Query 048501
Match_columns 143
No_of_seqs 131 out of 608
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 10:03:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048501.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048501hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00161 histone H3; Provision 100.0 4.5E-58 9.8E-63 348.3 10.4 128 9-142 1-129 (135)
2 PTZ00018 histone H3; Provision 100.0 5.6E-58 1.2E-62 348.7 10.6 130 9-142 1-135 (136)
3 PLN00121 histone H3; Provision 100.0 7.8E-58 1.7E-62 347.9 10.6 131 9-143 1-136 (136)
4 KOG1745 Histones H3 and H4 [Ch 100.0 6.4E-55 1.4E-59 331.5 8.5 131 9-143 1-137 (137)
5 smart00428 H3 Histone H3. 100.0 5.4E-50 1.2E-54 293.7 8.4 101 42-142 2-104 (105)
6 PLN00160 histone H3; Provision 100.0 8.1E-50 1.8E-54 289.1 7.6 94 49-142 1-95 (97)
7 COG2036 HHT1 Histones H3 and H 99.9 7.9E-26 1.7E-30 162.2 6.6 87 51-142 1-87 (91)
8 PF00125 Histone: Core histone 99.8 1.6E-21 3.4E-26 132.2 4.8 75 65-139 1-75 (75)
9 cd07981 TAF12 TATA Binding Pro 99.2 1.7E-11 3.8E-16 83.9 6.0 59 79-137 7-65 (72)
10 PLN00158 histone H2B; Provisio 98.7 2.3E-08 5E-13 74.8 6.0 69 71-139 25-93 (116)
11 PTZ00463 histone H2B; Provisio 98.7 2.4E-08 5.3E-13 74.7 5.8 68 72-139 27-94 (117)
12 smart00427 H2B Histone H2B. 98.7 4.1E-08 9E-13 70.5 6.2 66 74-139 2-67 (89)
13 cd00076 H4 Histone H4, one of 98.5 1.4E-07 2.9E-12 67.2 4.7 69 68-141 12-80 (85)
14 PLN00035 histone H4; Provision 98.4 3.7E-07 7.9E-12 67.1 4.8 67 70-141 30-96 (103)
15 KOG1744 Histone H2B [Chromatin 98.4 6E-07 1.3E-11 68.2 5.5 70 70-139 34-103 (127)
16 PTZ00015 histone H4; Provision 98.4 4.2E-07 9.1E-12 66.7 4.6 69 68-141 29-97 (102)
17 smart00803 TAF TATA box bindin 98.4 5.9E-07 1.3E-11 60.7 4.9 63 70-137 3-65 (65)
18 cd07979 TAF9 TATA Binding Prot 98.3 1.6E-06 3.4E-11 64.6 6.1 65 76-141 4-68 (117)
19 PF00808 CBFD_NFYB_HMF: Histon 98.3 2.1E-06 4.5E-11 56.9 5.5 58 79-136 8-65 (65)
20 smart00417 H4 Histone H4. 98.0 3.8E-06 8.3E-11 58.4 2.6 62 68-134 12-73 (74)
21 PF15630 CENP-S: Kinetochore c 97.9 1E-05 2.3E-10 56.3 3.4 63 75-137 7-71 (76)
22 PF03847 TFIID_20kDa: Transcri 97.7 0.0001 2.3E-09 50.3 5.3 58 80-137 6-63 (68)
23 PF02969 TAF: TATA box binding 97.6 0.00023 5.1E-09 48.4 5.6 59 78-137 8-66 (66)
24 PF02291 TFIID-31kDa: Transcri 97.5 0.00025 5.4E-09 53.9 5.8 65 76-141 15-79 (129)
25 smart00576 BTP Bromodomain tra 97.5 0.00021 4.6E-09 49.1 5.0 51 91-141 23-73 (77)
26 KOG0870 DNA polymerase epsilon 97.5 0.00014 3.1E-09 57.6 4.1 69 67-137 8-76 (172)
27 cd08050 TAF6 TATA Binding Prot 97.3 0.00053 1.1E-08 59.0 6.3 64 77-141 3-66 (343)
28 PF15511 CENP-T: Centromere ki 97.2 0.00045 9.8E-09 60.9 4.7 56 76-131 354-414 (414)
29 cd00074 H2A Histone 2A; H2A is 97.0 0.0005 1.1E-08 51.3 2.8 67 67-137 18-84 (115)
30 KOG1142 Transcription initiati 96.8 0.0014 3.1E-08 55.0 3.9 72 61-136 146-217 (258)
31 KOG3334 Transcription initiati 95.5 0.027 5.8E-07 43.9 4.7 65 77-142 17-81 (148)
32 PF07524 Bromo_TP: Bromodomain 94.9 0.074 1.6E-06 36.1 5.0 54 88-141 19-73 (77)
33 PF02269 TFIID-18kDa: Transcri 88.2 0.77 1.7E-05 32.7 3.7 63 75-137 3-65 (93)
34 COG5262 HTA1 Histone H2A [Chro 87.8 0.77 1.7E-05 35.0 3.7 58 79-136 32-89 (132)
35 KOG3467 Histone H4 [Chromatin 86.2 1.5 3.2E-05 31.9 4.2 48 94-141 49-96 (103)
36 KOG0869 CCAAT-binding factor, 85.1 2.2 4.8E-05 33.9 5.1 68 70-140 33-100 (168)
37 KOG0871 Class 2 transcription 83.1 1.9 4.2E-05 33.9 4.0 72 66-140 9-80 (156)
38 smart00414 H2A Histone 2A. 81.9 2.4 5.1E-05 31.2 3.9 66 68-137 8-73 (106)
39 KOG2549 Transcription initiati 81.7 2.5 5.3E-05 39.4 4.7 62 78-140 16-77 (576)
40 COG5094 TAF9 Transcription ini 81.4 2.2 4.7E-05 32.9 3.6 46 93-138 33-81 (145)
41 PLN00154 histone H2A; Provisio 80.6 2 4.4E-05 33.1 3.3 68 67-137 36-103 (136)
42 cd08045 TAF4 TATA Binding Prot 80.1 2.8 6E-05 33.7 4.1 55 68-123 43-97 (212)
43 PF05236 TAF4: Transcription i 78.8 1.5 3.2E-05 36.3 2.2 57 68-125 42-98 (264)
44 PTZ00017 histone H2A; Provisio 78.7 2.7 5.9E-05 32.3 3.4 67 67-137 25-91 (134)
45 KOG2389 Predicted bromodomain 70.8 10 0.00022 33.5 5.3 61 79-140 35-95 (353)
46 PLN00157 histone H2A; Provisio 69.3 5.5 0.00012 30.6 3.0 67 67-137 24-90 (132)
47 KOG4336 TBP-associated transcr 68.3 15 0.00032 32.1 5.7 50 92-141 23-72 (323)
48 PLN00156 histone H2AX; Provisi 67.8 7.4 0.00016 30.2 3.5 67 67-137 27-93 (139)
49 PF09123 DUF1931: Domain of un 66.7 8.2 0.00018 29.9 3.5 60 75-139 1-60 (138)
50 cd07978 TAF13 The TATA Binding 66.3 26 0.00056 25.0 5.8 57 80-137 9-65 (92)
51 PLN00153 histone H2A; Provisio 65.8 7.9 0.00017 29.6 3.3 67 67-137 22-88 (129)
52 COG5150 Class 2 transcription 65.1 8.8 0.00019 29.7 3.4 68 65-135 7-74 (148)
53 KOG1756 Histone 2A [Chromatin 63.7 12 0.00027 28.7 3.9 50 88-137 42-91 (131)
54 COG5208 HAP5 CCAAT-binding fac 62.9 13 0.00027 31.4 4.2 84 52-137 80-173 (286)
55 PF10911 DUF2717: Protein of u 55.6 19 0.0004 25.4 3.4 60 56-118 2-64 (77)
56 COG5248 TAF19 Transcription in 53.5 43 0.00094 25.3 5.3 61 75-137 11-71 (126)
57 PTZ00252 histone H2A; Provisio 52.9 22 0.00047 27.5 3.7 67 67-137 23-91 (134)
58 KOG1658 DNA polymerase epsilon 48.9 12 0.00026 29.7 1.8 63 71-135 58-121 (162)
59 KOG3901 Transcription initiati 44.0 82 0.0018 23.5 5.4 63 72-137 8-70 (109)
60 COG5095 TAF6 Transcription ini 38.2 54 0.0012 29.3 4.3 61 79-140 11-71 (450)
61 COG1224 TIP49 DNA helicase TIP 36.7 68 0.0015 29.2 4.8 71 68-138 354-431 (450)
62 PRK07452 DNA polymerase III su 35.9 68 0.0015 26.5 4.5 58 77-136 137-196 (326)
63 TIGR02902 spore_lonB ATP-depen 34.3 86 0.0019 28.6 5.2 59 79-137 268-330 (531)
64 PRK14562 haloacid dehalogenase 33.3 78 0.0017 25.4 4.3 27 87-113 70-96 (204)
65 KOG1657 CCAAT-binding factor, 32.8 63 0.0014 26.9 3.8 72 64-136 66-137 (236)
66 PHA03159 hypothetical protein; 30.5 80 0.0017 24.7 3.7 49 73-121 4-54 (160)
67 PF09415 CENP-X: CENP-S associ 30.2 53 0.0012 22.4 2.5 57 77-133 3-62 (72)
68 KOG2680 DNA helicase TIP49, TB 29.3 1.5E+02 0.0033 26.7 5.7 72 68-139 351-429 (454)
69 TIGR01924 rsbW_low_gc serine-p 27.8 83 0.0018 23.7 3.4 45 72-116 15-59 (159)
70 PF13581 HATPase_c_2: Histidin 25.7 1.4E+02 0.0031 20.6 4.2 43 77-119 9-51 (125)
71 PF01997 Translin: Translin fa 25.5 1.1E+02 0.0024 24.1 3.9 22 89-110 62-83 (200)
72 PF04604 L_biotic_typeA: Type- 24.9 62 0.0013 21.1 1.9 20 95-114 7-26 (51)
73 COG2178 Predicted RNA-binding 24.4 1E+02 0.0023 25.3 3.6 56 54-109 24-91 (204)
74 PF06075 DUF936: Plant protein 23.8 1.2E+02 0.0026 28.5 4.3 42 75-119 325-368 (579)
75 PF07105 DUF1367: Protein of u 23.4 99 0.0021 25.3 3.2 16 98-113 91-106 (196)
76 KOG1071 Mitochondrial translat 23.4 74 0.0016 28.1 2.6 86 52-141 114-206 (340)
77 TIGR00764 lon_rel lon-related 23.4 2.2E+02 0.0048 26.6 5.9 49 90-138 329-390 (608)
78 smart00188 IL10 Interleukin-10 22.1 2.4E+02 0.0052 21.7 5.0 60 55-124 11-71 (137)
79 PF10788 DUF2603: Protein of u 21.2 65 0.0014 24.9 1.7 32 53-85 97-128 (137)
80 KOG1757 Histone 2A [Chromatin 20.9 1.5E+02 0.0031 22.6 3.5 67 73-141 31-97 (131)
81 PRK08487 DNA polymerase III su 20.4 2.1E+02 0.0045 24.0 4.8 59 76-136 138-197 (328)
82 PF03172 Sp100: Sp100 domain; 20.2 2.3E+02 0.005 20.9 4.4 48 60-120 40-87 (103)
83 PRK05907 hypothetical protein; 20.2 1.6E+02 0.0034 25.1 4.0 67 70-136 131-200 (311)
84 COG5624 TAF61 Transcription in 20.2 38 0.00081 31.0 0.2 49 87-135 398-446 (505)
No 1
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=4.5e-58 Score=348.35 Aligned_cols=128 Identities=59% Similarity=0.846 Sum_probs=119.7
Q ss_pred hhccccCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCCcccCCCCchhhHHHHhhhhhhhhhhccCccchhHHHHHHhhh-
Q 048501 9 LARSRQQGSPPEGRHHVSSWPPRQLGNSTSATGGVKKPHCFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK- 87 (143)
Q Consensus 9 MartK~ta~k~~~~~~~~kaprk~~~ks~p~~~~~k~~~r~rpgt~alrEIr~yQkst~llI~k~pF~RLVrEI~~~~~- 87 (143)
||||||+ +++++ ||.|+|++... ...+++++++||+||++||+|||+||+||+|||||+||+||||||++++.
T Consensus 1 mar~k~~-~~~~~----~~~~~~~~~~~-~~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RLVREI~~~~~~ 74 (135)
T PLN00161 1 MARRLQG-KRFRK----GKKPQKEASGV-TRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEMLR 74 (135)
T ss_pred CCccccc-ccccC----CCCCcccCCCC-CCCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHHHHHHHHhcCC
Confidence 9999999 67777 88899888643 45577899999999999999999999999999999999999999999996
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhccC
Q 048501 88 TDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGER 142 (143)
Q Consensus 88 ~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~~ 142 (143)
+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+||.+|||+.
T Consensus 75 ~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~ 129 (135)
T PLN00161 75 EPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPI 129 (135)
T ss_pred CCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhcccc
Confidence 5899999999999999999999999999999999999999999999999999975
No 2
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=5.6e-58 Score=348.68 Aligned_cols=130 Identities=79% Similarity=1.155 Sum_probs=123.1
Q ss_pred hhccccCCCCCCCCCCCCCCCCCcCC-----CCCCCCCCCCCcccCCCCchhhHHHHhhhhhhhhhhccCccchhHHHHH
Q 048501 9 LARSRQQGSPPEGRHHVSSWPPRQLG-----NSTSATGGVKKPHCFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIA 83 (143)
Q Consensus 9 MartK~ta~k~~~~~~~~kaprk~~~-----ks~p~~~~~k~~~r~rpgt~alrEIr~yQkst~llI~k~pF~RLVrEI~ 83 (143)
|||||+++++++| +++|+++++ ++.+..++.++++||+||++||+|||+||+||+|||||+||+||||||+
T Consensus 1 MaRtk~~~~k~~~----~~~prk~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~ 76 (136)
T PTZ00018 1 MARTKQTARKSTG----GKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIA 76 (136)
T ss_pred CCCCCcCccCCCC----CCCCcccccccccccCCCCCCCCCCCcccCCchhHHHHHHHHcccchhccccccHHHHHHHHH
Confidence 9999999999999 899998886 3344557788999999999999999999999999999999999999999
Q ss_pred HhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhccC
Q 048501 84 QDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGER 142 (143)
Q Consensus 84 ~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~~ 142 (143)
+++.+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+|++||||++
T Consensus 77 ~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~ 135 (136)
T PTZ00018 77 QDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
T ss_pred HHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhcccC
Confidence 99999999999999999999999999999999999999999999999999999999986
No 3
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=7.8e-58 Score=347.88 Aligned_cols=131 Identities=82% Similarity=1.160 Sum_probs=123.8
Q ss_pred hhccccCCCCCCCCCCCCCCCCCcCC-----CCCCCCCCCCCcccCCCCchhhHHHHhhhhhhhhhhccCccchhHHHHH
Q 048501 9 LARSRQQGSPPEGRHHVSSWPPRQLG-----NSTSATGGVKKPHCFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIA 83 (143)
Q Consensus 9 MartK~ta~k~~~~~~~~kaprk~~~-----ks~p~~~~~k~~~r~rpgt~alrEIr~yQkst~llI~k~pF~RLVrEI~ 83 (143)
|||||+++++++| +++|+++++ ++.+..++.++++||+||++||+|||+||+||+|||||+||+||||||+
T Consensus 1 MaRtk~~~~k~~~----~~~p~~~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~ 76 (136)
T PLN00121 1 MARTKQTARKSTG----GKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIA 76 (136)
T ss_pred CCCCCcCccCCCC----CCCCcccccccccccCCCCCCCCCCCcccCchhHHHHHHHHhccccccccccccHHHHHHHHH
Confidence 9999999999999 999999886 3344567789999999999999999999999999999999999999999
Q ss_pred HhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhccCC
Q 048501 84 QDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGERA 143 (143)
Q Consensus 84 ~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~~~ 143 (143)
+++.+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+|+++|||++.
T Consensus 77 ~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~~ 136 (136)
T PLN00121 77 QDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
T ss_pred HHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHhccccC
Confidence 999999999999999999999999999999999999999999999999999999999863
No 4
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=100.00 E-value=6.4e-55 Score=331.50 Aligned_cols=131 Identities=79% Similarity=1.135 Sum_probs=123.1
Q ss_pred hhccccCCCCCCCCCCCCCCCCCcCC-CCCC-----CCCCCCCcccCCCCchhhHHHHhhhhhhhhhhccCccchhHHHH
Q 048501 9 LARSRQQGSPPEGRHHVSSWPPRQLG-NSTS-----ATGGVKKPHCFRPGTVALREIRKYQKSTELLIRKLPFQRLVREI 82 (143)
Q Consensus 9 MartK~ta~k~~~~~~~~kaprk~~~-ks~p-----~~~~~k~~~r~rpgt~alrEIr~yQkst~llI~k~pF~RLVrEI 82 (143)
|+|++++++++.+ +++|++.++ ++.. ..+..++++||+||+++++|||+||+||||||+|+||+|||+||
T Consensus 1 m~r~~~t~~k~~~----~~~~r~~~a~~~~~~~~~~~~~~~~k~~r~rpg~~al~eirkyQkstdLlI~K~PFqRlvrei 76 (137)
T KOG1745|consen 1 MARTKQTARKSTG----GKAPRKQLAGKAARKSAAPRTGRVKKPHRYRPGTVALREIRKYQKSTDLLIRKLPFQRLVREI 76 (137)
T ss_pred CCCCCcccccccC----CCCCccccccccccccccccccccCccccccCchHHHHHHHHHHhhhHHHhhcCcHHHHhHHH
Confidence 8999999999999 999999988 3332 23567889999999999999999999999999999999999999
Q ss_pred HHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhccCC
Q 048501 83 AQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGERA 143 (143)
Q Consensus 83 ~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~~~ 143 (143)
+++|.+|+|||+.||.|||||+|+|||+||||+|+||+|||||||||+|||||++|||++.
T Consensus 77 ~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg~~~ 137 (137)
T KOG1745|consen 77 AQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 137 (137)
T ss_pred HhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcccCCC
Confidence 9999999999999999999999999999999999999999999999999999999999863
No 5
>smart00428 H3 Histone H3.
Probab=100.00 E-value=5.4e-50 Score=293.67 Aligned_cols=101 Identities=83% Similarity=1.155 Sum_probs=98.5
Q ss_pred CCCCcccCCCCchhhHHHHhhhhhhhhhhccCccchhHHHHHHhhhc--cccchHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 048501 42 GVKKPHCFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKT--DLWFQSSAVAALQEAAEAYLVGLFEDTNLCT 119 (143)
Q Consensus 42 ~~k~~~r~rpgt~alrEIr~yQkst~llI~k~pF~RLVrEI~~~~~~--~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a 119 (143)
++++|+||+||++||+|||+||+||++||||+||+||||||++++.+ ++|||++|++||||++|+|||++|||||+||
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 56789999999999999999999999999999999999999999987 9999999999999999999999999999999
Q ss_pred hccCccccCcccHHHHHHHhccC
Q 048501 120 IHTKRVTIMPKDIQLARRIRGER 142 (143)
Q Consensus 120 ~HakRvTi~~kDiqLa~rirg~~ 142 (143)
+||||||||++||+||.+|||++
T Consensus 82 ~HAkRvTl~~kDi~La~rir~~~ 104 (105)
T smart00428 82 IHAKRVTIMPKDIQLARRIRGER 104 (105)
T ss_pred HHhCCccCcHhhHHHHHHHhccC
Confidence 99999999999999999999985
No 6
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=8.1e-50 Score=289.08 Aligned_cols=94 Identities=69% Similarity=1.044 Sum_probs=91.2
Q ss_pred CCCCchhhHHHHhhhhhhhhhhccCccchhHHHHHHhhh-ccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCcccc
Q 048501 49 FRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK-TDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTI 127 (143)
Q Consensus 49 ~rpgt~alrEIr~yQkst~llI~k~pF~RLVrEI~~~~~-~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi 127 (143)
|+||++||+|||+||+||++||||+||+||||||++++. +++|||++||+|||||||+|||+||||+|+||+|||||||
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 048501 128 MPKDIQLARRIRGER 142 (143)
Q Consensus 128 ~~kDiqLa~rirg~~ 142 (143)
|+||||||++|||+.
T Consensus 81 ~~kD~~L~~rirg~~ 95 (97)
T PLN00160 81 MPKDMQLARRIRGQT 95 (97)
T ss_pred chhhHHHHHHhhccc
Confidence 999999999999974
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.92 E-value=7.9e-26 Score=162.24 Aligned_cols=87 Identities=45% Similarity=0.674 Sum_probs=84.0
Q ss_pred CCchhhHHHHhhhhhhhhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcc
Q 048501 51 PGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPK 130 (143)
Q Consensus 51 pgt~alrEIr~yQkst~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~k 130 (143)
||+++++|||+||++++++||++||+|++|+...+ ||+.+|+++||++.|.|++.++|+|+.||.|++|+||+++
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 68999999999999999999999999999999886 9999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhccC
Q 048501 131 DIQLARRIRGER 142 (143)
Q Consensus 131 DiqLa~rirg~~ 142 (143)
||+|+.+.+|..
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=99.84 E-value=1.6e-21 Score=132.16 Aligned_cols=75 Identities=44% Similarity=0.612 Sum_probs=71.9
Q ss_pred hhhhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHh
Q 048501 65 STELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIR 139 (143)
Q Consensus 65 st~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rir 139 (143)
+|.++|++.||.|+++||..++..++||+++|+.+||+++|+|++.+||+|+.||.|+||+||+++||++|.+|+
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 467899999999999999999888899999999999999999999999999999999999999999999999985
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=99.24 E-value=1.7e-11 Score=83.89 Aligned_cols=59 Identities=22% Similarity=0.282 Sum_probs=52.7
Q ss_pred HHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 79 VREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 79 VrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
+.|.+.++.+..|++.+|.++||+.+|+|+..++++|..||.|++|.||.++||+|+..
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 34445555567999999999999999999999999999999999999999999999864
No 10
>PLN00158 histone H2B; Provisional
Probab=98.74 E-value=2.3e-08 Score=74.76 Aligned_cols=69 Identities=13% Similarity=0.202 Sum_probs=66.4
Q ss_pred ccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHh
Q 048501 71 RKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIR 139 (143)
Q Consensus 71 ~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rir 139 (143)
++..|..+|+.|+.++++|+.+++.||..|.....+++.++-.+|..++.+.+|-||+++|||.+.||.
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 467899999999999999999999999999999999999999999999999999999999999999985
No 11
>PTZ00463 histone H2B; Provisional
Probab=98.72 E-value=2.4e-08 Score=74.70 Aligned_cols=68 Identities=12% Similarity=0.116 Sum_probs=65.5
Q ss_pred cCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHh
Q 048501 72 KLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIR 139 (143)
Q Consensus 72 k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rir 139 (143)
+..|..+|+.++.++++|+.+++.||..|.....+++.++-.+|..++.+.+|-||+++|||.+.||.
T Consensus 27 ~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 27 YDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred cchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 45699999999999999999999999999999999999999999999999999999999999999985
No 12
>smart00427 H2B Histone H2B.
Probab=98.70 E-value=4.1e-08 Score=70.46 Aligned_cols=66 Identities=14% Similarity=0.209 Sum_probs=63.9
Q ss_pred ccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHh
Q 048501 74 PFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIR 139 (143)
Q Consensus 74 pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rir 139 (143)
.|..+|+.|+.++++|..+++.||..|...+.+++.++-.+|..++.+.||-||.++|||.|.||.
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 578899999999999999999999999999999999999999999999999999999999999985
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=98.53 E-value=1.4e-07 Score=67.17 Aligned_cols=69 Identities=23% Similarity=0.268 Sum_probs=62.8
Q ss_pred hhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 68 LLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 68 llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
--||+.|..||+|.- .--|++.+|.+.+.++.|.||..+..||...|-||+|.||+..||.++.+-.|.
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 348999999998854 347999999999999999999999999999999999999999999999998885
No 14
>PLN00035 histone H4; Provisional
Probab=98.42 E-value=3.7e-07 Score=67.14 Aligned_cols=67 Identities=21% Similarity=0.245 Sum_probs=61.5
Q ss_pred hccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 70 IRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 70 I~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
||+.|-.||.|.- .--|++.+|.+.|.++.|.||..+..||...|-||+|.||+..||.+|.+-.|.
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 8899988888754 247999999999999999999999999999999999999999999999988775
No 15
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=98.39 E-value=6e-07 Score=68.15 Aligned_cols=70 Identities=21% Similarity=0.270 Sum_probs=67.3
Q ss_pred hccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHh
Q 048501 70 IRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIR 139 (143)
Q Consensus 70 I~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rir 139 (143)
..+..|..+|+.++.++++|+.+.+.|+.+|.....+++.++...|+++|.+.||-||..+|||+|.+|.
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 4788899999999999999999999999999999999999999999999999999999999999999985
No 16
>PTZ00015 histone H4; Provisional
Probab=98.39 E-value=4.2e-07 Score=66.70 Aligned_cols=69 Identities=20% Similarity=0.213 Sum_probs=62.1
Q ss_pred hhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 68 LLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 68 llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
.-|++.|-.||++.- .--|++.+|.+.+.++.|.||..+..||..+|-||+|.||+..||.+|.+-.|.
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 348898888888754 347999999999999999999999999999999999999999999999988775
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=98.39 E-value=5.9e-07 Score=60.67 Aligned_cols=63 Identities=21% Similarity=0.256 Sum_probs=52.6
Q ss_pred hccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 70 IRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 70 I~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
+|+.|..|+. ...+-. +.+.+|...|.+..|.++-.+.++|..++.|+||.||++.||.+|.+
T Consensus 3 ~p~~~i~ria----~~~Gi~-ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 3 LPKETIKDVA----ESLGIG-NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCHHHHHHHH----HHCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 4555554444 444333 89999999999999999999999999999999999999999999863
No 18
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=98.31 E-value=1.6e-06 Score=64.57 Aligned_cols=65 Identities=20% Similarity=0.331 Sum_probs=59.1
Q ss_pred chhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 76 QRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 76 ~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
.++|..|+.+.+ -.+++..|+..|-|.++.|...+..||...|-||+|.||...||+||...++.
T Consensus 4 ~~~v~~iLk~~G-v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 4 ARVIAAILKSMG-ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHCC-CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 467888888653 35899999999999999999999999999999999999999999999998875
No 19
>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=98.28 E-value=2.1e-06 Score=56.86 Aligned_cols=58 Identities=28% Similarity=0.288 Sum_probs=49.4
Q ss_pred HHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHH
Q 048501 79 VREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLAR 136 (143)
Q Consensus 79 VrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~ 136 (143)
|+.|++....+.+++.+|+.+|+.++|.|+..|-.+|+..+-+.+|-||++.||..|.
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 4556665555678999999999999999999999999999999999999999998763
No 20
>smart00417 H4 Histone H4.
Probab=98.01 E-value=3.8e-06 Score=58.40 Aligned_cols=62 Identities=19% Similarity=0.197 Sum_probs=55.3
Q ss_pred hhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHH
Q 048501 68 LLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQL 134 (143)
Q Consensus 68 llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqL 134 (143)
.-||+.|..||+|.= .--|++.++.+.|.++.|.||..+..||..+|-|++|.||+..|+..
T Consensus 12 ~gI~k~~IrRLaRr~-----GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARRG-----GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 348999999998743 34699999999999999999999999999999999999999999853
No 21
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.91 E-value=1e-05 Score=56.35 Aligned_cols=63 Identities=25% Similarity=0.242 Sum_probs=52.4
Q ss_pred cchhHHHHHHhh--hccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 75 FQRLVREIAQDF--KTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 75 F~RLVrEI~~~~--~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
+.--|-+|+++. ..++.|++..|.+|-|.+=.++..+-.|--..|-||+|.||++.|+.|..|
T Consensus 7 l~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 7 LWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 344566777766 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=97.69 E-value=0.0001 Score=50.26 Aligned_cols=58 Identities=19% Similarity=0.220 Sum_probs=45.7
Q ss_pred HHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 80 REIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 80 rEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
.|++.++.++..+..++.++|.+.|++|+.+..+.|-.+|.|.+--||.++|+|+...
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 3444555788999999999999999999999999999999999999999999999853
No 23
>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=97.56 E-value=0.00023 Score=48.41 Aligned_cols=59 Identities=27% Similarity=0.316 Sum_probs=47.2
Q ss_pred hHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 78 LVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 78 LVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
-|+-|++.++- -..+.++..+|.+-+|.-|-.+.++|..++.|+||-++++.||..|.|
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 46777776652 136889999999999999999999999999999999999999999875
No 24
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=97.51 E-value=0.00025 Score=53.95 Aligned_cols=65 Identities=26% Similarity=0.341 Sum_probs=53.0
Q ss_pred chhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 76 QRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 76 ~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
.++|..|+.+.+- ..|+..++.-|-|.+=.|...+++||...|-||+|.+|...|++||...|..
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 4788888887753 2479999999999999999999999999999999999999999999887643
No 25
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.51 E-value=0.00021 Score=49.09 Aligned_cols=51 Identities=24% Similarity=0.195 Sum_probs=47.8
Q ss_pred cchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 91 WFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 91 rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
+.+.+|++.|.+..|.|+..|-+.+...+-|++|.++.+.|+.++..--|.
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 789999999999999999999999999999999999999999999766553
No 26
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=97.46 E-value=0.00014 Score=57.58 Aligned_cols=69 Identities=25% Similarity=0.270 Sum_probs=63.9
Q ss_pred hhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 67 ELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 67 ~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
++.+|..--.|||+|++.+. ++-++.+|..||+.+|--|+.-|--.|+-.|.-.+|-||++.|+-=++.
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 67889999999999999976 7899999999999999999999999999999999999999999876553
No 27
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=97.33 E-value=0.00053 Score=58.95 Aligned_cols=64 Identities=20% Similarity=0.255 Sum_probs=56.6
Q ss_pred hhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 77 RLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 77 RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
..|+.|++..+- -+...+|..+|-+-+|.++-.+.++|..+|.|+||.||+..||++|.+.++.
T Consensus 3 ~~i~~ia~~~Gi-~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~ 66 (343)
T cd08050 3 ESIKLIAESLGI-DSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNV 66 (343)
T ss_pred hHHHHHHHHcCC-CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCC
Confidence 357777775542 2789999999999999999999999999999999999999999999999864
No 28
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.20 E-value=0.00045 Score=60.94 Aligned_cols=56 Identities=27% Similarity=0.388 Sum_probs=43.7
Q ss_pred chhHHHHHHhh-----hccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCccc
Q 048501 76 QRLVREIAQDF-----KTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKD 131 (143)
Q Consensus 76 ~RLVrEI~~~~-----~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kD 131 (143)
+-+|+.+++.| ....++..+||.+|+.|+|-|+.+|-+|-...|-||+|.||...|
T Consensus 354 ~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 354 PGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred ccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 34567777666 257899999999999999999999999999999999999998776
No 29
>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=97.03 E-value=0.0005 Score=51.34 Aligned_cols=67 Identities=19% Similarity=0.170 Sum_probs=59.0
Q ss_pred hhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 67 ELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 67 ~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
.|.+|-.++.|+.++= ....|+..+|...|-.+-|.+...++|.|.-.|.|+++.+|+|+||+|+.+
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 5778888888888752 123799999999999999999999999999999999999999999999964
No 30
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.80 E-value=0.0014 Score=55.05 Aligned_cols=72 Identities=19% Similarity=0.257 Sum_probs=62.5
Q ss_pred hhhhhhhhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHH
Q 048501 61 KYQKSTELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLAR 136 (143)
Q Consensus 61 ~yQkst~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~ 136 (143)
.++-+++.++-|--...||++| ..+--+..++-+.|.|.|++|+.++-.-+-.+|.|.|--||.++||+|.+
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 5667777777777777777776 45677889999999999999999999999999999999999999999975
No 31
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.50 E-value=0.027 Score=43.92 Aligned_cols=65 Identities=23% Similarity=0.409 Sum_probs=54.5
Q ss_pred hhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhccC
Q 048501 77 RLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGER 142 (143)
Q Consensus 77 RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~~ 142 (143)
++|--|+.+++- --|....+.-|=|.+=.|.+.+++||...+-||++-||...|++||...++.+
T Consensus 17 ~~i~~iL~s~GI-~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~ 81 (148)
T KOG3334|consen 17 RVIASILKSLGI-QEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDH 81 (148)
T ss_pred HHHHHHHHHcCc-cccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhcc
Confidence 455566665441 23678899999999999999999999999999999999999999999887653
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=94.88 E-value=0.074 Score=36.07 Aligned_cols=54 Identities=20% Similarity=0.175 Sum_probs=48.3
Q ss_pred ccc-cchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 88 TDL-WFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 88 ~~~-rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
.+| ..+++||+.|-+.++.||..|...+...|-|+.|-...+.|+.++..=-|.
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 688999999999999999999999999999999999999999998765553
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=88.23 E-value=0.77 Score=32.73 Aligned_cols=63 Identities=14% Similarity=0.212 Sum_probs=31.4
Q ss_pred cchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 75 FQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 75 F~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
|..=|+.++--|+..-.=..+.+..|.+..-.|++.+...|..+|...++-+|.+.|+-.+.|
T Consensus 3 f~~eI~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 3 FSKEIRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp -CCCCHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred hHHHHHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 344455566556655556688899999999999999999999999999999999999988765
No 34
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=87.80 E-value=0.77 Score=34.97 Aligned_cols=58 Identities=19% Similarity=0.229 Sum_probs=49.7
Q ss_pred HHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHH
Q 048501 79 VREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLAR 136 (143)
Q Consensus 79 VrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~ 136 (143)
|+.++..-...+|+.+.|.-.|--..|.....++|-|.-.|.-.|-..|||+-+|||.
T Consensus 32 vkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAI 89 (132)
T COG5262 32 VKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAI 89 (132)
T ss_pred HHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHh
Confidence 3444444446789999999999998998889999999999999999999999999994
No 35
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=86.19 E-value=1.5 Score=31.93 Aligned_cols=48 Identities=21% Similarity=0.279 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 94 SSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 94 ~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
.-..+-...++..||.+..-+|..-+-||||.||+.-|+--++.-.|.
T Consensus 49 G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 49 GLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 334455667888899999999999999999999999999877665443
No 36
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=85.14 E-value=2.2 Score=33.88 Aligned_cols=68 Identities=16% Similarity=0.172 Sum_probs=53.2
Q ss_pred hccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhc
Q 048501 70 IRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRG 140 (143)
Q Consensus 70 I~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg 140 (143)
+|-+--.|+.+.++ ..+-.+..+|=+.+||.+-.|+-=+-..|+--..--||.||+-.||-.|+--.|
T Consensus 33 LPIANV~RIMK~~l---P~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 33 LPIANVSRIMKKAL---PANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred ccHHHHHHHHHhcC---CcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 44444444444433 467889999999999999999888888888877889999999999998876544
No 37
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=83.05 E-value=1.9 Score=33.88 Aligned_cols=72 Identities=17% Similarity=0.235 Sum_probs=62.6
Q ss_pred hhhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhc
Q 048501 66 TELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRG 140 (143)
Q Consensus 66 t~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg 140 (143)
.++-+||+--+..|.||+- .|+||..+|=+.|++++=.|+--+--.||..+---.+-||.+.-+.=|+.-.|
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 4667899998888888874 59999999999999999999999999999999999999999988877665444
No 38
>smart00414 H2A Histone 2A.
Probab=81.94 E-value=2.4 Score=31.21 Aligned_cols=66 Identities=23% Similarity=0.194 Sum_probs=51.2
Q ss_pred hhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 68 LLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 68 llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
|.+|---+.|+.++- ....|+.++|.--|--.-|.....++|-|...+...++..|+|+|++++.+
T Consensus 8 L~fPVgRi~r~Lk~~----~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 8 LQFPVGRIHRLLRKG----TYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred ccCchHHHHHHHHcC----ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 444444455555432 234589999998998889999999999998888888999999999999854
No 39
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=81.71 E-value=2.5 Score=39.41 Aligned_cols=62 Identities=21% Similarity=0.261 Sum_probs=51.5
Q ss_pred hHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhc
Q 048501 78 LVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRG 140 (143)
Q Consensus 78 LVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg 140 (143)
-|+-+++..+ --.+..+|..+|-+-+|.-+-.+.+||..++.|+||-+++..|+.-|.|.+.
T Consensus 16 s~k~vAEslG-i~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 16 SVKVVAESLG-ITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred HHHHHHHHhC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 3445555433 2347789999999999999999999999999999999999999999988763
No 40
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=81.44 E-value=2.2 Score=32.91 Aligned_cols=46 Identities=28% Similarity=0.328 Sum_probs=38.1
Q ss_pred hHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCc---ccHHHHHHH
Q 048501 93 QSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMP---KDIQLARRI 138 (143)
Q Consensus 93 q~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~---kDiqLa~ri 138 (143)
......-|-+.|--|..+++|||...|-|+.|-.+.+ .|+.||.--
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 3455566778999999999999999999998876666 999998654
No 41
>PLN00154 histone H2A; Provisional
Probab=80.57 E-value=2 Score=33.14 Aligned_cols=68 Identities=18% Similarity=0.125 Sum_probs=53.9
Q ss_pred hhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 67 ELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 67 ~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
.|.+|---..|+.+|-.. ...|+.++|.--|--+-|.....++|-|.-.|...++..|+|++|+||.+
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 455555555666665431 24588888888888888999999999999999999999999999999964
No 42
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=80.08 E-value=2.8 Score=33.66 Aligned_cols=55 Identities=18% Similarity=0.215 Sum_probs=49.1
Q ss_pred hhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccC
Q 048501 68 LLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTK 123 (143)
Q Consensus 68 llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~Hak 123 (143)
.++..-|++..+..|+.+.... .+..+.+..|-.|+|.+|-.|.++...++-|-.
T Consensus 43 ~fl~~~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~ 97 (212)
T cd08045 43 SFLNPSPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEERLRNLLEKLIEVSEHRV 97 (212)
T ss_pred hccCHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 5678889999999999876544 789999999999999999999999999999963
No 43
>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=78.83 E-value=1.5 Score=36.26 Aligned_cols=57 Identities=19% Similarity=0.241 Sum_probs=38.7
Q ss_pred hhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCcc
Q 048501 68 LLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRV 125 (143)
Q Consensus 68 llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRv 125 (143)
+++...|++..+.+|+.... ...+..+.+..|=.|+|.+|-.|.|++..++.|....
T Consensus 42 ~fL~~~~L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 42 PFLNPSPLQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp --S-HHHHHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred cccCHHHHHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 56678889999999997665 5678899999999999999999999999999996543
No 44
>PTZ00017 histone H2A; Provisional
Probab=78.69 E-value=2.7 Score=32.34 Aligned_cols=67 Identities=21% Similarity=0.175 Sum_probs=53.9
Q ss_pred hhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 67 ELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 67 ~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
.|.+|---+.|+.++- ....|+...|.--|--+-|.....++|-|.-.+...++..|+|++|+|+.+
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 4566666666666543 123488888888888889999999999999999999999999999999964
No 45
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=70.80 E-value=10 Score=33.51 Aligned_cols=61 Identities=23% Similarity=0.158 Sum_probs=50.7
Q ss_pred HHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhc
Q 048501 79 VREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRG 140 (143)
Q Consensus 79 VrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg 140 (143)
|..|++.+.- -.++..|++.|+..+-.|+-+|-+.|...+-|++|+-.+..||-++..-.|
T Consensus 35 vaQIcqslg~-~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls 95 (353)
T KOG2389|consen 35 VAQICQSLGY-SSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLS 95 (353)
T ss_pred HHHHHHhcCC-cccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhh
Confidence 4445554432 257788999999999999999999999999999999999999999876654
No 46
>PLN00157 histone H2A; Provisional
Probab=69.28 E-value=5.5 Score=30.60 Aligned_cols=67 Identities=22% Similarity=0.188 Sum_probs=52.3
Q ss_pred hhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 67 ELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 67 ~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
.|.+|---+.|+.++= ....|+.+.|.--|--.-|.....++|-|.-.+...++..|+|++|+|+.+
T Consensus 24 gL~FPVgRi~R~Lk~g----~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAG----KYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcC----chhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 3555555555555542 233588888888888888888889999999999999999999999999854
No 47
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=68.26 E-value=15 Score=32.13 Aligned_cols=50 Identities=14% Similarity=0.097 Sum_probs=43.3
Q ss_pred chHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 92 FQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 92 fq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
+...|++.|=|+.-.|+-.+|+.+-..+-|++|.-.++.|+.|+....|.
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 45567777777777899999999999999999999999999999887765
No 48
>PLN00156 histone H2AX; Provisional
Probab=67.85 E-value=7.4 Score=30.15 Aligned_cols=67 Identities=22% Similarity=0.187 Sum_probs=52.0
Q ss_pred hhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 67 ELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 67 ~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
.|.+|---+.|+.++- ....|+...|.--|--.-|.....++|-|.-.+...++..|+|+.|+|+.+
T Consensus 27 gL~FPVgRi~R~Lk~g----~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAG----KYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcC----ChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 3455555555555442 233588888888888888888889999999999999999999999999864
No 49
>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=66.68 E-value=8.2 Score=29.92 Aligned_cols=60 Identities=22% Similarity=0.298 Sum_probs=42.2
Q ss_pred cchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHh
Q 048501 75 FQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIR 139 (143)
Q Consensus 75 F~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rir 139 (143)
|+++.|+-+. +-...+=+.-+-+.+|.-|..||+-|+.-|.+..|-.|.+.|+-+...+.
T Consensus 1 fe~lFR~aa~-----LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPITkGlq 60 (138)
T PF09123_consen 1 FERLFRKAAG-----LDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPITKGLQ 60 (138)
T ss_dssp HHHHHHHHHS---------HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHHH
T ss_pred ChHHHHHHhc-----cCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCccHHHH
Confidence 4566665542 44556667778899999999999999999999999999999998876653
No 50
>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=66.25 E-value=26 Score=24.97 Aligned_cols=57 Identities=16% Similarity=0.207 Sum_probs=42.8
Q ss_pred HHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 80 REIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 80 rEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
+.++--++..-.=..+.+.+|.+..=.|++.|.-.|..+|. ..+--+.+.|+-.+.|
T Consensus 9 ~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 9 RQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 33333344333445788899999999999999999999998 5666669999987754
No 51
>PLN00153 histone H2A; Provisional
Probab=65.81 E-value=7.9 Score=29.64 Aligned_cols=67 Identities=22% Similarity=0.183 Sum_probs=52.6
Q ss_pred hhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 67 ELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 67 ~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
.|.+|---+.|+.++= ....|+.+.|.--|--.-|.....++|-|.-.+...+...|+|+.|+|+.+
T Consensus 22 gL~FpVgRi~R~Lr~g----~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKG----KYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcC----chhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 3555555555555441 233588888888888888988889999999999999999999999999864
No 52
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=65.09 E-value=8.8 Score=29.71 Aligned_cols=68 Identities=22% Similarity=0.215 Sum_probs=57.1
Q ss_pred hhhhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHH
Q 048501 65 STELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLA 135 (143)
Q Consensus 65 st~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa 135 (143)
+.++-+||+--|..|-+|+. .|+-|+.+|-+.+++++=.|+--|--.||..+---...||.+.-+--|
T Consensus 7 dDe~sLPKATVqKMvS~iLp---~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKA 74 (148)
T COG5150 7 DDENSLPKATVQKMVSSILP---KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKA 74 (148)
T ss_pred cccccCcHHHHHHHHHHhcc---ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHH
Confidence 34567899999999999976 789999999999999999999988888998888777788877665433
No 53
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=63.71 E-value=12 Score=28.72 Aligned_cols=50 Identities=22% Similarity=0.214 Sum_probs=42.0
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 88 TDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 88 ~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
.-.|+..+|.-.|--.-|.....++|.+...|.-.++..|+|+-++||.+
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 45677777777777666766778999999999999999999999999965
No 54
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=62.92 E-value=13 Score=31.40 Aligned_cols=84 Identities=20% Similarity=0.274 Sum_probs=61.2
Q ss_pred CchhhHHHHhhhhhhhh---------hhccCccchhHHHHHHhhhccc-cchHHHHHHHHHHHHHHHHHHhhhhhhhhhc
Q 048501 52 GTVALREIRKYQKSTEL---------LIRKLPFQRLVREIAQDFKTDL-WFQSSAVAALQEAAEAYLVGLFEDTNLCTIH 121 (143)
Q Consensus 52 gt~alrEIr~yQkst~l---------lI~k~pF~RLVrEI~~~~~~~~-rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~H 121 (143)
|...-+-+|.||+..+- -...+||.|+- .++. ...|. -+.++|=-..-.++|-|+..|---|-+.|--
T Consensus 80 g~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARIk-kvMK-tdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~ 157 (286)
T COG5208 80 GLLDERISRYWQQTIKAAEEERQILLKDHNLPLARIK-KVMK-TDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEE 157 (286)
T ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHHH-HHHh-cccchhheecccchHHHHHHHHHHHHHHHHHHHHHhH
Confidence 45556678899976422 22348999863 4443 12233 3566676777889999999999999999999
Q ss_pred cCccccCcccHHHHHH
Q 048501 122 TKRVTIMPKDIQLARR 137 (143)
Q Consensus 122 akRvTi~~kDiqLa~r 137 (143)
.||-||...||--|+.
T Consensus 158 NkRRtLQksDia~Av~ 173 (286)
T COG5208 158 NKRRTLQKSDIAAAVK 173 (286)
T ss_pred hhhhHHHHHHHHHHHH
Confidence 9999999999987754
No 55
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=55.63 E-value=19 Score=25.39 Aligned_cols=60 Identities=23% Similarity=0.437 Sum_probs=47.8
Q ss_pred hHHHHhhhhhhhhhhccCccchhHHHHHHh-hhccccchHHHHHHHHH--HHHHHHHHHhhhhhhh
Q 048501 56 LREIRKYQKSTELLIRKLPFQRLVREIAQD-FKTDLWFQSSAVAALQE--AAEAYLVGLFEDTNLC 118 (143)
Q Consensus 56 lrEIr~yQkst~llI~k~pF~RLVrEI~~~-~~~~~rfq~~Al~aLQe--aaEa~Lv~lfeda~l~ 118 (143)
|++|.+|+...+ =||-.| |.+.|-++. |+.++-.++..+..|+. -||+|+-+..+..+.|
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 678999988874 346554 677777764 67888889999999985 4899999999998887
No 56
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=53.46 E-value=43 Score=25.33 Aligned_cols=61 Identities=16% Similarity=0.190 Sum_probs=45.8
Q ss_pred cchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 75 FQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 75 F~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
|..=|+.++--|+....=..+.+++|.|.+-+|++.+.-+|-..|- .|=.+...|...+.|
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 3344455555556666666788999999999999999988877776 566677888888865
No 57
>PTZ00252 histone H2A; Provisional
Probab=52.89 E-value=22 Score=27.46 Aligned_cols=67 Identities=18% Similarity=0.162 Sum_probs=49.3
Q ss_pred hhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhc--cCccccCcccHHHHHH
Q 048501 67 ELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIH--TKRVTIMPKDIQLARR 137 (143)
Q Consensus 67 ~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~H--akRvTi~~kDiqLa~r 137 (143)
.|.+|---+.|+.++= ....|+.+.|.--|--.-|.....++|-|.-.|.. .|+..|+|++|+|+.+
T Consensus 23 GL~FPVgRi~R~Lr~g----~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRG----QYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcC----CcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 3445555555555432 23458888888888888888888999999888854 6778899999999864
No 58
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=48.94 E-value=12 Score=29.70 Aligned_cols=63 Identities=24% Similarity=0.353 Sum_probs=49.6
Q ss_pred ccCccchhHHHHHHhhhccccchHH-HHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHH
Q 048501 71 RKLPFQRLVREIAQDFKTDLWFQSS-AVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLA 135 (143)
Q Consensus 71 ~k~pF~RLVrEI~~~~~~~~rfq~~-Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa 135 (143)
.++|.+| |++|.. ..+|++|..+ |+.++-.++|.|+-.|=.+++-|+--.+|+|+.-+|+..+
T Consensus 58 ~rLpL~r-ik~vvk-l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~a 121 (162)
T KOG1658|consen 58 SRLPLAR-IKQVVK-LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTA 121 (162)
T ss_pred hhccHHH-HHhhcc-CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhccccc
Confidence 4555555 344432 3578888765 5567889999999999999999999999999999998765
No 59
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=43.98 E-value=82 Score=23.53 Aligned_cols=63 Identities=21% Similarity=0.237 Sum_probs=46.7
Q ss_pred cCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 72 KLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 72 k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
+--|+.=++-.+--|..+--=-.+.+++|.+.+=.|++.+...|.... +|=.+.+.|+..+.|
T Consensus 8 k~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 8 KHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred HHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 334666666666666666555678899999999999999966555554 888888999988754
No 60
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=38.16 E-value=54 Score=29.32 Aligned_cols=61 Identities=20% Similarity=0.279 Sum_probs=48.8
Q ss_pred HHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhc
Q 048501 79 VREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRG 140 (143)
Q Consensus 79 VrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg 140 (143)
++.+++...- --+..+++.||---.|.-+-.+-+.|...+.|.||.-++..||.-|.|-+.
T Consensus 11 ~KdvAeslGi-~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lN 71 (450)
T COG5095 11 LKDVAESLGI-SNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLN 71 (450)
T ss_pred HHHHHHHcCC-cccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcC
Confidence 4455543321 135578888888889999999999999999999999999999999988764
No 61
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=36.70 E-value=68 Score=29.16 Aligned_cols=71 Identities=23% Similarity=0.382 Sum_probs=58.4
Q ss_pred hhhccCccch-hHHHHHHhh--hccccchHHHHHHHHHHHHH----HHHHHhhhhhhhhhccCccccCcccHHHHHHH
Q 048501 68 LLIRKLPFQR-LVREIAQDF--KTDLWFQSSAVAALQEAAEA----YLVGLFEDTNLCTIHTKRVTIMPKDIQLARRI 138 (143)
Q Consensus 68 llI~k~pF~R-LVrEI~~~~--~~~~rfq~~Al~aLQeaaEa----~Lv~lfeda~l~a~HakRvTi~~kDiqLa~ri 138 (143)
|+|+-.||.+ =++||..-= ..++-.+.+|++-|-...|. |-++|++-|+..|--.+.-+|...|+.-|..+
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 6788889876 477776531 36788999999999766654 99999999999999999999999999887665
No 62
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=35.94 E-value=68 Score=26.50 Aligned_cols=58 Identities=17% Similarity=0.192 Sum_probs=45.7
Q ss_pred hhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhc--cCccccCcccHHHHH
Q 048501 77 RLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIH--TKRVTIMPKDIQLAR 136 (143)
Q Consensus 77 RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~H--akRvTi~~kDiqLa~ 136 (143)
..|++.++ ..++.+..+|+..|-+.++.=|..+-.+...++.+ .+.-+|+..|++.+.
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 33444433 35688999999999999999888888888888888 567789999998764
No 63
>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=34.35 E-value=86 Score=28.57 Aligned_cols=59 Identities=19% Similarity=0.255 Sum_probs=43.4
Q ss_pred HHHHHHhh--hccccchHHHHHHHHHHHH--HHHHHHhhhhhhhhhccCccccCcccHHHHHH
Q 048501 79 VREIAQDF--KTDLWFQSSAVAALQEAAE--AYLVGLFEDTNLCTIHTKRVTIMPKDIQLARR 137 (143)
Q Consensus 79 VrEI~~~~--~~~~rfq~~Al~aLQeaaE--a~Lv~lfeda~l~a~HakRvTi~~kDiqLa~r 137 (143)
+.+|++.. +.++.+..+|++.|-.-+. ..+..+++.|...|...+|.+|+.+|+.-+..
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 2457788888887655444 37888899988888888999999999988753
No 64
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=33.33 E-value=78 Score=25.41 Aligned_cols=27 Identities=33% Similarity=0.364 Sum_probs=21.4
Q ss_pred hccccchHHHHHHHHHHHHHHHHHHhh
Q 048501 87 KTDLWFQSSAVAALQEAAEAYLVGLFE 113 (143)
Q Consensus 87 ~~~~rfq~~Al~aLQeaaEa~Lv~lfe 113 (143)
.++++|+...-.++||.+|++..-.|=
T Consensus 70 ~~~~~y~~~~~~~lQEyvEA~~f~~~l 96 (204)
T PRK14562 70 HPELYYAGYVGTALQEYVEALLVYSLL 96 (204)
T ss_pred CchhhhhhhcchHHHHHHHHHHHHHHH
Confidence 367888888889999999997665543
No 65
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=32.76 E-value=63 Score=26.89 Aligned_cols=72 Identities=21% Similarity=0.210 Sum_probs=58.6
Q ss_pred hhhhhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHH
Q 048501 64 KSTELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLAR 136 (143)
Q Consensus 64 kst~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~ 136 (143)
...++.+..+|..|+. .|+..-..---+..+|.-.+-.|+|.|+..|-.-+..-+--++|-|+.-.|+.-++
T Consensus 66 ~~~d~~~~~lPlaRiK-kimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av 137 (236)
T KOG1657|consen 66 GQLDFKNHILPLARIK-KIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAV 137 (236)
T ss_pred cccchhhccCcHhhcc-ccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHh
Confidence 4567889999999965 45543221126899999999999999999999999999999999999999887654
No 66
>PHA03159 hypothetical protein; Provisional
Probab=30.51 E-value=80 Score=24.66 Aligned_cols=49 Identities=22% Similarity=0.440 Sum_probs=40.4
Q ss_pred CccchhHHHHHHhhhccccchHHHHHHHHHHHHHH--HHHHhhhhhhhhhc
Q 048501 73 LPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAY--LVGLFEDTNLCTIH 121 (143)
Q Consensus 73 ~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~--Lv~lfeda~l~a~H 121 (143)
.-||..|-.|+.++.....=|.+.+-|++..-..| +..|+.|-.+|+.-
T Consensus 4 i~fq~~ie~il~~cq~~~~~~dsivraihsvi~qynkfe~lmpdfs~c~hd 54 (160)
T PHA03159 4 IKFQKIIENILKECQDCHHQQDSIVRAIHSVIHQYNKFEALMPDFSICAHD 54 (160)
T ss_pred ccHHHHHHHHHHHHHhcchhhhHHHHHHHHHHHHHhhHHHhCCCchhhhhh
Confidence 46899999999988776677788888998888776 67888999999864
No 67
>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=30.19 E-value=53 Score=22.40 Aligned_cols=57 Identities=5% Similarity=0.039 Sum_probs=35.6
Q ss_pred hhHHHHHHhh--hccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccc-cCcccHH
Q 048501 77 RLVREIAQDF--KTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVT-IMPKDIQ 133 (143)
Q Consensus 77 RLVrEI~~~~--~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvT-i~~kDiq 133 (143)
-+|.+|.+.. +...+++.+|+.++.+-.+-|...-+.-|..-+---+-.. |.+.|++
T Consensus 3 ~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LE 62 (72)
T PF09415_consen 3 ELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLE 62 (72)
T ss_dssp HHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHH
T ss_pred HHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence 3566676643 3678999999999999888777766665555444444444 6666654
No 68
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=29.34 E-value=1.5e+02 Score=26.67 Aligned_cols=72 Identities=22% Similarity=0.359 Sum_probs=58.7
Q ss_pred hhhccCccch-hHHHHHHh-h-hccccchHHHHHHHHHHHHH----HHHHHhhhhhhhhhccCccccCcccHHHHHHHh
Q 048501 68 LLIRKLPFQR-LVREIAQD-F-KTDLWFQSSAVAALQEAAEA----YLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIR 139 (143)
Q Consensus 68 llI~k~pF~R-LVrEI~~~-~-~~~~rfq~~Al~aLQeaaEa----~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rir 139 (143)
++|.-.|+.+ =+++|+.- + ..|.-.+.+|+..|-...|+ |-..|...|++.+.-.|--++...||+-|-+|-
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 45666542 2 36888999999998877776 999999999999999999999999999988773
No 69
>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=27.79 E-value=83 Score=23.72 Aligned_cols=45 Identities=11% Similarity=0.115 Sum_probs=36.7
Q ss_pred cCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhh
Q 048501 72 KLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTN 116 (143)
Q Consensus 72 k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~ 116 (143)
.+-+-+.||..+..+-....|..+.+.-|+-+++..++..++.++
T Consensus 15 ~~~~~~~vr~~~~~~a~~~g~~~~~~~~l~lav~Ea~~Nai~ha~ 59 (159)
T TIGR01924 15 KPEYVGLIRLTLSGIASRAGYTYDDIEDLKIAVSEACTNAVKHAY 59 (159)
T ss_pred cHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhcc
Confidence 344567788888877778889999999999999999999888876
No 70
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=25.65 E-value=1.4e+02 Score=20.60 Aligned_cols=43 Identities=19% Similarity=0.145 Sum_probs=33.2
Q ss_pred hhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhh
Q 048501 77 RLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCT 119 (143)
Q Consensus 77 RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a 119 (143)
+.+++.+..+-....|....+..+.-+++-.++..++.++...
T Consensus 9 ~~~r~~~~~~~~~~~~~~~~~~~~~lav~E~~~Nav~H~~~~~ 51 (125)
T PF13581_consen 9 REARAFLREFLERLGLPEEDRDDLELAVSEALTNAVEHGYPGD 51 (125)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 3455555555556888899999999999999999998888643
No 71
>PF01997 Translin: Translin family; InterPro: IPR002848 Translins are DNA-binding proteins that specifically recognise consensus sequences at the breakpoint junctions in chromosomal translocations, mostly involving immunoglobulin (Ig)/T-cell receptor gene segments. They seem to recognise single-stranded DNA ends generated by staggered breaks occuring at recombination hot spots []. Translin folds into an alpha-alpha superhelix, consisting of two curved layers of alpha/alpha topology [, ].; GO: 0043565 sequence-specific DNA binding; PDB: 3QB5_K 3PJA_L 1J1J_D 3RIU_C 3AXJ_B 4DG7_C 2QVA_C 2QRX_A 1KEY_C.
Probab=25.47 E-value=1.1e+02 Score=24.08 Aligned_cols=22 Identities=23% Similarity=0.105 Sum_probs=16.0
Q ss_pred cccchHHHHHHHHHHHHHHHHH
Q 048501 89 DLWFQSSAVAALQEAAEAYLVG 110 (143)
Q Consensus 89 ~~rfq~~Al~aLQeaaEa~Lv~ 110 (143)
.++|....-.+|||.+|+..-.
T Consensus 62 ~~~y~~~~s~~lQE~vEa~~f~ 83 (200)
T PF01997_consen 62 FYRYHGAYSPGLQEYVEAISFY 83 (200)
T ss_dssp HHHHGGGTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777777889998886433
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=24.93 E-value=62 Score=21.06 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=18.4
Q ss_pred HHHHHHHHHHHHHHHHHhhh
Q 048501 95 SAVAALQEAAEAYLVGLFED 114 (143)
Q Consensus 95 ~Al~aLQeaaEa~Lv~lfed 114 (143)
+|+.+|||+++.-|..+...
T Consensus 7 ea~~~lqevs~eELd~ilGg 26 (51)
T PF04604_consen 7 EALNSLQEVSDEELDQILGG 26 (51)
T ss_pred HHHHHHHhcCHHHHHHHhCC
Confidence 89999999999999998875
No 73
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=24.42 E-value=1e+02 Score=25.33 Aligned_cols=56 Identities=25% Similarity=0.342 Sum_probs=40.6
Q ss_pred hhhHHHHhhhhhhhhhhccCccchhHH----------HHHHhh--hccccchHHHHHHHHHHHHHHHH
Q 048501 54 VALREIRKYQKSTELLIRKLPFQRLVR----------EIAQDF--KTDLWFQSSAVAALQEAAEAYLV 109 (143)
Q Consensus 54 ~alrEIr~yQkst~llI~k~pF~RLVr----------EI~~~~--~~~~rfq~~Al~aLQeaaEa~Lv 109 (143)
...|||.+|-+-.-.++.+-.|..-=. ++-..+ .+++-|...|=.++||-+||.+.
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 457899999888878888888865322 222122 27888999999999999999543
No 74
>PF06075 DUF936: Plant protein of unknown function (DUF936); InterPro: IPR010341 This family consists of several hypothetical proteins from plants. The function of this family is unknown.
Probab=23.84 E-value=1.2e+02 Score=28.48 Aligned_cols=42 Identities=38% Similarity=0.430 Sum_probs=28.9
Q ss_pred cchhHHHHHHhhhccccchHHHHHHHHHH--HHHHHHHHhhhhhhhh
Q 048501 75 FQRLVREIAQDFKTDLWFQSSAVAALQEA--AEAYLVGLFEDTNLCT 119 (143)
Q Consensus 75 F~RLVrEI~~~~~~~~rfq~~Al~aLQea--aEa~Lv~lfeda~l~a 119 (143)
...|-+|+++.=.. =+.-|++||||| +|..|-.|=..|++|.
T Consensus 325 L~kLGKEa~~~Rd~---A~~aA~eALqEASAaE~lir~Ls~fseL~s 368 (579)
T PF06075_consen 325 LAKLGKEAMQQRDA---AQKAAVEALQEASAAESLIRCLSMFSELCS 368 (579)
T ss_pred HHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56778888773221 246799999997 4666666666677773
No 75
>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=23.38 E-value=99 Score=25.30 Aligned_cols=16 Identities=50% Similarity=0.650 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHHhh
Q 048501 98 AALQEAAEAYLVGLFE 113 (143)
Q Consensus 98 ~aLQeaaEa~Lv~lfe 113 (143)
.+||++++.||..+-+
T Consensus 91 ~~l~~~A~~yL~~va~ 106 (196)
T PF07105_consen 91 DALQEAADQYLAKVAK 106 (196)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 8999999999988765
No 76
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=23.37 E-value=74 Score=28.09 Aligned_cols=86 Identities=24% Similarity=0.199 Sum_probs=49.7
Q ss_pred CchhhHHHHhhhhhhhhhhccCccchhHHHHHHhhhcc---ccchHHHHHH--HHHHHHHHHHHHhhhhhhhhhccCccc
Q 048501 52 GTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTD---LWFQSSAVAA--LQEAAEAYLVGLFEDTNLCTIHTKRVT 126 (143)
Q Consensus 52 gt~alrEIr~yQkst~llI~k~pF~RLVrEI~~~~~~~---~rfq~~Al~a--LQeaaEa~Lv~lfeda~l~a~HakRvT 126 (143)
|+.++-|+.. -|+|.-+-.+||+||..|+..+-.. +-=+.+.+.- =++. +-..-.+|++.+++.-|-..--
T Consensus 114 ~r~vlvElNC---ETDFVARn~~Fq~Lv~~iA~~~l~~~~~~~~~~s~~s~e~~l~~-~~~g~kl~~~~~~l~~~~d~~g 189 (340)
T KOG1071|consen 114 GRTVLVELNC---ETDFVARNDIFQDLVDQIALSVLAHCQTLKTKHSSYSKEKELEM-DGRGFKLSESLSLLPNLPDVEG 189 (340)
T ss_pred CeEEEEEeec---ccchhhccchHHHHHHHHHHHHHHhhhhcccChhhhhhhhhccc-cchHHHhhHHHhhccCCCCccc
Confidence 5556666654 3889999999999999999865321 1111111110 0000 3355678889988888865443
Q ss_pred --cCcccHHHHHHHhcc
Q 048501 127 --IMPKDIQLARRIRGE 141 (143)
Q Consensus 127 --i~~kDiqLa~rirg~ 141 (143)
.+..-+.++-.+-||
T Consensus 190 kvsl~d~l~~~i~~~GE 206 (340)
T KOG1071|consen 190 KVSLKDQLALAIGKLGE 206 (340)
T ss_pred ceeHHHHHHHHHHHhcc
Confidence 222234444444455
No 77
>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=23.37 E-value=2.2e+02 Score=26.56 Aligned_cols=49 Identities=18% Similarity=0.223 Sum_probs=39.0
Q ss_pred ccchHHHHHHHHH-HH------------HHHHHHHhhhhhhhhhccCccccCcccHHHHHHH
Q 048501 90 LWFQSSAVAALQE-AA------------EAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRI 138 (143)
Q Consensus 90 ~rfq~~Al~aLQe-aa------------Ea~Lv~lfeda~l~a~HakRvTi~~kDiqLa~ri 138 (143)
..|+.+|+..|-+ ++ +..|.++...|+..|...+..+|..+|++-|...
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 4799999998764 23 4678889999988888888899999999876543
No 78
>smart00188 IL10 Interleukin-10 family. Interleukin-10 inhibits the synthesis of a number of cytokines, including IFN-gamma, IL-2, IL-3, TNF and GM-CSF produced by activated macrophages and by helper T cells.
Probab=22.08 E-value=2.4e+02 Score=21.72 Aligned_cols=60 Identities=23% Similarity=0.263 Sum_probs=38.3
Q ss_pred hhHHHHhh-hhhhhhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCc
Q 048501 55 ALREIRKY-QKSTELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKR 124 (143)
Q Consensus 55 alrEIr~y-Qkst~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakR 124 (143)
+-.|||.| |..-++-.. .|-+++++++++.++= -+|.+.-.-||...|..|..+-.|-++
T Consensus 11 ~f~~Ik~~~q~kD~~~~v-----ll~~~ll~~~k~~~gC-----~~l~ell~FYLd~V~p~a~~~~~~~k~ 71 (137)
T smart00188 11 AFSRVKTFFQMKDQLDNI-----LLTESLLEDFKGYLGC-----QALSEMIQFYLEEVMPQAENHGPDIKE 71 (137)
T ss_pred HHHHHHHHHHccchHhhH-----hhhHHHHHHhCCCcch-----HHHHHHHHHHHHHHHHHHhcCCcchhh
Confidence 44566666 544433221 4566888888765432 456777888999999888776655554
No 79
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=21.16 E-value=65 Score=24.90 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=26.2
Q ss_pred chhhHHHHhhhhhhhhhhccCccchhHHHHHHh
Q 048501 53 TVALREIRKYQKSTELLIRKLPFQRLVREIAQD 85 (143)
Q Consensus 53 t~alrEIr~yQkst~llI~k~pF~RLVrEI~~~ 85 (143)
.||+.||+++..+...+ +...+-+||.+|=.+
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~ 128 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKE 128 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHh
Confidence 58999999997666555 888999999999653
No 80
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=20.88 E-value=1.5e+02 Score=22.62 Aligned_cols=67 Identities=22% Similarity=0.281 Sum_probs=44.9
Q ss_pred CccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHHHHhcc
Q 048501 73 LPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLARRIRGE 141 (143)
Q Consensus 73 ~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~rirg~ 141 (143)
.|..|.-|-+-......-|.-..|.--+-..-|..-...+|-|.-.+---|=..|+|+-+||| |||+
T Consensus 31 FpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLA--iRGD 97 (131)
T KOG1757|consen 31 FPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA--IRGD 97 (131)
T ss_pred cchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheee--ecCc
Confidence 455565555555445556666666555555556666677887777777767777889999998 5665
No 81
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=20.38 E-value=2.1e+02 Score=24.00 Aligned_cols=59 Identities=17% Similarity=0.068 Sum_probs=45.6
Q ss_pred chhHHHHHHhh-hccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHHH
Q 048501 76 QRLVREIAQDF-KTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLAR 136 (143)
Q Consensus 76 ~RLVrEI~~~~-~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa~ 136 (143)
..|++=|.+.+ ..++.++.+|+..|-+.++.=|..+-.+-..++.+++ +|+..|++.+.
T Consensus 138 ~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 138 REALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred HHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 33444444444 3678899999999999999988888888888888877 68889988754
No 82
>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=20.23 E-value=2.3e+02 Score=20.89 Aligned_cols=48 Identities=27% Similarity=0.384 Sum_probs=37.1
Q ss_pred HhhhhhhhhhhccCccchhHHHHHHhhhccccchHHHHHHHHHHHHHHHHHHhhhhhhhhh
Q 048501 60 RKYQKSTELLIRKLPFQRLVREIAQDFKTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTI 120 (143)
Q Consensus 60 r~yQkst~llI~k~pF~RLVrEI~~~~~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~ 120 (143)
..|+.+-+..-.+.|-++.|++|+..... ...-.+|..||.+.|+..+
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 56888877777889999999999886632 2345678888999998765
No 83
>PRK05907 hypothetical protein; Provisional
Probab=20.21 E-value=1.6e+02 Score=25.12 Aligned_cols=67 Identities=12% Similarity=0.026 Sum_probs=52.1
Q ss_pred hccCccchhHHHHHHhhh-ccccchHHHHHHHHHHH-HHHHHHHhhhhhhhhhc-cCccccCcccHHHHH
Q 048501 70 IRKLPFQRLVREIAQDFK-TDLWFQSSAVAALQEAA-EAYLVGLFEDTNLCTIH-TKRVTIMPKDIQLAR 136 (143)
Q Consensus 70 I~k~pF~RLVrEI~~~~~-~~~rfq~~Al~aLQeaa-Ea~Lv~lfeda~l~a~H-akRvTi~~kDiqLa~ 136 (143)
.+++.-+.|.+-|.+.++ .+..++.+|+..|=+.+ +.=|-.+...-..++.+ +.+-+|+..|++.+.
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 344445778888888774 67899999999988888 67777777777788888 668889999998653
No 84
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=20.18 E-value=38 Score=31.00 Aligned_cols=49 Identities=18% Similarity=0.125 Sum_probs=40.7
Q ss_pred hccccchHHHHHHHHHHHHHHHHHHhhhhhhhhhccCccccCcccHHHH
Q 048501 87 KTDLWFQSSAVAALQEAAEAYLVGLFEDTNLCTIHTKRVTIMPKDIQLA 135 (143)
Q Consensus 87 ~~~~rfq~~Al~aLQeaaEa~Lv~lfeda~l~a~HakRvTi~~kDiqLa 135 (143)
..+-.+..+.=+.|=+.|..|....-|-+-.+|.|.|--||.++|+||-
T Consensus 398 d~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlh 446 (505)
T COG5624 398 DEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLH 446 (505)
T ss_pred CcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceee
Confidence 3556677777788888888888777777777999999999999999984
Done!