Query psy17763
Match_columns 136
No_of_seqs 141 out of 607
Neff 5.5
Searched_HMMs 46136
Date Fri Aug 16 22:14:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17763.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17763hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00018 histone H3; Provision 100.0 7.3E-59 1.6E-63 347.6 11.4 135 1-135 1-135 (136)
2 PLN00121 histone H3; Provision 100.0 9.9E-59 2.1E-63 346.9 11.4 136 1-136 1-136 (136)
3 PLN00161 histone H3; Provision 100.0 2.5E-57 5.4E-62 338.3 10.7 128 1-135 1-129 (135)
4 KOG1745|consensus 100.0 8.8E-55 1.9E-59 325.0 9.1 136 1-136 1-137 (137)
5 PLN00160 histone H3; Provision 100.0 7.3E-50 1.6E-54 284.4 8.4 94 42-135 1-95 (97)
6 smart00428 H3 Histone H3. 100.0 1.2E-49 2.6E-54 287.0 9.2 101 35-135 2-104 (105)
7 COG2036 HHT1 Histones H3 and H 99.9 6.3E-26 1.4E-30 160.0 7.1 87 44-135 1-87 (91)
8 PF00125 Histone: Core histone 99.9 8.1E-22 1.8E-26 131.9 6.0 75 58-132 1-75 (75)
9 cd07981 TAF12 TATA Binding Pro 99.3 6E-12 1.3E-16 84.9 6.5 58 73-130 8-65 (72)
10 PTZ00463 histone H2B; Provisio 98.9 4.7E-09 1E-13 77.1 8.0 69 64-132 26-94 (117)
11 PLN00158 histone H2B; Provisio 98.9 5.7E-09 1.2E-13 76.6 6.6 69 64-132 25-93 (116)
12 smart00427 H2B Histone H2B. 98.8 1.1E-08 2.3E-13 72.1 6.8 66 67-132 2-67 (89)
13 cd00076 H4 Histone H4, one of 98.7 5.8E-08 1.3E-12 67.8 5.8 69 61-134 12-80 (85)
14 smart00803 TAF TATA box bindin 98.6 9.1E-08 2E-12 63.5 4.5 64 62-130 2-65 (65)
15 PLN00035 histone H4; Provision 98.6 1.5E-07 3.4E-12 67.9 5.9 67 63-134 30-96 (103)
16 PTZ00015 histone H4; Provision 98.5 2.1E-07 4.6E-12 67.1 5.7 69 61-134 29-97 (102)
17 KOG1744|consensus 98.5 1.7E-07 3.7E-12 69.8 5.2 70 63-132 34-103 (127)
18 PF00808 CBFD_NFYB_HMF: Histon 98.4 7.1E-07 1.5E-11 58.3 5.6 58 72-129 8-65 (65)
19 cd07979 TAF9 TATA Binding Prot 98.4 1.2E-06 2.6E-11 64.2 6.6 66 68-134 3-68 (117)
20 smart00417 H4 Histone H4. 98.3 9.7E-07 2.1E-11 60.3 4.0 62 61-127 12-73 (74)
21 PF15630 CENP-S: Kinetochore c 98.1 6.3E-06 1.4E-10 56.5 4.7 65 66-130 5-71 (76)
22 PF03847 TFIID_20kDa: Transcri 98.0 2.5E-05 5.4E-10 52.4 5.6 58 73-130 6-63 (68)
23 KOG0870|consensus 97.9 2.5E-05 5.5E-10 60.6 5.1 69 60-130 8-76 (172)
24 PF02969 TAF: TATA box binding 97.7 0.00011 2.4E-09 49.1 5.7 59 71-130 8-66 (66)
25 smart00576 BTP Bromodomain tra 97.6 0.00015 3.2E-09 49.1 5.1 52 83-134 22-73 (77)
26 cd08050 TAF6 TATA Binding Prot 97.5 0.00025 5.5E-09 60.1 6.5 63 71-134 4-66 (343)
27 PF02291 TFIID-31kDa: Transcri 97.5 0.00033 7.2E-09 52.4 6.3 65 69-134 15-79 (129)
28 cd00074 H2A Histone 2A; H2A is 97.3 0.00032 6.9E-09 51.5 3.7 67 60-130 18-84 (115)
29 KOG1142|consensus 97.2 0.00034 7.4E-09 57.7 4.0 72 54-129 146-217 (258)
30 PF15511 CENP-T: Centromere ki 97.1 0.00061 1.3E-08 59.3 4.5 55 70-124 355-414 (414)
31 KOG3334|consensus 96.2 0.021 4.6E-07 43.6 6.5 66 69-135 16-81 (148)
32 PF07524 Bromo_TP: Bromodomain 94.9 0.077 1.7E-06 35.4 5.1 53 82-134 20-73 (77)
33 KOG0869|consensus 92.4 0.28 6E-06 38.2 4.7 70 61-133 31-100 (168)
34 PF02269 TFIID-18kDa: Transcri 91.4 0.17 3.7E-06 35.5 2.4 59 72-130 7-65 (93)
35 KOG0871|consensus 90.5 0.62 1.3E-05 35.9 4.9 72 59-133 9-80 (156)
36 COG5262 HTA1 Histone H2A [Chro 89.2 0.59 1.3E-05 34.8 3.7 58 73-130 33-90 (132)
37 KOG3467|consensus 89.0 0.84 1.8E-05 32.5 4.2 51 83-133 45-95 (103)
38 PLN00154 histone H2A; Provisio 87.1 1.1 2.3E-05 34.0 4.1 68 60-130 36-103 (136)
39 cd08045 TAF4 TATA Binding Prot 86.8 1.6 3.5E-05 34.5 5.2 56 61-117 43-98 (212)
40 KOG2549|consensus 86.8 1.5 3.4E-05 40.0 5.6 61 72-133 17-77 (576)
41 smart00414 H2A Histone 2A. 86.1 0.77 1.7E-05 33.2 2.8 67 60-130 7-73 (106)
42 PTZ00017 histone H2A; Provisio 84.8 0.83 1.8E-05 34.5 2.5 67 60-130 25-91 (134)
43 PF05236 TAF4: Transcription i 84.6 0.97 2.1E-05 36.8 3.0 58 60-118 41-98 (264)
44 cd07978 TAF13 The TATA Binding 83.7 5.9 0.00013 27.8 6.4 62 68-130 4-65 (92)
45 COG5094 TAF9 Transcription ini 81.7 2.2 4.9E-05 32.2 3.7 47 85-131 32-81 (145)
46 PLN00153 histone H2A; Provisio 77.1 2.6 5.7E-05 31.6 2.8 67 60-130 22-88 (129)
47 COG5248 TAF19 Transcription in 76.3 12 0.00026 27.7 6.0 61 68-130 11-71 (126)
48 PLN00156 histone H2AX; Provisi 75.7 2.6 5.6E-05 32.1 2.5 67 60-130 27-93 (139)
49 KOG4336|consensus 75.6 8.9 0.00019 32.8 5.9 51 85-135 23-73 (323)
50 COG5150 Class 2 transcription 75.3 6.3 0.00014 29.8 4.5 68 59-129 8-75 (148)
51 PLN00157 histone H2A; Provisio 71.9 4.9 0.00011 30.3 3.2 67 60-130 24-90 (132)
52 PTZ00252 histone H2A; Provisio 71.7 4.9 0.00011 30.4 3.2 67 60-130 23-91 (134)
53 KOG1658|consensus 71.4 3.6 7.8E-05 32.0 2.4 63 64-128 58-121 (162)
54 KOG3901|consensus 70.4 22 0.00047 26.0 6.1 64 64-130 7-70 (109)
55 KOG2389|consensus 68.3 14 0.00031 32.0 5.6 50 84-133 46-95 (353)
56 COG5208 HAP5 CCAAT-binding fac 64.7 15 0.00033 30.3 4.9 84 45-130 80-173 (286)
57 KOG1756|consensus 63.9 13 0.00028 28.0 4.0 66 61-130 26-91 (131)
58 KOG1657|consensus 63.4 11 0.00024 30.9 3.9 72 57-129 66-137 (236)
59 PF09123 DUF1931: Domain of un 61.4 18 0.00038 27.6 4.4 60 68-132 1-60 (138)
60 COG5095 TAF6 Transcription ini 53.7 23 0.00049 31.0 4.3 61 72-133 11-71 (450)
61 PF10911 DUF2717: Protein of u 50.4 22 0.00048 24.5 3.0 60 49-111 2-64 (77)
62 TIGR01924 rsbW_low_gc serine-p 47.6 22 0.00048 26.5 3.0 46 65-110 15-60 (159)
63 COG1224 TIP49 DNA helicase TIP 46.5 39 0.00085 30.1 4.7 72 61-132 354-432 (450)
64 PRK07452 DNA polymerase III su 43.9 52 0.0011 26.8 5.0 59 69-129 136-196 (326)
65 PF09415 CENP-X: CENP-S associ 38.9 37 0.00081 22.7 2.8 56 71-126 4-62 (72)
66 PF13581 HATPase_c_2: Histidin 38.8 66 0.0014 22.1 4.2 44 69-112 8-51 (125)
67 COG5624 TAF61 Transcription in 38.1 12 0.00027 33.4 0.4 58 72-129 389-447 (505)
68 TIGR02902 spore_lonB ATP-depen 34.9 92 0.002 28.0 5.4 59 72-130 268-330 (531)
69 PF07278 DUF1441: Protein of u 33.1 1.6E+02 0.0035 22.6 5.8 64 48-111 75-149 (152)
70 TIGR00764 lon_rel lon-related 31.8 1.8E+02 0.0038 26.8 6.8 49 83-131 329-390 (608)
71 COG2178 Predicted RNA-binding 30.0 81 0.0018 25.5 3.8 56 47-102 24-91 (204)
72 PF04604 L_biotic_typeA: Type- 29.7 46 0.00099 21.2 1.9 20 88-107 7-26 (51)
73 PF13654 AAA_32: AAA domain; P 29.4 2.2E+02 0.0047 25.7 6.8 66 66-132 430-506 (509)
74 KOG2680|consensus 26.7 1.9E+02 0.0041 25.5 5.7 72 61-132 351-429 (454)
75 PRK14562 haloacid dehalogenase 26.5 83 0.0018 24.8 3.3 27 80-106 70-96 (204)
76 PF07105 DUF1367: Protein of u 26.5 96 0.0021 24.9 3.6 16 91-106 91-106 (196)
77 PRK08487 DNA polymerase III su 25.9 1.6E+02 0.0034 24.4 5.0 58 70-129 139-197 (328)
78 KOG1089|consensus 25.3 76 0.0016 29.4 3.2 35 67-112 417-451 (573)
79 TIGR03015 pepcterm_ATPase puta 25.1 1.8E+02 0.0039 22.5 5.0 49 82-130 213-264 (269)
80 PRK05907 hypothetical protein; 24.9 1.4E+02 0.0031 25.0 4.6 67 63-129 131-200 (311)
81 PRK04069 serine-protein kinase 24.1 1.6E+02 0.0035 21.7 4.3 46 65-110 15-60 (161)
82 KOG1969|consensus 24.0 1.3E+02 0.0029 29.1 4.6 80 45-126 449-531 (877)
83 PF03172 Sp100: Sp100 domain; 23.1 1.6E+02 0.0034 21.4 3.9 48 53-113 40-87 (103)
84 KOG1757|consensus 23.0 1.6E+02 0.0034 22.0 3.9 66 67-134 32-97 (131)
85 PHA02604 rI.-1 hypothetical pr 23.0 1.3E+02 0.0029 22.5 3.6 44 67-113 82-125 (126)
86 PF10788 DUF2603: Protein of u 22.8 70 0.0015 24.3 2.1 33 46-79 97-129 (137)
87 PF07962 Swi3: Replication For 22.4 71 0.0015 21.7 2.0 30 48-77 35-64 (83)
88 COG5304 Uncharacterized protei 22.3 67 0.0015 22.8 1.8 18 63-80 72-89 (92)
89 cd00913 PCD_DCoH_subfamily_a P 21.8 44 0.00096 22.0 0.8 13 120-132 62-74 (76)
90 PF10083 DUF2321: Uncharacteri 21.8 95 0.0021 24.1 2.7 22 77-98 72-93 (158)
No 1
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=7.3e-59 Score=347.61 Aligned_cols=135 Identities=96% Similarity=1.342 Sum_probs=129.6
Q ss_pred CCCccccccccCCCCCCccchhhhhcccCCCCCCCCCCCCcCCCCchhhHHHHhhhhhhhhhhhccchhHHHHHHHhhhc
Q psy17763 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 MartK~ta~ks~g~kaprk~~~~k~~~~~~p~~~~~k~~~r~~pg~~alrEIr~~Qkst~lli~k~pF~rlVreI~~~~~ 80 (136)
|||||+++++++|+++|+++.++++..++.+..++.++++||+||++||+|||+||+||+|||||+||+||||||+++|.
T Consensus 1 MaRtk~~~~k~~~~~~prk~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PTZ00018 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCCchhHHHHHHHHcccchhccccccHHHHHHHHHHHcC
Confidence 99999999999999999999988877777777778889999999999999999999999999999999999999999999
Q ss_pred cCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhccc
Q psy17763 81 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 81 ~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~~ 135 (136)
+++|||++||+|||||+|+|||+||||+|+||+||||||||++||+|++||||++
T Consensus 81 ~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~ 135 (136)
T PTZ00018 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
T ss_pred CcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhcccC
Confidence 9999999999999999999999999999999999999999999999999999986
No 2
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=9.9e-59 Score=346.90 Aligned_cols=136 Identities=98% Similarity=1.342 Sum_probs=130.4
Q ss_pred CCCccccccccCCCCCCccchhhhhcccCCCCCCCCCCCCcCCCCchhhHHHHhhhhhhhhhhhccchhHHHHHHHhhhc
Q psy17763 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 MartK~ta~ks~g~kaprk~~~~k~~~~~~p~~~~~k~~~r~~pg~~alrEIr~~Qkst~lli~k~pF~rlVreI~~~~~ 80 (136)
|||||+++++++++++|+++.++++..++.+..++.++++||+||+++|+|||+||+||+|||||+||+||||||++++.
T Consensus 1 MaRtk~~~~k~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PLN00121 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCchhHHHHHHHHhccccccccccccHHHHHHHHHHHhC
Confidence 99999999999999999999988877777777788899999999999999999999999999999999999999999999
Q ss_pred cCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcccC
Q psy17763 81 TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
Q Consensus 81 ~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~~~ 136 (136)
+++|||++||+|||||+|+|||+||||+|+||+|+||||||++||+|++||||+++
T Consensus 81 ~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~~ 136 (136)
T PLN00121 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
T ss_pred ccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHhccccC
Confidence 99999999999999999999999999999999999999999999999999999864
No 3
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=2.5e-57 Score=338.35 Aligned_cols=128 Identities=65% Similarity=0.959 Sum_probs=118.8
Q ss_pred CCCccccccccCCCCCCccchhhhhcccCCCCCCCCCCCCcCCCCchhhHHHHhhhhhhhhhhhccchhHHHHHHHhhhc
Q psy17763 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 MartK~ta~ks~g~kaprk~~~~k~~~~~~p~~~~~k~~~r~~pg~~alrEIr~~Qkst~lli~k~pF~rlVreI~~~~~ 80 (136)
||||||+ +++++|+.|++.+..+ ...++.++++||+||++||+|||+||+||++||||+||+||||||++++.
T Consensus 1 mar~k~~-~~~~~~~~~~~~~~~~------~~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RLVREI~~~~~ 73 (135)
T PLN00161 1 MARRLQG-KRFRKGKKPQKEASGV------TRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEML 73 (135)
T ss_pred CCccccc-ccccCCCCCcccCCCC------CCCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHHHHHHHHhcC
Confidence 9999999 7788999898876553 13456689999999999999999999999999999999999999999996
Q ss_pred -cCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhccc
Q psy17763 81 -TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 81 -~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~~ 135 (136)
+++|||++||+|||||+|+|||+||||+|+||+|+||||||++||+||++|||+.
T Consensus 74 ~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~ 129 (135)
T PLN00161 74 REPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPI 129 (135)
T ss_pred CCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhcccc
Confidence 5899999999999999999999999999999999999999999999999999974
No 4
>KOG1745|consensus
Probab=100.00 E-value=8.8e-55 Score=324.95 Aligned_cols=136 Identities=94% Similarity=1.296 Sum_probs=128.6
Q ss_pred CCCccccccccCCCCCCccchhhhhcccC-CCCCCCCCCCCcCCCCchhhHHHHhhhhhhhhhhhccchhHHHHHHHhhh
Q psy17763 1 MARTKQTARKSTGGKAPRKQLATKAARKS-APATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 79 (136)
Q Consensus 1 MartK~ta~ks~g~kaprk~~~~k~~~~~-~p~~~~~k~~~r~~pg~~alrEIr~~Qkst~lli~k~pF~rlVreI~~~~ 79 (136)
|+|++++++++.++++|++..+.+..+++ .|..+...++++|+||+++++|||+||+||||||+|+||+||||||.++|
T Consensus 1 m~r~~~t~~k~~~~~~~r~~~a~~~~~~~~~~~~~~~~k~~r~rpg~~al~eirkyQkstdLlI~K~PFqRlvrei~q~f 80 (137)
T KOG1745|consen 1 MARTKQTARKSTGGKAPRKQLAGKAARKSAAPRTGRVKKPHRYRPGTVALREIRKYQKSTDLLIRKLPFQRLVREIAQDF 80 (137)
T ss_pred CCCCCcccccccCCCCCccccccccccccccccccccCccccccCchHHHHHHHHHHhhhHHHhhcCcHHHHhHHHHhcc
Confidence 89999999999999999999988877765 34456668899999999999999999999999999999999999999999
Q ss_pred ccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcccC
Q psy17763 80 KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
Q Consensus 80 ~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~~~ 136 (136)
.+|+|||+.||.|||||+|+|||+||||+|+||+|||||||||+|||||++|+|++.
T Consensus 81 ~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg~~~ 137 (137)
T KOG1745|consen 81 KTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 137 (137)
T ss_pred cccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcccCCC
Confidence 999999999999999999999999999999999999999999999999999999863
No 5
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=7.3e-50 Score=284.39 Aligned_cols=94 Identities=70% Similarity=1.080 Sum_probs=91.2
Q ss_pred CCCCchhhHHHHhhhhhhhhhhhccchhHHHHHHHhhhc-cCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCcccc
Q psy17763 42 YRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI 120 (136)
Q Consensus 42 ~~pg~~alrEIr~~Qkst~lli~k~pF~rlVreI~~~~~-~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi 120 (136)
++||++||+|||+||+||++||||+||+||||||++++. +++|||++||+|||||+|+|||+||||+|+||+|||||||
T Consensus 1 ~rpGt~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl 80 (97)
T PLN00160 1 MRPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTI 80 (97)
T ss_pred CCCccHHHHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhccccc
Confidence 689999999999999999999999999999999999986 5699999999999999999999999999999999999999
Q ss_pred CcccHHHHHHHhccc
Q psy17763 121 MPKDIQLARRIRGER 135 (136)
Q Consensus 121 ~~kDi~La~rirg~~ 135 (136)
|+|||+||++|||+.
T Consensus 81 ~~kD~~L~~rirg~~ 95 (97)
T PLN00160 81 MPKDMQLARRIRGQT 95 (97)
T ss_pred chhhHHHHHHhhccc
Confidence 999999999999974
No 6
>smart00428 H3 Histone H3.
Probab=100.00 E-value=1.2e-49 Score=286.96 Aligned_cols=101 Identities=87% Similarity=1.230 Sum_probs=97.9
Q ss_pred CCCCCCcCCCCchhhHHHHhhhhhhhhhhhccchhHHHHHHHhhhcc--CccccHHHHHHHHHHHHHHHHHhhhhhhHhh
Q psy17763 35 GVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVMALQEASEAYLVGLFEDTNLCA 112 (136)
Q Consensus 35 ~~k~~~r~~pg~~alrEIr~~Qkst~lli~k~pF~rlVreI~~~~~~--~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a 112 (136)
++++++||+||++||+|||+||+||++||||+||+||||||++++.+ ++|||++||+||||++|+|||++|||||+||
T Consensus 2 ~~~~~~r~rpg~~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a 81 (105)
T smart00428 2 GKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLA 81 (105)
T ss_pred CCCCCcCCCCcchHHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999999999999999999999999999987 9999999999999999999999999999999
Q ss_pred hhcCccccCcccHHHHHHHhccc
Q psy17763 113 IHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 113 ~HakRvTi~~kDi~La~rirg~~ 135 (136)
+||||||||++||+||.+|||++
T Consensus 82 ~HAkRvTl~~kDi~La~rir~~~ 104 (105)
T smart00428 82 IHAKRVTIMPKDIQLARRIRGER 104 (105)
T ss_pred HHhCCccCcHhhHHHHHHHhccC
Confidence 99999999999999999999975
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.93 E-value=6.3e-26 Score=159.97 Aligned_cols=87 Identities=49% Similarity=0.708 Sum_probs=83.6
Q ss_pred CCchhhHHHHhhhhhhhhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcc
Q psy17763 44 PGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 123 (136)
Q Consensus 44 pg~~alrEIr~~Qkst~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~k 123 (136)
||...++|||+||++++++||++||.|++|+...+ ||+.+|+++||++.|.|++.++|+|+.||.|+||+||+++
T Consensus 1 ~~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~~-----Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~ 75 (91)
T COG2036 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGAE-----RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAE 75 (91)
T ss_pred CCcchHHHHHhhhhhhhhhcCchHHHHHHHHHhHH-----HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHH
Confidence 68899999999999999999999999999999875 9999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhccc
Q psy17763 124 DIQLARRIRGER 135 (136)
Q Consensus 124 Di~La~rirg~~ 135 (136)
||+|+.+++|..
T Consensus 76 DI~la~~~~~~~ 87 (91)
T COG2036 76 DIKLALKRLGRR 87 (91)
T ss_pred HHHHHHHHhccc
Confidence 999999999853
No 8
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=99.85 E-value=8.1e-22 Score=131.92 Aligned_cols=75 Identities=48% Similarity=0.659 Sum_probs=71.6
Q ss_pred hhhhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHh
Q psy17763 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 58 st~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rir 132 (136)
++.++||+.||.|+++||..++..+++|+.+|+.+||+++|+|++.+||+|+.||.|+||+||+++||++|.+|+
T Consensus 1 ~~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 1 RTRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred CcccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 466899999999999999999887799999999999999999999999999999999999999999999999985
No 9
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=99.31 E-value=6e-12 Score=84.85 Aligned_cols=58 Identities=22% Similarity=0.290 Sum_probs=52.4
Q ss_pred HHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 73 REIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
.|++.++.+..+++.+|.++||+.+|+|+..++++|..||.|++|.||.++||+|+..
T Consensus 8 ~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~ 65 (72)
T cd07981 8 QELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLE 65 (72)
T ss_pred HHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3445555667999999999999999999999999999999999999999999999964
No 10
>PTZ00463 histone H2B; Provisional
Probab=98.94 E-value=4.7e-09 Score=77.08 Aligned_cols=69 Identities=12% Similarity=0.134 Sum_probs=66.4
Q ss_pred hccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHh
Q psy17763 64 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rir 132 (136)
++.+|..||+.|+.++++|+.++..||..|.....|++.++-.+|..++.+.+|-||+++|||.+.||.
T Consensus 26 r~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 26 RYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred ccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 456799999999999999999999999999999999999999999999999999999999999999985
No 11
>PLN00158 histone H2B; Provisional
Probab=98.88 E-value=5.7e-09 Score=76.60 Aligned_cols=69 Identities=14% Similarity=0.204 Sum_probs=66.7
Q ss_pred hccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHh
Q psy17763 64 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rir 132 (136)
++..|..||+.|+.++++|+.++..||..|.....|++.++-.+|..++.+.+|-||+++|||.+.||.
T Consensus 25 r~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 25 KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 568899999999999999999999999999999999999999999999999999999999999999985
No 12
>smart00427 H2B Histone H2B.
Probab=98.84 E-value=1.1e-08 Score=72.12 Aligned_cols=66 Identities=15% Similarity=0.211 Sum_probs=64.2
Q ss_pred chhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHh
Q psy17763 67 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rir 132 (136)
.|..+|+.|+.++++|..++..||..|...+.|++.++-.+|..++.+.||-||+++|||.|.||.
T Consensus 2 sy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 2 TYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred cHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 688999999999999999999999999999999999999999999999999999999999999985
No 13
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=98.66 E-value=5.8e-08 Score=67.84 Aligned_cols=69 Identities=25% Similarity=0.280 Sum_probs=63.3
Q ss_pred hhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q psy17763 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~ 134 (136)
.-||+.|..||+|.- +--|++.++.+.+.++.|.||..+..||..++-|++|.||+..||.++.+-.|.
T Consensus 12 ~gi~k~~I~RLarr~-----GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~ 80 (85)
T cd00076 12 KGITKPAIRRLARRG-----GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred ccCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 349999999998752 467999999999999999999999999999999999999999999999998885
No 14
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.57 E-value=9.1e-08 Score=63.55 Aligned_cols=64 Identities=20% Similarity=0.207 Sum_probs=54.7
Q ss_pred hhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 62 li~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
.+|+.|..|+.+. . +--+.+.+|...|.+..|.++-.+.++|..++.|+||.||+..||.+|.+
T Consensus 2 ~~p~~~i~ria~~----~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAES----L-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHH----C-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 3566676666543 3 33489999999999999999999999999999999999999999998864
No 15
>PLN00035 histone H4; Provisional
Probab=98.57 E-value=1.5e-07 Score=67.88 Aligned_cols=67 Identities=22% Similarity=0.261 Sum_probs=62.0
Q ss_pred hhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q psy17763 63 IRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~ 134 (136)
||+.|..||+|.- .--|++.+|.+.|.++.|.||..+..||...+-|++|.||+..||.+|.+-.|.
T Consensus 30 ipk~~IrRLARr~-----GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~ 96 (103)
T PLN00035 30 ITKPAIRRLARRG-----GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred CCHHHHHHHHHHc-----CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC
Confidence 8999999998753 457999999999999999999999999999999999999999999999988775
No 16
>PTZ00015 histone H4; Provisional
Probab=98.53 E-value=2.1e-07 Score=67.08 Aligned_cols=69 Identities=22% Similarity=0.229 Sum_probs=62.7
Q ss_pred hhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q psy17763 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~ 134 (136)
.-|++.|..||++.- .--|++.+|.+.+.++.|.||..+..||..+|-|++|.||+..||.+|.+-.|.
T Consensus 29 ~gI~k~~IrRLarr~-----GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~ 97 (102)
T PTZ00015 29 RGITKGAIRRLARRG-----GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred cCCCHHHHHHHHHHc-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 348999999998752 567999999999999999999999999999999999999999999999988775
No 17
>KOG1744|consensus
Probab=98.52 E-value=1.7e-07 Score=69.80 Aligned_cols=70 Identities=23% Similarity=0.264 Sum_probs=66.9
Q ss_pred hhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHh
Q psy17763 63 IRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rir 132 (136)
..+..|..+|+.++.++++|+.++..|+.+|.....+++.++..+|+++|.+.||-||..+|||+|.+|.
T Consensus 34 ~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 34 RRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred cccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 4677899999999999999999999999999999999999999999999999999999999999999985
No 18
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=98.42 E-value=7.1e-07 Score=58.30 Aligned_cols=58 Identities=29% Similarity=0.314 Sum_probs=49.2
Q ss_pred HHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHH
Q psy17763 72 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~ 129 (136)
|+.|+....+..+++.+|..+|+.++|.|+..|-.+|+..+.+.+|-||++.||..|.
T Consensus 8 vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 8 VKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 3555555556678999999999999999999999999999999999999999998763
No 19
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=98.38 E-value=1.2e-06 Score=64.22 Aligned_cols=66 Identities=20% Similarity=0.318 Sum_probs=60.2
Q ss_pred hhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q psy17763 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~ 134 (136)
..++|..|+.+. +..+++..+...|-|.++.|...+..||...|-|++|.||...||+||...+++
T Consensus 3 d~~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 3 DARVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 357888888866 346999999999999999999999999999999999999999999999998875
No 20
>smart00417 H4 Histone H4.
Probab=98.28 E-value=9.7e-07 Score=60.27 Aligned_cols=62 Identities=21% Similarity=0.229 Sum_probs=56.1
Q ss_pred hhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHH
Q psy17763 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 127 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~L 127 (136)
.-||+.|..||+|. .+--|++.++.+.|.++.|.||..+..||..++-|++|.||+..|+..
T Consensus 12 ~gI~k~~IrRLaRr-----~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARR-----GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHH-----cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 44999999999874 356799999999999999999999999999999999999999999853
No 21
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.08 E-value=6.3e-06 Score=56.47 Aligned_cols=65 Identities=26% Similarity=0.251 Sum_probs=53.4
Q ss_pred cchhHHHHHHHhhh--ccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 66 LPFQRLVREIAQDF--KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 66 ~pF~rlVreI~~~~--~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
..+.--|-+|+++. ..+..++++.+.+|=|.+=.++..+-.|--..|.||||.||++.|+.|..|
T Consensus 5 aal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 5 AALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 33445566777766 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=97.95 E-value=2.5e-05 Score=52.41 Aligned_cols=58 Identities=19% Similarity=0.245 Sum_probs=46.1
Q ss_pred HHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 73 REIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
.|++.++.+...+.+++.++|.+.|++|+....+.|..+|.|.+--||.++|+++...
T Consensus 6 ~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 6 QELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 4455556789999999999999999999999999999999999999999999999864
No 23
>KOG0870|consensus
Probab=97.87 E-value=2.5e-05 Score=60.63 Aligned_cols=69 Identities=25% Similarity=0.305 Sum_probs=64.3
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
++.+|++-..|||+|++.+. +.-++.+|+.||+.+|--|+.-|---|+..|.-.+|.||++.|+-=++.
T Consensus 8 dl~lP~AiI~rlvke~l~E~--~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~ 76 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPES--NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD 76 (172)
T ss_pred HhhccHHHHHHHHHHhCccc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence 58899999999999999877 7899999999999999999999999999999999999999999876654
No 24
>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=97.72 E-value=0.00011 Score=49.07 Aligned_cols=59 Identities=27% Similarity=0.323 Sum_probs=47.2
Q ss_pred HHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 71 LVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 71 lVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
-|+-|++.++- -..+.++..+|-+-+|.-|-.+.++|..++.|+||-+|+..||..|.|
T Consensus 8 svk~iAes~Gi-~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 8 SVKDIAESLGI-SNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHHcCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 46667776642 247899999999999999999999999999999999999999999875
No 25
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.60 E-value=0.00015 Score=49.11 Aligned_cols=52 Identities=27% Similarity=0.190 Sum_probs=48.7
Q ss_pred ccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q psy17763 83 LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 83 ~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~ 134 (136)
-+.+++|++.|-+..|.|+..|-+.+...+-|++|.+..+.|+.++..-.|.
T Consensus 22 ~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi 73 (77)
T smart00576 22 DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGI 73 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Confidence 3889999999999999999999999999999999999999999999876664
No 26
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=97.51 E-value=0.00025 Score=60.05 Aligned_cols=63 Identities=21% Similarity=0.244 Sum_probs=56.6
Q ss_pred HHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q psy17763 71 LVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 71 lVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~ 134 (136)
.|+.|++..+ --+.+.+|..+|-+-+|.++-.+.++|..++.|+||.||+..||++|.+.++.
T Consensus 4 ~i~~ia~~~G-i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~ 66 (343)
T cd08050 4 SIKLIAESLG-IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNV 66 (343)
T ss_pred HHHHHHHHcC-CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCC
Confidence 4677777653 34899999999999999999999999999999999999999999999999865
No 27
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=97.50 E-value=0.00033 Score=52.37 Aligned_cols=65 Identities=28% Similarity=0.353 Sum_probs=53.2
Q ss_pred hHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q psy17763 69 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 69 ~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~ 134 (136)
.++|..|+.+.+ -..|+...+.-|-|.+=.|...+++||...+-||+|.+|...|++||...+.+
T Consensus 15 a~~i~~iL~~~G-v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~ 79 (129)
T PF02291_consen 15 ARVIHLILKSMG-VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLD 79 (129)
T ss_dssp HHHHHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT--
T ss_pred HHHHHHHHHHcC-CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHh
Confidence 578888988774 23589999999999999999999999999999999999999999999987743
No 28
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=97.26 E-value=0.00032 Score=51.52 Aligned_cols=67 Identities=22% Similarity=0.209 Sum_probs=59.6
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
.|.+|-.++.|+.++= ....|+..+|...|-..-|.+...++|-|...+.|.++.+|+|+||+|+.+
T Consensus 18 gL~fPV~ri~R~Lk~~----~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 18 GLQFPVGRIHRYLKKG----RYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred CccCcHHHHHHHHHcC----ccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 4889999999998651 123799999999999999999999999999999999999999999999875
No 29
>KOG1142|consensus
Probab=97.24 E-value=0.00034 Score=57.66 Aligned_cols=72 Identities=19% Similarity=0.273 Sum_probs=63.7
Q ss_pred hhhhhhhhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHH
Q psy17763 54 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 54 ~~Qkst~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~ 129 (136)
.++-+++.++-|--...||++| ..+..+..++-+.|.|.|++|+..+-.-+..+|.|.|--||.++||+|.+
T Consensus 146 ~~~~~~~~il~k~kl~dLvqqI----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhL 217 (258)
T KOG1142|consen 146 QDEPGNNPILSKRKLDDLVQQI----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHL 217 (258)
T ss_pred cccCCCCccccccchhHHHHhh----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeee
Confidence 5667777888777777777777 56778899999999999999999999999999999999999999999975
No 30
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.11 E-value=0.00061 Score=59.28 Aligned_cols=55 Identities=33% Similarity=0.450 Sum_probs=42.7
Q ss_pred HHHHHHHhhh-----ccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCccc
Q psy17763 70 RLVREIAQDF-----KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKD 124 (136)
Q Consensus 70 rlVreI~~~~-----~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kD 124 (136)
-+||.+++.| ....++..+||.+|..|+|-|+.+|-+|---.|.||+|.||...|
T Consensus 355 ~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 355 GVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp HHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred cHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3566666655 257899999999999999999999999999999999999998776
No 31
>KOG3334|consensus
Probab=96.16 E-value=0.021 Score=43.64 Aligned_cols=66 Identities=23% Similarity=0.400 Sum_probs=56.5
Q ss_pred hHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhccc
Q psy17763 69 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 69 ~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~~ 135 (136)
.+++--|+.+++ ---|.+..+.-|=|.+=.|.+.+++||...+-||++-||...|++||...+++.
T Consensus 16 a~~i~~iL~s~G-I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~ 81 (148)
T KOG3334|consen 16 ARVIASILKSLG-IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDH 81 (148)
T ss_pred HHHHHHHHHHcC-ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhcc
Confidence 356667776664 235678899999999999999999999999999999999999999999988753
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=94.93 E-value=0.077 Score=35.44 Aligned_cols=53 Identities=25% Similarity=0.194 Sum_probs=48.5
Q ss_pred Cc-cccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q psy17763 82 DL-RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 82 ~~-r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~ 134 (136)
.| ..+++||+.|-+.+..||..|...+...+-|++|-...+.|+.++..=.|.
T Consensus 20 GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi 73 (77)
T PF07524_consen 20 GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI 73 (77)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 44 688999999999999999999999999999999999999999998876654
No 33
>KOG0869|consensus
Probab=92.36 E-value=0.28 Score=38.18 Aligned_cols=70 Identities=16% Similarity=0.186 Sum_probs=56.1
Q ss_pred hhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q psy17763 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg 133 (136)
.++|-+--.|+.+.++ ..+-.+..+|=+.+||.+-.|+-=+-..|+.-..--||.||+..||-.|+--.|
T Consensus 31 r~LPIANV~RIMK~~l---P~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 31 RFLPIANVSRIMKKAL---PANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhccHHHHHHHHHhcC---CcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 3455555555555443 477899999999999999999988888888888889999999999999876555
No 34
>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=91.35 E-value=0.17 Score=35.53 Aligned_cols=59 Identities=15% Similarity=0.200 Sum_probs=30.8
Q ss_pred HHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 72 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
|+.++--|++.-.-..+....|.+..-.|++.+...|..+|.+.++-+|...|+-.+.|
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 45555556666677899999999999999999999999999999999999999987765
No 35
>KOG0871|consensus
Probab=90.53 E-value=0.62 Score=35.90 Aligned_cols=72 Identities=18% Similarity=0.258 Sum_probs=63.8
Q ss_pred hhhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q psy17763 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 59 t~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg 133 (136)
.++-+||+.....|+|++. .|+||..+|=+.|++++=.|+--+=..||..+---.+-||.+.-+.=|+.-.|
T Consensus 9 de~sLPkAtv~KmIke~lP---~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~Lg 80 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLP---KDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLG 80 (156)
T ss_pred ccccCcHHHHHHHHHHhCC---cccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcc
Confidence 4577999999999999864 69999999999999999999999999999999999999999998877765544
No 36
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=89.16 E-value=0.59 Score=34.85 Aligned_cols=58 Identities=22% Similarity=0.282 Sum_probs=49.5
Q ss_pred HHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 73 REIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
+.++..-...+|+.+.|...|--..|.....++|-|.-.|.-.|-..|||+-+|||-|
T Consensus 33 kr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 33 KRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred HHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 4444433467899999999999889988899999999999999999999999999843
No 37
>KOG3467|consensus
Probab=88.98 E-value=0.84 Score=32.46 Aligned_cols=51 Identities=22% Similarity=0.265 Sum_probs=42.6
Q ss_pred ccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q psy17763 83 LRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 83 ~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg 133 (136)
-|+..-..+-...++..||.....+|..-+-||||.||+.-|+--+..=.|
T Consensus 45 kRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G 95 (103)
T KOG3467|consen 45 KRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 95 (103)
T ss_pred chhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcC
Confidence 355556666777889999999999999999999999999999987766544
No 38
>PLN00154 histone H2A; Provisional
Probab=87.10 E-value=1.1 Score=34.03 Aligned_cols=68 Identities=19% Similarity=0.157 Sum_probs=56.7
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
.|.+|---..|+.+|-.. ...|+.+.|..-|--.-|.....++|-|.-.+...++..|+|++|+||.+
T Consensus 36 gL~FPVgRi~r~Lk~g~~---~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVS---AHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhh---hccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 467777777788776431 24588999998888888999999999999999999999999999999864
No 39
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=86.79 E-value=1.6 Score=34.47 Aligned_cols=56 Identities=18% Similarity=0.211 Sum_probs=50.1
Q ss_pred hhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCc
Q psy17763 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKR 117 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakR 117 (136)
.++...|+...+..|+.+.+-. .+..+.+..|..|+|.+|-.|.++...++-|...
T Consensus 43 ~fl~~~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~ 98 (212)
T cd08045 43 SFLNPSPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEERLRNLLEKLIEVSEHRVD 98 (212)
T ss_pred hccCHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 6788899999999999877543 8899999999999999999999999999999743
No 40
>KOG2549|consensus
Probab=86.76 E-value=1.5 Score=39.99 Aligned_cols=61 Identities=21% Similarity=0.311 Sum_probs=51.3
Q ss_pred HHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q psy17763 72 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg 133 (136)
++-+++.. +--.++.+|..+|-+-+|.-+-.+.+||..++.|+||-+++..||.-|.|.+.
T Consensus 17 ~k~vAEsl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 17 VKVVAESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred HHHHHHHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 44444433 23457899999999999999999999999999999999999999999988764
No 41
>smart00414 H2A Histone 2A.
Probab=86.09 E-value=0.77 Score=33.19 Aligned_cols=67 Identities=25% Similarity=0.226 Sum_probs=54.1
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
+|.+|-.-|.|+.++- .-..|+...|..-|=-.-|.....++|-|...+...++..|+|+|++++.+
T Consensus 7 gL~fPVgRi~r~Lk~~----~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 7 GLQFPVGRIHRLLRKG----TYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred CccCchHHHHHHHHcC----ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 3666777777776543 223589999998888888999999999998888899999999999999864
No 42
>PTZ00017 histone H2A; Provisional
Probab=84.81 E-value=0.83 Score=34.50 Aligned_cols=67 Identities=24% Similarity=0.197 Sum_probs=56.0
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
.|.+|-.-+.|+.++-. ...|+...|..-|=-.-|.....++|-|.-.+...+...|+|++|+|+.+
T Consensus 25 gL~FPVgRi~R~Lk~g~----~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGR----YAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhccc----hhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 47788888888876531 23488888988888888999999999999999999999999999999865
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=84.62 E-value=0.97 Score=36.82 Aligned_cols=58 Identities=21% Similarity=0.265 Sum_probs=38.9
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCcc
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV 118 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRv 118 (136)
.+++...|++..+.+|+..+. ...+..+.+..|-.|+|.+|-.|+|++..++.|....
T Consensus 41 ~~fL~~~~L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 41 EPFLNPSPLQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp ---S-HHHHHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred ccccCHHHHHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 367788889999999997665 5678999999999999999999999999999997654
No 44
>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=83.72 E-value=5.9 Score=27.77 Aligned_cols=62 Identities=18% Similarity=0.252 Sum_probs=48.2
Q ss_pred hhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
|..=++.++--+++.-.-..+...+|.+.+=.|++.+.-.|..+|. ..+--+.+.|+..+.|
T Consensus 4 f~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 4 FTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred cHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 4444455555555555678899999999999999999999999998 5666669999987764
No 45
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=81.67 E-value=2.2 Score=32.15 Aligned_cols=47 Identities=26% Similarity=0.375 Sum_probs=38.2
Q ss_pred ccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCc---ccHHHHHHH
Q psy17763 85 FQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMP---KDIQLARRI 131 (136)
Q Consensus 85 ~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~---kDi~La~ri 131 (136)
+......-|-+.|--|..+++|||...+-|++|-.+.. .|+.||.--
T Consensus 32 ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 32 YEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred hCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 34455566778999999999999999999998865555 999998753
No 46
>PLN00153 histone H2A; Provisional
Probab=77.07 E-value=2.6 Score=31.64 Aligned_cols=67 Identities=25% Similarity=0.222 Sum_probs=54.6
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
.|.+|---+.|+.++= ....|+...|..-|--.-|.....++|-|.-.+...+...|+|+.|+|+.+
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 3667777777776541 223588899988888888888889999999999999999999999999864
No 47
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=76.32 E-value=12 Score=27.71 Aligned_cols=61 Identities=18% Similarity=0.199 Sum_probs=49.8
Q ss_pred hhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
|..=|+.++--|+++..-..+.+++|.|.+-+|++.+.-+|-..|- .|=.+...|...+.|
T Consensus 11 F~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 11 FMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred HHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 5566677777778888888999999999999999999998888777 555667788888765
No 48
>PLN00156 histone H2AX; Provisional
Probab=75.71 E-value=2.6 Score=32.07 Aligned_cols=67 Identities=25% Similarity=0.226 Sum_probs=54.3
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
.|.+|---+.|+.++- ....|+...|..-|--.-|.....++|-|.-.+...++..|+|+.|+|+.+
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 3667777777776552 223588899988888888888889999999999999999999999999864
No 49
>KOG4336|consensus
Probab=75.55 E-value=8.9 Score=32.81 Aligned_cols=51 Identities=16% Similarity=0.112 Sum_probs=45.2
Q ss_pred ccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhccc
Q psy17763 85 FQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 85 ~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~~ 135 (136)
++..|++.|=++.-.|+-.+|+.+-..+-|++|.-.+..|+.|.....|..
T Consensus 23 is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~ 73 (323)
T KOG4336|consen 23 ISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK 73 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC
Confidence 556677778888889999999999999999999999999999999887763
No 50
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=75.29 E-value=6.3 Score=29.85 Aligned_cols=68 Identities=22% Similarity=0.198 Sum_probs=57.7
Q ss_pred hhhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHH
Q psy17763 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 59 t~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~ 129 (136)
.++-+||+--+..|.+|+. .|+-|+.+|-+.+++++=.|+--|=-.||..+-.-...||.+.-+--|.
T Consensus 8 De~sLPKATVqKMvS~iLp---~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKAL 75 (148)
T COG5150 8 DENSLPKATVQKMVSSILP---KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKAL 75 (148)
T ss_pred ccccCcHHHHHHHHHHhcc---ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHH
Confidence 3567899999999999876 7899999999999999999999998999988888888888876654443
No 51
>PLN00157 histone H2A; Provisional
Probab=71.94 E-value=4.9 Score=30.29 Aligned_cols=67 Identities=25% Similarity=0.227 Sum_probs=54.5
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
.|.+|---+.|+.++= ....|+...|..-|--.-|.....++|-|.-.+...++..|+|++|+|+.+
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 3667777777776552 123588888888888888888889999999999999999999999999864
No 52
>PTZ00252 histone H2A; Provisional
Probab=71.70 E-value=4.9 Score=30.40 Aligned_cols=67 Identities=21% Similarity=0.202 Sum_probs=52.2
Q ss_pred hhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhh--cCccccCcccHHHHHH
Q psy17763 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~H--akRvTi~~kDi~La~r 130 (136)
.|.+|-.-+.|+.++= ....|+...|..-|--.-|.....++|-|...+.. .|+..|+|++|+|+.+
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 3667777777776542 22458999998888888888888999999888854 6788999999999864
No 53
>KOG1658|consensus
Probab=71.41 E-value=3.6 Score=31.97 Aligned_cols=63 Identities=24% Similarity=0.365 Sum_probs=50.2
Q ss_pred hccchhHHHHHHHhhhccCccccHH-HHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHH
Q psy17763 64 RKLPFQRLVREIAQDFKTDLRFQSS-AVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLA 128 (136)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~-Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La 128 (136)
.++|.+|. ++|.. ..+|++|..+ |+.++-.++|.|+-.|=.+++-|+--.+|+|+.-+|+..+
T Consensus 58 ~rLpL~ri-k~vvk-l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~a 121 (162)
T KOG1658|consen 58 SRLPLARI-KQVVK-LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTA 121 (162)
T ss_pred hhccHHHH-Hhhcc-CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhccccc
Confidence 46666653 44443 3578888765 5677889999999999999999999999999999997654
No 54
>KOG3901|consensus
Probab=70.36 E-value=22 Score=26.02 Aligned_cols=64 Identities=22% Similarity=0.267 Sum_probs=51.5
Q ss_pred hccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 64 RKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 64 ~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
++--|++=++-.+--|+.+.---.+.+++|.+.+=.|++.+.+.|.... +|=.+...|+..+.|
T Consensus 7 rk~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 7 RKHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred HHHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 4445777788888788888888889999999999999999966666555 777788899987754
No 55
>KOG2389|consensus
Probab=68.27 E-value=14 Score=32.04 Aligned_cols=50 Identities=24% Similarity=0.143 Sum_probs=46.4
Q ss_pred cccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q psy17763 84 RFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 84 r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg 133 (136)
.++..||+.|+..+-.|+-+|-+.|...+-|++|+--...||-++..-.|
T Consensus 46 ~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls 95 (353)
T KOG2389|consen 46 STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLS 95 (353)
T ss_pred ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhh
Confidence 57788999999999999999999999999999999999999999987654
No 56
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=64.67 E-value=15 Score=30.26 Aligned_cols=84 Identities=23% Similarity=0.333 Sum_probs=62.2
Q ss_pred CchhhHHHHhhhhhhh---------hhhhccchhHHHHHHHhhhccCc-cccHHHHHHHHHHHHHHHHHhhhhhhHhhhh
Q psy17763 45 GTVALREIRRYQKSTE---------LLIRKLPFQRLVREIAQDFKTDL-RFQSSAVMALQEASEAYLVGLFEDTNLCAIH 114 (136)
Q Consensus 45 g~~alrEIr~~Qkst~---------lli~k~pF~rlVreI~~~~~~~~-r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~H 114 (136)
|...-+-+|.+|+..+ +-...+||.|+ +.++.. .+|. =++++|=...-.++|-|+..|---|-+.|-.
T Consensus 80 g~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARI-kkvMKt-dedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~ 157 (286)
T COG5208 80 GLLDERISRYWQQTIKAAEEERQILLKDHNLPLARI-KKVMKT-DEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEE 157 (286)
T ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHH-HHHHhc-ccchhheecccchHHHHHHHHHHHHHHHHHHHHHhH
Confidence 4445556788887532 22344899986 555542 2333 4677787778899999999999999999999
Q ss_pred cCccccCcccHHHHHH
Q psy17763 115 AKRVTIMPKDIQLARR 130 (136)
Q Consensus 115 akRvTi~~kDi~La~r 130 (136)
.||-||.-.||--|+.
T Consensus 158 NkRRtLQksDia~Av~ 173 (286)
T COG5208 158 NKRRTLQKSDIAAAVK 173 (286)
T ss_pred hhhhHHHHHHHHHHHH
Confidence 9999999999987764
No 57
>KOG1756|consensus
Probab=63.86 E-value=13 Score=28.02 Aligned_cols=66 Identities=26% Similarity=0.261 Sum_probs=48.9
Q ss_pred hhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 61 lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
+.+|---..|+.|+ -....|+...|...|--.-|.....++|.+...+.-.++..|+|+-++||.+
T Consensus 26 l~fPvgri~r~Lr~----~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 26 LQFPVGRIHRLLRK----GRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccCHHHHHHHHHc----cchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 33444444445444 2245677788887787666766778999999999999999999999999865
No 58
>KOG1657|consensus
Probab=63.36 E-value=11 Score=30.86 Aligned_cols=72 Identities=19% Similarity=0.219 Sum_probs=59.5
Q ss_pred hhhhhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHH
Q psy17763 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 57 kst~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~ 129 (136)
...+..+..+|..|+ |.|...-..---++.+|....-.|+|.|+..|=.-++.-+--++|-|+.-.|+.-++
T Consensus 66 ~~~d~~~~~lPlaRi-KkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av 137 (236)
T KOG1657|consen 66 GQLDFKNHILPLARI-KKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAV 137 (236)
T ss_pred cccchhhccCcHhhc-cccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHh
Confidence 456789999999996 556553322237999999999999999999999999999999999999999887654
No 59
>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=61.42 E-value=18 Score=27.56 Aligned_cols=60 Identities=23% Similarity=0.325 Sum_probs=42.5
Q ss_pred hhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHh
Q psy17763 68 FQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 68 F~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rir 132 (136)
|.++.|+-+ ++-...+-+.-+-+.+|.-|..||+-|+.-|...+|-.|.+.|+-+-..+.
T Consensus 1 fe~lFR~aa-----~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPITkGlq 60 (138)
T PF09123_consen 1 FERLFRKAA-----GLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPITKGLQ 60 (138)
T ss_dssp HHHHHHHHH-----S----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHHH
T ss_pred ChHHHHHHh-----ccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCccHHHH
Confidence 556655544 355567778888999999999999999999999999999999987766553
No 60
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=53.70 E-value=23 Score=30.97 Aligned_cols=61 Identities=20% Similarity=0.269 Sum_probs=49.9
Q ss_pred HHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhc
Q psy17763 72 VREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg 133 (136)
++.+++..+ ---+..+++.||---.|.-+-.+-++|...+.|.||.-++..||.-|.|-+.
T Consensus 11 ~KdvAeslG-i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lN 71 (450)
T COG5095 11 LKDVAESLG-ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLN 71 (450)
T ss_pred HHHHHHHcC-CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcC
Confidence 445554432 2246678899998889999999999999999999999999999999998764
No 61
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=50.41 E-value=22 Score=24.51 Aligned_cols=60 Identities=25% Similarity=0.421 Sum_probs=45.5
Q ss_pred hHHHHhhhhhhhhhhhccchhHHHHHHHhh-hccCccccHHHHHHHHH--HHHHHHHHhhhhhhHh
Q psy17763 49 LREIRRYQKSTELLIRKLPFQRLVREIAQD-FKTDLRFQSSAVMALQE--ASEAYLVGLFEDTNLC 111 (136)
Q Consensus 49 lrEIr~~Qkst~lli~k~pF~rlVreI~~~-~~~~~r~~~~Al~aLQe--aaE~~Lv~lfe~a~l~ 111 (136)
|++|.+|+...+ =||-.| |.+.|-++. |+.++-..+..+..|+. -+|+|+-++.+..+.|
T Consensus 2 L~~I~h~l~np~-DiP~ip--ra~aeyLqvrfN~~yl~~sG~i~~lr~~G~SE~~I~Gfl~Gl~~A 64 (77)
T PF10911_consen 2 LKPIQHLLDNPD-DIPDIP--RAAAEYLQVRFNAAYLMASGIISALRKQGWSESYILGFLAGLQYA 64 (77)
T ss_pred cchHHHHhcCCc-ccCCcc--HHHHHHHHHHhcHHHHHHhhhHHHHHHccccHHHHHHHHHHHHHH
Confidence 678888887763 355554 667776663 56777788888888875 5899999999998887
No 62
>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=47.62 E-value=22 Score=26.50 Aligned_cols=46 Identities=11% Similarity=0.096 Sum_probs=38.5
Q ss_pred ccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhH
Q psy17763 65 KLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNL 110 (136)
Q Consensus 65 k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l 110 (136)
..-+-+.|+..+..+-....|+.+.+.-++-+++..+++.++.++.
T Consensus 15 ~~~~~~~vr~~~~~~a~~~g~~~~~~~~l~lav~Ea~~Nai~ha~~ 60 (159)
T TIGR01924 15 KPEYVGLIRLTLSGIASRAGYTYDDIEDLKIAVSEACTNAVKHAYK 60 (159)
T ss_pred cHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhccC
Confidence 4456677888888887788899999999999999999999998863
No 63
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=46.54 E-value=39 Score=30.09 Aligned_cols=72 Identities=24% Similarity=0.378 Sum_probs=59.8
Q ss_pred hhhhccchhH-HHHHHHhhh--ccCccccHHHHHHHHHHHH----HHHHHhhhhhhHhhhhcCccccCcccHHHHHHHh
Q psy17763 61 LLIRKLPFQR-LVREIAQDF--KTDLRFQSSAVMALQEASE----AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 61 lli~k~pF~r-lVreI~~~~--~~~~r~~~~Al~aLQeaaE----~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rir 132 (136)
++|+-.||.+ =++||..-- ..++-.+.+||+-|-...| -|-++|++-|+..|.-.+.-+|...|+.-|..|-
T Consensus 354 lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~lF 432 (450)
T COG1224 354 LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKELF 432 (450)
T ss_pred eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHHH
Confidence 6788899986 578887632 2688999999999866554 7999999999999999999999999998887663
No 64
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=43.92 E-value=52 Score=26.80 Aligned_cols=59 Identities=19% Similarity=0.228 Sum_probs=46.9
Q ss_pred hHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhh--cCccccCcccHHHHH
Q psy17763 69 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLAR 129 (136)
Q Consensus 69 ~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~H--akRvTi~~kDi~La~ 129 (136)
..+|++.++. .++.++.+|+..|-+.++.=|..+-.+-..++.+ .+.-+|+..|++.+.
T Consensus 136 ~~~i~~~~~~--~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v 196 (326)
T PRK07452 136 KQLVERTAQE--LGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALV 196 (326)
T ss_pred HHHHHHHHHH--cCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHh
Confidence 3444444432 4678999999999999999888888888889888 568889999998764
No 65
>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=38.88 E-value=37 Score=22.72 Aligned_cols=56 Identities=7% Similarity=0.074 Sum_probs=36.2
Q ss_pred HHHHHHhhh--ccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccc-cCcccHH
Q psy17763 71 LVREIAQDF--KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVT-IMPKDIQ 126 (136)
Q Consensus 71 lVreI~~~~--~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvT-i~~kDi~ 126 (136)
+|.+|++.. +..++++.+|+.++.+-.+-|...-+.-|..-+.--+--. |.+.|++
T Consensus 4 li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LE 62 (72)
T PF09415_consen 4 LIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLE 62 (72)
T ss_dssp HHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHH
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence 556666643 3679999999999998888887776666666554444444 6666665
No 66
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=38.78 E-value=66 Score=22.06 Aligned_cols=44 Identities=18% Similarity=0.119 Sum_probs=34.8
Q ss_pred hHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhh
Q psy17763 69 QRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCA 112 (136)
Q Consensus 69 ~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a 112 (136)
-+.+++.+..+.....|..+.+..+.-+++..+++.++.++...
T Consensus 8 i~~~r~~~~~~~~~~~~~~~~~~~~~lav~E~~~Nav~H~~~~~ 51 (125)
T PF13581_consen 8 IREARAFLREFLERLGLPEEDRDDLELAVSEALTNAVEHGYPGD 51 (125)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 34455666666566889999999999999999999999988743
No 67
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=38.08 E-value=12 Score=33.38 Aligned_cols=58 Identities=17% Similarity=0.143 Sum_probs=47.0
Q ss_pred HHHHHhhh-ccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHH
Q psy17763 72 VREIAQDF-KTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 72 VreI~~~~-~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~ 129 (136)
.+|+.+.. ..+-.+..+.=+.|=+.|..|....=|-+..+|.|.|--||.++|+||-.
T Consensus 389 L~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhl 447 (505)
T COG5624 389 LEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHL 447 (505)
T ss_pred HHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeee
Confidence 34444443 46677888888888899999998888888889999999999999999853
No 68
>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=34.91 E-value=92 Score=27.97 Aligned_cols=59 Identities=19% Similarity=0.269 Sum_probs=43.2
Q ss_pred HHHHHhhh--ccCccccHHHHHHHHHHHH--HHHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 72 VREIAQDF--KTDLRFQSSAVMALQEASE--AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 72 VreI~~~~--~~~~r~~~~Al~aLQeaaE--~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
+.+|++.. ..++.++.+|++.|-.-+. ..++.+++.|...+...+|.+|+.+|+.-+..
T Consensus 268 i~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~ 330 (531)
T TIGR02902 268 IKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE 330 (531)
T ss_pred HHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence 34444443 2457788999887654443 56888899988888888999999999987753
No 69
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=33.07 E-value=1.6e+02 Score=22.62 Aligned_cols=64 Identities=17% Similarity=0.193 Sum_probs=48.5
Q ss_pred hhHHHHhhhhhhhhhhhccc----hhHHHHHHHhhh-------ccCccccHHHHHHHHHHHHHHHHHhhhhhhHh
Q psy17763 48 ALREIRRYQKSTELLIRKLP----FQRLVREIAQDF-------KTDLRFQSSAVMALQEASEAYLVGLFEDTNLC 111 (136)
Q Consensus 48 alrEIr~~Qkst~lli~k~p----F~rlVreI~~~~-------~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~ 111 (136)
+-+|--+|++.+.-|||-.= |+.+++-|.+.+ ..|..|+++++..+|.+.-+...+|-+..+.+
T Consensus 75 sE~eRlk~e~e~g~Lipa~eV~~~~s~~~Kav~q~LetlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~ 149 (152)
T PF07278_consen 75 SENERLKFEKETGQLIPAEEVRREMSEMAKAVVQVLETLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEA 149 (152)
T ss_pred HHHHHHHHHHHHcccCcHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666778999999999764 455555555544 25789999999999999999998887765443
No 70
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=31.81 E-value=1.8e+02 Score=26.79 Aligned_cols=49 Identities=20% Similarity=0.231 Sum_probs=39.1
Q ss_pred ccccHHHHHHHHH-HH------------HHHHHHhhhhhhHhhhhcCccccCcccHHHHHHH
Q psy17763 83 LRFQSSAVMALQE-AS------------EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 83 ~r~~~~Al~aLQe-aa------------E~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~ri 131 (136)
..|+.+|+..|-+ ++ +.-|..++..|+..|...+..+|+.+|++-|...
T Consensus 329 ~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~ 390 (608)
T TIGR00764 329 PHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKL 390 (608)
T ss_pred CcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHH
Confidence 4899999998764 22 4678888999988888888899999999876543
No 71
>COG2178 Predicted RNA-binding protein of the translin family [Translation, ribosomal structure and biogenesis]
Probab=30.00 E-value=81 Score=25.47 Aligned_cols=56 Identities=29% Similarity=0.323 Sum_probs=40.3
Q ss_pred hhhHHHHhhhhhhhhhhhccchhHH----------HHHHHhhh--ccCccccHHHHHHHHHHHHHHHH
Q psy17763 47 VALREIRRYQKSTELLIRKLPFQRL----------VREIAQDF--KTDLRFQSSAVMALQEASEAYLV 102 (136)
Q Consensus 47 ~alrEIr~~Qkst~lli~k~pF~rl----------VreI~~~~--~~~~r~~~~Al~aLQeaaE~~Lv 102 (136)
...|||.++-+-.-.++.+-.|..- |.++-..+ .+++-|+..+=.++||-+|+.+.
T Consensus 24 ~lsRei~r~s~~aI~~~H~~~~eeA~~~l~~a~~~v~~Lk~~l~~~pel~~ag~~~~a~QEyvEA~~l 91 (204)
T COG2178 24 KLSREIVRLSGEAIFLLHRGDFEEAEKKLKKASEAVEKLKRLLAGFPELYFAGFVTTALQEYVEATLL 91 (204)
T ss_pred HHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHhhcchHHHHHHHHHH
Confidence 4578899888777788888888653 33322222 26788889999999999998653
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=29.68 E-value=46 Score=21.22 Aligned_cols=20 Identities=30% Similarity=0.336 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHhhhh
Q psy17763 88 SAVMALQEASEAYLVGLFED 107 (136)
Q Consensus 88 ~Al~aLQeaaE~~Lv~lfe~ 107 (136)
+|+.+|||.++.-|.++...
T Consensus 7 ea~~~lqevs~eELd~ilGg 26 (51)
T PF04604_consen 7 EALNSLQEVSDEELDQILGG 26 (51)
T ss_pred HHHHHHHhcCHHHHHHHhCC
Confidence 89999999999999999876
No 73
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=29.41 E-value=2.2e+02 Score=25.74 Aligned_cols=66 Identities=26% Similarity=0.292 Sum_probs=48.2
Q ss_pred cchhHHHHHHHhhhccCccccHHHHHHHHHHHH-----------HHHHHhhhhhhHhhhhcCccccCcccHHHHHHHh
Q psy17763 66 LPFQRLVREIAQDFKTDLRFQSSAVMALQEASE-----------AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 66 ~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE-----------~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rir 132 (136)
..|.++|..++++. .-..|+.+|+..|=+.+- ..|..|+..|+..|--.+.-.|...||+-|..-|
T Consensus 430 ~~~~~~i~~~~~~~-~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 430 RQYARFIASICQKE-GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHH-SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHhC-CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 34777888887765 234789999988655443 5789999999999998889999999999887654
No 74
>KOG2680|consensus
Probab=26.73 E-value=1.9e+02 Score=25.53 Aligned_cols=72 Identities=21% Similarity=0.356 Sum_probs=59.2
Q ss_pred hhhhccchhH-HHHHHHhh-h-ccCccccHHHHHHHHHHHH----HHHHHhhhhhhHhhhhcCccccCcccHHHHHHHh
Q psy17763 61 LLIRKLPFQR-LVREIAQD-F-KTDLRFQSSAVMALQEASE----AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 61 lli~k~pF~r-lVreI~~~-~-~~~~r~~~~Al~aLQeaaE----~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rir 132 (136)
++|.-.|+.+ =+++|+.- | ..|.-.+++|++.|-...| -|-.+|...|++.+...|--++...||+-|.+|-
T Consensus 351 lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~LF 429 (454)
T KOG2680|consen 351 LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRLF 429 (454)
T ss_pred heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHHH
Confidence 6778888865 46666653 2 3788999999999876665 5889999999999999999999999999988874
No 75
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=26.51 E-value=83 Score=24.84 Aligned_cols=27 Identities=33% Similarity=0.263 Sum_probs=20.3
Q ss_pred ccCccccHHHHHHHHHHHHHHHHHhhh
Q psy17763 80 KTDLRFQSSAVMALQEASEAYLVGLFE 106 (136)
Q Consensus 80 ~~~~r~~~~Al~aLQeaaE~~Lv~lfe 106 (136)
.++++|+...-.++||.+|++..-.|=
T Consensus 70 ~~~~~y~~~~~~~lQEyvEA~~f~~~l 96 (204)
T PRK14562 70 HPELYYAGYVGTALQEYVEALLVYSLL 96 (204)
T ss_pred CchhhhhhhcchHHHHHHHHHHHHHHH
Confidence 367788888888999999876654443
No 76
>PF07105 DUF1367: Protein of unknown function (DUF1367); InterPro: IPR009797 This entry is represented by Bacteriophage VT2phi_272, P37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Probab=26.46 E-value=96 Score=24.89 Aligned_cols=16 Identities=44% Similarity=0.567 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHhhh
Q psy17763 91 MALQEASEAYLVGLFE 106 (136)
Q Consensus 91 ~aLQeaaE~~Lv~lfe 106 (136)
++||++++.||..+-+
T Consensus 91 ~~l~~~A~~yL~~va~ 106 (196)
T PF07105_consen 91 DALQEAADQYLAKVAK 106 (196)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 8999999999988765
No 77
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=25.95 E-value=1.6e+02 Score=24.40 Aligned_cols=58 Identities=21% Similarity=0.098 Sum_probs=45.1
Q ss_pred HHHHHHHhhhc-cCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHH
Q psy17763 70 RLVREIAQDFK-TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 70 rlVreI~~~~~-~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~ 129 (136)
.+++=|.+.+. .+..++.+|+..|-+.++.=|..+-.+-..++.+++ +|+..||+.+.
T Consensus 139 ~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 139 EALELLQERAKELGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 34333433332 568899999999999999989888888888889877 68999988754
No 78
>KOG1089|consensus
Probab=25.33 E-value=76 Score=29.39 Aligned_cols=35 Identities=23% Similarity=0.439 Sum_probs=29.4
Q ss_pred chhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhh
Q psy17763 67 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCA 112 (136)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a 112 (136)
-|-..|..++.++...|.| .|.||..||+.++.|-
T Consensus 417 qFLDcvwQl~~QfP~~FEF-----------ne~fLi~L~~h~ys~q 451 (573)
T KOG1089|consen 417 QFLDCVWQLLEQFPCAFEF-----------NERFLIKLHEHAYSSQ 451 (573)
T ss_pred HHHHHHHHHHhhCCcceeh-----------hHHHHHHHHHhhHHhh
Confidence 4778889999988877766 8999999999998774
No 79
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=25.07 E-value=1.8e+02 Score=22.53 Aligned_cols=49 Identities=16% Similarity=0.116 Sum_probs=38.2
Q ss_pred CccccHHHHHHHHHHHHH---HHHHhhhhhhHhhhhcCccccCcccHHHHHH
Q psy17763 82 DLRFQSSAVMALQEASEA---YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 82 ~~r~~~~Al~aLQeaaE~---~Lv~lfe~a~l~a~HakRvTi~~kDi~La~r 130 (136)
+..|+.+++..|-+.+.- ++..+...+.+.|.-.+--+|+..||.-+.+
T Consensus 213 ~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~ 264 (269)
T TIGR03015 213 APVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIA 264 (269)
T ss_pred CCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 456999999999999986 6777777777776666677899988876653
No 80
>PRK05907 hypothetical protein; Provisional
Probab=24.89 E-value=1.4e+02 Score=24.96 Aligned_cols=67 Identities=12% Similarity=0.035 Sum_probs=52.2
Q ss_pred hhccchhHHHHHHHhhhc-cCccccHHHHHHHHHHH-HHHHHHhhhhhhHhhhh-cCccccCcccHHHHH
Q psy17763 63 IRKLPFQRLVREIAQDFK-TDLRFQSSAVMALQEAS-EAYLVGLFEDTNLCAIH-AKRVTIMPKDIQLAR 129 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~-~~~r~~~~Al~aLQeaa-E~~Lv~lfe~a~l~a~H-akRvTi~~kDi~La~ 129 (136)
.+...-..|.+-|.+.+. .+..++.+|+..|=+.+ +.-|-.+..+-..++.+ +.+-+|+..||+.+.
T Consensus 131 ~~~l~e~~L~~Wi~~~~~~~g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv 200 (311)
T PRK05907 131 WFADRDKRIAQLLIQRAKELGISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFV 200 (311)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHh
Confidence 444444677777777774 67899999999988888 67777888888888888 668899999998653
No 81
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=24.08 E-value=1.6e+02 Score=21.71 Aligned_cols=46 Identities=9% Similarity=0.127 Sum_probs=36.6
Q ss_pred ccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhH
Q psy17763 65 KLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNL 110 (136)
Q Consensus 65 k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l 110 (136)
..-+-+.||..+..+.....|..+.+..|+-+++..+.+..+.++.
T Consensus 15 ~~~~~~~vr~~v~~~~~~~g~~~~~~~~l~lav~Ea~~Nai~Hg~~ 60 (161)
T PRK04069 15 KAEYVSIIRLTLSGVANRMGFSYDDIEDMKIAVSEACTNAVQHAYK 60 (161)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhccC
Confidence 4456678888888887788899999988888888888888777653
No 82
>KOG1969|consensus
Probab=24.00 E-value=1.3e+02 Score=29.11 Aligned_cols=80 Identities=23% Similarity=0.226 Sum_probs=55.9
Q ss_pred CchhhHHHHhhhhhhhhhhhccchhHHHHHHHhhhc-cCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCcc--ccC
Q psy17763 45 GTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRV--TIM 121 (136)
Q Consensus 45 g~~alrEIr~~Qkst~lli~k~pF~rlVreI~~~~~-~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRv--Ti~ 121 (136)
.+.|||..|.|-.= ..++.-+=.+||..+-.-|+ ++++..+.||.+|=|.++.-+-.-..--+.++..++|. -|.
T Consensus 449 YaPaLR~Lr~~A~i--i~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L~el~~~DIRsCINtLQfLa~~~~r~ds~i~ 526 (877)
T KOG1969|consen 449 YAPALRPLRPFAEI--IAFVPPSQSRLVERLNEICHRENMRADSKALNALCELTQNDIRSCINTLQFLASNVDRRDSSIS 526 (877)
T ss_pred cchhhhhcccceEE--EEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcchHHHHHHHHHHHHHhcccccccch
Confidence 67899999987542 34455566778855444443 78999999999999999877766666666777776664 244
Q ss_pred cccHH
Q psy17763 122 PKDIQ 126 (136)
Q Consensus 122 ~kDi~ 126 (136)
.+|++
T Consensus 527 ~~~i~ 531 (877)
T KOG1969|consen 527 VKLIC 531 (877)
T ss_pred hhhhh
Confidence 45544
No 83
>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=23.06 E-value=1.6e+02 Score=21.36 Aligned_cols=48 Identities=27% Similarity=0.376 Sum_probs=36.6
Q ss_pred HhhhhhhhhhhhccchhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhh
Q psy17763 53 RRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAI 113 (136)
Q Consensus 53 r~~Qkst~lli~k~pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~ 113 (136)
+.|+.+-+..--+.|-++.|+.|+..... ...-.+|..||.+.|+..+
T Consensus 40 ~~y~e~~e~crnlvpv~rvvY~vLs~Lek-------------~f~~~fl~~LFs~~nL~~Y 87 (103)
T PF03172_consen 40 QMYKESQEACRNLVPVQRVVYNVLSWLEK-------------TFIRSFLEALFSDYNLKEY 87 (103)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHHH-------------HhhHHHHHHHhhHHHHHHC
Confidence 46777777777888999999999886632 2345788889999888765
No 84
>KOG1757|consensus
Probab=23.03 E-value=1.6e+02 Score=21.98 Aligned_cols=66 Identities=24% Similarity=0.308 Sum_probs=43.7
Q ss_pred chhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhhhcCccccCcccHHHHHHHhcc
Q psy17763 67 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~HakRvTi~~kDi~La~rirg~ 134 (136)
|-.|+-|-+-......-|.-+.|..-+-..-|......+|-|.-.+---|=..|+|+-+||| |||+
T Consensus 32 pVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLA--iRGD 97 (131)
T KOG1757|consen 32 PVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLA--IRGD 97 (131)
T ss_pred chHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheee--ecCc
Confidence 44455444444444556666666555555556666677888877777777778899999997 4555
No 85
>PHA02604 rI.-1 hypothetical protein; Provisional
Probab=22.99 E-value=1.3e+02 Score=22.49 Aligned_cols=44 Identities=11% Similarity=0.052 Sum_probs=31.9
Q ss_pred chhHHHHHHHhhhccCccccHHHHHHHHHHHHHHHHHhhhhhhHhhh
Q psy17763 67 PFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAI 113 (136)
Q Consensus 67 pF~rlVreI~~~~~~~~r~~~~Al~aLQeaaE~~Lv~lfe~a~l~a~ 113 (136)
.+.-+|++|+++...-++ .....||.+.++++.-+..--+++++
T Consensus 82 d~~~~l~~~l~~a~~i~~---~l~s~L~N~~DdI~~~~~qt~YkLtL 125 (126)
T PHA02604 82 DTIAFLDELLQEAEEIYK---ELPSALQSTLDDITGLCYQTKYKLTL 125 (126)
T ss_pred CHHHHHHHHHHHHHHHHH---HhhHHHHHHHHHHHHHHHHHHHHHhc
Confidence 677888888887654333 44566999999988887776666653
No 86
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=22.84 E-value=70 Score=24.27 Aligned_cols=33 Identities=24% Similarity=0.519 Sum_probs=26.4
Q ss_pred chhhHHHHhhhhhhhhhhhccchhHHHHHHHhhh
Q psy17763 46 TVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 79 (136)
Q Consensus 46 ~~alrEIr~~Qkst~lli~k~pF~rlVreI~~~~ 79 (136)
.+|+.||+++..+...+ +...+-+||++|=.++
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~H 129 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKEH 129 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHhC
Confidence 57999999996655444 8999999999997644
No 87
>PF07962 Swi3: Replication Fork Protection Component Swi3; InterPro: IPR012923 Replication fork pausing is required to initiate recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1. Together they define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks []. This complex is required for accurate replication, fork protection and replication checkpoint signalling [, ].; GO: 0006974 response to DNA damage stimulus, 0007049 cell cycle, 0048478 replication fork protection, 0005634 nucleus
Probab=22.41 E-value=71 Score=21.74 Aligned_cols=30 Identities=20% Similarity=0.322 Sum_probs=24.2
Q ss_pred hhHHHHhhhhhhhhhhhccchhHHHHHHHh
Q psy17763 48 ALREIRRYQKSTELLIRKLPFQRLVREIAQ 77 (136)
Q Consensus 48 alrEIr~~Qkst~lli~k~pF~rlVreI~~ 77 (136)
.-+=+..||.=...|.|+++|...|..|-.
T Consensus 35 L~~ll~~Yq~W~h~LfPk~~F~d~i~~vE~ 64 (83)
T PF07962_consen 35 LRRLLQFYQLWAHRLFPKASFEDFIERVEK 64 (83)
T ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHHHH
Confidence 344467899888999999999999877654
No 88
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.31 E-value=67 Score=22.80 Aligned_cols=18 Identities=33% Similarity=0.719 Sum_probs=14.9
Q ss_pred hhccchhHHHHHHHhhhc
Q psy17763 63 IRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 63 i~k~pF~rlVreI~~~~~ 80 (136)
-.-+|+|+|++||+....
T Consensus 72 a~GlpYQtyIreiLh~~~ 89 (92)
T COG5304 72 AEGLPYQTYIREILHKYS 89 (92)
T ss_pred hcCCcHHHHHHHHHHhhc
Confidence 467899999999998653
No 89
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=21.77 E-value=44 Score=22.04 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=11.1
Q ss_pred cCcccHHHHHHHh
Q psy17763 120 IMPKDIQLARRIR 132 (136)
Q Consensus 120 i~~kDi~La~rir 132 (136)
|+.+|+.||.+|=
T Consensus 62 lT~~D~~lA~~id 74 (76)
T cd00913 62 LSENDFIMAAKID 74 (76)
T ss_pred CCHHHHHHHHHHh
Confidence 7789999999883
No 90
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.75 E-value=95 Score=24.14 Aligned_cols=22 Identities=18% Similarity=0.199 Sum_probs=19.6
Q ss_pred hhhccCccccHHHHHHHHHHHH
Q psy17763 77 QDFKTDLRFQSSAVMALQEASE 98 (136)
Q Consensus 77 ~~~~~~~r~~~~Al~aLQeaaE 98 (136)
.+++..|-|+..+|++.+|.+|
T Consensus 72 ~~CGkpyPWt~~~L~aa~el~e 93 (158)
T PF10083_consen 72 HNCGKPYPWTENALEAANELIE 93 (158)
T ss_pred HhCCCCCchHHHHHHHHHHHHH
Confidence 4567899999999999999998
Done!