=21.77 Aligned_cols=44 Identities=7% Similarity=0.205 Sum_probs=35.8
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhhhc--CCCCcHHHHHHHHhh
Q 033783 32 LPETVALVEDIVVEYVTDLAHKAQDIGSK--GGKLSVEDFLYLIRK 75 (111)
Q Consensus 32 ~~eTv~l~Ediv~~~i~~l~~~A~~~a~~--Rgki~~eDl~F~lR~ 75 (111)
...+..+|.-+|.+..-.|..+|..+|.. |..|+..+|--++|-
T Consensus 47 S~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrL 92 (116)
T PLN00158 47 SSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRL 92 (116)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 55677888888888888899999999874 445999999988873
No 50
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=37.82 E-value=87 Score=21.79 Aligned_cols=69 Identities=14% Similarity=0.225 Sum_probs=38.0
Q ss_pred CCcchhhhhHHHHHHhhhhhCCCCCC----cHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCcHHHHHHHHhhChhH
Q 033783 6 LSASEESFKKIVIQHMMYGFGDDPNP----LPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIRKDLPK 79 (111)
Q Consensus 6 ~~~~~~~~~~~EI~~mMy~fGD~~~P----~~eTv~l~Ediv~~~i~~l~~~A~~~a~--~Rgki~~eDl~F~lR~D~~K 79 (111)
+|-+++-....-|+.+--- |.++.- ..||..+ ...||.+.+.-|+-.+. .|..++.-|+++.|.+.-.+
T Consensus 23 LsDnIqgitKpaIRRlARr-~GVkRi~G~~yeE~~~~----~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 23 LRDNIQGITKPAIRRLARR-GGVKRISGLIYEETRGV----LKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred HHhhccccchHHHHHHHHh-cCcchhchhhHHHHHHH----HHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 3444444444444444322 223332 3455444 45555566666655543 46669999999999876544
No 51
>COG4008 Predicted metal-binding transcription factor [Transcription]
Probab=36.84 E-value=46 Score=24.73 Aligned_cols=38 Identities=21% Similarity=0.352 Sum_probs=29.5
Q ss_pred CccccCCcchhhhhHHHHHHhhhhhCCCCCCcHHHHHHHHH
Q 033783 1 MKQLHLSASEESFKKIVIQHMMYGFGDDPNPLPETVALVED 41 (111)
Q Consensus 1 ~~~~~~~~~~~~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ed 41 (111)
|++.|+||.|-....+.+..-+.| ..+|..|+|.++-+
T Consensus 86 l~ri~mS~~EYM~lKkqLae~il~---~s~~~~e~v~v~a~ 123 (153)
T COG4008 86 LNRINMSPEEYMELKKQLAEYILG---HSEPPVEEVEVLAD 123 (153)
T ss_pred HHhcCCCHHHHHHHHHHHHHHHhc---cCCCcHHHHHHHHH
Confidence 468899999999999888776655 56788888886543
No 52
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=36.49 E-value=91 Score=18.28 Aligned_cols=53 Identities=15% Similarity=0.349 Sum_probs=31.6
Q ss_pred hhhhhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHH
Q 033783 10 EESFKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLI 73 (111)
Q Consensus 10 ~~~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~l 73 (111)
.+.+..+|+..++-..|-... ++-+.+.+..++..+=. ...|.|+.++|.-++
T Consensus 14 ~G~i~~~el~~~~~~~~~~~~---------~~~~~~~~~~~~~~~D~--d~dG~i~~~Ef~~~~ 66 (66)
T PF13499_consen 14 DGYISKEELRRALKHLGRDMS---------DEESDEMIDQIFREFDT--DGDGRISFDEFLNFM 66 (66)
T ss_dssp SSEEEHHHHHHHHHHTTSHST---------HHHHHHHHHHHHHHHTT--TSSSSEEHHHHHHHH
T ss_pred cCCCCHHHHHHHHHHhccccc---------HHHHHHHHHHHHHHhCC--CCcCCCcHHHHhccC
Confidence 455667799999988887543 22233333333333221 256889999987543
No 53
>PHA00724 hypothetical protein
Probab=36.27 E-value=28 Score=23.33 Aligned_cols=35 Identities=29% Similarity=0.283 Sum_probs=30.2
Q ss_pred hhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHH
Q 033783 21 MMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQ 55 (111)
Q Consensus 21 mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~ 55 (111)
||=+.||+-.-.---+-++--|+++|+.++.--.+
T Consensus 1 mmsalgdviyilgil~p~lgli~rnyl~nlmgfvm 35 (83)
T PHA00724 1 MMSALGDVIYILGILIPLLGLIVRNYLVNLMGFVM 35 (83)
T ss_pred CcchhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78899999988888888999999999999976554
No 54
>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=36.03 E-value=82 Score=18.24 Aligned_cols=42 Identities=21% Similarity=0.313 Sum_probs=32.4
Q ss_pred cHHHHHHHHhhChhHHhHHHHHHHHHHHHHHHHh-hcCcchhh
Q 033783 65 SVEDFLYLIRKDLPKLNRCTELLSMQEELKQARK-AFEVDEEK 106 (111)
Q Consensus 65 ~~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik~ark-~fd~d~~~ 106 (111)
+++.|+=.+++||.-..+|...-...+.++-|+. +|+-+.++
T Consensus 5 ~l~~Fl~~~~~d~~l~~~l~~~~~~~e~~~lA~~~Gy~ft~~e 47 (49)
T PF07862_consen 5 SLKAFLEKVKSDPELREQLKACQNPEEVVALAREAGYDFTEEE 47 (49)
T ss_pred HHHHHHHHHhcCHHHHHHHHhcCCHHHHHHHHHHcCCCCCHHH
Confidence 3567788888999988888888888888888876 55555444
No 55
>PTZ00463 histone H2B; Provisional
Probab=35.56 E-value=1.6e+02 Score=21.19 Aligned_cols=43 Identities=16% Similarity=0.265 Sum_probs=35.0
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhhhc--CCCCcHHHHHHHHh
Q 033783 32 LPETVALVEDIVVEYVTDLAHKAQDIGSK--GGKLSVEDFLYLIR 74 (111)
Q Consensus 32 ~~eTv~l~Ediv~~~i~~l~~~A~~~a~~--Rgki~~eDl~F~lR 74 (111)
...+..+|--+|.+-.-.+..+|..+|.. |..|+..+|-.++|
T Consensus 48 S~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr 92 (117)
T PTZ00463 48 SRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR 92 (117)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh
Confidence 56677888888888888889999998874 44499999988887
No 56
>PLN00161 histone H3; Provisional
Probab=35.32 E-value=1.8e+02 Score=21.37 Aligned_cols=57 Identities=7% Similarity=0.104 Sum_probs=42.0
Q ss_pred HHHhhhhhC-CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHh
Q 033783 18 IQHMMYGFG-DDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 74 (111)
Q Consensus 18 I~~mMy~fG-D~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR 74 (111)
++.++--|. ..-.=..+++..+.+..-.|++++...|.-+|...++ |...|+..+.|
T Consensus 65 VREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 65 VREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred HHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 444444442 2235568899999999999999999999988876666 66688876643
No 57
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=34.91 E-value=1.3e+02 Score=23.96 Aligned_cols=50 Identities=16% Similarity=0.289 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhChhHHhHHHHHHH
Q 033783 38 LVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKDLPKLNRCTELLS 88 (111)
Q Consensus 38 l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D~~Kl~Rl~~lL~ 88 (111)
++-.-+--|+..||..+++++..||. ++.+-|.-++-+++ |+.-|++++.
T Consensus 39 iisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~-~FdFLk~~v~ 90 (224)
T KOG1659|consen 39 IISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDP-KFDFLKEVVE 90 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccc-hhHHHHHHHH
Confidence 45566677999999999999988874 99999999998887 4555555443
No 58
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=33.54 E-value=1.7e+02 Score=21.77 Aligned_cols=45 Identities=9% Similarity=-0.025 Sum_probs=31.5
Q ss_pred CcHHHHHHHHHHHHH---HHHHHHHHHHHhhhcCCC--CcHHHHHHHHhh
Q 033783 31 PLPETVALVEDIVVE---YVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 75 (111)
Q Consensus 31 P~~eTv~l~Ediv~~---~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~ 75 (111)
=.++.+..+-++... .|..+|..|...|..+|+ |+.+++..+++.
T Consensus 216 ~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~ 265 (269)
T TIGR03015 216 FSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAE 265 (269)
T ss_pred cCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 345666666666554 788888888887765554 888888877763
No 59
>PTZ00252 histone H2A; Provisional
Probab=32.78 E-value=1e+02 Score=22.63 Aligned_cols=37 Identities=19% Similarity=0.198 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHh-hhcCCCCcHHHHHHHHhhChh
Q 033783 42 IVVEYVTDLAHKAQDI-GSKGGKLSVEDFLYLIRKDLP 78 (111)
Q Consensus 42 iv~~~i~~l~~~A~~~-a~~Rgki~~eDl~F~lR~D~~ 78 (111)
+++.-|.+|.-+|..- ...+.+|+.+.|.-++|+|..
T Consensus 58 YLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDeE 95 (134)
T PTZ00252 58 YLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDDD 95 (134)
T ss_pred HHHHHHHHHHHHHHHhccCCcccccHHHHHhhccChHH
Confidence 3333344554444321 123456999999999999974
No 60
>PLN00157 histone H2A; Provisional
Probab=32.39 E-value=1.1e+02 Score=22.45 Aligned_cols=36 Identities=19% Similarity=0.204 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChh
Q 033783 42 IVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLP 78 (111)
Q Consensus 42 iv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~ 78 (111)
++..-|.+|.-+|..-. .+.+|+..+|.-++|+|..
T Consensus 59 YLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~nDeE 94 (132)
T PLN00157 59 YLAAEVLELAGNAARDN-KKSRIVPRHIQLAVRNDEE 94 (132)
T ss_pred HHHHHHHHHHHHHHHhc-CCccccHHHHhhcccCcHH
Confidence 33333555555543322 3446999999999999975
No 61
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=32.14 E-value=1.1e+02 Score=26.10 Aligned_cols=46 Identities=17% Similarity=0.234 Sum_probs=34.2
Q ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHhh--hcCCCCcHHHHHHHHhh
Q 033783 30 NPLPETVALVEDIVVEYVTDLAHKAQDIG--SKGGKLSVEDFLYLIRK 75 (111)
Q Consensus 30 ~P~~eTv~l~Ediv~~~i~~l~~~A~~~a--~~Rgki~~eDl~F~lR~ 75 (111)
+-.++....+--=+---|.++|++|.+.- +.|..++++|+-+++|.
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 45556666555555566889999998764 35667999999999995
No 62
>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=31.47 E-value=90 Score=25.69 Aligned_cols=52 Identities=13% Similarity=0.219 Sum_probs=34.4
Q ss_pred hhhHHHHHHhhhhhCCCCCCcHHHHHHHHHH------HHHHHHHHHHHHHHhhhcCCC
Q 033783 12 SFKKIVIQHMMYGFGDDPNPLPETVALVEDI------VVEYVTDLAHKAQDIGSKGGK 63 (111)
Q Consensus 12 ~~~~~EI~~mMy~fGD~~~P~~eTv~l~Edi------v~~~i~~l~~~A~~~a~~Rgk 63 (111)
++-..||..++|-|||.+++..-...+++.- -+.++.+++..|.....++++
T Consensus 141 ~~se~~L~~I~~~yGee~~a~~IA~~Iv~~R~~~pi~tT~~L~~iI~~~~~~~~~~~~ 198 (310)
T PF01795_consen 141 TYSEEELARIFREYGEEKFARRIARAIVEARKKKPITTTKELAEIIEKAVPKKRRRRK 198 (310)
T ss_dssp HS-HHHHHHHHHHHH--TTHHHHHHHHHHHHHHSS--BHHHHHHHHHHHS-HHHCC-S
T ss_pred hcCHHHHHHHHHhcCchhHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhCCccccccc
Confidence 3455699999999999988777777777665 367777788877765554443
No 63
>PF14164 YqzH: YqzH-like protein
Probab=31.14 E-value=47 Score=21.54 Aligned_cols=20 Identities=35% Similarity=0.649 Sum_probs=17.6
Q ss_pred CCCcHHHHHHHHHHHHHHHH
Q 033783 29 PNPLPETVALVEDIVVEYVT 48 (111)
Q Consensus 29 ~~P~~eTv~l~Ediv~~~i~ 48 (111)
.+|..+--.+|||+|-+||+
T Consensus 44 ~~~~~Dl~eiVeDvVY~yiT 63 (64)
T PF14164_consen 44 EEPDEDLHEIVEDVVYDYIT 63 (64)
T ss_pred cCCCchHHHHHHHHHHHHhc
Confidence 57888888999999999986
No 64
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=30.91 E-value=2e+02 Score=21.03 Aligned_cols=44 Identities=11% Similarity=0.228 Sum_probs=36.3
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHh
Q 033783 31 PLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 74 (111)
Q Consensus 31 P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR 74 (111)
-..++..+|.-++.+.+-.+..+|.++|..+|+ |+-.++.-++|
T Consensus 56 is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~r 101 (127)
T KOG1744|consen 56 ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVR 101 (127)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHH
Confidence 567888899999999999999999999987776 77777766666
No 65
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=30.62 E-value=48 Score=28.31 Aligned_cols=43 Identities=12% Similarity=0.159 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhh
Q 033783 33 PETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 75 (111)
Q Consensus 33 ~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~ 75 (111)
.+-+...+.+.-..|..+|.+|...|.++|+ |+.+||.-++++
T Consensus 379 ~~la~~t~g~sgAdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~ 423 (438)
T PTZ00361 379 EEFIMAKDELSGADIKAICTEAGLLALRERRMKVTQADFRKAKEK 423 (438)
T ss_pred HHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHH
Confidence 3444455666777788999999998887764 999999988775
No 66
>PLN00160 histone H3; Provisional
Probab=30.43 E-value=1.9e+02 Score=20.04 Aligned_cols=57 Identities=7% Similarity=0.094 Sum_probs=42.2
Q ss_pred HHHhhhhh-CCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHh
Q 033783 18 IQHMMYGF-GDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIR 74 (111)
Q Consensus 18 I~~mMy~f-GD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR 74 (111)
++.+.-.| ++.-.=.+++...+.+..-.|++.+...|.-+|...++ |...|+..+.|
T Consensus 31 VREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 31 VREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred HHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 33344334 34356678889999999999999999999988876666 66788876643
No 67
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=30.20 E-value=2.4e+02 Score=21.70 Aligned_cols=38 Identities=18% Similarity=0.135 Sum_probs=31.1
Q ss_pred hCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 033783 25 FGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG 62 (111)
Q Consensus 25 fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg 62 (111)
-+...-+.+--+.||-=....||.++...|.+.+..|+
T Consensus 98 ~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~ 135 (176)
T KOG3423|consen 98 KAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRT 135 (176)
T ss_pred hcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 34456677778889999999999999999999887655
No 68
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=29.82 E-value=2.6e+02 Score=23.89 Aligned_cols=69 Identities=20% Similarity=0.317 Sum_probs=45.1
Q ss_pred hhhhhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhh--cCCCCcHHHHHHHHhhChhHHhHHHHHH
Q 033783 10 EESFKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGS--KGGKLSVEDFLYLIRKDLPKLNRCTELL 87 (111)
Q Consensus 10 ~~~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~--~Rgki~~eDl~F~lR~D~~Kl~Rl~~lL 87 (111)
...|....+-+.+.|.||. +.++|.+-... + -.+|.+.+. ..|+++.+||+-.++. =.|++-+..++
T Consensus 274 le~f~~~~~~~~ilgmgd~-------~~l~e~~~~~~--~-~~~~~~~~~~~~~~~f~l~d~~~q~~~-~~kmG~~~~~~ 342 (437)
T PRK00771 274 LERFDPDRFISRLLGMGDL-------ESLLEKVEEAL--D-EEEEEKDVEKMMKGKFTLKDMYKQLEA-MNKMGPLKQIL 342 (437)
T ss_pred CCcCCHHHHHHHHhCCCCh-------HHHHHHHHHhh--h-HHHHHHHHHHHHcCCcCHHHHHHHHHH-HHhcCCHHHHH
Confidence 4556778899999999996 35555443211 1 122333332 3588999999999875 45677777776
Q ss_pred HH
Q 033783 88 SM 89 (111)
Q Consensus 88 ~~ 89 (111)
+|
T Consensus 343 ~m 344 (437)
T PRK00771 343 QM 344 (437)
T ss_pred Hh
Confidence 66
No 69
>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=29.46 E-value=1.4e+02 Score=18.35 Aligned_cols=35 Identities=17% Similarity=0.178 Sum_probs=29.9
Q ss_pred CCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcC
Q 033783 27 DDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKG 61 (111)
Q Consensus 27 D~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~R 61 (111)
....+.+-.+.+|-=....||.+++..|++.+..|
T Consensus 16 G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r 50 (51)
T PF03540_consen 16 GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIR 50 (51)
T ss_pred CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34557888899999999999999999999988654
No 70
>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=27.59 E-value=78 Score=23.42 Aligned_cols=74 Identities=22% Similarity=0.276 Sum_probs=46.9
Q ss_pred hhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhc-------CCCCcHHHHHHHHhhChhHHhH--HHHHHHHHHHHH
Q 033783 24 GFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSK-------GGKLSVEDFLYLIRKDLPKLNR--CTELLSMQEELK 94 (111)
Q Consensus 24 ~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~-------Rgki~~eDl~F~lR~D~~Kl~R--l~~lL~~k~~ik 94 (111)
||+|...-+.-++.+.|=|-.+--++++..+..+... .-..++++|..++. |=+=||| ++.||+|...+.
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 5555555555556555544444445777777766542 12477777777764 5556676 889999987777
Q ss_pred HHHh
Q 033783 95 QARK 98 (111)
Q Consensus 95 ~ark 98 (111)
+.-.
T Consensus 92 ~~~~ 95 (159)
T PF11861_consen 92 KELG 95 (159)
T ss_pred HHHh
Confidence 6543
No 71
>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=27.17 E-value=1.7e+02 Score=18.52 Aligned_cols=44 Identities=18% Similarity=0.193 Sum_probs=29.8
Q ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHh
Q 033783 31 PLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIR 74 (111)
Q Consensus 31 P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR 74 (111)
+.|-..+++|-..-++-++-+-.+..-|-.+|+|+++.++=.+|
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 45556667766666666666666666666789999998876665
No 72
>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=27.09 E-value=87 Score=22.45 Aligned_cols=33 Identities=15% Similarity=0.260 Sum_probs=25.1
Q ss_pred hhhCCCCCCcHHHHH-HHHHHHHHHHHHHHHHHH
Q 033783 23 YGFGDDPNPLPETVA-LVEDIVVEYVTDLAHKAQ 55 (111)
Q Consensus 23 y~fGD~~~P~~eTv~-l~Ediv~~~i~~l~~~A~ 55 (111)
|--+....+..+||. ++||.|-.+|+-+|.+=.
T Consensus 22 Fe~~~~~~~~~~Tv~d~vee~ia~~im~vc~Qnp 55 (113)
T PF12290_consen 22 FESSQSGDTGDETVEDVVEEQIASQIMAVCEQNP 55 (113)
T ss_pred hcCCCCCCcccchHHHHHHHHHHHHHHHHHccCC
Confidence 444566677888887 999999999999886543
No 73
>COG1422 Predicted membrane protein [Function unknown]
Probab=25.67 E-value=95 Score=24.32 Aligned_cols=27 Identities=19% Similarity=0.400 Sum_probs=19.2
Q ss_pred hChhHHhHHHHHHH-HHHHHHHHHhhcC
Q 033783 75 KDLPKLNRCTELLS-MQEELKQARKAFE 101 (111)
Q Consensus 75 ~D~~Kl~Rl~~lL~-~k~~ik~ark~fd 101 (111)
-|.+|++|+++..+ .|++.++|++.-|
T Consensus 69 iD~ekm~~~qk~m~efq~e~~eA~~~~d 96 (201)
T COG1422 69 IDQEKMKELQKMMKEFQKEFREAQESGD 96 (201)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 47888888877664 5777888877533
No 74
>PTZ00017 histone H2A; Provisional
Probab=25.11 E-value=1.8e+02 Score=21.29 Aligned_cols=38 Identities=21% Similarity=0.215 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChh
Q 033783 40 EDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLP 78 (111)
Q Consensus 40 Ediv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~ 78 (111)
=|++...|.++.-++..-. .+.+|+..+|.-++|+|..
T Consensus 58 LEYLtaEILELAgNaa~d~-kk~RItPrHi~lAI~nDeE 95 (134)
T PTZ00017 58 LEYLTAEVLELAGNAAKDN-KKKRITPRHIQLAIRNDEE 95 (134)
T ss_pred HHHHHHHHHHHHHHHHHhc-CCCeecHHHHHhhccCcHH
Confidence 3344444555555554322 3445999999999999975
No 75
>PRK05481 lipoyl synthase; Provisional
Probab=25.02 E-value=19 Score=28.66 Aligned_cols=24 Identities=17% Similarity=0.333 Sum_probs=19.1
Q ss_pred HHhhhhhCCCCCCcHHHHHHHHHH
Q 033783 19 QHMMYGFGDDPNPLPETVALVEDI 42 (111)
Q Consensus 19 ~~mMy~fGD~~~P~~eTv~l~Edi 42 (111)
..||+|||++.+-..+|...++++
T Consensus 200 t~~IvGfGET~ed~~~tl~~lrel 223 (289)
T PRK05481 200 SGLMVGLGETDEEVLEVMDDLRAA 223 (289)
T ss_pred eeeEEECCCCHHHHHHHHHHHHhc
Confidence 458899999988777777777765
No 76
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=24.94 E-value=3.6e+02 Score=21.49 Aligned_cols=45 Identities=24% Similarity=0.304 Sum_probs=34.2
Q ss_pred CcHHHHHHHHHHH------HHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhh
Q 033783 31 PLPETVALVEDIV------VEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 75 (111)
Q Consensus 31 P~~eTv~l~Ediv------~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~ 75 (111)
-.++.+.++-+.+ ..++.++|..|...|..+|+ |+.+|+.=++..
T Consensus 229 ~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~ 281 (394)
T PRK00411 229 VDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEK 281 (394)
T ss_pred CCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHH
Confidence 4567777777777 56778999999988876664 899999766653
No 77
>COG1004 Ugd Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]
Probab=24.85 E-value=94 Score=26.84 Aligned_cols=46 Identities=11% Similarity=-0.038 Sum_probs=34.6
Q ss_pred hhhhHHHHHHhhhhhCCCC--CCcHHHHHHHHHHHHHHHHHHHHHHHH
Q 033783 11 ESFKKIVIQHMMYGFGDDP--NPLPETVALVEDIVVEYVTDLAHKAQD 56 (111)
Q Consensus 11 ~~~~~~EI~~mMy~fGD~~--~P~~eTv~l~Ediv~~~i~~l~~~A~~ 56 (111)
+|-|.||++++++.+.|.. .++-+++--+-+-=..++.+++.+...
T Consensus 260 GsCfPKD~~AL~~~a~~~~~~~~ll~avv~vN~~qk~~~~~~i~~~~~ 307 (414)
T COG1004 260 GSCFPKDTKALIANAEELGYDPNLLEAVVEVNERRKDKLAEKILNHLG 307 (414)
T ss_pred CcCCcHhHHHHHHHHHhcCCchHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4668999999999999998 455555555556666777777777766
No 78
>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=24.42 E-value=83 Score=21.10 Aligned_cols=35 Identities=23% Similarity=0.405 Sum_probs=25.6
Q ss_pred cHHHHHHHHhhC--hhHHhHHHHHHHHHHHHHHHHhh
Q 033783 65 SVEDFLYLIRKD--LPKLNRCTELLSMQEELKQARKA 99 (111)
Q Consensus 65 ~~eDl~F~lR~D--~~Kl~Rl~~lL~~k~~ik~ark~ 99 (111)
.+.++.|++|+. +.|+.+++.+|.+=-++.+....
T Consensus 19 dL~s~kFLl~~~i~k~kle~~~s~Ldlf~eLEk~~~l 55 (83)
T cd08813 19 ELKSFKFLLQNELPKSKLDDETTLLDIFIEMEKKGIL 55 (83)
T ss_pred HHhhhHHHhhccccchHHhhhccHHHHHHHHHhhCCC
Confidence 356788999865 57888888888887777766554
No 79
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=23.97 E-value=2.7e+02 Score=19.81 Aligned_cols=72 Identities=11% Similarity=0.070 Sum_probs=46.7
Q ss_pred HHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCC--CCcHHHHHHHHhhChhHHhHHHHHHHH
Q 033783 17 VIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGG--KLSVEDFLYLIRKDLPKLNRCTELLSM 89 (111)
Q Consensus 17 EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rg--ki~~eDl~F~lR~D~~Kl~Rl~~lL~~ 89 (111)
-|..+|-.=-|.-.-..-|--++-.-+--||+.|+...++.|...| +++.|-|.-++-+|+ |+.-|++.+..
T Consensus 28 r~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sde-kFdFL~~~~~~ 101 (113)
T COG5247 28 RLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDE-KFDFLKNMEQF 101 (113)
T ss_pred HHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhH-HHHHHHHHHHh
Confidence 3555565544443333333344555566788888888888876554 499999999998886 46666666543
No 80
>PF07887 Calmodulin_bind: Calmodulin binding protein-like; InterPro: IPR012416 The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members (for example, Q8H6T7 from SWISSPROT), are known to be involved in the induction of plant defence responses []. However, their precise function in this regard is as yet unknown.
Probab=23.73 E-value=1.4e+02 Score=24.72 Aligned_cols=36 Identities=39% Similarity=0.604 Sum_probs=29.8
Q ss_pred CCCCcHHHHHHHHhhChhHHhHHHHHHH-------HHHHHHHHHhh
Q 033783 61 GGKLSVEDFLYLIRKDLPKLNRCTELLS-------MQEELKQARKA 99 (111)
Q Consensus 61 Rgki~~eDl~F~lR~D~~Kl~Rl~~lL~-------~k~~ik~ark~ 99 (111)
.|--+++||+=++-.||.||. ++|. |+..++-|++.
T Consensus 183 ~~I~tV~dFl~l~~~d~~~Lr---~ilg~~ms~k~We~~v~HA~tC 225 (299)
T PF07887_consen 183 NGINTVEDFLKLLNKDPQKLR---EILGSGMSNKMWETTVEHAKTC 225 (299)
T ss_pred cCCccHHHHHHHHhcCHHHHH---HHHhcCCChhhHHHHHHHHHhc
Confidence 456899999999999998775 6665 88889999875
No 81
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=23.63 E-value=2.7e+02 Score=21.87 Aligned_cols=43 Identities=14% Similarity=0.202 Sum_probs=31.8
Q ss_pred cHHHHHHHHHHHH------HHHHHHHHHHHHhhhcCC--CCcHHHHHHHHh
Q 033783 32 LPETVALVEDIVV------EYVTDLAHKAQDIGSKGG--KLSVEDFLYLIR 74 (111)
Q Consensus 32 ~~eTv~l~Ediv~------~~i~~l~~~A~~~a~~Rg--ki~~eDl~F~lR 74 (111)
.++.+.++.+++. ..+.++|..|...|..+| .|+.+|+.-++.
T Consensus 222 ~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~ 272 (365)
T TIGR02928 222 DDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQE 272 (365)
T ss_pred ChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3566677777663 578889999998887655 499999886654
No 82
>PF09778 Guanylate_cyc_2: Guanylylate cyclase; InterPro: IPR018616 Members of this family of proteins catalyse the conversion of guanosine triphosphate (GTP) to 3',5'-cyclic guanosine monophosphate (cGMP) and pyrophosphate.
Probab=23.45 E-value=48 Score=26.01 Aligned_cols=16 Identities=50% Similarity=0.756 Sum_probs=12.2
Q ss_pred HHHHHHHhhcCcchhh
Q 033783 91 EELKQARKAFEVDEEK 106 (111)
Q Consensus 91 ~~ik~ark~fd~d~~~ 106 (111)
.-+.+||+.|++|||-
T Consensus 193 ~~ld~AR~s~GTDeDi 208 (212)
T PF09778_consen 193 EALDEARKSFGTDEDI 208 (212)
T ss_pred HHHHHHHhccCCCcce
Confidence 4578888888888874
No 83
>PRK12928 lipoyl synthase; Provisional
Probab=23.44 E-value=21 Score=28.62 Aligned_cols=22 Identities=23% Similarity=0.443 Sum_probs=15.7
Q ss_pred HhhhhhCCCCCCcHHHHHHHHH
Q 033783 20 HMMYGFGDDPNPLPETVALVED 41 (111)
Q Consensus 20 ~mMy~fGD~~~P~~eTv~l~Ed 41 (111)
.||+|||++.+-..+|...+.+
T Consensus 209 ~iIvG~GET~ed~~etl~~Lre 230 (290)
T PRK12928 209 GLMLGLGETEDEVIETLRDLRA 230 (290)
T ss_pred cEEEeCCCCHHHHHHHHHHHHh
Confidence 6899999987666666555554
No 84
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=22.55 E-value=1.3e+02 Score=27.21 Aligned_cols=57 Identities=21% Similarity=0.291 Sum_probs=36.2
Q ss_pred HHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhChhHHhHHHHHHHHHHHHHHHHhhcCcch
Q 033783 46 YVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKDLPKLNRCTELLSMQEELKQARKAFEVDE 104 (111)
Q Consensus 46 ~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D~~Kl~Rl~~lL~~k~~ik~ark~fd~d~ 104 (111)
.+.+|+..|..+|...|+ |+.+|+.-++++..-..+++.+-.. +.++.....+....
T Consensus 367 dl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~~~~e~~l~e~~~--~~~~~~~~li~t~G 425 (647)
T COG1067 367 DLGNLVREAGDIAVSEGRKLITAEDVEEALQKRELREGQLAERYI--EDIKGGQILIETEG 425 (647)
T ss_pred HHHHHHHHhhHHHhcCCcccCcHHHHHHHHHhhhhHHHHHHHHHH--HHHhcceEEEeecc
Confidence 466677777777776554 8999999999887666666655332 44443433444333
No 85
>PLN00156 histone H2AX; Provisional
Probab=22.54 E-value=2.4e+02 Score=20.84 Aligned_cols=37 Identities=19% Similarity=0.223 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChh
Q 033783 41 DIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLP 78 (111)
Q Consensus 41 div~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~ 78 (111)
|++...|.+|.-+|..-. .+.+|+...|.-++|+|..
T Consensus 61 EYLtaEVLELAgNaa~d~-kk~RItPrHi~lAIrnDeE 97 (139)
T PLN00156 61 EYLAAEVLELAGNAARDN-KKNRIVPRHIQLAVRNDEE 97 (139)
T ss_pred HHHHHHHHHHHHHHHHHc-CCCcCcHHHHHhhccCcHH
Confidence 444444666665554322 3446999999999999975
No 86
>PRK07194 fliG flagellar motor switch protein G; Reviewed
Probab=22.39 E-value=1.7e+02 Score=23.82 Aligned_cols=23 Identities=26% Similarity=0.196 Sum_probs=20.5
Q ss_pred HHHHhhhhhCCCCCCcHHHHHHH
Q 033783 17 VIQHMMYGFGDDPNPLPETVALV 39 (111)
Q Consensus 17 EI~~mMy~fGD~~~P~~eTv~l~ 39 (111)
+|+..||.|-|-.+=.|.|++++
T Consensus 230 ~Ir~~mF~FedL~~~~~qtia~i 252 (334)
T PRK07194 230 EIEDNMYDFFILSRQSEETLQRL 252 (334)
T ss_pred HHHHhcCCHHHHhcCCHHHHHHH
Confidence 79999999999999889988854
No 87
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=22.32 E-value=3e+02 Score=19.68 Aligned_cols=53 Identities=21% Similarity=0.248 Sum_probs=34.0
Q ss_pred HHHHHhhh-cCCCCcHHHHHHHHhhChhHHhH-HHHHHHHHHHHHHHHhhcCcchhhh
Q 033783 52 HKAQDIGS-KGGKLSVEDFLYLIRKDLPKLNR-CTELLSMQEELKQARKAFEVDEEKL 107 (111)
Q Consensus 52 ~~A~~~a~-~Rgki~~eDl~F~lR~D~~Kl~R-l~~lL~~k~~ik~ark~fd~d~~~~ 107 (111)
++|..+|. .||+--.+.+.+ |..-|+|-+| +..+|. .-+.+|...++.|.+++
T Consensus 23 kk~r~Va~~IrG~~v~~A~~~-L~~~pkKaa~~v~KvL~--sA~aNAe~n~gLd~d~L 77 (120)
T COG0091 23 KKARLVADLIRGKKVAEALAI-LEFVPKKAAKLVKKVLE--SAIANAENNKGLDPDKL 77 (120)
T ss_pred HHHHHHHHHHcCCcHHHHHHH-HHhChHHHHHHHHHHHH--HHHhhHHhccCCChHHE
Confidence 44555554 577755566666 7777999999 556655 45667766556665543
No 88
>KOG0034 consensus Ca2+/calmodulin-dependent protein phosphatase (calcineurin subunit B), EF-Hand superfamily protein [Signal transduction mechanisms]
Probab=22.13 E-value=3.4e+02 Score=20.55 Aligned_cols=34 Identities=26% Similarity=0.431 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHhhh--cCCCCcHHHHHHHHhhChh
Q 033783 45 EYVTDLAHKAQDIGS--KGGKLSVEDFLYLIRKDLP 78 (111)
Q Consensus 45 ~~i~~l~~~A~~~a~--~Rgki~~eDl~F~lR~D~~ 78 (111)
+++.+++.+...-|- +-|+|+.||+.-++.+.|.
T Consensus 143 e~~~~i~d~t~~e~D~d~DG~IsfeEf~~~v~~~P~ 178 (187)
T KOG0034|consen 143 EQLEDIVDKTFEEADTDGDGKISFEEFCKVVEKQPD 178 (187)
T ss_pred HHHHHHHHHHHHHhCCCCCCcCcHHHHHHHHHcCcc
Confidence 444455555555553 4588999999999988764
No 89
>PF06769 Plasmid_Txe: Plasmid encoded toxin Txe; InterPro: IPR009614 The Axe-Txe pair in Enterococcus faecium (Streptococcus faecium) and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This family describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by match to IPR006442 from INTERPRO [].; GO: 0004519 endonuclease activity, 0006401 RNA catabolic process; PDB: 3OEI_L 2A6R_F 2A6Q_E 2A6S_D.
Probab=21.92 E-value=1.2e+02 Score=20.05 Aligned_cols=23 Identities=26% Similarity=0.456 Sum_probs=19.6
Q ss_pred HHHHHHHHhhChhHHhHHHHHHH
Q 033783 66 VEDFLYLIRKDLPKLNRCTELLS 88 (111)
Q Consensus 66 ~eDl~F~lR~D~~Kl~Rl~~lL~ 88 (111)
.+|+.+.-.+|++-+.|+.++|.
T Consensus 6 ~~d~~~~~~~d~kl~kki~~li~ 28 (80)
T PF06769_consen 6 WEDYKYWKKSDKKLLKKINKLIK 28 (80)
T ss_dssp HHHHHHHHCC-HHHHHHHHHHHH
T ss_pred HHHHHHHHHhCHHHHHHHHHHHH
Confidence 58999999999999999998886
No 90
>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=21.71 E-value=5.7e+02 Score=22.70 Aligned_cols=40 Identities=20% Similarity=0.208 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhChhHHhHHH
Q 033783 45 EYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKDLPKLNRCT 84 (111)
Q Consensus 45 ~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D~~Kl~Rl~ 84 (111)
..+.+++..|..+|..+|+ |+.+|+.=+++.-....+++.
T Consensus 358 R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~~~~~~i~ 399 (608)
T TIGR00764 358 RELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAKTLEKQLA 399 (608)
T ss_pred HHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHHHHHHHHH
Confidence 6788888888777766664 888888877765544444443
No 91
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=21.56 E-value=92 Score=26.11 Aligned_cols=42 Identities=14% Similarity=0.115 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhhC
Q 033783 35 TVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRKD 76 (111)
Q Consensus 35 Tv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~D 76 (111)
-+...+.+.-..|..+|.+|...|.++++ |+.+||.-++++-
T Consensus 343 la~~t~g~sgaDI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 343 FVSRPEKISAADIAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHcCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 33444556667788999999988877765 9999999888763
No 92
>PLN00153 histone H2A; Provisional
Probab=21.37 E-value=2.6e+02 Score=20.34 Aligned_cols=37 Identities=22% Similarity=0.230 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChh
Q 033783 41 DIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLP 78 (111)
Q Consensus 41 div~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~ 78 (111)
|+++.-|.++.-+|..-. .+.+|+...|.-++|+|..
T Consensus 56 EYLtaEVLELAgnaa~d~-kk~RItPrHi~lAI~nDeE 92 (129)
T PLN00153 56 EYLTAEVLELAGNAARDN-KKNRIVPRHIQLAIRNDEE 92 (129)
T ss_pred HHHHHHHHHHHHHHHHhc-CCCccChHHHHhhccCcHH
Confidence 334433555555554322 3456999999999999964
No 93
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=21.26 E-value=1.7e+02 Score=20.44 Aligned_cols=76 Identities=24% Similarity=0.332 Sum_probs=44.7
Q ss_pred hhhhHHHHHHhhhhhCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCCCcHHHHHHHHhhChhHHhHHHHHHHHH
Q 033783 11 ESFKKIVIQHMMYGFGDDPNPLPETVALVEDIVVEYVTDLAHKAQDIGSKGGKLSVEDFLYLIRKDLPKLNRCTELLSMQ 90 (111)
Q Consensus 11 ~~~~~~EI~~mMy~fGD~~~P~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgki~~eDl~F~lR~D~~Kl~Rl~~lL~~k 90 (111)
+-....|+...|-.+|-. |..+ .+.++..+.-. ..-|.|+.++|.-++.+......--. .-.
T Consensus 23 G~i~~~el~~~lr~lg~~--~t~~-----------el~~~~~~~D~--dg~g~I~~~eF~~l~~~~~~~~~~~~---~~~ 84 (151)
T KOG0027|consen 23 GKISVEELGAVLRSLGQN--PTEE-----------ELRDLIKEIDL--DGDGTIDFEEFLDLMEKLGEEKTDEE---ASS 84 (151)
T ss_pred CcccHHHHHHHHHHcCCC--CCHH-----------HHHHHHHHhCC--CCCCeEcHHHHHHHHHhhhccccccc---ccH
Confidence 334567888888888876 2221 12222222211 14577999999999886532211111 345
Q ss_pred HHHHHHHhhcCcch
Q 033783 91 EELKQARKAFEVDE 104 (111)
Q Consensus 91 ~~ik~ark~fd~d~ 104 (111)
+++++|-+.||.|.
T Consensus 85 ~el~eaF~~fD~d~ 98 (151)
T KOG0027|consen 85 EELKEAFRVFDKDG 98 (151)
T ss_pred HHHHHHHHHHccCC
Confidence 68888988998874
No 94
>PF09432 THP2: Tho complex subunit THP2; InterPro: IPR018557 The THO complex plays a role in coupling transcription elongation to mRNA export. It is composed of subunits THP2, HPR1, THO2 and MFT1 [].
Probab=20.79 E-value=89 Score=22.98 Aligned_cols=19 Identities=32% Similarity=0.737 Sum_probs=11.5
Q ss_pred HHHHhhhhhCCCCCCcHHHHH
Q 033783 17 VIQHMMYGFGDDPNPLPETVA 37 (111)
Q Consensus 17 EI~~mMy~fGD~~~P~~eTv~ 37 (111)
.|..||| ||.++....-.+
T Consensus 103 ~iE~~mF--GD~pnSmkkMl~ 121 (132)
T PF09432_consen 103 NIEMLMF--GDGPNSMKKMLQ 121 (132)
T ss_pred HHHHHHh--cCChHHHHHHHH
Confidence 4777885 677665544433
No 95
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=20.09 E-value=1e+02 Score=24.83 Aligned_cols=44 Identities=14% Similarity=0.262 Sum_probs=31.1
Q ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHhhhcCCC--CcHHHHHHHHhh
Q 033783 32 LPETVALVEDIVVEYVTDLAHKAQDIGSKGGK--LSVEDFLYLIRK 75 (111)
Q Consensus 32 ~~eTv~l~Ediv~~~i~~l~~~A~~~a~~Rgk--i~~eDl~F~lR~ 75 (111)
..+.+...+...-..|..+|..|...|-++|+ |+.+||.-++++
T Consensus 317 ~~~la~~t~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 317 LEAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 34444555556666788889988888866654 999999877754
No 96
>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=20.05 E-value=80 Score=23.80 Aligned_cols=15 Identities=40% Similarity=0.570 Sum_probs=8.0
Q ss_pred CCCcHHHHHHHHhhC
Q 033783 62 GKLSVEDFLYLIRKD 76 (111)
Q Consensus 62 gki~~eDl~F~lR~D 76 (111)
|-++++||+=.++..
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 446667766555553
Done!