Query 032654
Match_columns 136
No_of_seqs 141 out of 617
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 04:14:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032654.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032654hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00018 histone H3; Provision 100.0 4E-59 8.6E-64 349.3 11.2 135 1-135 1-135 (136)
2 PLN00121 histone H3; Provision 100.0 5.6E-59 1.2E-63 348.5 11.2 136 1-136 1-136 (136)
3 PLN00161 histone H3; Provision 100.0 1.6E-57 3.5E-62 339.7 10.5 128 1-135 1-129 (135)
4 KOG1745 Histones H3 and H4 [Ch 100.0 2.1E-55 4.6E-60 328.5 8.8 136 1-136 1-137 (137)
5 PLN00160 histone H3; Provision 100.0 6.2E-50 1.3E-54 285.0 8.2 94 42-135 1-95 (97)
6 smart00428 H3 Histone H3. 100.0 1.2E-49 2.7E-54 287.1 9.0 101 35-135 2-104 (105)
7 COG2036 HHT1 Histones H3 and H 99.9 5.4E-26 1.2E-30 160.5 7.0 87 44-135 1-87 (91)
8 PF00125 Histone: Core histone 99.9 7.1E-22 1.5E-26 132.3 5.8 75 58-132 1-75 (75)
9 cd07981 TAF12 TATA Binding Pro 99.3 4.9E-12 1.1E-16 85.3 6.3 59 72-130 7-65 (72)
10 PTZ00463 histone H2B; Provisio 98.9 6.6E-09 1.4E-13 76.4 7.6 69 64-132 26-94 (117)
11 PLN00158 histone H2B; Provisio 98.8 7.9E-09 1.7E-13 75.9 6.4 69 64-132 25-93 (116)
12 smart00427 H2B Histone H2B. 98.8 1.5E-08 3.2E-13 71.5 6.5 66 67-132 2-67 (89)
13 cd00076 H4 Histone H4, one of 98.6 7.2E-08 1.6E-12 67.4 5.6 69 61-134 12-80 (85)
14 PLN00035 histone H4; Provision 98.5 2E-07 4.3E-12 67.4 5.7 67 63-134 30-96 (103)
15 PTZ00015 histone H4; Provision 98.5 2.7E-07 5.9E-12 66.5 5.5 69 61-134 29-97 (102)
16 KOG1744 Histone H2B [Chromatin 98.5 2.2E-07 4.7E-12 69.3 5.1 70 63-132 34-103 (127)
17 smart00803 TAF TATA box bindin 98.5 2.7E-07 5.9E-12 61.3 5.0 63 63-130 3-65 (65)
18 PF00808 CBFD_NFYB_HMF: Histon 98.4 6.3E-07 1.4E-11 58.6 5.5 58 72-129 8-65 (65)
19 cd07979 TAF9 TATA Binding Prot 98.3 1.4E-06 2.9E-11 64.0 6.3 66 68-134 3-68 (117)
20 smart00417 H4 Histone H4. 98.2 2.2E-06 4.9E-11 58.5 4.7 62 61-127 12-73 (74)
21 PF15630 CENP-S: Kinetochore c 98.1 6.5E-06 1.4E-10 56.4 4.5 65 66-130 5-71 (76)
22 PF03847 TFIID_20kDa: Transcri 97.9 2.7E-05 5.8E-10 52.3 5.4 58 73-130 6-63 (68)
23 KOG0870 DNA polymerase epsilon 97.8 3.8E-05 8.2E-10 59.7 5.0 69 60-130 8-76 (172)
24 smart00576 BTP Bromodomain tra 97.7 0.0002 4.4E-09 48.4 6.5 51 84-134 23-73 (77)
25 PF02969 TAF: TATA box binding 97.6 0.00017 3.6E-09 48.3 5.6 59 71-130 8-66 (66)
26 cd08050 TAF6 TATA Binding Prot 97.5 0.00029 6.2E-09 59.8 6.2 63 71-134 4-66 (343)
27 PF02291 TFIID-31kDa: Transcri 97.4 0.00036 7.8E-09 52.2 5.8 65 69-134 15-79 (129)
28 cd00074 H2A Histone 2A; H2A is 97.2 0.00036 7.7E-09 51.3 3.6 67 60-130 18-84 (115)
29 KOG1142 Transcription initiati 97.2 0.00037 8E-09 57.5 3.9 72 54-129 146-217 (258)
30 PF15511 CENP-T: Centromere ki 97.1 0.0005 1.1E-08 59.8 4.3 55 70-124 355-414 (414)
31 KOG3334 Transcription initiati 95.8 0.031 6.7E-07 42.8 6.1 65 70-135 17-81 (148)
32 PF07524 Bromo_TP: Bromodomain 94.8 0.08 1.7E-06 35.4 4.9 54 81-134 19-73 (77)
33 PF02269 TFIID-18kDa: Transcri 90.4 0.26 5.7E-06 34.6 2.6 61 70-130 5-65 (93)
34 KOG0869 CCAAT-binding factor, 90.2 0.91 2E-05 35.4 5.6 69 62-133 32-100 (168)
35 KOG0871 Class 2 transcription 90.1 0.68 1.5E-05 35.7 4.8 72 59-133 9-80 (156)
36 COG5262 HTA1 Histone H2A [Chro 89.6 0.45 9.8E-06 35.5 3.4 58 73-130 33-90 (132)
37 KOG3467 Histone H4 [Chromatin 89.3 0.72 1.6E-05 32.9 4.1 51 83-133 45-95 (103)
38 PLN00154 histone H2A; Provisio 85.9 1.2 2.7E-05 33.7 3.9 68 60-130 36-103 (136)
39 cd08045 TAF4 TATA Binding Prot 85.7 1.9 4.1E-05 34.1 5.1 56 61-117 43-98 (212)
40 smart00414 H2A Histone 2A. 84.3 1.7 3.8E-05 31.4 3.9 67 60-130 7-73 (106)
41 KOG2549 Transcription initiati 84.1 2.3 5E-05 38.9 5.4 61 72-133 17-77 (576)
42 PF05236 TAF4: Transcription i 83.7 1 2.2E-05 36.7 2.8 58 60-118 41-98 (264)
43 COG5094 TAF9 Transcription ini 81.7 2.2 4.8E-05 32.2 3.7 46 86-131 33-81 (145)
44 PTZ00017 histone H2A; Provisio 81.6 1.9 4.2E-05 32.6 3.4 67 60-130 25-91 (134)
45 cd07978 TAF13 The TATA Binding 79.3 9.4 0.0002 26.8 6.1 62 68-130 4-65 (92)
46 COG5150 Class 2 transcription 74.3 6.6 0.00014 29.8 4.3 67 59-128 8-74 (148)
47 PLN00157 histone H2A; Provisio 73.4 3.8 8.3E-05 30.9 2.9 66 61-130 25-90 (132)
48 KOG4336 TBP-associated transcr 73.2 10 0.00022 32.5 5.7 50 85-134 23-72 (323)
49 PLN00156 histone H2AX; Provisi 72.3 5.1 0.00011 30.5 3.4 66 61-130 28-93 (139)
50 PLN00153 histone H2A; Provisio 70.4 5.4 0.00012 30.0 3.2 66 61-130 23-88 (129)
51 KOG1658 DNA polymerase epsilon 70.3 3.6 7.7E-05 32.0 2.2 64 63-128 57-121 (162)
52 COG5248 TAF19 Transcription in 70.2 18 0.00039 26.8 5.8 61 68-130 11-71 (126)
53 COG5208 HAP5 CCAAT-binding fac 69.8 8.9 0.00019 31.7 4.5 84 45-130 80-173 (286)
54 PTZ00252 histone H2A; Provisio 69.5 5.4 0.00012 30.2 3.0 66 61-130 24-91 (134)
55 KOG2389 Predicted bromodomain 69.0 12 0.00026 32.5 5.3 50 84-133 46-95 (353)
56 KOG1756 Histone 2A [Chromatin 66.0 9.9 0.00021 28.7 3.7 50 81-130 42-91 (131)
57 PF09123 DUF1931: Domain of un 64.1 13 0.00029 28.2 4.2 59 68-131 1-59 (138)
58 KOG3901 Transcription initiati 63.4 32 0.00068 25.2 5.8 64 64-130 7-70 (109)
59 KOG1657 CCAAT-binding factor, 60.9 13 0.00027 30.5 3.8 72 57-129 66-137 (236)
60 PF10911 DUF2717: Protein of u 47.4 25 0.00055 24.2 3.0 60 49-111 2-64 (77)
61 COG5095 TAF6 Transcription ini 47.1 32 0.00069 30.1 4.2 61 72-133 11-71 (450)
62 PRK07452 DNA polymerase III su 39.2 65 0.0014 26.3 4.8 58 70-129 137-196 (326)
63 COG1224 TIP49 DNA helicase TIP 38.2 60 0.0013 29.0 4.6 71 61-131 354-431 (450)
64 PF09415 CENP-X: CENP-S associ 35.9 37 0.0008 22.8 2.4 56 71-126 4-62 (72)
65 COG5624 TAF61 Transcription in 35.0 15 0.00032 32.9 0.4 57 73-129 390-447 (505)
66 PF13581 HATPase_c_2: Histidin 33.6 76 0.0017 21.7 3.8 44 69-112 8-51 (125)
67 TIGR02902 spore_lonB ATP-depen 32.2 1E+02 0.0022 27.7 5.3 59 72-130 268-330 (531)
68 TIGR01924 rsbW_low_gc serine-p 29.8 91 0.002 23.2 3.9 45 65-109 15-59 (159)
69 COG2178 Predicted RNA-binding 29.5 75 0.0016 25.7 3.5 56 47-102 24-91 (204)
70 TIGR00764 lon_rel lon-related 28.7 2E+02 0.0042 26.5 6.5 49 83-131 329-390 (608)
71 PF03172 Sp100: Sp100 domain; 27.4 1E+02 0.0022 22.3 3.6 48 53-113 40-87 (103)
72 PF04604 L_biotic_typeA: Type- 26.8 50 0.0011 21.1 1.7 20 88-107 7-26 (51)
73 KOG2680 DNA helicase TIP49, TB 26.4 1.7E+02 0.0037 25.9 5.4 72 61-132 351-429 (454)
74 PF13654 AAA_32: AAA domain; P 25.6 2.5E+02 0.0055 25.3 6.6 66 66-132 430-506 (509)
75 PF07278 DUF1441: Protein of u 25.5 2.4E+02 0.0052 21.7 5.5 64 48-111 75-149 (152)
76 PF07105 DUF1367: Protein of u 25.5 92 0.002 25.0 3.4 16 91-106 91-106 (196)
77 KOG1089 Myotubularin-related p 25.0 71 0.0015 29.6 3.0 35 67-112 417-451 (573)
78 PRK14562 haloacid dehalogenase 24.2 87 0.0019 24.7 3.0 27 80-106 70-96 (204)
79 KOG1757 Histone 2A [Chromatin 22.4 1.4E+02 0.003 22.3 3.6 66 67-134 32-97 (131)
80 PRK08487 DNA polymerase III su 21.8 1.9E+02 0.0042 23.8 4.8 58 70-129 139-197 (328)
81 PF07962 Swi3: Replication For 21.4 69 0.0015 21.8 1.7 30 48-77 35-64 (83)
82 PRK05907 hypothetical protein; 21.3 1.8E+02 0.0038 24.4 4.5 67 63-129 131-200 (311)
83 COG5304 Uncharacterized protei 21.3 63 0.0014 23.0 1.5 18 63-80 72-89 (92)
84 TIGR03015 pepcterm_ATPase puta 21.1 2.2E+02 0.0047 22.1 4.8 49 82-130 213-264 (269)
85 cd00913 PCD_DCoH_subfamily_a P 20.8 47 0.001 22.0 0.8 13 120-132 62-74 (76)
86 PHA02604 rI.-1 hypothetical pr 20.7 1.6E+02 0.0034 22.1 3.6 44 67-113 82-125 (126)
87 PRK04069 serine-protein kinase 20.6 1.8E+02 0.004 21.4 4.1 45 65-109 15-59 (161)
88 KOG1969 DNA replication checkp 20.4 1.7E+02 0.0037 28.4 4.6 80 45-126 449-531 (877)
89 PF10788 DUF2603: Protein of u 20.1 82 0.0018 23.9 2.0 33 46-79 97-129 (137)
No 1
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=4e-59 Score=349.31 Aligned_cols=135 Identities=96% Similarity=1.336 Sum_probs=129.8
Q ss_pred CCcccccccccCCCCCCCchhhhhhcccCCCCCCCCCCCCcCCCCchhhHHHHhhhhchhhhhhccchhHHHHHHHhhhc
Q 032654 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 MARtK~~a~ks~g~kaprk~~a~k~~~k~~p~~~~~~~~~r~~pg~~al~EIr~~Qkst~lli~k~pF~rlVreI~~~~~ 80 (136)
|||||+++++++|+++|+++.++++..++.+..++.++++||+||+++|+|||+||+||++||||+||+||||||++++.
T Consensus 1 MaRtk~~~~k~~~~~~prk~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PTZ00018 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCCchhHHHHHHHHcccchhccccccHHHHHHHHHHHcC
Confidence 99999999999999999999988877777777778899999999999999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhccc
Q 032654 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 81 ~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~~ 135 (136)
+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+|++||||++
T Consensus 81 ~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~ 135 (136)
T PTZ00018 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
T ss_pred CcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhcccC
Confidence 9999999999999999999999999999999999999999999999999999986
No 2
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=5.6e-59 Score=348.48 Aligned_cols=136 Identities=98% Similarity=1.338 Sum_probs=130.6
Q ss_pred CCcccccccccCCCCCCCchhhhhhcccCCCCCCCCCCCCcCCCCchhhHHHHhhhhchhhhhhccchhHHHHHHHhhhc
Q 032654 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 MARtK~~a~ks~g~kaprk~~a~k~~~k~~p~~~~~~~~~r~~pg~~al~EIr~~Qkst~lli~k~pF~rlVreI~~~~~ 80 (136)
|||||+++++++|+++|+++.++++..++.+..++.++++||+||+++|+|||+||+||++||||+||+||||||++++.
T Consensus 1 MaRtk~~~~k~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PLN00121 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCchhHHHHHHHHhccccccccccccHHHHHHHHHHHhC
Confidence 99999999999999999999988877777777788899999999999999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcccC
Q 032654 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGERA 136 (136)
Q Consensus 81 ~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~~~ 136 (136)
+++|||++||+|||||+|+|||+||||+|+||+|+||||||++||+|+++|||+++
T Consensus 81 ~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~~ 136 (136)
T PLN00121 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
T ss_pred ccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHhccccC
Confidence 99999999999999999999999999999999999999999999999999999863
No 3
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=1.6e-57 Score=339.68 Aligned_cols=128 Identities=66% Similarity=0.962 Sum_probs=119.1
Q ss_pred CCcccccccccCCCCCCCchhhhhhcccCCCCCCCCCCCCcCCCCchhhHHHHhhhhchhhhhhccchhHHHHHHHhhhc
Q 032654 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 MARtK~~a~ks~g~kaprk~~a~k~~~k~~p~~~~~~~~~r~~pg~~al~EIr~~Qkst~lli~k~pF~rlVreI~~~~~ 80 (136)
||||||+ +++++||.|++++..+ ...+++++++||+||++||+|||+||+||++||||+||+||||||++++.
T Consensus 1 mar~k~~-~~~~~~~~~~~~~~~~------~~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RLVREI~~~~~ 73 (135)
T PLN00161 1 MARRLQG-KRFRKGKKPQKEASGV------TRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEML 73 (135)
T ss_pred CCccccc-ccccCCCCCcccCCCC------CCCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHHHHHHHHhcC
Confidence 9999999 7788999998887653 23456689999999999999999999999999999999999999999996
Q ss_pred -ccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhccc
Q 032654 81 -TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 81 -~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~~ 135 (136)
+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+||++|||+.
T Consensus 74 ~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~ 129 (135)
T PLN00161 74 REPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPI 129 (135)
T ss_pred CCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhcccc
Confidence 5899999999999999999999999999999999999999999999999999974
No 4
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=100.00 E-value=2.1e-55 Score=328.54 Aligned_cols=136 Identities=94% Similarity=1.293 Sum_probs=128.8
Q ss_pred CCcccccccccCCCCCCCchhhhhhcccC-CCCCCCCCCCCcCCCCchhhHHHHhhhhchhhhhhccchhHHHHHHHhhh
Q 032654 1 MARTKQTARKSTGGKAPRKQLATKAARKS-APTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDF 79 (136)
Q Consensus 1 MARtK~~a~ks~g~kaprk~~a~k~~~k~-~p~~~~~~~~~r~~pg~~al~EIr~~Qkst~lli~k~pF~rlVreI~~~~ 79 (136)
|+|++++++++.++++|++..+.+..+++ .|..+...++++|+||+++++|||+||+||||||+|+||+|||+||.++|
T Consensus 1 m~r~~~t~~k~~~~~~~r~~~a~~~~~~~~~~~~~~~~k~~r~rpg~~al~eirkyQkstdLlI~K~PFqRlvrei~q~f 80 (137)
T KOG1745|consen 1 MARTKQTARKSTGGKAPRKQLAGKAARKSAAPRTGRVKKPHRYRPGTVALREIRKYQKSTDLLIRKLPFQRLVREIAQDF 80 (137)
T ss_pred CCCCCcccccccCCCCCccccccccccccccccccccCccccccCchHHHHHHHHHHhhhHHHhhcCcHHHHhHHHHhcc
Confidence 89999999999999999999998877765 34456668899999999999999999999999999999999999999999
Q ss_pred cccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcccC
Q 032654 80 KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGERA 136 (136)
Q Consensus 80 ~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~~~ 136 (136)
.+|+|||+.||.|||||+|+|||+||||+|+||+|||||||||+|||||++|||++.
T Consensus 81 ~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg~~~ 137 (137)
T KOG1745|consen 81 KTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 137 (137)
T ss_pred cccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcccCCC
Confidence 999999999999999999999999999999999999999999999999999999863
No 5
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=6.2e-50 Score=284.99 Aligned_cols=94 Identities=70% Similarity=1.080 Sum_probs=91.2
Q ss_pred CCCCchhhHHHHhhhhchhhhhhccchhHHHHHHHhhhc-ccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCcccc
Q 032654 42 YRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTI 120 (136)
Q Consensus 42 ~~pg~~al~EIr~~Qkst~lli~k~pF~rlVreI~~~~~-~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi 120 (136)
++||++||+|||+||+||++||||+||+||||||++++. +++|||++||+|||||+|+|||+||||+|+||+|||||||
T Consensus 1 ~rpGt~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl 80 (97)
T PLN00160 1 MRPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTI 80 (97)
T ss_pred CCCccHHHHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhccccc
Confidence 689999999999999999999999999999999999986 5699999999999999999999999999999999999999
Q ss_pred CcccHHHHHHHhccc
Q 032654 121 MPKDIQLARRIRGER 135 (136)
Q Consensus 121 ~~kDiqLa~rirg~~ 135 (136)
|+||||||++|||+.
T Consensus 81 ~~kD~~L~~rirg~~ 95 (97)
T PLN00160 81 MPKDMQLARRIRGQT 95 (97)
T ss_pred chhhHHHHHHhhccc
Confidence 999999999999974
No 6
>smart00428 H3 Histone H3.
Probab=100.00 E-value=1.2e-49 Score=287.12 Aligned_cols=101 Identities=86% Similarity=1.221 Sum_probs=98.0
Q ss_pred CCCCCCcCCCCchhhHHHHhhhhchhhhhhccchhHHHHHHHhhhcc--cccccHHHHHHHHHHHHHHhhhhhhhhhHhh
Q 032654 35 GVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSHAVLALQEAAEAYLVGLFEDTNLCA 112 (136)
Q Consensus 35 ~~~~~~r~~pg~~al~EIr~~Qkst~lli~k~pF~rlVreI~~~~~~--~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a 112 (136)
++++++||+||++||+|||+||+||++||||+||+||||||++++.+ ++|||++||+||||++|+|||++|||||+||
T Consensus 2 ~~~~~~r~rpg~~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a 81 (105)
T smart00428 2 GKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLA 81 (105)
T ss_pred CCCCCcCCCCcchHHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999999999999999999999999999987 9999999999999999999999999999999
Q ss_pred hhcCccccCcccHHHHHHHhccc
Q 032654 113 IHARRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 113 ~HakRvTi~~kDiqLa~rirg~~ 135 (136)
+||||||||++||+||.+|||++
T Consensus 82 ~HAkRvTl~~kDi~La~rir~~~ 104 (105)
T smart00428 82 IHAKRVTIMPKDIQLARRIRGER 104 (105)
T ss_pred HHhCCccCcHhhHHHHHHHhccC
Confidence 99999999999999999999985
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.93 E-value=5.4e-26 Score=160.45 Aligned_cols=87 Identities=46% Similarity=0.690 Sum_probs=83.6
Q ss_pred CCchhhHHHHhhhhchhhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcc
Q 032654 44 PGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPK 123 (136)
Q Consensus 44 pg~~al~EIr~~Qkst~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~k 123 (136)
||+..++|||+||++++++||++||.|++|+...+ ||+.+|+++||++.|.|++.++|+|+.||.|+||+||+++
T Consensus 1 ~~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~-----Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~ 75 (91)
T COG2036 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAE 75 (91)
T ss_pred CCcchHHHHHhhhhhhhhhcCchHHHHHHHHHhHH-----HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHH
Confidence 58899999999999999999999999999999875 9999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhccc
Q 032654 124 DIQLARRIRGER 135 (136)
Q Consensus 124 DiqLa~rirg~~ 135 (136)
||+|+.+.+|..
T Consensus 76 DI~la~~~~~~~ 87 (91)
T COG2036 76 DIKLALKRLGRR 87 (91)
T ss_pred HHHHHHHHhccc
Confidence 999999999853
No 8
>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=99.85 E-value=7.1e-22 Score=132.25 Aligned_cols=75 Identities=47% Similarity=0.662 Sum_probs=71.7
Q ss_pred chhhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHh
Q 032654 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIR 132 (136)
Q Consensus 58 st~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rir 132 (136)
++..+||+.||.|+++||..++..+++|+.+|+.+||+++|+|++.+||+|+.||.|+||+||+++||++|.+|+
T Consensus 1 ~~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 1 RTRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred CcccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 366899999999999999999887799999999999999999999999999999999999999999999999985
No 9
>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=99.31 E-value=4.9e-12 Score=85.34 Aligned_cols=59 Identities=22% Similarity=0.295 Sum_probs=52.9
Q ss_pred HHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 72 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
+.|++.++.+..+++.+|.++||+.+|+|+..++++|..||.|++|.||.++||+|+..
T Consensus 7 l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~ 65 (72)
T cd07981 7 LQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLE 65 (72)
T ss_pred HHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 34455555677999999999999999999999999999999999999999999999864
No 10
>PTZ00463 histone H2B; Provisional
Probab=98.90 E-value=6.6e-09 Score=76.36 Aligned_cols=69 Identities=13% Similarity=0.146 Sum_probs=66.4
Q ss_pred hccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHh
Q 032654 64 RKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIR 132 (136)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rir 132 (136)
++.+|..||+.|+.++++|..++..||..|.....|++.++-.+|..++.+.+|-||+++|||.+.||.
T Consensus 26 r~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 26 RYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred ccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 466799999999999999999999999999999999999999999999999999999999999999985
No 11
>PLN00158 histone H2B; Provisional
Probab=98.84 E-value=7.9e-09 Score=75.93 Aligned_cols=69 Identities=13% Similarity=0.206 Sum_probs=66.7
Q ss_pred hccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHh
Q 032654 64 RKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIR 132 (136)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rir 132 (136)
++..|..||+.|+.++++|..++..||..|.....+++.++-.+|..++.+.+|-||.++|||.+.||.
T Consensus 25 r~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 25 KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 568899999999999999999999999999999999999999999999999999999999999999985
No 12
>smart00427 H2B Histone H2B.
Probab=98.81 E-value=1.5e-08 Score=71.51 Aligned_cols=66 Identities=14% Similarity=0.213 Sum_probs=64.1
Q ss_pred chhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHh
Q 032654 67 PFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIR 132 (136)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rir 132 (136)
+|..+|+.|+.++++|..++..||..|...+.+++.++-.+|..++.+.||-||.++|||.+.||.
T Consensus 2 sy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 2 TYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred cHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 688999999999999999999999999999999999999999999999999999999999999985
No 13
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=98.63 E-value=7.2e-08 Score=67.43 Aligned_cols=69 Identities=23% Similarity=0.269 Sum_probs=63.0
Q ss_pred hhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
.-||+.|..||+|.- +--|++.++.+.+.++.|.||..+..||..++-|++|.||+..||.++.+-.|.
T Consensus 12 ~gi~k~~I~RLarr~-----GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~ 80 (85)
T cd00076 12 KGITKPAIRRLARRG-----GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred ccCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 348999999998742 457999999999999999999999999999999999999999999999998885
No 14
>PLN00035 histone H4; Provisional
Probab=98.53 E-value=2e-07 Score=67.36 Aligned_cols=67 Identities=24% Similarity=0.273 Sum_probs=61.8
Q ss_pred hhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 63 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
||+.|..||+|.- .--|++.+|.+.|.++.|.||..+..||...+-|++|.||+..||.++.+-.|.
T Consensus 30 ipk~~IrRLARr~-----GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~ 96 (103)
T PLN00035 30 ITKPAIRRLARRG-----GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred CCHHHHHHHHHHc-----CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC
Confidence 8999999998653 457999999999999999999999999999999999999999999999988775
No 15
>PTZ00015 histone H4; Provisional
Probab=98.49 E-value=2.7e-07 Score=66.55 Aligned_cols=69 Identities=23% Similarity=0.238 Sum_probs=62.3
Q ss_pred hhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
.-|++.|..||++.- .--|++.+|.+.+.++.|.||..+..||..+|-||+|.||+..||.++.+-.|.
T Consensus 29 ~gI~k~~IrRLarr~-----GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~ 97 (102)
T PTZ00015 29 RGITKGAIRRLARRG-----GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred cCCCHHHHHHHHHHc-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 348999999998642 457999999999999999999999999999999999999999999999988774
No 16
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=98.49 E-value=2.2e-07 Score=69.33 Aligned_cols=70 Identities=21% Similarity=0.265 Sum_probs=67.0
Q ss_pred hhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHh
Q 032654 63 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIR 132 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rir 132 (136)
..+..|..+|+.++.++++|+.++..|+.+|.....+++.++...|+++|.+.||-||..+|||+|.+|.
T Consensus 34 ~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 34 RRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred cccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 4678899999999999999999999999999999999999999999999999999999999999999985
No 17
>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=98.48 E-value=2.7e-07 Score=61.30 Aligned_cols=63 Identities=19% Similarity=0.215 Sum_probs=53.9
Q ss_pred hhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 63 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
+|+.|..|+.+. .+ --+++.+|...|.+..|.++-.+.++|..++.|+||.||+..||.+|.+
T Consensus 3 ~p~~~i~ria~~----~G-i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 3 LPKETIKDVAES----LG-IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCHHHHHHHHHH----CC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 566666666543 33 3489999999999999999999999999999999999999999998863
No 18
>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=98.42 E-value=6.3e-07 Score=58.57 Aligned_cols=58 Identities=29% Similarity=0.315 Sum_probs=49.3
Q ss_pred HHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHH
Q 032654 72 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLAR 129 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~ 129 (136)
|+.|++...+..+++.+|..+|+.++|.|+..|-.+|+..+.+.+|-||++.||..|.
T Consensus 8 vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 8 VKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 3555555556678999999999999999999999999999999999999999998763
No 19
>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=98.35 E-value=1.4e-06 Score=63.97 Aligned_cols=66 Identities=21% Similarity=0.325 Sum_probs=60.0
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 68 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
..++|..|+.+.+ ..+++..+...|-|.++.|...+..||...|-||+|.||...||+||...++.
T Consensus 3 d~~~v~~iLk~~G-v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 3 DARVIAAILKSMG-ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHHCC-CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 3578888888663 45999999999999999999999999999999999999999999999998875
No 20
>smart00417 H4 Histone H4.
Probab=98.22 E-value=2.2e-06 Score=58.53 Aligned_cols=62 Identities=23% Similarity=0.240 Sum_probs=55.8
Q ss_pred hhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHH
Q 032654 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQL 127 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqL 127 (136)
.-||+.|..||+|. .+--|++.++.+.|.++.|.||..+..||..++-|++|.||+..|+..
T Consensus 12 ~gI~k~~IrRLaRr-----~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARR-----GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHH-----cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 34899999999864 245799999999999999999999999999999999999999999853
No 21
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.07 E-value=6.5e-06 Score=56.44 Aligned_cols=65 Identities=26% Similarity=0.260 Sum_probs=54.0
Q ss_pred cchhHHHHHHHhhh--cccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 66 LPFQRLVREIAQDF--KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 66 ~pF~rlVreI~~~~--~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
..+.--|-+|+++. ..+..++++.+.+|-|.+=.++..+-.|--..|.||+|.||++.|+.|..|
T Consensus 5 aal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 5 AALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 34555677777776 367899999999999999999999999999999999999999999999754
No 22
>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=97.93 E-value=2.7e-05 Score=52.29 Aligned_cols=58 Identities=19% Similarity=0.244 Sum_probs=46.1
Q ss_pred HHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 73 REIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
.|++.++.++..+..++.++|.+.|++|+....+.|..+|.|.+--||.++|+|+...
T Consensus 6 ~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 6 QELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 4455556789999999999999999999999999999999999999999999999764
No 23
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=97.80 E-value=3.8e-05 Score=59.74 Aligned_cols=69 Identities=26% Similarity=0.316 Sum_probs=64.1
Q ss_pred hhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
++.+|++-..|||+|++.+. +.-++.+|+.||+.+|--|+.-|--.|+-.|.-.+|-||++.|+-=++.
T Consensus 8 dl~lP~AiI~rlvke~l~E~--~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~ 76 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPES--NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD 76 (172)
T ss_pred HhhccHHHHHHHHHHhCccc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence 58899999999999999877 7899999999999999999999999999999999999999999865543
No 24
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.66 E-value=0.0002 Score=48.45 Aligned_cols=51 Identities=25% Similarity=0.205 Sum_probs=48.0
Q ss_pred cccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 84 RFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 84 r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
+.+.+|++.|.+..|.|+..|-+.+...+-|++|.+..+.|+.++..--|.
T Consensus 23 ~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi 73 (77)
T smart00576 23 SFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGI 73 (77)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Confidence 889999999999999999999999999999999999999999999876554
No 25
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.63 E-value=0.00017 Score=48.27 Aligned_cols=59 Identities=25% Similarity=0.324 Sum_probs=46.8
Q ss_pred HHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 71 LVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 71 lVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
-|+-|++.++- -..+.++..+|-+-+|.-|-.+.++|..++.|+||-+|++.||..|.|
T Consensus 8 svk~iAes~Gi-~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 8 SVKDIAESLGI-SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHHcCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 46666666542 247899999999999999999999999999999999999999998875
No 26
>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=97.46 E-value=0.00029 Score=59.76 Aligned_cols=63 Identities=19% Similarity=0.245 Sum_probs=56.3
Q ss_pred HHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 71 LVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 71 lVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
.|+.|++..+ --+.+.+|..+|-+-+|.++-.+.++|..++.|+||.||+..||++|.+.++.
T Consensus 4 ~i~~ia~~~G-i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~ 66 (343)
T cd08050 4 SIKLIAESLG-IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNV 66 (343)
T ss_pred HHHHHHHHcC-CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCC
Confidence 4677777553 23889999999999999999999999999999999999999999999999865
No 27
>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=97.44 E-value=0.00036 Score=52.20 Aligned_cols=65 Identities=29% Similarity=0.375 Sum_probs=53.2
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 69 QRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 69 ~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
.++|..|+.+.+- ..++...+.-|-|.+=.|...+++||...+-||+|.+|...|++||...|..
T Consensus 15 a~~i~~iL~~~Gv-~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~ 79 (129)
T PF02291_consen 15 ARVIHLILKSMGV-TEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLD 79 (129)
T ss_dssp HHHHHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT--
T ss_pred HHHHHHHHHHcCC-cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHh
Confidence 5788889887752 3579999999999999999999999999999999999999999999987753
No 28
>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=97.22 E-value=0.00036 Score=51.29 Aligned_cols=67 Identities=21% Similarity=0.203 Sum_probs=59.3
Q ss_pred hhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
.|.+|-.++.|+.++= ....|+..+|...|-..-|.+...++|-|...+.|.++.+|+|+||+|+.+
T Consensus 18 gL~fPV~ri~R~Lk~~----~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 18 GLQFPVGRIHRYLKKG----RYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred CccCcHHHHHHHHHcC----ccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 4789999999998651 123799999999999999999999999999999999999999999999865
No 29
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.21 E-value=0.00037 Score=57.51 Aligned_cols=72 Identities=19% Similarity=0.272 Sum_probs=63.3
Q ss_pred hhhhchhhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHH
Q 032654 54 KYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLAR 129 (136)
Q Consensus 54 ~~Qkst~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~ 129 (136)
.++-+++.++-|--...||++| ..+-.+..++-+.|.|.|++|+..+-.-+..+|.|.|--||.++||+|.+
T Consensus 146 ~~~~~~~~il~k~kl~dLvqqI----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhL 217 (258)
T KOG1142|consen 146 QDEPGNNPILSKRKLDDLVQQI----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHL 217 (258)
T ss_pred cccCCCCccccccchhHHHHhh----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeee
Confidence 5667777888777777777766 56778899999999999999999999999999999999999999999975
No 30
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.15 E-value=0.0005 Score=59.80 Aligned_cols=55 Identities=31% Similarity=0.438 Sum_probs=42.6
Q ss_pred HHHHHHHhhh-----cccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCccc
Q 032654 70 RLVREIAQDF-----KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKD 124 (136)
Q Consensus 70 rlVreI~~~~-----~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kD 124 (136)
-+|+.++..| ....++..+||.+|..|+|-|+.+|-+|--..|.||+|.||...|
T Consensus 355 ~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 355 GVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp HHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred cHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3556666655 257899999999999999999999999999999999999998776
No 31
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.85 E-value=0.031 Score=42.78 Aligned_cols=65 Identities=23% Similarity=0.411 Sum_probs=55.4
Q ss_pred HHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhccc
Q 032654 70 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 70 rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~~ 135 (136)
+++--|+.+++ ---|....+.-|=|.+=.|.+.+++||...+-||++-||...|++||...++.+
T Consensus 17 ~~i~~iL~s~G-I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~ 81 (148)
T KOG3334|consen 17 RVIASILKSLG-IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDH 81 (148)
T ss_pred HHHHHHHHHcC-ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhcc
Confidence 56666666554 234677889999999999999999999999999999999999999999888753
No 32
>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=94.79 E-value=0.08 Score=35.38 Aligned_cols=54 Identities=22% Similarity=0.179 Sum_probs=48.5
Q ss_pred ccc-cccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 81 TDL-RFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 81 ~~~-r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
.+| ..+++||+.|-+.+..||..|...+...+-|+.|-...+.|+.++..=-|.
T Consensus 19 ~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi 73 (77)
T PF07524_consen 19 AGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI 73 (77)
T ss_pred cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 344 688999999999999999999999999999999999999999988765553
No 33
>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=90.39 E-value=0.26 Score=34.57 Aligned_cols=61 Identities=15% Similarity=0.195 Sum_probs=31.4
Q ss_pred HHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 70 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 70 rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
.=|+.++--|+..-.-..+....|.+..-.|++.+...|..+|.+.++-+|.+.|+-.+.|
T Consensus 5 ~eI~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 5 KEIRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp CCCHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred HHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 3345555556666677889999999999999999999999999999999999999987765
No 34
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=90.15 E-value=0.91 Score=35.38 Aligned_cols=69 Identities=14% Similarity=0.198 Sum_probs=54.3
Q ss_pred hhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q 032654 62 LIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 62 li~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg 133 (136)
++|-+--.|+.+.++ ..+-.+..+|=+.+||.+-.|+-=+--.|+.-..--||.||+..||-.|+--.|
T Consensus 32 ~LPIANV~RIMK~~l---P~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 32 FLPIANVSRIMKKAL---PANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hccHHHHHHHHHhcC---CcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 344444445444443 467899999999999999999988888888888889999999999998876554
No 35
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=90.12 E-value=0.68 Score=35.74 Aligned_cols=72 Identities=18% Similarity=0.256 Sum_probs=63.4
Q ss_pred hhhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q 032654 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 59 t~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg 133 (136)
.++-+||+.....|+|++- .|+||..+|=+.|++++=.|+--+=-.||..+---.+-||.|.-+.=|+.-.|
T Consensus 9 de~sLPkAtv~KmIke~lP---~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~Lg 80 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLP---KDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLG 80 (156)
T ss_pred ccccCcHHHHHHHHHHhCC---cccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcc
Confidence 3577999999999998864 69999999999999999999999999999999999999999998877765444
No 36
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=89.65 E-value=0.45 Score=35.50 Aligned_cols=58 Identities=21% Similarity=0.275 Sum_probs=49.5
Q ss_pred HHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 73 REIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
+.++..-....|+.+.|...|--..|.....++|-|.-.|.-.|-..|||+-+|||-|
T Consensus 33 kr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 33 KRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred HHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 4444433467899999999999888988899999999999999999999999999843
No 37
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=89.31 E-value=0.72 Score=32.85 Aligned_cols=51 Identities=20% Similarity=0.264 Sum_probs=42.6
Q ss_pred ccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q 032654 83 LRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 83 ~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg 133 (136)
-|+..-..+-...++..||.....+|..-+-||||.||+.-|+--+..=-|
T Consensus 45 kRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G 95 (103)
T KOG3467|consen 45 KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 95 (103)
T ss_pred chhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcC
Confidence 355566667778889999999999999999999999999999987765444
No 38
>PLN00154 histone H2A; Provisional
Probab=85.88 E-value=1.2 Score=33.72 Aligned_cols=68 Identities=18% Similarity=0.152 Sum_probs=55.6
Q ss_pred hhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
.|.+|---..|+.+|-.. ...|+.+.|..-|--.-|.....++|-|.-.+...++..|+|++|+|+.+
T Consensus 36 gL~FPVgRi~r~Lk~g~~---~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVS---AHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhh---hccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 366777777777766431 24588889988888888988899999999999999999999999999864
No 39
>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=85.65 E-value=1.9 Score=34.09 Aligned_cols=56 Identities=18% Similarity=0.208 Sum_probs=50.0
Q ss_pred hhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCc
Q 032654 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARR 117 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakR 117 (136)
.++...|+...+..|+.+.+-. .+..+.+..|..|+|.+|-.|.++...++-|...
T Consensus 43 ~fl~~~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~ 98 (212)
T cd08045 43 SFLNPSPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEERLRNLLEKLIEVSEHRVD 98 (212)
T ss_pred hccCHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 6788899999999999876543 8899999999999999999999999999999743
No 40
>smart00414 H2A Histone 2A.
Probab=84.29 E-value=1.7 Score=31.36 Aligned_cols=67 Identities=24% Similarity=0.220 Sum_probs=53.4
Q ss_pred hhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
+|.+|-.-|.|+.++- .-..|+...|..-|--.-|.....++|-|...+...++..|+|+|++++.+
T Consensus 7 gL~fPVgRi~r~Lk~~----~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 7 GLQFPVGRIHRLLRKG----TYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred CccCchHHHHHHHHcC----ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 3556666666766542 223588999988888888999999999999889999999999999999864
No 41
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=84.14 E-value=2.3 Score=38.94 Aligned_cols=61 Identities=21% Similarity=0.322 Sum_probs=50.8
Q ss_pred HHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q 032654 72 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg 133 (136)
++-+++.. +--.++.+|..+|-+-+|.-+-.+.+||..++.|+||-+++..||.-|.|.+.
T Consensus 17 ~k~vAEsl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 17 VKVVAESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred HHHHHHHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 33444433 23457889999999999999999999999999999999999999999988764
No 42
>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=83.68 E-value=1 Score=36.70 Aligned_cols=58 Identities=22% Similarity=0.266 Sum_probs=38.8
Q ss_pred hhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCcc
Q 032654 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRV 118 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRv 118 (136)
.+++...|++..+.+|+..++ ...+..+.+..|-.|+|.+|-.|+|++..++.|....
T Consensus 41 ~~fL~~~~L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 41 EPFLNPSPLQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp ---S-HHHHHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred ccccCHHHHHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 367788889999999997665 5678899999999999999999999999999997654
No 43
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=81.74 E-value=2.2 Score=32.22 Aligned_cols=46 Identities=30% Similarity=0.369 Sum_probs=37.6
Q ss_pred cHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCc---ccHHHHHHH
Q 032654 86 QSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMP---KDIQLARRI 131 (136)
Q Consensus 86 ~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~---kDiqLa~ri 131 (136)
......-|-+.|--|..+++|||...+-|++|-.+.+ .|+.||.--
T Consensus 33 e~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 33 EPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred CccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 3444555678999999999999999999998876665 999998754
No 44
>PTZ00017 histone H2A; Provisional
Probab=81.61 E-value=1.9 Score=32.58 Aligned_cols=67 Identities=22% Similarity=0.208 Sum_probs=55.2
Q ss_pred hhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
.|.+|---+.|+.++- ....|+...|..-|--.-|.....++|-|.-.+...++..|+|++|+|+.+
T Consensus 25 gL~FPVgRi~R~Lk~g----~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKG----RYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhcc----chhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 3677777777877553 123488888888888888999999999999999999999999999999865
No 45
>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=79.29 E-value=9.4 Score=26.77 Aligned_cols=62 Identities=19% Similarity=0.265 Sum_probs=47.1
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 68 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
|..=++.++--++..-.-..+....|.+.+=.|++.+.-.|..+|. ..+--+.+.|+-.+.|
T Consensus 4 f~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 4 FTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred cHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 3333444454455555667889999999999999999999999998 5555569999987764
No 46
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=74.33 E-value=6.6 Score=29.80 Aligned_cols=67 Identities=22% Similarity=0.210 Sum_probs=57.2
Q ss_pred hhhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHH
Q 032654 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLA 128 (136)
Q Consensus 59 t~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa 128 (136)
.++.+||+--+..|-+|+. .|+-|+.+|-+.+++++=.|+--|=-.||..+-.-...||.+.-+--|
T Consensus 8 De~sLPKATVqKMvS~iLp---~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKA 74 (148)
T COG5150 8 DENSLPKATVQKMVSSILP---KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKA 74 (148)
T ss_pred ccccCcHHHHHHHHHHhcc---ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHH
Confidence 3567899999999998875 789999999999999999999999999998888888888887665443
No 47
>PLN00157 histone H2A; Provisional
Probab=73.38 E-value=3.8 Score=30.90 Aligned_cols=66 Identities=24% Similarity=0.229 Sum_probs=53.1
Q ss_pred hhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
|.+|---+.|+.++= ....|+.+.|..-|--.-|.....++|-|.-.+...++..|+|++|+|+.+
T Consensus 25 L~FPVgRi~R~Lk~g----~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 25 LQFPVGRIARYLKAG----KYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred cccchHHHHHHHhcC----chhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 666666667776541 123588888888888888888889999999999999999999999999864
No 48
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=73.16 E-value=10 Score=32.53 Aligned_cols=50 Identities=16% Similarity=0.085 Sum_probs=44.8
Q ss_pred ccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 85 FQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 85 ~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
++..|++.|=++.-.|+-.+|+.+-..+-|++|.-.++.|+.|....-|.
T Consensus 23 is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI 72 (323)
T KOG4336|consen 23 ISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNI 72 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCC
Confidence 55677888888888999999999999999999999999999999987775
No 49
>PLN00156 histone H2AX; Provisional
Probab=72.27 E-value=5.1 Score=30.50 Aligned_cols=66 Identities=24% Similarity=0.227 Sum_probs=53.0
Q ss_pred hhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
|.+|---+.|+.++- ....|+...|..-|--.-|.....++|-|.-.+...++..|+|+.|+|+.+
T Consensus 28 L~FPVgRi~R~Lk~g----~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 28 LQFPVGRIARFLKAG----KYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred cccchHHHHHHHhcC----ChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 566666666766542 223488888888888888888889999999999999999999999999864
No 50
>PLN00153 histone H2A; Provisional
Probab=70.45 E-value=5.4 Score=29.97 Aligned_cols=66 Identities=24% Similarity=0.219 Sum_probs=53.2
Q ss_pred hhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
|.+|---+.|+.++ -....|+.+.|..-|--.-|.....++|-|.-.+...+...|+|+.|+|+.+
T Consensus 23 L~FpVgRi~R~Lr~----g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 23 LQFPVGRIARYLKK----GKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred cccchHHHHHHHhc----CchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 66666666676644 1223588888888888888888889999999999999999999999999864
No 51
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=70.34 E-value=3.6 Score=32.02 Aligned_cols=64 Identities=23% Similarity=0.375 Sum_probs=50.7
Q ss_pred hhccchhHHHHHHHhhhcccccccHH-HHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHH
Q 032654 63 IRKLPFQRLVREIAQDFKTDLRFQSH-AVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLA 128 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~~~~r~~~~-Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa 128 (136)
+.++|.+|. ++|.. ..+|++|..+ |+.++-.++|.|+-.|=.+++-|+--.+|+|+.-+|+..+
T Consensus 57 l~rLpL~ri-k~vvk-l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~a 121 (162)
T KOG1658|consen 57 LSRLPLARI-KQVVK-LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTA 121 (162)
T ss_pred hhhccHHHH-Hhhcc-CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhccccc
Confidence 356666653 44443 4578888765 4667889999999999999999999999999999997654
No 52
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=70.21 E-value=18 Score=26.78 Aligned_cols=61 Identities=18% Similarity=0.199 Sum_probs=48.5
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 68 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
|..=|+.++--|+.+..-..+.+++|.|.+-+|++.+.-.|-..|- .|=.+...|...+.|
T Consensus 11 F~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 11 FMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred HHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 5555666666677777788899999999999999999988887776 555667788888765
No 53
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=69.84 E-value=8.9 Score=31.67 Aligned_cols=84 Identities=20% Similarity=0.298 Sum_probs=62.1
Q ss_pred CchhhHHHHhhhhchhh---------hhhccchhHHHHHHHhhhcccc-cccHHHHHHHHHHHHHHhhhhhhhhhHhhhh
Q 032654 45 GTVALREIRKYQKSTEL---------LIRKLPFQRLVREIAQDFKTDL-RFQSHAVLALQEAAEAYLVGLFEDTNLCAIH 114 (136)
Q Consensus 45 g~~al~EIr~~Qkst~l---------li~k~pF~rlVreI~~~~~~~~-r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~H 114 (136)
|...-+-+|.||+..+. -...+||.|+ +.++. ..+|. =++++|=...-.++|-|+..|---|-+.|-.
T Consensus 80 g~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARI-kkvMK-tdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~ 157 (286)
T COG5208 80 GLLDERISRYWQQTIKAAEEERQILLKDHNLPLARI-KKVMK-TDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEE 157 (286)
T ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHH-HHHHh-cccchhheecccchHHHHHHHHHHHHHHHHHHHHHhH
Confidence 44455567888876432 2334899886 45554 22333 4677777778889999999999999999999
Q ss_pred cCccccCcccHHHHHH
Q 032654 115 ARRVTIMPKDIQLARR 130 (136)
Q Consensus 115 akRvTi~~kDiqLa~r 130 (136)
.||-||.-.||--|+.
T Consensus 158 NkRRtLQksDia~Av~ 173 (286)
T COG5208 158 NKRRTLQKSDIAAAVK 173 (286)
T ss_pred hhhhHHHHHHHHHHHH
Confidence 9999999999987764
No 54
>PTZ00252 histone H2A; Provisional
Probab=69.50 E-value=5.4 Score=30.19 Aligned_cols=66 Identities=18% Similarity=0.200 Sum_probs=50.9
Q ss_pred hhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhh--cCccccCcccHHHHHH
Q 032654 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIH--ARRVTIMPKDIQLARR 130 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~H--akRvTi~~kDiqLa~r 130 (136)
|.+|---+.|+.++= ....|+.+.|..-|--.-|.....++|-|...+.. .|+..|+|++|+|+.+
T Consensus 24 L~FPVgRi~R~Lr~g----~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 24 LIFPVGRVGSLLRRG----QYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred ccCchHHHHHHHHcC----CcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 566666677776442 22358889998888888888888999999888854 6778999999999864
No 55
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=69.00 E-value=12 Score=32.53 Aligned_cols=50 Identities=22% Similarity=0.124 Sum_probs=46.2
Q ss_pred cccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q 032654 84 RFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 84 r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg 133 (136)
.++..||+-|+..+-.|+-+|-+.|...+-|++|+--...||-++..-.|
T Consensus 46 ~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls 95 (353)
T KOG2389|consen 46 STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLS 95 (353)
T ss_pred ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhh
Confidence 57788999999999999999999999999999999999999999886654
No 56
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=66.03 E-value=9.9 Score=28.67 Aligned_cols=50 Identities=24% Similarity=0.258 Sum_probs=41.7
Q ss_pred ccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 81 ~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
.-.|+...|...|--.-|.....++|.+...|.-.++..|+|+-++||.+
T Consensus 42 ~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 42 YAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred hhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 34677777877777666666678999999999999999999999999865
No 57
>PF09123 DUF1931: Domain of unknown function (DUF1931); InterPro: IPR015207 This entry represents a set of hypothetical bacterial proteins containing a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined []. ; PDB: 1WWS_A 1WWI_A 1R4V_A.
Probab=64.13 E-value=13 Score=28.20 Aligned_cols=59 Identities=24% Similarity=0.326 Sum_probs=42.0
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHH
Q 032654 68 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRI 131 (136)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~ri 131 (136)
|.++.|+-+ ++-...+-+.-+-+.+|.-|..||+-|+.-|...+|-.|.+.|+-+-..+
T Consensus 1 fe~lFR~aa-----~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPITkGl 59 (138)
T PF09123_consen 1 FERLFRKAA-----GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPITKGL 59 (138)
T ss_dssp HHHHHHHHH-----S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHH
T ss_pred ChHHHHHHh-----ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCccHHH
Confidence 455655543 35556777888899999999999999999999999999999998776655
No 58
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=63.43 E-value=32 Score=25.20 Aligned_cols=64 Identities=20% Similarity=0.266 Sum_probs=50.3
Q ss_pred hccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 64 RKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
++--|+.=++-.+--|+.+.---.+.+++|.+.+=.|++.+.+.|..+. +|=.+...|+..+.|
T Consensus 7 rk~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 7 RKHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred HHHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 3445777777777777777777889999999999999999966665555 777888899987654
No 59
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=60.89 E-value=13 Score=30.51 Aligned_cols=72 Identities=18% Similarity=0.221 Sum_probs=59.3
Q ss_pred hchhhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHH
Q 032654 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLAR 129 (136)
Q Consensus 57 kst~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~ 129 (136)
...++.+..+|..|+ +.|...-..---+..+|....-.|+|.|+..|=.-++.-+--++|-|+.-.|+.-++
T Consensus 66 ~~~d~~~~~lPlaRi-KkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av 137 (236)
T KOG1657|consen 66 GQLDFKNHILPLARI-KKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAV 137 (236)
T ss_pred cccchhhccCcHhhc-cccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHh
Confidence 355788999999997 556553222237999999999999999999999999999999999999999887654
No 60
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=47.44 E-value=25 Score=24.22 Aligned_cols=60 Identities=23% Similarity=0.416 Sum_probs=45.2
Q ss_pred hHHHHhhhhchhhhhhccchhHHHHHHHh-hhcccccccHHHHHHHHH--HHHHHhhhhhhhhhHh
Q 032654 49 LREIRKYQKSTELLIRKLPFQRLVREIAQ-DFKTDLRFQSHAVLALQE--AAEAYLVGLFEDTNLC 111 (136)
Q Consensus 49 l~EIr~~Qkst~lli~k~pF~rlVreI~~-~~~~~~r~~~~Al~aLQe--aaE~~Lv~lfe~a~l~ 111 (136)
|++|.+|+...+ =||-.| |.+.|-++ .|+.++-..+..+..|+. -+|+|+-++++..+.|
T Consensus 2 L~~I~h~l~np~-DiP~ip--ra~aeyLqvrfN~~yl~~sG~i~~lr~~G~SE~~I~Gfl~Gl~~A 64 (77)
T PF10911_consen 2 LKPIQHLLDNPD-DIPDIP--RAAAEYLQVRFNAAYLMASGIISALRKQGWSESYILGFLAGLQYA 64 (77)
T ss_pred cchHHHHhcCCc-ccCCcc--HHHHHHHHHHhcHHHHHHhhhHHHHHHccccHHHHHHHHHHHHHH
Confidence 678888887763 355554 66667666 356777788888888875 5899999999999887
No 61
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=47.06 E-value=32 Score=30.15 Aligned_cols=61 Identities=18% Similarity=0.268 Sum_probs=49.4
Q ss_pred HHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q 032654 72 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg 133 (136)
++.+++..+ ---+..+++.||---.|.-+-.+-+.|...+.|.||.-++..||.-|.|-+.
T Consensus 11 ~KdvAeslG-i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lN 71 (450)
T COG5095 11 LKDVAESLG-ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLN 71 (450)
T ss_pred HHHHHHHcC-CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcC
Confidence 444444332 1246678898998889999999999999999999999999999999988764
No 62
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=39.22 E-value=65 Score=26.26 Aligned_cols=58 Identities=19% Similarity=0.216 Sum_probs=45.8
Q ss_pred HHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhh--cCccccCcccHHHHH
Q 032654 70 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIH--ARRVTIMPKDIQLAR 129 (136)
Q Consensus 70 rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~H--akRvTi~~kDiqLa~ 129 (136)
.+|++.++ ..++.+..+|+..|-+.++.=|..+-..-..++.+ .+.-+|+..|++.+.
T Consensus 137 ~~i~~~~~--~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v 196 (326)
T PRK07452 137 QLVERTAQ--ELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALV 196 (326)
T ss_pred HHHHHHHH--HcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHh
Confidence 44444443 24688999999999999998888888888888888 567889999998764
No 63
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=38.21 E-value=60 Score=29.01 Aligned_cols=71 Identities=24% Similarity=0.395 Sum_probs=58.9
Q ss_pred hhhhccchhH-HHHHHHhhh--cccccccHHHHHHHHHHHH----HHhhhhhhhhhHhhhhcCccccCcccHHHHHHH
Q 032654 61 LLIRKLPFQR-LVREIAQDF--KTDLRFQSHAVLALQEAAE----AYLVGLFEDTNLCAIHARRVTIMPKDIQLARRI 131 (136)
Q Consensus 61 lli~k~pF~r-lVreI~~~~--~~~~r~~~~Al~aLQeaaE----~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~ri 131 (136)
++|+-.||.+ =++||..-- ..++-.+.+||+-|-...| -|-++|++-|+..|.-.+.-+|...|+.-|..|
T Consensus 354 lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~l 431 (450)
T COG1224 354 LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKEL 431 (450)
T ss_pred eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHH
Confidence 6788889976 577777632 2688999999999866554 799999999999999999999999999887765
No 64
>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=35.88 E-value=37 Score=22.78 Aligned_cols=56 Identities=7% Similarity=0.076 Sum_probs=36.2
Q ss_pred HHHHHHhhh--cccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccc-cCcccHH
Q 032654 71 LVREIAQDF--KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVT-IMPKDIQ 126 (136)
Q Consensus 71 lVreI~~~~--~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvT-i~~kDiq 126 (136)
+|.+|++.. +...+++.+|+..+.+-.+-|...-+.-|+.-+.--+--+ |.+.|++
T Consensus 4 li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LE 62 (72)
T PF09415_consen 4 LIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLE 62 (72)
T ss_dssp HHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHH
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence 455666643 3678999999999999888888777666666554444444 6666665
No 65
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=34.95 E-value=15 Score=32.90 Aligned_cols=57 Identities=18% Similarity=0.137 Sum_probs=45.6
Q ss_pred HHHHhhh-cccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHH
Q 032654 73 REIAQDF-KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLAR 129 (136)
Q Consensus 73 reI~~~~-~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~ 129 (136)
+|+.+.. ..+-.+..+.=+.|-+.|..|....=|-+..+|.|.|--||.++|+||-.
T Consensus 390 ~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhl 447 (505)
T COG5624 390 EELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHL 447 (505)
T ss_pred HHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeee
Confidence 4444433 45667778888888889999988888888889999999999999999853
No 66
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=33.60 E-value=76 Score=21.74 Aligned_cols=44 Identities=18% Similarity=0.121 Sum_probs=34.4
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhh
Q 032654 69 QRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCA 112 (136)
Q Consensus 69 ~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a 112 (136)
-..+++.+..+-....|....+..+.-+++..++..++.++...
T Consensus 8 i~~~r~~~~~~~~~~~~~~~~~~~~~lav~E~~~Nav~H~~~~~ 51 (125)
T PF13581_consen 8 IREARAFLREFLERLGLPEEDRDDLELAVSEALTNAVEHGYPGD 51 (125)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 34455566666566889999999999999999999999888643
No 67
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=32.16 E-value=1e+02 Score=27.69 Aligned_cols=59 Identities=22% Similarity=0.307 Sum_probs=42.9
Q ss_pred HHHHHhhh--cccccccHHHHHHHHHHHH--HHhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 72 VREIAQDF--KTDLRFQSHAVLALQEAAE--AYLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 72 VreI~~~~--~~~~r~~~~Al~aLQeaaE--~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
+.+|++.. ..++.++.+|++.|-.-+. ..+..+++.|...+...+|.+|+.+|+.-+..
T Consensus 268 i~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~ 330 (531)
T TIGR02902 268 IKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE 330 (531)
T ss_pred HHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence 34444443 2457788888887654443 56788889988888888999999999987753
No 68
>TIGR01924 rsbW_low_gc serine-protein kinase RsbW. This model describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter. RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex. Low ATP level or environmental stress causes the dephosphorylation of RsbV.
Probab=29.84 E-value=91 Score=23.15 Aligned_cols=45 Identities=11% Similarity=0.115 Sum_probs=37.6
Q ss_pred ccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhh
Q 032654 65 KLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTN 109 (136)
Q Consensus 65 k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~ 109 (136)
..-+-+.|+..+..+-....|+.+.+..++-+++..++..++.++
T Consensus 15 ~~~~~~~vr~~~~~~a~~~g~~~~~~~~l~lav~Ea~~Nai~ha~ 59 (159)
T TIGR01924 15 KPEYVGLIRLTLSGIASRAGYTYDDIEDLKIAVSEACTNAVKHAY 59 (159)
T ss_pred cHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhcc
Confidence 445667788888888778889999999999999999999998886
No 69
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=29.52 E-value=75 Score=25.70 Aligned_cols=56 Identities=27% Similarity=0.329 Sum_probs=40.2
Q ss_pred hhhHHHHhhhhchhhhhhccchhHH----------HHHHHhhh--cccccccHHHHHHHHHHHHHHhh
Q 032654 47 VALREIRKYQKSTELLIRKLPFQRL----------VREIAQDF--KTDLRFQSHAVLALQEAAEAYLV 102 (136)
Q Consensus 47 ~al~EIr~~Qkst~lli~k~pF~rl----------VreI~~~~--~~~~r~~~~Al~aLQeaaE~~Lv 102 (136)
...+||.+|-+-.-.++.+-.|..- |.++-..+ .+++-|...+=.++||-+|+.+.
T Consensus 24 ~lsRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~~~pel~~ag~~~~a~QEyvEA~~l 91 (204)
T COG2178 24 KLSREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRLLAGFPELYFAGFVTTALQEYVEATLL 91 (204)
T ss_pred HHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhcchHHHHHHHHHH
Confidence 4568899888877788888888653 32322222 26788888999999999998653
No 70
>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=28.69 E-value=2e+02 Score=26.52 Aligned_cols=49 Identities=20% Similarity=0.223 Sum_probs=39.0
Q ss_pred ccccHHHHHHHHH-HH------------HHHhhhhhhhhhHhhhhcCccccCcccHHHHHHH
Q 032654 83 LRFQSHAVLALQE-AA------------EAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRI 131 (136)
Q Consensus 83 ~r~~~~Al~aLQe-aa------------E~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~ri 131 (136)
..|+.+|+..|-+ ++ +.-|..++..|+..|...+..+|..+|++-|...
T Consensus 329 ~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~ 390 (608)
T TIGR00764 329 PHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKL 390 (608)
T ss_pred CcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHH
Confidence 4899999998764 23 4678888888888888888899999999876544
No 71
>PF03172 Sp100: Sp100 domain; InterPro: IPR004865 The Sp100 and promyelocytic leukemia proteins (PML) are constituents of nuclear domains, known as nuclear dots (NDs or NBs - nuclear bodies or PML bodies), and are both covalently modified by the small ubiquitin-related protein SUMO-1. NBs play a role in autoimmunity, virus infections, and in the etiology of acute promyelocytic leukemia []. A functional nuclear localization signal and an NB-targeting region that coincides with an Sp100 homodimerization domain have been mapped. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins, which include the autoimmune regulator proteins (AIRE) and other numerous other transiently or permanently localised proteins. PML is expressed as a family of isoforms (PML I-VII) as a result of alternative splicing, most of which are found in the nucleus. Although there are many other functions of PML NBs in a wide range of cellular pathways, there is accumulating evidence that they represent preferential targets for viral infections and that PML plays a role in the mechanism of the antiviral action of interferon []. The Sp100 domain is usually found at the amino terminus of proteins that contain a SAND domain IPR000770 from INTERPRO. ; GO: 0005634 nucleus
Probab=27.37 E-value=1e+02 Score=22.33 Aligned_cols=48 Identities=27% Similarity=0.385 Sum_probs=36.9
Q ss_pred HhhhhchhhhhhccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhh
Q 032654 53 RKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAI 113 (136)
Q Consensus 53 r~~Qkst~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~ 113 (136)
..|+.+-+..--+.|-++.|+.|+..... ...-.+|..||.+.|+..+
T Consensus 40 ~~y~e~~e~crnlvpv~rvvY~vLs~Lek-------------~f~~~fl~~LFs~~nL~~Y 87 (103)
T PF03172_consen 40 QMYKESQEACRNLVPVQRVVYNVLSWLEK-------------TFIRSFLEALFSDYNLKEY 87 (103)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHHH-------------HhhHHHHHHHhhHHHHHHC
Confidence 46777777777889999999999886632 2345788889999988765
No 72
>PF04604 L_biotic_typeA: Type-A lantibiotic; InterPro: IPR007682 Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyllanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [].; GO: 0019748 secondary metabolic process, 0005576 extracellular region
Probab=26.85 E-value=50 Score=21.06 Aligned_cols=20 Identities=25% Similarity=0.308 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHhhhhhhh
Q 032654 88 HAVLALQEAAEAYLVGLFED 107 (136)
Q Consensus 88 ~Al~aLQeaaE~~Lv~lfe~ 107 (136)
+|+.+|||.++.-|.++...
T Consensus 7 ea~~~lqevs~eELd~ilGg 26 (51)
T PF04604_consen 7 EALNSLQEVSDEELDQILGG 26 (51)
T ss_pred HHHHHHHhcCHHHHHHHhCC
Confidence 89999999999999998875
No 73
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=26.38 E-value=1.7e+02 Score=25.86 Aligned_cols=72 Identities=19% Similarity=0.349 Sum_probs=58.7
Q ss_pred hhhhccchhH-HHHHHHhh-h-cccccccHHHHHHHHHHHH----HHhhhhhhhhhHhhhhcCccccCcccHHHHHHHh
Q 032654 61 LLIRKLPFQR-LVREIAQD-F-KTDLRFQSHAVLALQEAAE----AYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIR 132 (136)
Q Consensus 61 lli~k~pF~r-lVreI~~~-~-~~~~r~~~~Al~aLQeaaE----~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rir 132 (136)
++|.-.|+.. =+++|+.- + ..|.-.+++|++.|-...| -|-.+|...|++.+...|--++...||+-|.+|-
T Consensus 351 lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~LF 429 (454)
T KOG2680|consen 351 LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRLF 429 (454)
T ss_pred heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHHH
Confidence 6777788864 46666652 2 3688999999999876665 5889999999999999999999999999888874
No 74
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=25.60 E-value=2.5e+02 Score=25.32 Aligned_cols=66 Identities=23% Similarity=0.272 Sum_probs=47.7
Q ss_pred cchhHHHHHHHhhhcccccccHHHHHHHHHHHH-----------HHhhhhhhhhhHhhhhcCccccCcccHHHHHHHh
Q 032654 66 LPFQRLVREIAQDFKTDLRFQSHAVLALQEAAE-----------AYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIR 132 (136)
Q Consensus 66 ~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE-----------~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rir 132 (136)
..|.++|..++++. .-..|+.+|+..|=+.+- ..|..|+..|+..|--.+.-.|...||+-|..-|
T Consensus 430 ~~~~~~i~~~~~~~-~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 430 RQYARFIASICQKE-GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHH-SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHhC-CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 34777887777755 234789999988655442 5788999999999998889999999999887654
No 75
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=25.49 E-value=2.4e+02 Score=21.70 Aligned_cols=64 Identities=19% Similarity=0.199 Sum_probs=48.1
Q ss_pred hhHHHHhhhhchhhhhhccc----hhHHHHHHHhhhc-------ccccccHHHHHHHHHHHHHHhhhhhhhhhHh
Q 032654 48 ALREIRKYQKSTELLIRKLP----FQRLVREIAQDFK-------TDLRFQSHAVLALQEAAEAYLVGLFEDTNLC 111 (136)
Q Consensus 48 al~EIr~~Qkst~lli~k~p----F~rlVreI~~~~~-------~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~ 111 (136)
+-.|--+|++.+.-|||-.- |+.+++-|.+.+. .|..++++++..+|.+.-+...+|-+..+-+
T Consensus 75 sE~eRlk~e~e~g~Lipa~eV~~~~s~~~Kav~q~LetlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~ 149 (152)
T PF07278_consen 75 SENERLKFEKETGQLIPAEEVRREMSEMAKAVVQVLETLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEA 149 (152)
T ss_pred HHHHHHHHHHHHcccCcHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566678899999999764 5555655555442 5789999999999999999988887765443
No 76
>PF07105 DUF1367: Protein of unknown function (DUF1367); InterPro: IPR009797 This entry is represented by Bacteriophage VT2phi_272, P37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Probab=25.45 E-value=92 Score=25.02 Aligned_cols=16 Identities=50% Similarity=0.574 Sum_probs=14.1
Q ss_pred HHHHHHHHHHhhhhhh
Q 032654 91 LALQEAAEAYLVGLFE 106 (136)
Q Consensus 91 ~aLQeaaE~~Lv~lfe 106 (136)
++||++++.||..+-+
T Consensus 91 ~~l~~~A~~yL~~va~ 106 (196)
T PF07105_consen 91 DALQEAADQYLAKVAK 106 (196)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 8899999999988755
No 77
>KOG1089 consensus Myotubularin-related phosphatidylinositol 3-phosphate 3-phosphatase MTM6 [General function prediction only]
Probab=24.99 E-value=71 Score=29.58 Aligned_cols=35 Identities=23% Similarity=0.428 Sum_probs=29.4
Q ss_pred chhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhh
Q 032654 67 PFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCA 112 (136)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a 112 (136)
-|=.+|..+++++...|.| .|.||..||+.++.|-
T Consensus 417 qFLDcvwQl~~QfP~~FEF-----------ne~fLi~L~~h~ys~q 451 (573)
T KOG1089|consen 417 QFLDCVWQLLEQFPCAFEF-----------NERFLIKLHEHAYSSQ 451 (573)
T ss_pred HHHHHHHHHHhhCCcceeh-----------hHHHHHHHHHhhHHhh
Confidence 4778899999988877766 8999999999998774
No 78
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=24.16 E-value=87 Score=24.74 Aligned_cols=27 Identities=33% Similarity=0.265 Sum_probs=20.4
Q ss_pred cccccccHHHHHHHHHHHHHHhhhhhh
Q 032654 80 KTDLRFQSHAVLALQEAAEAYLVGLFE 106 (136)
Q Consensus 80 ~~~~r~~~~Al~aLQeaaE~~Lv~lfe 106 (136)
.++++|+...-.++||.+|++..-.|=
T Consensus 70 ~~~~~y~~~~~~~lQEyvEA~~f~~~l 96 (204)
T PRK14562 70 HPELYYAGYVGTALQEYVEALLVYSLL 96 (204)
T ss_pred CchhhhhhhcchHHHHHHHHHHHHHHH
Confidence 367788888888999999976654443
No 79
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=22.39 E-value=1.4e+02 Score=22.26 Aligned_cols=66 Identities=23% Similarity=0.302 Sum_probs=43.1
Q ss_pred chhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q 032654 67 PFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~rirg~ 134 (136)
|-.|+-|-+-......-|.-+.|..-+-..-|......+|-|.-.+---|=..|+|+-+||+ |||+
T Consensus 32 pVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLA--iRGD 97 (131)
T KOG1757|consen 32 PVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA--IRGD 97 (131)
T ss_pred chHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheee--ecCc
Confidence 44454444444344556666666555555556666677888877777777777889999997 4554
No 80
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=21.83 E-value=1.9e+02 Score=23.85 Aligned_cols=58 Identities=21% Similarity=0.087 Sum_probs=44.7
Q ss_pred HHHHHHHhhhc-ccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCccccCcccHHHHH
Q 032654 70 RLVREIAQDFK-TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRVTIMPKDIQLAR 129 (136)
Q Consensus 70 rlVreI~~~~~-~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~ 129 (136)
.+++=|.+.+. .+..++.+|+..|-+.++.=|..+-..-..++.+++ +|+..|++.+.
T Consensus 139 ~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 139 EALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 34433444342 568899999999999999888888888888888877 68999988754
No 81
>PF07962 Swi3: Replication Fork Protection Component Swi3; InterPro: IPR012923 Replication fork pausing is required to initiate recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1. Together they define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks []. This complex is required for accurate replication, fork protection and replication checkpoint signalling [, ].; GO: 0006974 response to DNA damage stimulus, 0007049 cell cycle, 0048478 replication fork protection, 0005634 nucleus
Probab=21.42 E-value=69 Score=21.82 Aligned_cols=30 Identities=20% Similarity=0.321 Sum_probs=24.3
Q ss_pred hhHHHHhhhhchhhhhhccchhHHHHHHHh
Q 032654 48 ALREIRKYQKSTELLIRKLPFQRLVREIAQ 77 (136)
Q Consensus 48 al~EIr~~Qkst~lli~k~pF~rlVreI~~ 77 (136)
.-+=+..||.=...|.|+++|...|..|-.
T Consensus 35 L~~ll~~Yq~W~h~LfPk~~F~d~i~~vE~ 64 (83)
T PF07962_consen 35 LRRLLQFYQLWAHRLFPKASFEDFIERVEK 64 (83)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 445577899888999999999999877644
No 82
>PRK05907 hypothetical protein; Provisional
Probab=21.33 E-value=1.8e+02 Score=24.43 Aligned_cols=67 Identities=10% Similarity=0.022 Sum_probs=51.4
Q ss_pred hhccchhHHHHHHHhhhc-ccccccHHHHHHHHHHH-HHHhhhhhhhhhHhhhh-cCccccCcccHHHHH
Q 032654 63 IRKLPFQRLVREIAQDFK-TDLRFQSHAVLALQEAA-EAYLVGLFEDTNLCAIH-ARRVTIMPKDIQLAR 129 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~-~~~r~~~~Al~aLQeaa-E~~Lv~lfe~a~l~a~H-akRvTi~~kDiqLa~ 129 (136)
.++..-..|.+-|.+.+. .+..++.+|+..|=+.+ +.=|-.+...-..++.+ +.+-+|+..||+.+.
T Consensus 131 ~~~l~e~~L~~Wi~~~~~~~g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv 200 (311)
T PRK05907 131 WFADRDKRIAQLLIQRAKELGISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFV 200 (311)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHh
Confidence 444444677777777774 67899999999988888 67777777777788888 668899999998653
No 83
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.29 E-value=63 Score=22.96 Aligned_cols=18 Identities=33% Similarity=0.719 Sum_probs=15.0
Q ss_pred hhccchhHHHHHHHhhhc
Q 032654 63 IRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~ 80 (136)
-.-+|+|+|++||+....
T Consensus 72 a~GlpYQtyIreiLh~~~ 89 (92)
T COG5304 72 AEGLPYQTYIREILHKYS 89 (92)
T ss_pred hcCCcHHHHHHHHHHhhc
Confidence 467999999999998653
No 84
>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=21.12 E-value=2.2e+02 Score=22.09 Aligned_cols=49 Identities=14% Similarity=0.085 Sum_probs=37.5
Q ss_pred cccccHHHHHHHHHHHHH---HhhhhhhhhhHhhhhcCccccCcccHHHHHH
Q 032654 82 DLRFQSHAVLALQEAAEA---YLVGLFEDTNLCAIHARRVTIMPKDIQLARR 130 (136)
Q Consensus 82 ~~r~~~~Al~aLQeaaE~---~Lv~lfe~a~l~a~HakRvTi~~kDiqLa~r 130 (136)
+..|+.+++..|-+.+.- ++..+...+-+.|.-.+--+|...||.-+..
T Consensus 213 ~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~ 264 (269)
T TIGR03015 213 APVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIA 264 (269)
T ss_pred CCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 456999999999999986 6667777776766666667888888876643
No 85
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=20.81 E-value=47 Score=21.95 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=11.0
Q ss_pred cCcccHHHHHHHh
Q 032654 120 IMPKDIQLARRIR 132 (136)
Q Consensus 120 i~~kDiqLa~rir 132 (136)
|+.+|+.||.+|=
T Consensus 62 lT~~D~~lA~~id 74 (76)
T cd00913 62 LSENDFIMAAKID 74 (76)
T ss_pred CCHHHHHHHHHHh
Confidence 7789999999883
No 86
>PHA02604 rI.-1 hypothetical protein; Provisional
Probab=20.66 E-value=1.6e+02 Score=22.13 Aligned_cols=44 Identities=11% Similarity=0.055 Sum_probs=31.8
Q ss_pred chhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhhHhhh
Q 032654 67 PFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAI 113 (136)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~ 113 (136)
.+.-+|++|+++...-++ .....||.+.++++.-+..--+++++
T Consensus 82 d~~~~l~~~l~~a~~i~~---~l~s~L~N~~DdI~~~~~qt~YkLtL 125 (126)
T PHA02604 82 DTIAFLDELLQEAEEIYK---ELPSALQSTLDDITGLCYQTKYKLTL 125 (126)
T ss_pred CHHHHHHHHHHHHHHHHH---HhhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 677888888887654333 44466999999988887776666653
No 87
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=20.60 E-value=1.8e+02 Score=21.38 Aligned_cols=45 Identities=9% Similarity=0.146 Sum_probs=35.3
Q ss_pred ccchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHhhhhhhhhh
Q 032654 65 KLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTN 109 (136)
Q Consensus 65 k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~ 109 (136)
..-+-++||..+..+.....|..+.+..|+-+++..+....+.++
T Consensus 15 ~~~~~~~vr~~v~~~~~~~g~~~~~~~~l~lav~Ea~~Nai~Hg~ 59 (161)
T PRK04069 15 KAEYVSIIRLTLSGVANRMGFSYDDIEDMKIAVSEACTNAVQHAY 59 (161)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 445667888888888778889998888888888877777777665
No 88
>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=20.36 E-value=1.7e+02 Score=28.40 Aligned_cols=80 Identities=23% Similarity=0.228 Sum_probs=54.9
Q ss_pred CchhhHHHHhhhhchhhhhhccchhHHHHHHHhhh-cccccccHHHHHHHHHHHHHHhhhhhhhhhHhhhhcCcc--ccC
Q 032654 45 GTVALREIRKYQKSTELLIRKLPFQRLVREIAQDF-KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHARRV--TIM 121 (136)
Q Consensus 45 g~~al~EIr~~Qkst~lli~k~pF~rlVreI~~~~-~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRv--Ti~ 121 (136)
.+.+|+..|.|-.= ..++..+=.+||..+-.-| .++++....||.+|=|.++.=+-.-..--+.++..++|. -|.
T Consensus 449 YaPaLR~Lr~~A~i--i~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L~el~~~DIRsCINtLQfLa~~~~r~ds~i~ 526 (877)
T KOG1969|consen 449 YAPALRPLRPFAEI--IAFVPPSQSRLVERLNEICHRENMRADSKALNALCELTQNDIRSCINTLQFLASNVDRRDSSIS 526 (877)
T ss_pred cchhhhhcccceEE--EEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcchHHHHHHHHHHHHHhcccccccch
Confidence 67799998887543 3445555667874443333 378999999999999999876666666666777776664 244
Q ss_pred cccHH
Q 032654 122 PKDIQ 126 (136)
Q Consensus 122 ~kDiq 126 (136)
.+|++
T Consensus 527 ~~~i~ 531 (877)
T KOG1969|consen 527 VKLIC 531 (877)
T ss_pred hhhhh
Confidence 45544
No 89
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=20.06 E-value=82 Score=23.92 Aligned_cols=33 Identities=27% Similarity=0.524 Sum_probs=26.4
Q ss_pred chhhHHHHhhhhchhhhhhccchhHHHHHHHhhh
Q 032654 46 TVALREIRKYQKSTELLIRKLPFQRLVREIAQDF 79 (136)
Q Consensus 46 ~~al~EIr~~Qkst~lli~k~pF~rlVreI~~~~ 79 (136)
.+|+.||+++..+...+ +...+-+||++|=.++
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~H 129 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKEH 129 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHhC
Confidence 57999999996665455 8899999999997644
Done!