Query psy17765
Match_columns 475
No_of_seqs 364 out of 1023
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 22:16:45 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17765.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17765hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00153 histone H2A; Provisio 100.0 2.2E-42 4.7E-47 308.2 10.5 116 125-240 5-120 (129)
2 PLN00156 histone H2AX; Provisi 100.0 3.7E-42 8.1E-47 309.5 10.3 116 125-240 10-125 (139)
3 PLN00157 histone H2A; Provisio 100.0 6.2E-42 1.4E-46 306.3 10.5 113 128-240 10-122 (132)
4 PTZ00017 histone H2A; Provisio 100.0 2.9E-41 6.3E-46 302.9 10.0 110 131-240 14-123 (134)
5 PTZ00252 histone H2A; Provisio 100.0 4.9E-41 1.1E-45 300.1 9.6 107 133-239 13-122 (134)
6 smart00414 H2A Histone 2A. 100.0 1.2E-40 2.6E-45 289.6 9.5 105 136-240 1-105 (106)
7 PLN00154 histone H2A; Provisio 100.0 4.6E-40 9.9E-45 294.8 10.0 109 131-240 25-134 (136)
8 cd00074 H2A Histone 2A; H2A is 100.0 1.6E-39 3.4E-44 286.3 10.8 112 128-239 4-115 (115)
9 KOG1756|consensus 100.0 4.9E-39 1.1E-43 283.7 9.2 109 132-240 15-123 (131)
10 PLN00158 histone H2B; Provisio 100.0 2.1E-38 4.6E-43 276.9 11.1 112 6-123 5-116 (116)
11 PTZ00463 histone H2B; Provisio 100.0 6.7E-38 1.5E-42 273.5 10.2 111 12-122 4-116 (117)
12 COG5262 HTA1 Histone H2A [Chro 100.0 7.5E-37 1.6E-41 266.3 9.1 118 123-240 3-122 (132)
13 smart00427 H2B Histone H2B. 100.0 6.2E-35 1.3E-39 245.6 10.1 89 34-122 1-89 (89)
14 PLN00158 histone H2B; Provisio 100.0 3.2E-35 6.9E-40 257.0 3.2 88 360-453 5-93 (116)
15 PTZ00463 histone H2B; Provisio 100.0 5.3E-35 1.2E-39 255.4 3.9 75 379-453 19-94 (117)
16 KOG1757|consensus 100.0 1.9E-32 4.1E-37 237.2 3.3 108 132-240 18-126 (131)
17 smart00427 H2B Histone H2B. 100.0 8.6E-32 1.9E-36 226.6 2.4 66 388-453 1-67 (89)
18 KOG1744|consensus 100.0 1.5E-30 3.2E-35 230.9 8.1 99 25-123 28-126 (127)
19 KOG1744|consensus 100.0 5.8E-29 1.3E-33 220.7 5.5 76 378-453 27-103 (127)
20 PLN00155 histone H2A; Provisio 99.7 2E-18 4.2E-23 134.8 4.6 54 125-178 5-58 (58)
21 PF00125 Histone: Core histone 99.3 6.7E-12 1.4E-16 101.6 5.4 73 138-210 2-75 (75)
22 PF00125 Histone: Core histone 99.0 6.3E-10 1.4E-14 90.1 4.2 69 31-99 2-74 (75)
23 COG5247 BUR6 Class 2 transcrip 98.7 2.1E-08 4.6E-13 86.7 6.6 78 142-219 21-98 (113)
24 KOG1659|consensus 98.2 1.8E-06 3.9E-11 83.5 6.6 75 143-217 12-86 (224)
25 PF00808 CBFD_NFYB_HMF: Histon 97.9 2.7E-05 5.8E-10 61.8 6.6 64 144-207 2-65 (65)
26 cd07981 TAF12 TATA Binding Pro 97.4 0.00057 1.2E-08 55.9 7.5 63 39-101 6-68 (72)
27 PF00808 CBFD_NFYB_HMF: Histon 97.2 0.001 2.2E-08 52.8 6.3 59 38-97 6-65 (65)
28 smart00803 TAF TATA box bindin 97.1 0.0014 3E-08 52.9 6.6 64 144-208 2-65 (65)
29 COG2036 HHT1 Histones H3 and H 97.0 0.0017 3.7E-08 55.9 5.7 67 141-208 16-82 (91)
30 COG2036 HHT1 Histones H3 and H 96.9 0.0018 4E-08 55.7 5.4 65 37-102 22-86 (91)
31 PLN00035 histone H4; Provision 96.9 0.0035 7.6E-08 55.1 7.0 63 37-100 32-94 (103)
32 PLN00035 histone H4; Provision 96.8 0.0022 4.8E-08 56.3 5.2 64 145-209 30-93 (103)
33 cd00076 H4 Histone H4, one of 96.4 0.0092 2E-07 50.8 6.5 64 145-209 14-77 (85)
34 cd00074 H2A Histone 2A; H2A is 96.3 0.011 2.3E-07 53.0 6.7 68 37-106 23-90 (115)
35 smart00803 TAF TATA box bindin 96.2 0.015 3.2E-07 47.0 6.4 60 38-98 6-65 (65)
36 PF03847 TFIID_20kDa: Transcri 96.1 0.026 5.6E-07 46.1 7.0 62 39-100 4-65 (68)
37 cd07981 TAF12 TATA Binding Pro 95.9 0.028 6E-07 46.0 6.7 66 145-210 2-67 (72)
38 cd00076 H4 Histone H4, one of 95.9 0.033 7.3E-07 47.4 7.3 62 37-99 16-77 (85)
39 PTZ00015 histone H4; Provision 95.8 0.029 6.2E-07 49.4 6.7 64 144-208 30-93 (102)
40 smart00417 H4 Histone H4. 95.7 0.019 4E-07 47.8 4.8 60 145-205 14-73 (74)
41 PTZ00015 histone H4; Provision 95.6 0.048 1E-06 48.0 7.3 63 36-99 32-94 (102)
42 smart00428 H3 Histone H3. 95.5 0.057 1.2E-06 47.7 7.3 68 32-99 31-100 (105)
43 KOG0871|consensus 94.6 0.09 2E-06 49.0 6.3 79 38-121 16-96 (156)
44 cd07979 TAF9 TATA Binding Prot 94.3 0.17 3.7E-06 45.3 7.2 65 37-102 4-68 (117)
45 PLN00156 histone H2AX; Provisi 94.2 0.11 2.4E-06 48.0 6.1 68 37-106 32-99 (139)
46 KOG0869|consensus 94.2 0.14 3E-06 48.2 6.7 67 37-103 35-103 (168)
47 KOG1657|consensus 94.0 0.053 1.2E-06 54.1 3.9 78 142-219 72-149 (236)
48 smart00417 H4 Histone H4. 93.5 0.23 5.1E-06 41.3 6.1 57 37-94 16-72 (74)
49 cd07979 TAF9 TATA Binding Prot 93.4 0.22 4.8E-06 44.6 6.4 63 148-211 5-67 (117)
50 COG5208 HAP5 CCAAT-binding fac 93.3 0.19 4E-06 49.7 6.1 76 143-218 108-183 (286)
51 cd08048 TAF11 TATA Binding Pro 93.2 0.35 7.6E-06 41.2 7.0 63 145-208 17-82 (85)
52 PTZ00017 histone H2A; Provisio 93.2 0.2 4.4E-06 46.1 5.8 68 37-106 30-97 (134)
53 PLN00153 histone H2A; Provisio 93.1 0.21 4.6E-06 45.7 5.8 68 37-106 27-94 (129)
54 PF02969 TAF: TATA box binding 92.5 0.45 9.8E-06 38.8 6.4 64 144-208 3-66 (66)
55 PLN00154 histone H2A; Provisio 92.2 0.44 9.5E-06 44.0 6.6 70 37-108 41-111 (136)
56 KOG1142|consensus 92.1 0.15 3.2E-06 51.4 3.8 65 36-100 156-220 (258)
57 KOG1756|consensus 92.0 0.38 8.2E-06 43.9 5.9 69 37-107 30-98 (131)
58 PF02969 TAF: TATA box binding 92.0 0.43 9.3E-06 38.9 5.7 47 52-98 20-66 (66)
59 PLN00157 histone H2A; Provisio 91.9 0.34 7.4E-06 44.5 5.6 68 37-106 29-96 (132)
60 PTZ00252 histone H2A; Provisio 91.4 0.64 1.4E-05 42.8 6.8 70 35-106 25-97 (134)
61 smart00414 H2A Histone 2A. 91.4 0.42 9.1E-06 42.3 5.4 68 37-106 12-79 (106)
62 smart00576 BTP Bromodomain tra 90.5 1 2.2E-05 37.1 6.6 61 38-99 10-70 (77)
63 COG5262 HTA1 Histone H2A [Chro 90.5 0.51 1.1E-05 42.6 5.1 69 37-107 29-97 (132)
64 KOG0869|consensus 90.2 0.25 5.5E-06 46.5 3.1 53 394-446 38-91 (168)
65 PF03847 TFIID_20kDa: Transcri 89.8 0.23 4.9E-06 40.6 2.1 55 394-448 5-59 (68)
66 cd08050 TAF6 TATA Binding Prot 88.9 0.77 1.7E-05 47.9 5.8 58 158-215 12-71 (343)
67 KOG0870|consensus 88.5 3.5 7.6E-05 39.3 9.2 63 38-100 14-78 (172)
68 smart00428 H3 Histone H3. 88.4 1.5 3.2E-05 38.9 6.4 67 142-208 27-99 (105)
69 PF15630 CENP-S: Kinetochore c 88.1 1.2 2.7E-05 37.2 5.4 62 38-99 9-72 (76)
70 PF04719 TAFII28: hTAFII28-lik 88.0 1.2 2.7E-05 38.4 5.5 63 145-208 24-88 (90)
71 KOG3219|consensus 86.9 0.95 2.1E-05 44.1 4.7 66 143-209 111-177 (195)
72 cd08050 TAF6 TATA Binding Prot 86.8 1.3 2.9E-05 46.2 6.1 49 52-100 16-64 (343)
73 PLN00121 histone H3; Provision 86.5 2 4.3E-05 39.8 6.3 65 35-99 67-131 (136)
74 PTZ00018 histone H3; Provision 86.2 2.1 4.6E-05 39.6 6.4 65 35-99 67-131 (136)
75 smart00325 RhoGEF Guanine nucl 86.2 0.16 3.4E-06 46.3 -1.0 68 286-357 22-94 (180)
76 smart00576 BTP Bromodomain tra 84.0 3.8 8.3E-05 33.7 6.4 58 151-209 13-70 (77)
77 cd00160 RhoGEF Guanine nucleot 82.9 0.28 6E-06 44.8 -0.9 69 286-358 25-98 (181)
78 PF15510 CENP-W: Centromere ki 82.0 1.6 3.5E-05 37.9 3.4 63 38-102 20-98 (102)
79 PF07524 Bromo_TP: Bromodomain 80.1 7.3 0.00016 31.8 6.6 48 52-99 23-70 (77)
80 PLN00161 histone H3; Provision 79.5 6.9 0.00015 36.3 6.9 65 35-99 60-125 (135)
81 PLN00160 histone H3; Provision 76.4 9.6 0.00021 33.4 6.6 67 33-99 24-91 (97)
82 PF15630 CENP-S: Kinetochore c 75.8 8.6 0.00019 32.2 5.9 48 166-213 26-76 (76)
83 cd07978 TAF13 The TATA Binding 75.5 16 0.00035 31.5 7.7 62 36-99 4-66 (92)
84 PF09415 CENP-X: CENP-S associ 72.4 16 0.00034 30.3 6.6 60 146-205 1-63 (72)
85 PF02269 TFIID-18kDa: Transcri 67.8 6.7 0.00015 33.7 3.6 48 52-99 19-66 (93)
86 KOG1142|consensus 62.4 8.8 0.00019 39.0 3.8 56 394-449 160-215 (258)
87 KOG2549|consensus 61.8 19 0.00041 40.4 6.5 49 52-100 28-76 (576)
88 KOG0871|consensus 59.9 5.9 0.00013 37.2 2.0 69 394-462 18-88 (156)
89 PF02291 TFIID-31kDa: Transcri 59.9 15 0.00032 33.7 4.5 63 38-101 16-78 (129)
90 PF15511 CENP-T: Centromere ki 59.6 17 0.00037 39.2 5.6 56 37-92 354-414 (414)
91 cd08048 TAF11 TATA Binding Pro 58.2 47 0.001 28.3 7.0 62 38-100 20-84 (85)
92 PF02861 Clp_N: Clp amino term 56.1 12 0.00026 27.5 2.8 34 186-219 1-36 (53)
93 PF02291 TFIID-31kDa: Transcri 55.7 42 0.00091 30.8 6.7 60 147-210 15-77 (129)
94 PLN00160 histone H3; Provision 54.8 37 0.0008 29.9 5.9 67 142-208 19-90 (97)
95 PLN00161 histone H3; Provision 47.6 62 0.0013 30.1 6.5 67 142-208 53-124 (135)
96 PTZ00018 histone H3; Provision 47.1 46 0.00099 31.0 5.5 67 142-208 60-130 (136)
97 COG1466 HolA DNA polymerase II 46.9 50 0.0011 34.1 6.5 73 35-109 144-216 (334)
98 cd07978 TAF13 The TATA Binding 46.1 47 0.001 28.6 5.2 30 182-212 40-69 (92)
99 KOG0870|consensus 44.9 64 0.0014 31.1 6.2 66 142-208 8-76 (172)
100 PF04719 TAFII28: hTAFII28-lik 44.8 82 0.0018 27.3 6.4 64 37-100 26-90 (90)
101 PLN00121 histone H3; Provision 43.6 43 0.00093 31.2 4.8 67 142-208 60-130 (136)
102 PRK08487 DNA polymerase III su 43.2 62 0.0013 33.3 6.5 69 36-108 140-208 (328)
103 KOG1757|consensus 42.3 32 0.0007 31.1 3.6 65 37-107 33-102 (131)
104 PF00621 RhoGEF: RhoGEF domain 40.9 6.4 0.00014 35.3 -1.0 67 286-357 22-93 (180)
105 PF02269 TFIID-18kDa: Transcri 40.8 19 0.0004 31.0 1.9 41 173-213 27-70 (93)
106 PF09415 CENP-X: CENP-S associ 35.5 67 0.0014 26.6 4.3 56 40-95 5-63 (72)
107 COG5150 Class 2 transcription 34.7 81 0.0018 29.2 5.0 71 49-123 27-97 (148)
108 TIGR01128 holA DNA polymerase 34.4 1.4E+02 0.003 29.4 7.3 69 34-104 114-182 (302)
109 smart00350 MCM minichromosome 33.3 1.3E+02 0.0029 33.0 7.5 66 34-101 421-505 (509)
110 PF07524 Bromo_TP: Bromodomain 32.3 1.1E+02 0.0024 24.8 5.2 48 161-208 22-69 (77)
111 PRK07452 DNA polymerase III su 31.2 74 0.0016 32.2 4.8 62 36-99 135-198 (326)
112 KOG0787|consensus 30.5 17 0.00038 39.0 0.1 63 166-230 252-315 (414)
113 TIGR02442 Cob-chelat-sub cobal 30.0 1E+02 0.0022 35.0 6.1 60 46-105 243-309 (633)
114 PF15511 CENP-T: Centromere ki 29.9 69 0.0015 34.6 4.5 72 131-202 338-414 (414)
115 PF14687 DUF4460: Domain of un 29.9 64 0.0014 28.8 3.6 36 35-70 10-53 (112)
116 PRK05574 holA DNA polymerase I 29.4 1.5E+02 0.0033 29.8 6.7 73 33-107 148-220 (340)
117 KOG3334|consensus 28.2 1.2E+02 0.0025 28.7 5.0 59 38-100 17-78 (148)
118 PF00725 3HCDH: 3-hydroxyacyl- 26.5 1.6E+02 0.0035 24.3 5.3 84 64-165 3-92 (97)
119 PRK00411 cdc6 cell division co 25.8 3.1E+02 0.0067 28.3 8.3 66 37-102 213-284 (394)
120 PF04604 L_biotic_typeA: Type- 25.3 42 0.00092 26.3 1.4 22 209-233 16-37 (51)
121 PRK06585 holA DNA polymerase I 25.2 1.8E+02 0.0039 29.7 6.4 71 36-108 147-218 (343)
122 KOG1745|consensus 23.9 83 0.0018 29.4 3.3 64 36-99 69-132 (137)
123 PRK05907 hypothetical protein; 23.8 90 0.002 32.4 3.9 70 37-108 140-211 (311)
124 COG5095 TAF6 Transcription ini 23.0 79 0.0017 33.6 3.3 57 44-100 11-70 (450)
125 TIGR00764 lon_rel lon-related 21.9 2.7E+02 0.0059 31.6 7.5 65 36-100 314-391 (608)
126 KOG3523|consensus 21.6 16 0.00034 41.4 -2.2 68 286-357 278-353 (695)
127 PF03297 Ribosomal_S25: S25 ri 21.2 53 0.0011 29.2 1.4 40 66-113 44-83 (105)
128 COG5150 Class 2 transcription 20.9 1.5E+02 0.0033 27.5 4.2 42 167-210 36-78 (148)
No 1
>PLN00153 histone H2A; Provisional
Probab=100.00 E-value=2.2e-42 Score=308.18 Aligned_cols=116 Identities=74% Similarity=1.114 Sum_probs=110.2
Q ss_pred CCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHH
Q psy17765 125 GKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ 204 (475)
Q Consensus 125 g~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~ 204 (475)
|++++.+++..|||+||||||||+||||||++++|+.||+++||||||||||||++||||||||.|++++++||+|+||+
T Consensus 5 ~~~~~~~~k~~srS~ragL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~ 84 (129)
T PLN00153 5 GKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQ 84 (129)
T ss_pred CCCCccccCccCcccccCcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHH
Confidence 44444445778999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765 205 LAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240 (475)
Q Consensus 205 lAI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~ 240 (475)
+||+||+||++||+++||++|||+|+||++|+|+++
T Consensus 85 lAI~nDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~ 120 (129)
T PLN00153 85 LAIRNDEELGKLLGEVTIASGGVLPNIHAVLLPKKT 120 (129)
T ss_pred hhccCcHHHHHHHCCCccCCCccCCCcchhhcCccc
Confidence 999999999999999999999999999999999987
No 2
>PLN00156 histone H2AX; Provisional
Probab=100.00 E-value=3.7e-42 Score=309.52 Aligned_cols=116 Identities=72% Similarity=1.096 Sum_probs=112.0
Q ss_pred CCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHH
Q psy17765 125 GKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQ 204 (475)
Q Consensus 125 g~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~ 204 (475)
|+|++++++..|||+||||||||+||||||++++|+.||+++||||||||||||++||||||||.|++++++||+|+||+
T Consensus 10 ~~g~~~~~k~~srS~rAgL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~ 89 (139)
T PLN00156 10 GRGKPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQ 89 (139)
T ss_pred CCCcccccCCcCcccccCcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHH
Confidence 45666667889999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765 205 LAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240 (475)
Q Consensus 205 lAI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~ 240 (475)
+||+||+||+.||+++||++|||+|+||++|+|+++
T Consensus 90 lAIrnDeEL~~Ll~~vTIa~GGV~P~i~~~l~~kk~ 125 (139)
T PLN00156 90 LAVRNDEELSKLLGSVTIAAGGVLPNIHQTLLPKKV 125 (139)
T ss_pred hhccCcHHHHHHHCCCccCCCccCCCccHhhccccc
Confidence 999999999999999999999999999999999998
No 3
>PLN00157 histone H2A; Provisional
Probab=100.00 E-value=6.2e-42 Score=306.26 Aligned_cols=113 Identities=73% Similarity=1.118 Sum_probs=109.2
Q ss_pred CCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHH
Q psy17765 128 GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI 207 (475)
Q Consensus 128 ~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI 207 (475)
++.+++..|+|+||||||||+||||+|++++|++||+++|+||||||||||++||||||||.|++++++||+|+||++||
T Consensus 10 ~~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI 89 (132)
T PLN00157 10 GGGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAV 89 (132)
T ss_pred CccCcCCcCcccccCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcc
Confidence 34456789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765 208 RNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240 (475)
Q Consensus 208 ~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~ 240 (475)
+||+||++||+++||++|||+|+||++|+|+++
T Consensus 90 ~nDeEL~~Ll~~vtIa~GGV~P~i~~~ll~kk~ 122 (132)
T PLN00157 90 RNDEELSKLLGGVTIAAGGVLPNIHSVLLPKKS 122 (132)
T ss_pred cCcHHHHHHHcCceecCCccCCCcchhhcCCCC
Confidence 999999999999999999999999999999988
No 4
>PTZ00017 histone H2A; Provisional
Probab=100.00 E-value=2.9e-41 Score=302.89 Aligned_cols=110 Identities=75% Similarity=1.151 Sum_probs=107.4
Q ss_pred CCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765 131 KTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND 210 (475)
Q Consensus 131 ~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD 210 (475)
+++..|||+||||||||+||||||++++|++||+++|||||+||||||++||||||||+|++++++||+|+||++||+||
T Consensus 14 ~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~nD 93 (134)
T PTZ00017 14 KKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRND 93 (134)
T ss_pred CcCcccccccCCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccCc
Confidence 44678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhcCceecCCcccCCcccccccccc
Q psy17765 211 EELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240 (475)
Q Consensus 211 ~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~ 240 (475)
+||+.||+++||++|||+|+||++|+|+++
T Consensus 94 eEL~~Ll~~vtIa~GGV~P~i~~~l~~k~~ 123 (134)
T PTZ00017 94 EELNKLLAGVTIASGGVLPNIHKVLLPKKS 123 (134)
T ss_pred HHHHHHHcCCcccCCccCCCccHhhccCCC
Confidence 999999999999999999999999999988
No 5
>PTZ00252 histone H2A; Provisional
Probab=100.00 E-value=4.9e-41 Score=300.13 Aligned_cols=107 Identities=50% Similarity=0.863 Sum_probs=102.4
Q ss_pred CccC-cCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHh--cCCcccchhHHHHHHhc
Q psy17765 133 KSKT-RSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARD--NKKTRIIPRHLQLAIRN 209 (475)
Q Consensus 133 ~~~s-rSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~--~k~~rItP~hI~lAI~n 209 (475)
+..+ ||+|||||||||||||||++++|+.||+++||||||||||||++||||||||.|++ ++++||+|+||++||+|
T Consensus 13 ~~~~~rS~rAGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 13 KSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred ccccccccccCccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 3445 99999999999999999999999999999999999999999999999999999976 78899999999999999
Q ss_pred cHHHHhhhcCceecCCcccCCccccccccc
Q psy17765 210 DEELNKLLSGVTIAQGGVLPNIQAVRVLEQ 239 (475)
Q Consensus 210 D~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~ 239 (475)
|+||++||+++||++|||+|+||++|+|++
T Consensus 93 DeEL~~Ll~~vTIa~GGVlP~i~~~l~~k~ 122 (134)
T PTZ00252 93 DDDLGSLLKNVTLSRGGVMPSLNKALAKKH 122 (134)
T ss_pred hHHHHHHHcCCccCCCccCCCccHhhcccc
Confidence 999999999999999999999999999983
No 6
>smart00414 H2A Histone 2A.
Probab=100.00 E-value=1.2e-40 Score=289.59 Aligned_cols=105 Identities=85% Similarity=1.235 Sum_probs=103.3
Q ss_pred CcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHh
Q psy17765 136 TRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNK 215 (475)
Q Consensus 136 srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~ 215 (475)
|||+|||||||||||||||++++|++||+++|+|||+||||||++||||||||+|++++++||+|+||++||+||+|||+
T Consensus 1 srS~ragL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~nD~EL~~ 80 (106)
T smart00414 1 SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELNK 80 (106)
T ss_pred CccccCCccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccCCHHHHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCceecCCcccCCcccccccccc
Q psy17765 216 LLSGVTIAQGGVLPNIQAVRVLEQT 240 (475)
Q Consensus 216 Lf~~~tIa~gGV~p~i~~~ll~~~~ 240 (475)
||+++||++|||+|+||+.|+|+++
T Consensus 81 L~~~vti~~ggv~p~i~~~l~~~~~ 105 (106)
T smart00414 81 LLKGVTIAQGGVLPNIHKVLLPKKT 105 (106)
T ss_pred HHcCcccCCCccCCCcchhhcccCC
Confidence 9999999999999999999999986
No 7
>PLN00154 histone H2A; Provisional
Probab=100.00 E-value=4.6e-40 Score=294.83 Aligned_cols=109 Identities=62% Similarity=0.893 Sum_probs=104.8
Q ss_pred CCCccCcCCCCCcccchhHHHHHHhhcC-cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765 131 KTKSKTRSSRAGLQFPVGRIHRLLRKGN-YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN 209 (475)
Q Consensus 131 ~~~~~srSsRagL~FPVsRi~r~Lke~~-~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n 209 (475)
+++..|||+||||||||+||||+||+++ |++||+++|||||+||||||++||||||||+|++++++||+|+||++||+|
T Consensus 25 ~~k~~srS~rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 25 KKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred CcCCcCcccccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 4567899999999999999999999997 578999999999999999999999999999999999999999999999999
Q ss_pred cHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765 210 DEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240 (475)
Q Consensus 210 D~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~ 240 (475)
|+||++||+ +||++|||+|+||++|+|+++
T Consensus 105 DeEL~~Ll~-~TIa~GGVlP~i~~~l~~k~~ 134 (136)
T PLN00154 105 DEELDTLIK-GTIAGGGVIPHIHKSLINKST 134 (136)
T ss_pred cHHHHHHhc-CCccCCccCCCcchhhccccc
Confidence 999999998 699999999999999999986
No 8
>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=100.00 E-value=1.6e-39 Score=286.28 Aligned_cols=112 Identities=79% Similarity=1.190 Sum_probs=108.1
Q ss_pred CCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHH
Q psy17765 128 GKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI 207 (475)
Q Consensus 128 ~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI 207 (475)
||.+++.+|+|+||||+|||+||||||++++|++||+++|+|||+||||||++||||+|+|.|+++++++|+|+||++||
T Consensus 4 ~k~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi 83 (115)
T cd00074 4 GKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAV 83 (115)
T ss_pred CccCcCccccccccCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHH
Confidence 36667788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccHHHHhhhcCceecCCcccCCccccccccc
Q psy17765 208 RNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQ 239 (475)
Q Consensus 208 ~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~ 239 (475)
+||+|||+||+++||++|||+|+||+.|+|++
T Consensus 84 ~nD~EL~~L~~~vtI~~ggv~p~i~~~l~~~~ 115 (115)
T cd00074 84 RNDEELNKLLKGVTIASGGVLPNIHKVLLPKK 115 (115)
T ss_pred hccHHHHHHHcCCcccCCccCCCcchhhcCCC
Confidence 99999999999999999999999999999874
No 9
>KOG1756|consensus
Probab=100.00 E-value=4.9e-39 Score=283.69 Aligned_cols=109 Identities=83% Similarity=1.191 Sum_probs=106.3
Q ss_pred CCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccH
Q psy17765 132 TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDE 211 (475)
Q Consensus 132 ~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~ 211 (475)
+...|+|.|+|||||||||+|+|++++|.+||+.+|||||+||||||++||||+|||+|+++++.||+|+||++||+||+
T Consensus 15 ~~~~srs~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~NDe 94 (131)
T KOG1756|consen 15 KAKSSRSSRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRNDE 94 (131)
T ss_pred hhhcchhhhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhCcH
Confidence 45668899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhhcCceecCCcccCCcccccccccc
Q psy17765 212 ELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240 (475)
Q Consensus 212 EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~ 240 (475)
||+.|++++||++|||+|+||+.+||+++
T Consensus 95 EL~~lL~~vtIa~GGvlPnI~~~lLpKk~ 123 (131)
T KOG1756|consen 95 ELNKLLGKVTIAQGGVLPNIQAILLPKKT 123 (131)
T ss_pred HHHHHhccceeccCCcccccchhhccccc
Confidence 99999999999999999999999999987
No 10
>PLN00158 histone H2B; Provisional
Probab=100.00 E-value=2.1e-38 Score=276.89 Aligned_cols=112 Identities=73% Similarity=1.037 Sum_probs=102.5
Q ss_pred CCcchhhhhhccccccccccccccccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCC
Q psy17765 6 SSGKAVKKAGKAQKNIAKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 85 (475)
Q Consensus 6 ~k~~~~~k~gka~~~~~~~~kk~~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr 85 (475)
|.+++++|+++++ ++|++++++++|++||||||||||||++||++||.+||||++||||||+.||++|+++|++
T Consensus 5 ~~~k~~~~~~~~~------~kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr 78 (116)
T PLN00158 5 PSKKPAKKAAKGA------KKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKK 78 (116)
T ss_pred cchhhhhhccccc------cccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 4566666665554 4566777899999999999999999999999999999999999999999999999999999
Q ss_pred CCCChHHHHHHHHHhCcHHHHHHHHHHhhhhhhhcccc
Q psy17765 86 STITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 123 (475)
Q Consensus 86 ~TlT~rdIqtAVrllLPgeLaKhAvseG~kAV~ky~sS 123 (475)
+|||+||||+|||++|||||+|||++||++||++|.++
T Consensus 79 ~TltsrEIqtAvrLvLpgELaKhAvsEGtkAv~k~~~~ 116 (116)
T PLN00158 79 PTVTSREIQTAVRLILPGELAKHAVSEGTKAVTKFTSA 116 (116)
T ss_pred CcCCHHHHHHHHHHhccHHHHHHHHHHHHHHHHHhhcC
Confidence 99999999999999999999999999999999999764
No 11
>PTZ00463 histone H2B; Provisional
Probab=100.00 E-value=6.7e-38 Score=273.54 Aligned_cols=111 Identities=67% Similarity=0.995 Sum_probs=99.8
Q ss_pred hhhhcccccc--ccccccccccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCC
Q psy17765 12 KKAGKAQKNI--AKSDKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTIT 89 (475)
Q Consensus 12 ~k~gka~~~~--~~~~kk~~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT 89 (475)
+|+|++++.. .+++++++++++++|+.||||||||||||++||++||.+||||++|||||||.||++|+++++++|||
T Consensus 4 ~~~~~~~~~~~~~~~~kk~~~kr~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~Tlt 83 (117)
T PTZ00463 4 KKPAKAKKAATGPDGKKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLS 83 (117)
T ss_pred ccccccccCCCCCCccccccccccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCC
Confidence 3455555432 33345667778999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHhCcHHHHHHHHHHhhhhhhhccc
Q psy17765 90 SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS 122 (475)
Q Consensus 90 ~rdIqtAVrllLPgeLaKhAvseG~kAV~ky~s 122 (475)
+||||+||||+|||||+|||++||++||++|.+
T Consensus 84 srEIQtAvrLlLpGELaKhAvsEGtkAv~k~~~ 116 (117)
T PTZ00463 84 SREIQTAIRLVLPGELAKHAVSEGTKAVTKFTS 116 (117)
T ss_pred HHHHHHHHhhcccHHHHHhhhhHHHHHHHHhhc
Confidence 999999999999999999999999999999964
No 12
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=100.00 E-value=7.5e-37 Score=266.28 Aligned_cols=118 Identities=75% Similarity=1.114 Sum_probs=109.5
Q ss_pred cCCCCCCC-C-CCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccch
Q psy17765 123 SKGKGGKA-K-TKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIP 200 (475)
Q Consensus 123 Skg~~~k~-~-~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP 200 (475)
+.|||||+ . +...|+|.++||+|||+||+|+|++++|..||++.|+||++||||||++||||+|||+|++++++||+|
T Consensus 3 ~~GKGgK~a~~r~~~s~sa~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~P 82 (132)
T COG5262 3 SGGKGGKAADARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIP 82 (132)
T ss_pred cCCcCcccccchhccchhhhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceech
Confidence 34666662 2 345689999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHhccHHHHhhhcCceecCCcccCCcccccccccc
Q psy17765 201 RHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240 (475)
Q Consensus 201 ~hI~lAI~nD~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~ 240 (475)
+|||+|||||+||+.|++++||++|||+|+||+.+||+..
T Consensus 83 rHlqlAIrnD~EL~~l~~~~tIa~GGvlp~I~~~ll~k~s 122 (132)
T COG5262 83 RHLQLAIRNDEELNKLLGDVTIAQGGVLPNINPGLLPKSS 122 (132)
T ss_pred HHHHHHhcCcHHHHHHhhhheeecCCcccccChhhhhhhh
Confidence 9999999999999999999999999999999999998754
No 13
>smart00427 H2B Histone H2B.
Probab=100.00 E-value=6.2e-35 Score=245.59 Aligned_cols=89 Identities=89% Similarity=1.240 Sum_probs=87.2
Q ss_pred hhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHHHHHHh
Q psy17765 34 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEG 113 (475)
Q Consensus 34 ~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKhAvseG 113 (475)
++|++||||||||||||++||++||.+||||++|+|||||.||++|+++++|+|||+||||+|||++|||||+|||++||
T Consensus 1 esy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~LpgeLakhAvsEg 80 (89)
T smart00427 1 ETYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 80 (89)
T ss_pred CcHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHccHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhccc
Q psy17765 114 TKAVTKYTS 122 (475)
Q Consensus 114 ~kAV~ky~s 122 (475)
++||++|.+
T Consensus 81 tkAv~k~~~ 89 (89)
T smart00427 81 TKAVTKYSS 89 (89)
T ss_pred HHHHHhhcC
Confidence 999999963
No 14
>PLN00158 histone H2B; Provisional
Probab=100.00 E-value=3.2e-35 Score=256.97 Aligned_cols=88 Identities=60% Similarity=0.860 Sum_probs=77.3
Q ss_pred cCccchhccccccccccccCCccCcCCCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCC
Q psy17765 360 SSGKAVKKAGKAQKNITKSDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKR 439 (475)
Q Consensus 360 ~~~k~~~~~~~~~~~~~~~~~k~~~~~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr 439 (475)
+++|+.+++++.+ ++|++++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|
T Consensus 5 ~~~k~~~~~~~~~------~kk~~~kr~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr 78 (116)
T PLN00158 5 PSKKPAKKAAKGA------KKKGSKSKTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKK 78 (116)
T ss_pred cchhhhhhccccc------cccccccccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 4566665554432 4556777899999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCCc-hhheehc
Q psy17765 440 STITKDL-CPSVCLY 453 (475)
Q Consensus 440 ~Tltsr~-~~~~~~~ 453 (475)
+|||+|| |+||+|+
T Consensus 79 ~TltsrEIqtAvrLv 93 (116)
T PLN00158 79 PTVTSREIQTAVRLI 93 (116)
T ss_pred CcCCHHHHHHHHHHh
Confidence 9999987 7899984
No 15
>PTZ00463 histone H2B; Provisional
Probab=100.00 E-value=5.3e-35 Score=255.38 Aligned_cols=75 Identities=53% Similarity=0.862 Sum_probs=70.6
Q ss_pred CCccCcCCCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheehc
Q psy17765 379 DKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCLY 453 (475)
Q Consensus 379 ~~k~~~~~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~~ 453 (475)
++|++++|+|+|++||||||||||||+|||++||+||||||||||||||.||++|++||+|+|||+|| |+||+|+
T Consensus 19 ~kk~~~kr~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 19 KKKRKKSRYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred cccccccccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 45567778999999999999999999999999999999999999999999999999999999999986 9999984
No 16
>KOG1757|consensus
Probab=99.97 E-value=1.9e-32 Score=237.18 Aligned_cols=108 Identities=60% Similarity=0.891 Sum_probs=101.8
Q ss_pred CCccCcCCCCCcccchhHHHHHHhhcCc-ccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765 132 TKSKTRSSRAGLQFPVGRIHRLLRKGNY-AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND 210 (475)
Q Consensus 132 ~~~~srSsRagL~FPVsRi~r~Lke~~~-~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD 210 (475)
.+..|+|+|+||||||+||||.|+.... ..||++.++||.+|+||||++|+||||||.+++.+.+||||+|+|+||+.|
T Consensus 18 ~k~vs~s~raGlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRGD 97 (131)
T KOG1757|consen 18 AKAVSRSARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGD 97 (131)
T ss_pred hhhhhHHHhcccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecCc
Confidence 5678999999999999999999998654 579999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhcCceecCCcccCCcccccccccc
Q psy17765 211 EELNKLLSGVTIAQGGVLPNIQAVRVLEQT 240 (475)
Q Consensus 211 ~EL~~Lf~~~tIa~gGV~p~i~~~ll~~~~ 240 (475)
+||+.|++ .||++|||+||||..|+-+++
T Consensus 98 eELDtLIk-~TiagGgViPhihk~l~~k~~ 126 (131)
T KOG1757|consen 98 EELDTLIK-ATIAGGGVIPHIHKSLINKKG 126 (131)
T ss_pred HHHHHHHH-HhhccCccccchHHHHhcccc
Confidence 99999997 589999999999999987766
No 17
>smart00427 H2B Histone H2B.
Probab=99.97 E-value=8.6e-32 Score=226.61 Aligned_cols=66 Identities=76% Similarity=1.062 Sum_probs=63.8
Q ss_pred ccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheehc
Q psy17765 388 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCLY 453 (475)
Q Consensus 388 esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~~ 453 (475)
|+|++||||||||||||+|||++||+||||||||||||||.||++|++||||+|||+|| |+||+|+
T Consensus 1 esy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 1 ETYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred CcHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999987 7899884
No 18
>KOG1744|consensus
Probab=99.96 E-value=1.5e-30 Score=230.87 Aligned_cols=99 Identities=85% Similarity=1.178 Sum_probs=95.5
Q ss_pred cccccccCchhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHH
Q psy17765 25 DKKKKHRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGE 104 (475)
Q Consensus 25 ~kk~~~k~~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPge 104 (475)
+|++..++.++|+.|++|||||||||++|+.+||.+||+|+||||++||.||++|+++++++|||++|||+||+|+|||+
T Consensus 28 gk~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLllPge 107 (127)
T KOG1744|consen 28 GKKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLLLPGE 107 (127)
T ss_pred cccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHhCchH
Confidence 36677888999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhhhhhhcccc
Q psy17765 105 LAKHAVSEGTKAVTKYTSS 123 (475)
Q Consensus 105 LaKhAvseG~kAV~ky~sS 123 (475)
|++||++||++||.+|.++
T Consensus 108 l~khA~seGtkav~ky~~s 126 (127)
T KOG1744|consen 108 LAKHAVSEGTKAVTKYTSS 126 (127)
T ss_pred HhhhhhcccchhheeeccC
Confidence 9999999999999999876
No 19
>KOG1744|consensus
Probab=99.95 E-value=5.8e-29 Score=220.71 Aligned_cols=76 Identities=68% Similarity=0.995 Sum_probs=70.9
Q ss_pred cCCccCcCCCccceeehhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc-hhheehc
Q psy17765 378 SDKKKKPRRKESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL-CPSVCLY 453 (475)
Q Consensus 378 ~~~k~~~~~~esy~~Yi~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~-~~~~~~~ 453 (475)
.+|++..++.|+|+.||||||||||||+|||++||+||||||||||||||+||++|++||+|+|||||| |++++|+
T Consensus 27 ~gk~~~~~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 27 AGKKRSTRRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ccccCcccccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 346677889999999999999999999999999999999999999999999999999999999999987 8888873
No 20
>PLN00155 histone H2A; Provisional
Probab=99.73 E-value=2e-18 Score=134.80 Aligned_cols=54 Identities=70% Similarity=1.167 Sum_probs=48.2
Q ss_pred CCCCCCCCCccCcCCCCCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHH
Q psy17765 125 GKGGKAKTKSKTRSSRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYL 178 (475)
Q Consensus 125 g~~~k~~~~~~srSsRagL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYL 178 (475)
|++++.+++..|+|+||||||||+||||+|++++|+.||+++||||||||||||
T Consensus 5 g~g~~~~~k~~srS~rAgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEYL 58 (58)
T PLN00155 5 GKGKTSGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL 58 (58)
T ss_pred CCCCccccCccCcccccccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHhC
Confidence 333444456789999999999999999999999999999999999999999997
No 21
>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=99.26 E-value=6.7e-12 Score=101.61 Aligned_cols=73 Identities=41% Similarity=0.607 Sum_probs=68.4
Q ss_pred CCCCCcccchhHHHHHHhhcCccc-ccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765 138 SSRAGLQFPVGRIHRLLRKGNYAE-RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND 210 (475)
Q Consensus 138 SsRagL~FPVsRi~r~Lke~~~~~-RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD 210 (475)
+.+..+.||+.|+.+-+.++.+.+ ||++.|.+||.+++||++.+|++.|++.|.+.++.+|+|+||++|+++|
T Consensus 2 ~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 2 TRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred cccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 346789999999999999988774 9999999999999999999999999999999999999999999999876
No 22
>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=98.95 E-value=6.3e-10 Score=90.08 Aligned_cols=69 Identities=30% Similarity=0.423 Sum_probs=65.1
Q ss_pred cCchhHHHHHHHHhhccCCC----CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 31 RRKESYAIYIYKVLKQVHPD----TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 31 k~~~sf~~yI~KVLKQVhPd----~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
++...+..+|+|++++++++ ..||.+|+.+|++++.+++.+|..+|..++.+++|.||+++|||.|+++
T Consensus 2 ~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 2 TRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp HSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred cccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 34567899999999999998 8999999999999999999999999999999999999999999999986
No 23
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=98.74 E-value=2.1e-08 Score=86.65 Aligned_cols=78 Identities=23% Similarity=0.437 Sum_probs=73.6
Q ss_pred CcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhcC
Q psy17765 142 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSG 219 (475)
Q Consensus 142 gL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~~ 219 (475)
.-.||++|+.++||-+....+|+..+||...-.||.+.++|+.+++..|+....+|||.+||..|+.+|+.++.|=..
T Consensus 21 ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~ 98 (113)
T COG5247 21 KTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNM 98 (113)
T ss_pred hhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHH
Confidence 457999999999999999999999999999999999999999999999999999999999999999999999877543
No 24
>KOG1659|consensus
Probab=98.25 E-value=1.8e-06 Score=83.51 Aligned_cols=75 Identities=20% Similarity=0.401 Sum_probs=71.7
Q ss_pred cccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhh
Q psy17765 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLL 217 (475)
Q Consensus 143 L~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf 217 (475)
-.||++||+++||-+....||...+||.+.-.||.++.+||..++..++..+-++++++||..||.||+.++.|=
T Consensus 12 trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk 86 (224)
T KOG1659|consen 12 TRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK 86 (224)
T ss_pred ccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence 469999999999999999999999999999999999999999999999999999999999999999999988763
No 25
>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=97.94 E-value=2.7e-05 Score=61.85 Aligned_cols=64 Identities=20% Similarity=0.288 Sum_probs=57.4
Q ss_pred ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHH
Q psy17765 144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAI 207 (475)
Q Consensus 144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI 207 (475)
.||.++|.|+||......+|+..|...++-..|.++.+|..-|...|.+.+++.|+++||..||
T Consensus 2 ~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 5999999999999866679999999999999999999999999999999999999999999886
No 26
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=97.44 E-value=0.00057 Score=55.90 Aligned_cols=63 Identities=16% Similarity=0.353 Sum_probs=59.1
Q ss_pred HHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhC
Q psy17765 39 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL 101 (475)
Q Consensus 39 yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllL 101 (475)
-|...++++.|+..++.+|...|..+..++.+.++..|.+|+.+.+++|+..+|||-+++..+
T Consensus 6 ~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~ 68 (72)
T cd07981 6 KLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNW 68 (72)
T ss_pred HHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Confidence 377889999999999999999999999999999999999999999999999999999988753
No 27
>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=97.21 E-value=0.001 Score=52.83 Aligned_cols=59 Identities=27% Similarity=0.449 Sum_probs=52.8
Q ss_pred HHHHHHhhccCCCC-CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHH
Q psy17765 38 IYIYKVLKQVHPDT-GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAV 97 (475)
Q Consensus 38 ~yI~KVLKQVhPd~-~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAV 97 (475)
.-|.|+.|+. |+. .+|.+|...|......+++.|+.+|...+..++|+|++.+||..||
T Consensus 6 a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 6 ARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 4589999998 664 6999999999999999999999999999999999999999999886
No 28
>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=97.14 E-value=0.0014 Score=52.88 Aligned_cols=64 Identities=22% Similarity=0.267 Sum_probs=58.5
Q ss_pred ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
.+|..-|.|+.+... ..||+..+.-.|+-.+||...+|+.-|.+++++.+++.++++||..|+.
T Consensus 2 ~~p~~~i~ria~~~G-i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLG-IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 478889999998755 4599999999999999999999999999999999999999999999863
No 29
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=96.95 E-value=0.0017 Score=55.86 Aligned_cols=67 Identities=30% Similarity=0.415 Sum_probs=60.9
Q ss_pred CCcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 141 AGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 141 agL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
..+.+|+-=|.|+|++.. ..||+.+|...|..++|-+..+|.+-|...|.+.+++.|+++||++|+.
T Consensus 16 ~~~~Lp~apv~Ri~r~~~-~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~ 82 (91)
T COG2036 16 TDLLLPKAPVRRILRKAG-AERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALK 82 (91)
T ss_pred hhhhcCchHHHHHHHHHh-HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH
Confidence 347889999999998743 4599999999999999999999999999999999999999999999975
No 30
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=96.89 E-value=0.0018 Score=55.65 Aligned_cols=65 Identities=25% Similarity=0.378 Sum_probs=58.9
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCc
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP 102 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLP 102 (475)
..-|.|++|++-++ .+|.+|...|+..+..+++-|+.+|..++...+|+|++..||+-|.+.+-.
T Consensus 22 ~apv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~ 86 (91)
T COG2036 22 KAPVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGR 86 (91)
T ss_pred chHHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcc
Confidence 34577888888777 899999999999999999999999999999999999999999999998754
No 31
>PLN00035 histone H4; Provisional
Probab=96.85 E-value=0.0035 Score=55.08 Aligned_cols=63 Identities=11% Similarity=0.136 Sum_probs=56.1
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 100 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll 100 (475)
...|.|+++..- --.||.++.+-+...+..+++.|+.+|..++.+.+|+|+|..||..|++..
T Consensus 32 k~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 32 KPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred HHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence 467888888764 346999999999999999999999999999999999999999999988763
No 32
>PLN00035 histone H4; Provisional
Probab=96.79 E-value=0.0022 Score=56.34 Aligned_cols=64 Identities=16% Similarity=0.232 Sum_probs=60.3
Q ss_pred cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765 145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN 209 (475)
Q Consensus 145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n 209 (475)
+|..-|.|+.+.+. ..||+..+..-|..+||.+..+|+.-|..++...+++.|+.+||.+|+..
T Consensus 30 ipk~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr 93 (103)
T PLN00035 30 ITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKR 93 (103)
T ss_pred CCHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 89999999999876 78999999999999999999999999999999999999999999999864
No 33
>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=96.44 E-value=0.0092 Score=50.78 Aligned_cols=64 Identities=19% Similarity=0.296 Sum_probs=59.8
Q ss_pred cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765 145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN 209 (475)
Q Consensus 145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n 209 (475)
+|..-|.|+.+.+. ..||+..+-.-+..+||.+..+|+.-|..++.+.+++.|+.+||.+|+..
T Consensus 14 i~k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr 77 (85)
T cd00076 14 ITKPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR 77 (85)
T ss_pred CCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 78889999999876 78999999999999999999999999999999999999999999999864
No 34
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=96.35 E-value=0.011 Score=53.02 Aligned_cols=68 Identities=25% Similarity=0.219 Sum_probs=60.1
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA 106 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa 106 (475)
...|+|.|++-.-...|+..|..+|...+..+...|.+.|...+..+++++||+++|+.|++- ..||.
T Consensus 23 V~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n--D~EL~ 90 (115)
T cd00074 23 VGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN--DEELN 90 (115)
T ss_pred HHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc--cHHHH
Confidence 578999999866667899999999999999999999999999999999999999999999987 44443
No 35
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=96.23 E-value=0.015 Score=46.95 Aligned_cols=60 Identities=23% Similarity=0.314 Sum_probs=52.6
Q ss_pred HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHH
Q psy17765 38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR 98 (475)
Q Consensus 38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVr 98 (475)
..|+++.++.-=+ .||.++..-|...+...+..|+++|..++...+|+|+|..||..|++
T Consensus 6 ~~i~ria~~~Gi~-ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 6 ETIKDVAESLGIG-NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred HHHHHHHHHCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 4578888876332 59999999999999999999999999999999999999999988764
No 36
>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=96.06 E-value=0.026 Score=46.09 Aligned_cols=62 Identities=18% Similarity=0.353 Sum_probs=50.7
Q ss_pred HHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765 39 YIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 100 (475)
Q Consensus 39 yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll 100 (475)
-|...++||-|+..+..++.+.|-.+..++.+.++..+++||.+.+..|+..+|||.....-
T Consensus 4 ~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~ 65 (68)
T PF03847_consen 4 KLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN 65 (68)
T ss_dssp HHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence 37788999999999999999999999999999999999999999999999999999887653
No 37
>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=95.93 E-value=0.028 Score=46.05 Aligned_cols=66 Identities=17% Similarity=0.280 Sum_probs=59.0
Q ss_pred cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765 145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRND 210 (475)
Q Consensus 145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD 210 (475)
++-..+..++++..-..|++..|...|..+.|-+..+|++.|...|++.++..|.++||++++..+
T Consensus 2 ~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 2 LTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred CcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 345667788887666789999999999999999999999999999999999999999999998765
No 38
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=95.90 E-value=0.033 Score=47.40 Aligned_cols=62 Identities=13% Similarity=0.186 Sum_probs=54.9
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
...|.|+.+..- --.||.++.+-+...+..+++.|+.+|..++.+.+|+|+|..||..|++.
T Consensus 16 k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr 77 (85)
T cd00076 16 KPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKR 77 (85)
T ss_pred HHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHH
Confidence 467888888753 34699999999999999999999999999999999999999999988875
No 39
>PTZ00015 histone H4; Provisional
Probab=95.80 E-value=0.029 Score=49.36 Aligned_cols=64 Identities=16% Similarity=0.255 Sum_probs=58.6
Q ss_pred ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
-+|..-|.|+.+.+ =..||+..+-.-+..+||.+..+|+.-|..++...+++.|+.+||.+|+.
T Consensus 30 gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlK 93 (102)
T PTZ00015 30 GITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALK 93 (102)
T ss_pred CCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence 47778999999875 36899999999999999999999999999999999999999999999975
No 40
>smart00417 H4 Histone H4.
Probab=95.69 E-value=0.019 Score=47.78 Aligned_cols=60 Identities=15% Similarity=0.180 Sum_probs=54.9
Q ss_pred cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHH
Q psy17765 145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQL 205 (475)
Q Consensus 145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~l 205 (475)
+|..-|.|+++.+. ..||+..+-..+..+||.+..+|+..|..++...+++.|+.+||..
T Consensus 14 I~k~~IrRLaRr~G-vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 14 ITKPAIRRLARRGG-VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred CCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 67889999999764 6899999999999999999999999999999999999999999864
No 41
>PTZ00015 histone H4; Provisional
Probab=95.62 E-value=0.048 Score=47.98 Aligned_cols=63 Identities=14% Similarity=0.242 Sum_probs=55.5
Q ss_pred HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
=...|.|+++..- --.||.++.+.+...+..+++.|+.+|..++.+.+|+|+|..||..|++.
T Consensus 32 ~k~~IrRLarr~G-vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr 94 (102)
T PTZ00015 32 TKGAIRRLARRGG-VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKR 94 (102)
T ss_pred CHHHHHHHHHHcC-CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHh
Confidence 3578888888752 24699999999999999999999999999999999999999999988875
No 42
>smart00428 H3 Histone H3.
Probab=95.46 E-value=0.057 Score=47.74 Aligned_cols=68 Identities=22% Similarity=0.312 Sum_probs=62.6
Q ss_pred CchhHHHHHHHHhhccCC--CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 32 RKESYAIYIYKVLKQVHP--DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 32 ~~~sf~~yI~KVLKQVhP--d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
++-.|+-.++.+..+..+ ++.++.+|+.-|.......+..+..+|..++.+.+|.|++++||+-|.++
T Consensus 31 ~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ri 100 (105)
T smart00428 31 RKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRI 100 (105)
T ss_pred ccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHH
Confidence 345699999999999888 88999999999999999999999999999999999999999999998876
No 43
>KOG0871|consensus
Probab=94.58 E-value=0.09 Score=48.99 Aligned_cols=79 Identities=16% Similarity=0.312 Sum_probs=66.3
Q ss_pred HHHHHHhhccCC-CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh-CcHHHHHHHHHHhhh
Q psy17765 38 IYIYKVLKQVHP-DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL-LPGELAKHAVSEGTK 115 (475)
Q Consensus 38 ~yI~KVLKQVhP-d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll-LPgeLaKhAvseG~k 115 (475)
.-|.|+.+.+-| |+.+..+|-+++...+..++..|+.||.+.|....|+||....|+.|..-+ |-.. +.++.+
T Consensus 16 Atv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eY-----iee~~~ 90 (156)
T KOG0871|consen 16 ATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEY-----IEEAEE 90 (156)
T ss_pred HHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHH-----HHHHHH
Confidence 348889999999 999999999999999999999999999999999999999999999999987 4422 334444
Q ss_pred hhhhcc
Q psy17765 116 AVTKYT 121 (475)
Q Consensus 116 AV~ky~ 121 (475)
++..|.
T Consensus 91 vl~~~K 96 (156)
T KOG0871|consen 91 VLENCK 96 (156)
T ss_pred HHHHHH
Confidence 454443
No 44
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=94.27 E-value=0.17 Score=45.28 Aligned_cols=65 Identities=12% Similarity=0.182 Sum_probs=57.0
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCc
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP 102 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLP 102 (475)
...|+++|+.-. ....+.++...|-.|+.+....|+.+|..++.+.+|+|++..||..|++....
T Consensus 4 ~~~v~~iLk~~G-v~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 4 ARVIAAILKSMG-ITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHCC-CCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 356888888752 24679999999999999999999999999999999999999999999988653
No 45
>PLN00156 histone H2AX; Provisional
Probab=94.24 E-value=0.11 Score=47.97 Aligned_cols=68 Identities=25% Similarity=0.227 Sum_probs=58.2
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA 106 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa 106 (475)
...|+|.|+.-+-...|+..|.-+|...+..+...|.+.|..-++.+++..||++.||.||+- ..||.
T Consensus 32 VgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn--DeEL~ 99 (139)
T PLN00156 32 VGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN--DEELS 99 (139)
T ss_pred hHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC--cHHHH
Confidence 467999999987777899999999988888888888888888889999999999999999987 44444
No 46
>KOG0869|consensus
Probab=94.21 E-value=0.14 Score=48.19 Aligned_cols=67 Identities=19% Similarity=0.323 Sum_probs=59.1
Q ss_pred HHHHHHHhhccCCCC-CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh-CcH
Q psy17765 37 AIYIYKVLKQVHPDT-GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL-LPG 103 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~-~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll-LPg 103 (475)
..-|-|+.|+.-|.. .||.+|-+.|...|..+..-|..||+.-|..-+|+|||-.||..|+--+ |+.
T Consensus 35 IANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~ 103 (168)
T KOG0869|consen 35 IANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFEN 103 (168)
T ss_pred HHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHh
Confidence 344678888887764 6999999999999999999999999999999999999999999999877 554
No 47
>KOG1657|consensus
Probab=94.02 E-value=0.053 Score=54.11 Aligned_cols=78 Identities=19% Similarity=0.293 Sum_probs=72.5
Q ss_pred CcccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhcC
Q psy17765 142 GLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSG 219 (475)
Q Consensus 142 gL~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~~ 219 (475)
...||.+||.+.||-+.....|...|||.++-..|++..|+=..+...+..+++..+.-.||.-++.+..-++.|...
T Consensus 72 ~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~Di 149 (236)
T KOG1657|consen 72 NHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDI 149 (236)
T ss_pred hccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceecc
Confidence 479999999999999988899999999999999999999999889999999999999999999999999999888863
No 48
>smart00417 H4 Histone H4.
Probab=93.47 E-value=0.23 Score=41.30 Aligned_cols=57 Identities=11% Similarity=0.178 Sum_probs=49.7
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQ 94 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIq 94 (475)
...|.|+++..- --.||..+.+-+..++..+++.|+.+|..++.+.+++|+|..||.
T Consensus 16 k~~IrRLaRr~G-vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~ 72 (74)
T smart00417 16 KPAIRRLARRGG-VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVV 72 (74)
T ss_pred HHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhe
Confidence 567888888652 235999999999999999999999999999999999999999984
No 49
>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=93.44 E-value=0.22 Score=44.58 Aligned_cols=63 Identities=17% Similarity=0.086 Sum_probs=55.8
Q ss_pred hHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccH
Q psy17765 148 GRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDE 211 (475)
Q Consensus 148 sRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~ 211 (475)
--|+++|++. -..+++..++..|.-.++-.+.+|+.-|..+|++.+++.|+.+||++||..--
T Consensus 5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~ 67 (117)
T cd07979 5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRV 67 (117)
T ss_pred HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHh
Confidence 3578899873 34689999999999999999999999999999999999999999999998643
No 50
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=93.32 E-value=0.19 Score=49.67 Aligned_cols=76 Identities=22% Similarity=0.388 Sum_probs=69.3
Q ss_pred cccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhccHHHHhhhc
Q psy17765 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLS 218 (475)
Q Consensus 143 L~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~nD~EL~~Lf~ 218 (475)
+.+|..||.++||-+....-|++.|||.++-+-|-+.+|+--.|--.|..+++..+--.||..|+...+-++.|+.
T Consensus 108 h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLid 183 (286)
T COG5208 108 HNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLID 183 (286)
T ss_pred ccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhh
Confidence 6799999999999888888999999999999999999998888877788888888899999999999999888885
No 51
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=93.24 E-value=0.35 Score=41.15 Aligned_cols=63 Identities=25% Similarity=0.419 Sum_probs=55.1
Q ss_pred cchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcC---CcccchhHHHHHHh
Q psy17765 145 FPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK---KTRIIPRHLQLAIR 208 (475)
Q Consensus 145 FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k---~~rItP~hI~lAI~ 208 (475)
||-..+.|++.. ...+.++....+.++++---++.||.|.|.......+ ...|.|.||+.|.+
T Consensus 17 f~k~~iKr~~~~-~~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~r 82 (85)
T cd08048 17 FPKAAIKRLIQS-VTGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYR 82 (85)
T ss_pred ccHHHHHHHHHH-HcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHH
Confidence 888889999874 5678999999999999999999999999988866544 47899999998875
No 52
>PTZ00017 histone H2A; Provisional
Probab=93.16 E-value=0.2 Score=46.06 Aligned_cols=68 Identities=24% Similarity=0.220 Sum_probs=57.4
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA 106 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa 106 (475)
...|+|.|+..+....|+..|.-+|-..+..+...|.+.|..-++.+++..||+++||.||+- ..||.
T Consensus 30 VgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n--DeEL~ 97 (134)
T PTZ00017 30 VGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN--DEELN 97 (134)
T ss_pred hHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC--cHHHH
Confidence 578999999886667888889888888888888888888888888999999999999999986 44554
No 53
>PLN00153 histone H2A; Provisional
Probab=93.09 E-value=0.21 Score=45.66 Aligned_cols=68 Identities=22% Similarity=0.218 Sum_probs=58.5
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA 106 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa 106 (475)
...|+|.|++-+....|+..|.-+|-..+..+...|.+.|..-++.+++..||++.||.||+- ..||.
T Consensus 27 VgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n--DeEL~ 94 (129)
T PLN00153 27 VGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN--DEELG 94 (129)
T ss_pred hHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC--cHHHH
Confidence 468999999987777899999999988888888888888888889999999999999999986 44444
No 54
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=92.53 E-value=0.45 Score=38.77 Aligned_cols=64 Identities=20% Similarity=0.272 Sum_probs=46.8
Q ss_pred ccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 144 QFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 144 ~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
.||.+-|..+-..-. ...++..+.-.|+-=+||-..||+.-|.+..++.+++++|++||..|++
T Consensus 3 ~~~~esvk~iAes~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 456666665553322 2468999999999999999999999999999999999999999999874
No 55
>PLN00154 histone H2A; Provisional
Probab=92.17 E-value=0.44 Score=44.00 Aligned_cols=70 Identities=21% Similarity=0.151 Sum_probs=55.4
Q ss_pred HHHHHHHhhccCC-CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765 37 AIYIYKVLKQVHP-DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKH 108 (475)
Q Consensus 37 ~~yI~KVLKQVhP-d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKh 108 (475)
...|+|.||.... ...|+..|.-+|-..+..+...|.+.|..-++.++++.||+++||.||+- ..||.+-
T Consensus 41 VgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn--DeEL~~L 111 (136)
T PLN00154 41 VGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG--DEELDTL 111 (136)
T ss_pred hHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC--cHHHHHH
Confidence 5789999999753 45778888888777777777777777777778899999999999999987 5555543
No 56
>KOG1142|consensus
Probab=92.10 E-value=0.15 Score=51.41 Aligned_cols=65 Identities=18% Similarity=0.250 Sum_probs=60.0
Q ss_pred HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765 36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 100 (475)
Q Consensus 36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll 100 (475)
+..-|...++||-++..|..++-++|-.+..|+.+.|..-++.||.+.+..||-++||+..++..
T Consensus 156 ~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~ 220 (258)
T KOG1142|consen 156 SKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERN 220 (258)
T ss_pred cccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeecc
Confidence 44558899999999999999999999999999999999999999999999999999999888775
No 57
>KOG1756|consensus
Probab=92.01 E-value=0.38 Score=43.92 Aligned_cols=69 Identities=25% Similarity=0.253 Sum_probs=54.5
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK 107 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK 107 (475)
...|.|.|+.-+....|+..|--+|.--+..+...|.+.|..-++.|++..+|++.|+-||+- ..||.+
T Consensus 30 vgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N--DeEL~~ 98 (131)
T KOG1756|consen 30 VGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN--DEELNK 98 (131)
T ss_pred HHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC--cHHHHH
Confidence 348999999988788899999888877666666666666666778899999999999999985 444443
No 58
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=92.01 E-value=0.43 Score=38.89 Aligned_cols=47 Identities=23% Similarity=0.355 Sum_probs=39.9
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHH
Q psy17765 52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVR 98 (475)
Q Consensus 52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVr 98 (475)
.++.++...|..-+..-+..|.++|.++++..+|.++|+.||..|.|
T Consensus 20 ~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 20 NLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp -B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 47899999999999999999999999999999999999999999875
No 59
>PLN00157 histone H2A; Provisional
Probab=91.92 E-value=0.34 Score=44.52 Aligned_cols=68 Identities=28% Similarity=0.234 Sum_probs=58.3
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA 106 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa 106 (475)
...|+|.|++.+-...|+..|.-+|...+..+...|.+.|..-++.+++..||+++||.||+- ..||.
T Consensus 29 VgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n--DeEL~ 96 (132)
T PLN00157 29 VGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN--DEELS 96 (132)
T ss_pred hHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC--cHHHH
Confidence 478999999987777899999999888888888888888888888999999999999999987 44544
No 60
>PTZ00252 histone H2A; Provisional
Probab=91.43 E-value=0.64 Score=42.83 Aligned_cols=70 Identities=16% Similarity=0.191 Sum_probs=54.3
Q ss_pred hH-HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhh--cCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765 35 SY-AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAH--YNKRSTITSREIQTAVRLLLPGELA 106 (475)
Q Consensus 35 sf-~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~--~~kr~TlT~rdIqtAVrllLPgeLa 106 (475)
.| ...|+|.|++-+-...|+..|.-+|-..+..+...|.+.|..-++ .+++..||+++||.||+- ..||.
T Consensus 25 ~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN--DeEL~ 97 (134)
T PTZ00252 25 IFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH--DDDLG 97 (134)
T ss_pred cCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC--hHHHH
Confidence 34 468999999988777899999888888777777777666666663 378889999999999986 44444
No 61
>smart00414 H2A Histone 2A.
Probab=91.39 E-value=0.42 Score=42.30 Aligned_cols=68 Identities=22% Similarity=0.225 Sum_probs=56.0
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELA 106 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLa 106 (475)
...|+|.|+..+....|+..|.-+|-..+..+...|.+.|..-+..+++..||+++|+.|++- ..||.
T Consensus 12 VgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n--D~EL~ 79 (106)
T smart00414 12 VGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN--DEELN 79 (106)
T ss_pred hHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC--CHHHH
Confidence 457999999887666889889888888887777777777888888889999999999999987 44554
No 62
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=90.48 E-value=1 Score=37.11 Aligned_cols=61 Identities=10% Similarity=0.183 Sum_probs=49.7
Q ss_pred HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
..+-++|+..- =-.++..|++.|-.++.+.+..|+.++..++...+|.+.+..||..|+.-
T Consensus 10 ~~Vaqil~~~G-f~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 10 IAVAQILESAG-FDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHHHHcC-ccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 34445555431 12478999999999999999999999999999999999999999988764
No 63
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=90.46 E-value=0.51 Score=42.60 Aligned_cols=69 Identities=22% Similarity=0.228 Sum_probs=59.4
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK 107 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK 107 (475)
...|+|.||.-.-.+.|+.+|.-++...+..+...|.+.|..-++.++++.|+++.+|-|+|- ..||.+
T Consensus 29 vgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn--D~EL~~ 97 (132)
T COG5262 29 VGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN--DEELNK 97 (132)
T ss_pred HHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC--cHHHHH
Confidence 457999999777778899999999888888888888888888889999999999999999986 556554
No 64
>KOG0869|consensus
Probab=90.25 E-value=0.25 Score=46.54 Aligned_cols=53 Identities=23% Similarity=0.369 Sum_probs=48.7
Q ss_pred hhhhhccccCC-CCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCc
Q psy17765 394 IYKVLKQVHPD-TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDL 446 (475)
Q Consensus 394 i~kvLkqvhp~-~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~ 446 (475)
|-|+.|+.-|. .-||+.|-.+|.-.|...--=|+.||+--|+-.||.||+..+
T Consensus 38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdD 91 (168)
T KOG0869|consen 38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDD 91 (168)
T ss_pred HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHH
Confidence 67888988877 669999999999999999999999999999999999999976
No 65
>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=89.79 E-value=0.23 Score=40.62 Aligned_cols=55 Identities=18% Similarity=0.347 Sum_probs=43.7
Q ss_pred hhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCchh
Q psy17765 394 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCP 448 (475)
Q Consensus 394 i~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~~~ 448 (475)
+-..++||-|+..+...+..++-.+.+|--+.+..-|++||++.+..||..++++
T Consensus 5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~ 59 (68)
T PF03847_consen 5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQ 59 (68)
T ss_dssp HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHH
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHH
Confidence 4567899999999999999999999999999999999999999999999998865
No 66
>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=88.86 E-value=0.77 Score=47.94 Aligned_cols=58 Identities=22% Similarity=0.284 Sum_probs=50.9
Q ss_pred CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh--ccHHHHh
Q psy17765 158 NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR--NDEELNK 215 (475)
Q Consensus 158 ~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~--nD~EL~~ 215 (475)
.-..|++..|...|+..+||...+|++.|.+.+++.++++++++||..|++ |.+.|.+
T Consensus 12 ~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG 71 (343)
T cd08050 12 LGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYG 71 (343)
T ss_pred cCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccC
Confidence 335699999999999999999999999999999999999999999999987 4444433
No 67
>KOG0870|consensus
Probab=88.47 E-value=3.5 Score=39.35 Aligned_cols=63 Identities=21% Similarity=0.297 Sum_probs=48.8
Q ss_pred HHHHHHhhccCCC--CCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765 38 IYIYKVLKQVHPD--TGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 100 (475)
Q Consensus 38 ~yI~KVLKQVhPd--~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll 100 (475)
.-|.|+.|.+-|+ ..||.+|...|.---.=+...+..-+..+|..++|+||+..||-.|+.-+
T Consensus 14 AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Ei 78 (172)
T KOG0870|consen 14 AIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEI 78 (172)
T ss_pred HHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHh
Confidence 3466677777665 58999998887654444455566667779999999999999999999877
No 68
>smart00428 H3 Histone H3.
Probab=88.43 E-value=1.5 Score=38.92 Aligned_cols=67 Identities=25% Similarity=0.310 Sum_probs=56.7
Q ss_pred CcccchhHHHHHHhhc--Cc----ccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 142 GLQFPVGRIHRLLRKG--NY----AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 142 gL~FPVsRi~r~Lke~--~~----~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
+|.+|-.-|.|+.++= .+ ..|+.++|-.-|-...|....++.|-|...|...++..|+|+|+++|.+
T Consensus 27 ~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 27 DLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred ccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 4777777777777652 11 3599999999999999999999999999999999999999999999854
No 69
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=88.09 E-value=1.2 Score=37.16 Aligned_cols=62 Identities=19% Similarity=0.274 Sum_probs=49.5
Q ss_pred HHHHHHhhcc--CCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 38 IYIYKVLKQV--HPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 38 ~yI~KVLKQV--hPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
..+-|+.++. ..+..+|.+.+.-|..++.+.++.++.+.-.+++..+|+||+..||.-..|.
T Consensus 9 ~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 9 YTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 3455566655 4667899999999999999999999999999999999999999999765553
No 70
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=87.95 E-value=1.2 Score=38.36 Aligned_cols=63 Identities=21% Similarity=0.348 Sum_probs=47.1
Q ss_pred cchhHHHHHHhhcCcc-cccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcC-CcccchhHHHHHHh
Q psy17765 145 FPVGRIHRLLRKGNYA-ERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNK-KTRIIPRHLQLAIR 208 (475)
Q Consensus 145 FPVsRi~r~Lke~~~~-~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k-~~rItP~hI~lAI~ 208 (475)
||=+-|.++++. ..+ +-|+....+.++++--.+..||+|.|.......+ ...|.|.||.-|.+
T Consensus 24 ~~k~~ikkli~~-~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~r 88 (90)
T PF04719_consen 24 FNKAAIKKLINQ-VLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYR 88 (90)
T ss_dssp --HHHHHHHHHH-HHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHH
T ss_pred CCHHHHHHHHHH-HcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence 788889999986 455 8999999999999999999999999988765543 45899999998864
No 71
>KOG3219|consensus
Probab=86.92 E-value=0.95 Score=44.10 Aligned_cols=66 Identities=21% Similarity=0.374 Sum_probs=55.5
Q ss_pred cccchhHHHHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhc-CCcccchhHHHHHHhc
Q psy17765 143 LQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDN-KKTRIIPRHLQLAIRN 209 (475)
Q Consensus 143 L~FPVsRi~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~-k~~rItP~hI~lAI~n 209 (475)
-.||-+.|.+++.. ..++-|+..+.|.++++-.-++.||+|.|....... ....+-|.||..|.+-
T Consensus 111 s~f~Ka~iKkL~~~-itg~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rr 177 (195)
T KOG3219|consen 111 SAFPKAQIKKLMSS-ITGQSVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRR 177 (195)
T ss_pred hcCCHHHHHHHHHH-HhCCccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHH
Confidence 36999999999986 445559999999999999999999999998875543 3568999999988753
No 72
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=86.83 E-value=1.3 Score=46.20 Aligned_cols=49 Identities=20% Similarity=0.355 Sum_probs=46.8
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765 52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 100 (475)
Q Consensus 52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll 100 (475)
.++.+|...+..-+......|+.||..+++..+|+|+|..||..|++..
T Consensus 16 ~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~ 64 (343)
T cd08050 16 SLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLR 64 (343)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHh
Confidence 6899999999999999999999999999999999999999999999875
No 73
>PLN00121 histone H3; Provisional
Probab=86.52 E-value=2 Score=39.81 Aligned_cols=65 Identities=18% Similarity=0.251 Sum_probs=57.4
Q ss_pred hHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 35 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 35 sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
.|+-.++.+.....+++.++.+|+.-|..-....+..+-+++...+.+.+|-||.++|||-+.++
T Consensus 67 pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PLN00121 67 PFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred cHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHh
Confidence 38888888888888889999999999988888888888888888888999999999999988765
No 74
>PTZ00018 histone H3; Provisional
Probab=86.25 E-value=2.1 Score=39.61 Aligned_cols=65 Identities=18% Similarity=0.251 Sum_probs=57.3
Q ss_pred hHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 35 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 35 sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
.|+-.++.+..+..+++.++.+|+.-|..-..+.+..+-+++...+.+.+|-||..+|||-+.++
T Consensus 67 pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PTZ00018 67 PFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred cHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHh
Confidence 38888888888888889999999999998888888888888888888999999999999988765
No 75
>smart00325 RhoGEF Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases. Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains. Improved coverage.
Probab=86.22 E-value=0.16 Score=46.33 Aligned_cols=68 Identities=13% Similarity=-0.033 Sum_probs=54.9
Q ss_pred hhHHHHHHhcccccc-----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765 286 VLEEHLENATGLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA 357 (475)
Q Consensus 286 Vfre~l~~~~~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~ 357 (475)
+|.++|.....++.+ +|+|+.+|+.+...++..|++.++-.. ...+.+|.||..+ ..-+++|..|...
T Consensus 22 ~y~~~l~~~~~~~~~~~~~~iF~~i~~i~~~h~~~l~~l~~~~~~~~--~~~~~i~~~f~~~--~~~~~~Y~~Y~~~ 94 (180)
T smart00325 22 VFLKPLKKELKLLSPNELETLFGNIEEIYEFHRDFLDELEERIEEWD--DSPERIGDVFLKL--EEFFKIYSEYCSN 94 (180)
T ss_pred HHHHHHHHhhCCCCHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhccc--ccccHHHHHHHHh--hHHHHHHHHHHHh
Confidence 677778776544443 999999999999999999998876532 3579999999999 5568999999775
No 76
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=84.03 E-value=3.8 Score=33.73 Aligned_cols=58 Identities=17% Similarity=0.104 Sum_probs=49.9
Q ss_pred HHHHhhcCcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHhc
Q psy17765 151 HRLLRKGNYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIRN 209 (475)
Q Consensus 151 ~r~Lke~~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~n 209 (475)
-++|+.. -+.++..+|.-.|+-++|-...+|.+.+-+++...+++..++.||..|+.+
T Consensus 13 aqil~~~-Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~ 70 (77)
T smart00576 13 AQILESA-GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN 70 (77)
T ss_pred HHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 3455542 347999999999999999999999999999999999999999999999864
No 77
>cd00160 RhoGEF Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases; Also called Dbl-homologous (DH) domain. It appears that PH domains invariably occur C-terminal to RhoGEF/DH domains.
Probab=82.86 E-value=0.28 Score=44.78 Aligned_cols=69 Identities=13% Similarity=-0.046 Sum_probs=55.1
Q ss_pred hhHHHHHHhcc-ccc----cccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhccC
Q psy17765 286 VLEEHLENATG-LLV----DESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAAG 358 (475)
Q Consensus 286 Vfre~l~~~~~-l~~----~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~~ 358 (475)
+|.++|..... +.. .+|+|+-+|+.+...++..|++.++-.. .+.+.+|.||..... -+++|..|....
T Consensus 25 ~y~~~l~~~~~~~~~~~~~~iF~~i~~i~~~h~~~l~~l~~~~~~~~--~~~~~i~~~f~~~~~--~~~~Y~~Y~~~~ 98 (181)
T cd00160 25 VFLKPLDKELLPLSPEEVELLFGNIEEIYEFHRIFLKSLEERVEEWD--KSGPRIGDVFLKLAP--FFKIYSEYCSNH 98 (181)
T ss_pred HHHHHHHhccCCCCHHHHHHHhcCHHHHHHHHHHHHHHHHHHHhccC--cccchHHHHHHHhhh--HHHHHHHHHhCh
Confidence 57777776554 222 2999999999999999999998887644 257899999999988 789999997763
No 78
>PF15510 CENP-W: Centromere kinetochore component W
Probab=81.99 E-value=1.6 Score=37.91 Aligned_cols=63 Identities=24% Similarity=0.372 Sum_probs=50.9
Q ss_pred HHHHHHhhccCCCCC--cChHHH--------------HHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhC
Q psy17765 38 IYIYKVLKQVHPDTG--VSSKAM--------------SIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL 101 (475)
Q Consensus 38 ~yI~KVLKQVhPd~~--IS~~Am--------------~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllL 101 (475)
.+++||+|+--|.+. -+.+.| -.+|.++ ++.|+|+|+-.-+..|+..+|..+.|..|.+.+|
T Consensus 20 gfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLL--FvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaKviL 97 (102)
T PF15510_consen 20 GFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLL--FVHRLAEEARTNACENKCGTIKKEHVLAAAKVIL 97 (102)
T ss_pred HHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHH--HHHHHHHHHHHHHHHHhhccccHHHHHHHHHHHH
Confidence 468999998888865 445555 4455555 6789999999999999999999999999998877
Q ss_pred c
Q psy17765 102 P 102 (475)
Q Consensus 102 P 102 (475)
-
T Consensus 98 K 98 (102)
T PF15510_consen 98 K 98 (102)
T ss_pred H
Confidence 4
No 79
>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=80.09 E-value=7.3 Score=31.80 Aligned_cols=48 Identities=13% Similarity=0.273 Sum_probs=43.8
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
+++..|++.+..++.+.+..|+..+...+...+|...+..||..|..-
T Consensus 23 ~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~ 70 (77)
T PF07524_consen 23 SASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEE 70 (77)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 589999999999999999999999999999999988999999877654
No 80
>PLN00161 histone H3; Provisional
Probab=79.53 E-value=6.9 Score=36.27 Aligned_cols=65 Identities=17% Similarity=0.244 Sum_probs=55.1
Q ss_pred hHHHHHHHHhhccCC-CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 35 SYAIYIYKVLKQVHP-DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 35 sf~~yI~KVLKQVhP-d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
.|+--++.+..+..+ ++.++.+|+.-|..-....+..+-+++...+.+.+|-||.++|||-+.++
T Consensus 60 PF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ri 125 (135)
T PLN00161 60 PFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRI 125 (135)
T ss_pred cHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHh
Confidence 388888888777655 58899999999988888888888888888888999999999999988776
No 81
>PLN00160 histone H3; Provisional
Probab=76.39 E-value=9.6 Score=33.44 Aligned_cols=67 Identities=16% Similarity=0.188 Sum_probs=54.7
Q ss_pred chhHHHHHHHHhhccCC-CCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 33 KESYAIYIYKVLKQVHP-DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 33 ~~sf~~yI~KVLKQVhP-d~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
+-.|+--++.+.....+ ++.++..|+.-|..-....+..+-+.+...+.+.+|-||.++|+|-+.++
T Consensus 24 k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ri 91 (97)
T PLN00160 24 RLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRI 91 (97)
T ss_pred cccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHh
Confidence 44588888888766543 48899999999988888888888888887888999999999999988765
No 82
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=75.81 E-value=8.6 Score=32.16 Aligned_cols=48 Identities=23% Similarity=0.353 Sum_probs=37.1
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhH---HHHhcCCcccchhHHHHHHhccHHH
Q psy17765 166 GAPVYLAAVMEYLAAEVLELAGN---AARDNKKTRIIPRHLQLAIRNDEEL 213 (475)
Q Consensus 166 ~A~VYLaAVLEYLtaEILELAgn---~A~~~k~~rItP~hI~lAI~nD~EL 213 (475)
-++-|++|+-|-....+-.++.. .|+.-+++.|++.|+.+..+.++.|
T Consensus 26 ~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~L 76 (76)
T PF15630_consen 26 VSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPSL 76 (76)
T ss_dssp E-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HHH
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCCC
Confidence 56888999999888888777744 3788899999999999999999876
No 83
>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=75.53 E-value=16 Score=31.52 Aligned_cols=62 Identities=10% Similarity=0.240 Sum_probs=46.0
Q ss_pred HHHHHHHHhhccCCCC-CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 36 YAIYIYKVLKQVHPDT-GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 36 f~~yI~KVLKQVhPd~-~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
|..-|..++- ++.|. .-..++..+|+.+|.+.+..|+.+|..++. ..+..++..|+..++|.
T Consensus 4 f~~ei~~mmy-~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~ 66 (92)
T cd07978 4 FTKEIRQMMY-GFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRK 66 (92)
T ss_pred cHHHHHHHHH-HcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhc
Confidence 4444444333 23343 346799999999999999999999999998 44455699999888865
No 84
>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=72.42 E-value=16 Score=30.27 Aligned_cols=60 Identities=20% Similarity=0.237 Sum_probs=46.4
Q ss_pred chhHHHHHHhhc--CcccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcc-cchhHHHH
Q psy17765 146 PVGRIHRLLRKG--NYAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTR-IIPRHLQL 205 (475)
Q Consensus 146 PVsRi~r~Lke~--~~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~r-ItP~hI~l 205 (475)
|..-|.|+|+.. .-.-||+..|---++..|+-++.|-+-.|...+++.+... |..+||+.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEk 63 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEK 63 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence 556677888742 2346999999999999999999999999999898888877 99999985
No 85
>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=67.81 E-value=6.7 Score=33.72 Aligned_cols=48 Identities=10% Similarity=0.202 Sum_probs=23.8
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
....++..+|+.++.+-+..++.+|..++...+++.++..|+..++|.
T Consensus 19 ~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 19 EPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp S--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 357899999999999999999999999999988889999999887775
No 86
>KOG1142|consensus
Probab=62.37 E-value=8.8 Score=39.04 Aligned_cols=56 Identities=16% Similarity=0.227 Sum_probs=50.1
Q ss_pred hhhhhccccCCCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCCchhh
Q psy17765 394 IYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKDLCPS 449 (475)
Q Consensus 394 i~kvLkqvhp~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr~~~~ 449 (475)
+...++||-+++-|....-.+|--...|--|-|..-|++||++.|..||-.||++=
T Consensus 160 l~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqL 215 (258)
T KOG1142|consen 160 LDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQL 215 (258)
T ss_pred hhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheee
Confidence 78889999999999999999888777777788888999999999999999998653
No 87
>KOG2549|consensus
Probab=61.77 E-value=19 Score=40.35 Aligned_cols=49 Identities=18% Similarity=0.312 Sum_probs=46.1
Q ss_pred CcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765 52 GVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 100 (475)
Q Consensus 52 ~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll 100 (475)
.|+.++...|..-+..=+..|+++|.+.....+|.++|+.||..|.|.+
T Consensus 28 nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~ 76 (576)
T KOG2549|consen 28 NLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSL 76 (576)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhc
Confidence 4889999999999999999999999999999999999999999999876
No 88
>KOG0871|consensus
Probab=59.88 E-value=5.9 Score=37.24 Aligned_cols=69 Identities=16% Similarity=0.327 Sum_probs=59.6
Q ss_pred hhhhhccccC-CCCCchHHHHHHhhHHHHHHhHhHHhhhcccccCCCcCCCCC-chhheehccccchhhhh
Q psy17765 394 IYKVLKQVHP-DTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITKD-LCPSVCLYSYTLYERTC 462 (475)
Q Consensus 394 i~kvLkqvhp-~~giS~kam~imnsfv~Diferia~Eas~L~~~~kr~Tltsr-~~~~~~~~~~~~~~~~~ 462 (475)
|-|..|.+-| |.-+...|-.+++..--.-..-|+.||...|.-..|.||... .+.|.--|-|+.|---|
T Consensus 18 v~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee~ 88 (156)
T KOG0871|consen 18 VNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEEA 88 (156)
T ss_pred HHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHHH
Confidence 7888999999 999999999988776666677899999999999999999994 68898889998875443
No 89
>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=59.88 E-value=15 Score=33.74 Aligned_cols=63 Identities=19% Similarity=0.219 Sum_probs=47.4
Q ss_pred HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhC
Q psy17765 38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLL 101 (475)
Q Consensus 38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllL 101 (475)
..|+.+|+.-- =..-...+...|-.|+.+-...|..+|...+.+.++.+++..||+.|+...+
T Consensus 16 ~~i~~iL~~~G-v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~ 78 (129)
T PF02291_consen 16 RVIHLILKSMG-VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRL 78 (129)
T ss_dssp HHHHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-
T ss_pred HHHHHHHHHcC-CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHH
Confidence 44666776541 1234678888888999999999999999999999999999999999999654
No 90
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=59.60 E-value=17 Score=39.19 Aligned_cols=56 Identities=16% Similarity=0.227 Sum_probs=40.9
Q ss_pred HHHHHHHhhcc-----CCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHH
Q psy17765 37 AIYIYKVLKQV-----HPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSRE 92 (475)
Q Consensus 37 ~~yI~KVLKQV-----hPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rd 92 (475)
...|+|++... .-+..|+.+||..|......+|+.|+....-.+.+.+|+||...|
T Consensus 354 ~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 354 PGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred ccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 33455555444 345779999999999999999999999999999999999997654
No 91
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=58.16 E-value=47 Score=28.32 Aligned_cols=62 Identities=16% Similarity=0.219 Sum_probs=49.6
Q ss_pred HHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCC---CCCCChHHHHHHHHHh
Q psy17765 38 IYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNK---RSTITSREIQTAVRLL 100 (475)
Q Consensus 38 ~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~k---r~TlT~rdIqtAVrll 100 (475)
.-++|+..++-. .+++.....+|..+-.-+.-.|.++|..+..... ..+|.++.|..|.|.+
T Consensus 20 ~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 20 AAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred HHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 347777777765 6788888888888888888899999988887544 4889999999999875
No 92
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=56.11 E-value=12 Score=27.47 Aligned_cols=34 Identities=32% Similarity=0.431 Sum_probs=26.8
Q ss_pred HhHHHHhcCCcccchhHHHHHHhccH--HHHhhhcC
Q psy17765 186 AGNAARDNKKTRIIPRHLQLAIRNDE--ELNKLLSG 219 (475)
Q Consensus 186 Agn~A~~~k~~rItP~hI~lAI~nD~--EL~~Lf~~ 219 (475)
|-+.|+..+...|+|+||-+|+-.|+ ....+|+.
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~~~~~~~il~~ 36 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDPDSIAARILKK 36 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHTTSHHHHHHHH
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhhhHHHHHHHHH
Confidence 44678889999999999999988766 77777764
No 93
>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=55.72 E-value=42 Score=30.82 Aligned_cols=60 Identities=23% Similarity=0.303 Sum_probs=41.7
Q ss_pred hhHHHHHHhhcCcccccCCChhHHHHHHHHH---HHHHHHHHHhHHHHhcCCcccchhHHHHHHhcc
Q psy17765 147 VGRIHRLLRKGNYAERVGAGAPVYLAAVMEY---LAAEVLELAGNAARDNKKTRIIPRHLQLAIRND 210 (475)
Q Consensus 147 VsRi~r~Lke~~~~~RI~~~A~VYLaAVLEY---LtaEILELAgn~A~~~k~~rItP~hI~lAI~nD 210 (475)
+--|+.+|++... ...-+-...-.||+ .+.+||+-|-.+|...++..|+..|+++||..-
T Consensus 15 a~~i~~iL~~~Gv----~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r 77 (129)
T PF02291_consen 15 ARVIHLILKSMGV----TEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSR 77 (129)
T ss_dssp HHHHHHHHHHTT-------B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT
T ss_pred HHHHHHHHHHcCC----cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHH
Confidence 4567888887643 33444444555555 467899999999999999999999999999854
No 94
>PLN00160 histone H3; Provisional
Probab=54.79 E-value=37 Score=29.85 Aligned_cols=67 Identities=27% Similarity=0.239 Sum_probs=53.9
Q ss_pred CcccchhHHHHHHhhcC-----cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 142 GLQFPVGRIHRLLRKGN-----YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 142 gL~FPVsRi~r~Lke~~-----~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
+|.+|-.-|.|+.++-. ...|+.++|-.-|=-.-|...-.++|-+.-.|...++..|.|.|++++.+
T Consensus 19 ~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 19 DLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred hhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 47777777777776521 12688888888888888999999999888888888999999999999854
No 95
>PLN00161 histone H3; Provisional
Probab=47.56 E-value=62 Score=30.11 Aligned_cols=67 Identities=27% Similarity=0.253 Sum_probs=53.7
Q ss_pred CcccchhHHHHHHhhcC--c---ccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 142 GLQFPVGRIHRLLRKGN--Y---AERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 142 gL~FPVsRi~r~Lke~~--~---~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
+|.+|-.-|.|+.++=. + ..|+.+.|-.-|=-+-|..+-.++|-+.-.|...++..|.|.||+++.+
T Consensus 53 ~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 53 ELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred ccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 47777777777776521 1 3688888888888888988899999888888888999999999998854
No 96
>PTZ00018 histone H3; Provisional
Probab=47.08 E-value=46 Score=30.98 Aligned_cols=67 Identities=25% Similarity=0.254 Sum_probs=55.7
Q ss_pred CcccchhHHHHHHhhcC----cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 142 GLQFPVGRIHRLLRKGN----YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 142 gL~FPVsRi~r~Lke~~----~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
+|.||-.-|.|+.++=. -..|+..+|-.-|--+-|..+..++|-+...+...++..|.|.||+++.+
T Consensus 60 ~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PTZ00018 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred hhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHH
Confidence 47888877888777621 23699999999999999999999999998888888999999999998853
No 97
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=46.91 E-value=50 Score=34.14 Aligned_cols=73 Identities=19% Similarity=0.221 Sum_probs=63.0
Q ss_pred hHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHHH
Q psy17765 35 SYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHA 109 (475)
Q Consensus 35 sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKhA 109 (475)
....+|.+.+++. ++.|+.+|++.+...+..=+.-|+.|...|+.+.+-..||..||+..|-........+++
T Consensus 144 ~l~~~i~~~~~~~--~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~~~~~~f~l~ 216 (334)
T COG1466 144 ELPQWIKKRAKEL--GLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDVAEFNIFDLA 216 (334)
T ss_pred HHHHHHHHHHHHc--CCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhccccCCHHHHH
Confidence 4666788887776 478899999999999998899999999999999888899999999999998877776653
No 98
>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=46.11 E-value=47 Score=28.65 Aligned_cols=30 Identities=17% Similarity=0.338 Sum_probs=22.3
Q ss_pred HHHHHhHHHHhcCCcccchhHHHHHHhccHH
Q psy17765 182 VLELAGNAARDNKKTRIIPRHLQLAIRNDEE 212 (475)
Q Consensus 182 ILELAgn~A~~~k~~rItP~hI~lAI~nD~E 212 (475)
++-.|.+.|. .++.+|+++|+.-+|++|+.
T Consensus 40 l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~ 69 (92)
T cd07978 40 LCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPK 69 (92)
T ss_pred HHHHHHHHHH-cCCCCCCHHHHHHHHhcCHH
Confidence 3334444554 57778899999999999986
No 99
>KOG0870|consensus
Probab=44.95 E-value=64 Score=31.07 Aligned_cols=66 Identities=20% Similarity=0.302 Sum_probs=48.0
Q ss_pred CcccchhHHHHHHhhcCccc---ccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 142 GLQFPVGRIHRLLRKGNYAE---RVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 142 gL~FPVsRi~r~Lke~~~~~---RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
-|.||-+-|-|+.++ .+.. -|+..|..-++-.-=-++..+...|++.|++.+++.|++.|+--|+.
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 DLNLPNAIITRLVKE-VLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD 76 (172)
T ss_pred HhhccHHHHHHHHHH-hCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence 478999999988775 3333 35555555554444445566677888899999999999999998875
No 100
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=44.84 E-value=82 Score=27.29 Aligned_cols=64 Identities=17% Similarity=0.232 Sum_probs=46.0
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhc-CCCCCCChHHHHHHHHHh
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHY-NKRSTITSREIQTAVRLL 100 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~-~kr~TlT~rdIqtAVrll 100 (475)
..-|+|+..++-.+.+++....-.|..+-.=+.-.|.++|...... ....+|.+.++..|.|.+
T Consensus 26 k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 26 KAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 4579999999887788899888888888888888888888887763 334589999999998864
No 101
>PLN00121 histone H3; Provisional
Probab=43.63 E-value=43 Score=31.16 Aligned_cols=67 Identities=25% Similarity=0.254 Sum_probs=55.3
Q ss_pred CcccchhHHHHHHhhcC----cccccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 142 GLQFPVGRIHRLLRKGN----YAERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 142 gL~FPVsRi~r~Lke~~----~~~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
+|.+|-.-|.|+.++=. ...|+..+|-.-|--.-|..+..++|-+.-.+...++..|.|.||+++.+
T Consensus 60 ~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~r 130 (136)
T PLN00121 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
T ss_pred ccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHH
Confidence 47888877788777621 13699999999999999999999999988888888999999999998853
No 102
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=43.18 E-value=62 Score=33.27 Aligned_cols=69 Identities=20% Similarity=0.159 Sum_probs=56.6
Q ss_pred HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765 36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKH 108 (475)
Q Consensus 36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKh 108 (475)
...+|.+.+++- +..|+.+|+..+...+..=+..|..|.-.|+.|.+ +||..||+..|-......+..+
T Consensus 140 l~~~i~~~~~~~--g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v~~~~e~~vF~l 208 (328)
T PRK08487 140 ALELLQERAKEL--GLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELVFGLGSVSFEDF 208 (328)
T ss_pred HHHHHHHHHHHh--CCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHhcccccccHHHH
Confidence 355677777775 46789999999999999889999999999999954 7999999998877766666544
No 103
>KOG1757|consensus
Probab=42.28 E-value=32 Score=31.11 Aligned_cols=65 Identities=32% Similarity=0.292 Sum_probs=42.7
Q ss_pred HHHHHHHhhccCCCCC-cChHHHHHHHHHHHHHHHHHHHHHhhhhhc----CCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765 37 AIYIYKVLKQVHPDTG-VSSKAMSIMNSFVNDIFERIAAESSRLAHY----NKRSTITSREIQTAVRLLLPGELAK 107 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~-IS~~Am~imns~v~diferIa~EA~~L~~~----~kr~TlT~rdIqtAVrllLPgeLaK 107 (475)
.-.|+|-||+-....+ +-..+.-++.+ ++|-+..|...|+.. -+-+.||+|..|-|+|- ..||+-
T Consensus 33 VgRihr~LK~r~t~h~rVGataavy~aa----ileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRG--DeELDt 102 (131)
T KOG1757|consen 33 VGRIHRHLKTRTTSHGRVGATAAVYSAA----ILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG--DEELDT 102 (131)
T ss_pred hHHHHHHHHHhcccccccchHHHHHHHH----HHHHHHHHHHHHcccccccceeeeccchhheeeecC--cHHHHH
Confidence 3468999998654433 33444444444 456667777777653 35567999999999986 566654
No 104
>PF00621 RhoGEF: RhoGEF domain; InterPro: IPR000219 The Rho family GTPases Rho, Rac and CDC42 regulate a diverse array of cellular processes. Like all members of the Ras superfamily, the Rho proteins cycle between active GTP-bound and inactive GDP-bound conformational states. Activation of Rho proteins through release of bound GDP and subsequent binding of GTP, is catalysed by guanine nucleotide exchange factors (GEFs) in the Dbl family. The proteins encoded by members of the Dbl family share a common domain, presented in this entry, of about 200 residues (designated the Dbl homology or DH domain) that has been shown to encode a GEF activity specific for a number of Rho family members. In addition, all family members possess a second, shared domain designated the pleckstrin homology (PH) domain (IPR001849 from INTERPRO). Trio and its homologue UNC-73 are unique within the Dbl family insomuch as they encode two distinct DH/PH domain modules. The PH domain is invariably located immediately C-terminal to the DH domain and this invariant topography suggests a functional interdependence between these two structural modules. Biochemical data have established the role of the conserved DH domain in Rho GTPase interaction and activation, and the role of the tandem PH domain in intracellular targeting and/or regulation of DH domain function. The DH domain of Dbl has been shown to mediate oligomerisation that is mostly homophilic in nature. In addition to the tandem DH/PH domains Dbl family GEFs contain diverse structural motifs like serine/threonine kinase, RBD, PDZ, RGS, IQ, REM, Cdc25, RasGEF, CH, SH2, SH3, EF, spectrin or Ig. The DH domain is composed of three structurally conserved regions separated by more variable regions. It does not share significant sequence homology with other subtypes of small G-protein GEF motifs such as the Cdc25 domain and the Sec7 domain, which specifically interact with Ras and ARF family small GTPases, respectively, nor with other Rho protein interactive motifs, indicating that the Dbl family proteins are evolutionarily unique. The DH domain is composed of 11 alpha helices that are folded into a flattened, elongated alpha-helix bundle in which two of the three conserved regions, conserved region 1 (CR1) and conserved region 3 (CR3), are exposed near the centre of one surface. CR1 and CR3, together with a part of alpha-6 and the DH/PH junction site, constitute the Rho GTPase interacting pocket.; GO: 0005089 Rho guanyl-nucleotide exchange factor activity, 0035023 regulation of Rho protein signal transduction, 0005622 intracellular; PDB: 3MPX_A 2RGN_E 2Z0Q_A 3T06_A 3KZ1_A 1XCG_E 2KR9_A 1BY1_A 1RJ2_J 1KZG_C ....
Probab=40.85 E-value=6.4 Score=35.25 Aligned_cols=67 Identities=13% Similarity=0.075 Sum_probs=49.2
Q ss_pred hhHHHHHHhccccc-----cccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765 286 VLEEHLENATGLLV-----DESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA 357 (475)
Q Consensus 286 Vfre~l~~~~~l~~-----~~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~ 357 (475)
+|..++......+. .+|+|+-+++++.+.++..|++.+ ++....+.+|.||-++.+ -+++|..|...
T Consensus 22 ~~~~~l~~~~~~l~~~~~~~lf~~i~~l~~~h~~ll~~L~~~~---~~~~~~~~i~~if~~~~~--~~~~Y~~Y~~~ 93 (180)
T PF00621_consen 22 VFLKPLRKRSPLLSEDEIKSLFGNIEELIEIHQQLLESLEERM---KEWSNIQSIGDIFLKFEP--FLKVYISYCSN 93 (180)
T ss_dssp HTHHHHHHHTTSSHHHHHHHHHTTHHHHHHHHHHHHHHHHHHH---HTTSSGGGHHHHHHHHTT--GGHHHHHHHHH
T ss_pred HHHHHHHhccccCCHHHHHHHhcchhhhhhHHHHHHHHHHHHH---Hhhhccchhhhhhhhccc--cccceeccchh
Confidence 66666666333332 399999999999999999999865 334678999999977444 56677777554
No 105
>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=40.77 E-value=19 Score=31.02 Aligned_cols=41 Identities=20% Similarity=0.275 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHH---hHHHHhcCCcccchhHHHHHHhccHHH
Q psy17765 173 AVMEYLAAEVLELA---GNAARDNKKTRIIPRHLQLAIRNDEEL 213 (475)
Q Consensus 173 AVLEYLtaEILELA---gn~A~~~k~~rItP~hI~lAI~nD~EL 213 (475)
.|-|+++.+|.++. .+.|...+..+|+++|+.-++++|+.-
T Consensus 27 lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~K 70 (93)
T PF02269_consen 27 LVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKK 70 (93)
T ss_dssp HHHHHHHHHHHHHHHHHHC-------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHH
Confidence 34445555555544 455655667799999999999999864
No 106
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=35.47 E-value=67 Score=26.61 Aligned_cols=56 Identities=13% Similarity=0.236 Sum_probs=34.6
Q ss_pred HHHHhhcc--CCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCC-CChHHHHH
Q psy17765 40 IYKVLKQV--HPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRST-ITSREIQT 95 (475)
Q Consensus 40 I~KVLKQV--hPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~T-lT~rdIqt 95 (475)
|.|+|+.- ++++.|+.+|+..+..++.-+...-...|...+...+... +...|++.
T Consensus 5 i~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEk 63 (72)
T PF09415_consen 5 IARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEK 63 (72)
T ss_dssp HHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred HHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence 56777753 4678899999988777775555444555555555566656 78888765
No 107
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=34.72 E-value=81 Score=29.22 Aligned_cols=71 Identities=14% Similarity=0.151 Sum_probs=55.9
Q ss_pred CCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHHHHHHhhhhhhhcccc
Q psy17765 49 PDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSS 123 (475)
Q Consensus 49 Pd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKhAvseG~kAV~ky~sS 123 (475)
.|+..+.+|-+++-.-...++..+..||...|..-.++||....|-.|..-+== +.=|.++++-...|.+.
T Consensus 27 ~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef----~eyi~~~~e~~~n~k~~ 97 (148)
T COG5150 27 KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEF----EEYIESCMEEHENYKSY 97 (148)
T ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccH----HHHHHHHHHHHHHHHHH
Confidence 357899999999998888999999999999999999999999999999876621 22234455555566554
No 108
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=34.45 E-value=1.4e+02 Score=29.45 Aligned_cols=69 Identities=22% Similarity=0.272 Sum_probs=54.4
Q ss_pred hhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHH
Q psy17765 34 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGE 104 (475)
Q Consensus 34 ~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPge 104 (475)
.....+|.+.++.. +..|+.++...+.+.+..=+..+..|..+|+.+.+..++|..||+..+.......
T Consensus 114 ~~~~~~i~~~~~~~--g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~~~~~ 182 (302)
T TIGR01128 114 QELPRWIQARLKKL--GLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDSARFN 182 (302)
T ss_pred HHHHHHHHHHHHHc--CCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhhhcCC
Confidence 34566788887775 5678999999999888776778899999999987666899999988776554433
No 109
>smart00350 MCM minichromosome maintenance proteins.
Probab=33.33 E-value=1.3e+02 Score=33.03 Aligned_cols=66 Identities=23% Similarity=0.269 Sum_probs=47.6
Q ss_pred hhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHH-------------------HHHHHHHhhhhhcCCCCCCChHHHH
Q psy17765 34 ESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIF-------------------ERIAAESSRLAHYNKRSTITSREIQ 94 (475)
Q Consensus 34 ~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~dif-------------------erIa~EA~~L~~~~kr~TlT~rdIq 94 (475)
+....||.-+-+.++|. +|.++..++..+...+= +-|.+-|.-+++...+.+++..||+
T Consensus 421 ~~l~~yi~~ar~~~~P~--ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~Dv~ 498 (509)
T smart00350 421 EFLRKYIAYAREKIKPK--LSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEADVE 498 (509)
T ss_pred HHHHHHHHHHHhcCCCC--CCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHHHHH
Confidence 34566776655457887 59999998877665432 4555666667777888889999999
Q ss_pred HHHHHhC
Q psy17765 95 TAVRLLL 101 (475)
Q Consensus 95 tAVrllL 101 (475)
.|++++.
T Consensus 499 ~ai~l~~ 505 (509)
T smart00350 499 EAIRLLR 505 (509)
T ss_pred HHHHHHH
Confidence 9998864
No 110
>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=32.32 E-value=1.1e+02 Score=24.79 Aligned_cols=48 Identities=15% Similarity=0.115 Sum_probs=42.6
Q ss_pred cccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhHHHHHHh
Q psy17765 161 ERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRHLQLAIR 208 (475)
Q Consensus 161 ~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~hI~lAI~ 208 (475)
..+..+|---|+-+++....+|...+-.+|...+++..++.|+..|+.
T Consensus 22 ~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~ 69 (77)
T PF07524_consen 22 DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALE 69 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 577888888999999888899999999999888999999999998874
No 111
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=31.16 E-value=74 Score=32.21 Aligned_cols=62 Identities=18% Similarity=0.291 Sum_probs=50.8
Q ss_pred HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhc--CCCCCCChHHHHHHHHH
Q psy17765 36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHY--NKRSTITSREIQTAVRL 99 (475)
Q Consensus 36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~--~kr~TlT~rdIqtAVrl 99 (475)
...+|.+.++.- +..|+.+|...+-..+..=+..+..|..+|+.+ .+..+||..||+..|..
T Consensus 135 l~~~i~~~~~~~--g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~ 198 (326)
T PRK07452 135 LKQLVERTAQEL--GVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSN 198 (326)
T ss_pred HHHHHHHHHHHc--CCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhcc
Confidence 455666666554 467899999999999988889999999999998 45778999999987754
No 112
>KOG0787|consensus
Probab=30.54 E-value=17 Score=39.04 Aligned_cols=63 Identities=17% Similarity=0.273 Sum_probs=41.8
Q ss_pred ChhHHHHHHHHHHHHHHHHHHhHHHHhcCC-cccchhHHHHHHhccHHHHhhhcCceecCCcccCC
Q psy17765 166 GAPVYLAAVMEYLAAEVLELAGNAARDNKK-TRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPN 230 (475)
Q Consensus 166 ~A~VYLaAVLEYLtaEILELAgn~A~~~k~-~rItP~hI~lAI~nD~EL~~Lf~~~tIa~gGV~p~ 230 (475)
...||+-..|+|+..||++-|..+...... ..-.+..|++.|.+..| +-+++ +.--+|||.+.
T Consensus 252 ~~~vyvPshL~ymlfElfKNamrATve~h~~~~~~~ppI~V~V~~gde-Dl~ik-ISDrGGGV~~~ 315 (414)
T KOG0787|consen 252 SFTVYVPSHLYYMLFELFKNAMRATVEHHGDDGDELPPIKVTVAKGDE-DLLIK-ISDRGGGVPHR 315 (414)
T ss_pred cCccccchHHHHHHHHHHHHHHHHHHHHhccCCCCCCCeEEEEecCCc-ceEEE-EecCCCCcChh
Confidence 344789999999999999999887555432 22237777777664444 23444 44467777665
No 113
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=30.02 E-value=1e+02 Score=34.95 Aligned_cols=60 Identities=18% Similarity=0.332 Sum_probs=49.2
Q ss_pred ccCCCCCcChHHHHHHHHHHHHH-------HHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHH
Q psy17765 46 QVHPDTGVSSKAMSIMNSFVNDI-------FERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGEL 105 (475)
Q Consensus 46 QVhPd~~IS~~Am~imns~v~di-------ferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeL 105 (475)
+..|...|+.+.+.++..+...+ ...+++-|.-++..+.+.+++..||+.|++++|++-+
T Consensus 243 ~~~~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~lvL~hR~ 309 (633)
T TIGR02442 243 SLLPSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAELVLPHRR 309 (633)
T ss_pred HhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHhhhhc
Confidence 45677889999999888877553 3556677777888899999999999999999998766
No 114
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=29.87 E-value=69 Score=34.60 Aligned_cols=72 Identities=13% Similarity=0.147 Sum_probs=43.1
Q ss_pred CCCccCcCCCCCcccchhHHHHHHhh----cCcc-cccCCChhHHHHHHHHHHHHHHHHHHhHHHHhcCCcccchhH
Q psy17765 131 KTKSKTRSSRAGLQFPVGRIHRLLRK----GNYA-ERVGAGAPVYLAAVMEYLAAEVLELAGNAARDNKKTRIIPRH 202 (475)
Q Consensus 131 ~~~~~srSsRagL~FPVsRi~r~Lke----~~~~-~RI~~~A~VYLaAVLEYLtaEILELAgn~A~~~k~~rItP~h 202 (475)
++++.||-.-.+..+|.+-|++++.. +.|+ .||+..|.--|.-++|++...+-+=-..||++.+++.|.+.|
T Consensus 338 k~~k~Skhgi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 338 KQKKVSKHGIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp --------------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred cccCCCCCCCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 34555666667788999999888753 2233 699999999999999999999998777899999999998865
No 115
>PF14687 DUF4460: Domain of unknown function (DUF4460)
Probab=29.87 E-value=64 Score=28.83 Aligned_cols=36 Identities=19% Similarity=0.369 Sum_probs=28.2
Q ss_pred hHHHHHHHHhhccCCCCC--------cChHHHHHHHHHHHHHHH
Q psy17765 35 SYAIYIYKVLKQVHPDTG--------VSSKAMSIMNSFVNDIFE 70 (475)
Q Consensus 35 sf~~yI~KVLKQVhPd~~--------IS~~Am~imns~v~dife 70 (475)
.-..+++.....||||+- +-++++..+++++..+..
T Consensus 10 ~l~~aLr~Fy~~VHPDlF~~~P~~k~~Ne~SLk~Ln~~Ld~l~~ 53 (112)
T PF14687_consen 10 DLRSALRPFYFAVHPDLFGQHPEEKQVNEESLKLLNSYLDSLKK 53 (112)
T ss_pred HHHHHHHHHHHHhCCcccccChHHHHhhHHHHHHHHHHHHHHhc
Confidence 467789999999999963 677888888888866554
No 116
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=29.40 E-value=1.5e+02 Score=29.82 Aligned_cols=73 Identities=19% Similarity=0.196 Sum_probs=56.3
Q ss_pred chhHHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHH
Q psy17765 33 KESYAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAK 107 (475)
Q Consensus 33 ~~sf~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaK 107 (475)
...+..+|...+++. +..|+.+|++.+-..+..=+..+..|.-+|+.+.+...+|..||+..+-......+..
T Consensus 148 ~~~~~~~i~~~~~~~--g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~~~~~~f~ 220 (340)
T PRK05574 148 EAELPQWIQQRLKQQ--GLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPDSARFDVFD 220 (340)
T ss_pred HHHHHHHHHHHHHHc--CCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhhhcCCHHH
Confidence 344677888888874 4678999999999999877889999999999886444499999988777655444433
No 117
>KOG3334|consensus
Probab=28.21 E-value=1.2e+02 Score=28.70 Aligned_cols=59 Identities=15% Similarity=0.312 Sum_probs=44.7
Q ss_pred HHHHHHhhccCCCCCc---ChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765 38 IYIYKVLKQVHPDTGV---SSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 100 (475)
Q Consensus 38 ~yI~KVLKQVhPd~~I---S~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll 100 (475)
.-|.-+|+. +|| ....+..|=.|-.+-...|...|.-.+.+.++.+|+..||+.|++..
T Consensus 17 ~~i~~iL~s----~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~ 78 (148)
T KOG3334|consen 17 RVIASILKS----LGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMR 78 (148)
T ss_pred HHHHHHHHH----cCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHH
Confidence 345555554 344 34555666666677778899999999999999999999999998875
No 118
>PF00725 3HCDH: 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain; InterPro: IPR006108 3-hydroxyacyl-CoA dehydrogenase (1.1.1.35 from EC) (HCDH) [] is an enzyme involved in fatty acid metabolism, it catalyzes the reduction of 3-hydroxyacyl-CoA to 3-oxoacyl-CoA. Most eukaryotic cells have 2 fatty-acid beta-oxidation systems, one located in mitochondria and the other in peroxisomes. In peroxisomes 3-hydroxyacyl-CoA dehydrogenase forms, with enoyl-CoA hydratase (ECH) and 3,2-trans-enoyl-CoA isomerase (ECI) a multifunctional enzyme where the N-terminal domain bears the hydratase/isomerase activities and the C-terminal domain the dehydrogenase activity. There are two mitochondrial enzymes: one which is monofunctional and the other which is, like its peroxisomal counterpart, multifunctional. In Escherichia coli (gene fadB) and Pseudomonas fragi (gene faoA) HCDH is part of a multifunctional enzyme which also contains an ECH/ECI domain as well as a 3-hydroxybutyryl-CoA epimerase domain []. There are two major region of similarities in the sequences of proteins of the HCDH family, the first one located in the N-terminal, corresponds to the NAD-binding site, the second one is located in the centre of the sequence. This represents the C-terminal domain which is also found in lambda crystallin. Some proteins include two copies of this domain.; GO: 0003857 3-hydroxyacyl-CoA dehydrogenase activity, 0016491 oxidoreductase activity, 0006631 fatty acid metabolic process, 0055114 oxidation-reduction process; PDB: 3MOG_A 2WTB_A 3ADP_A 3ADO_A 1WDL_B 2D3T_B 1WDK_A 1WDM_B 3K6J_A 1ZCJ_A ....
Probab=26.50 E-value=1.6e+02 Score=24.34 Aligned_cols=84 Identities=19% Similarity=0.274 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh--CcHHHHHHHHHHhhhhhhhc----cccCCCCCCCCCCccCc
Q psy17765 64 FVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRLL--LPGELAKHAVSEGTKAVTKY----TSSKGKGGKAKTKSKTR 137 (475)
Q Consensus 64 ~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll--LPgeLaKhAvseG~kAV~ky----~sSkg~~~k~~~~~~sr 137 (475)
++|+++-.+..||.+|+...- .|++||..+++.- +|.-....+-.-|...+..- ....+.
T Consensus 3 i~nRl~~~~~~ea~~l~~egv---as~~~ID~~~~~~~G~p~Gpf~l~D~~Gl~~~~~~~~~~~~~~~~----------- 68 (97)
T PF00725_consen 3 IVNRLLAALLNEAARLVEEGV---ASPEDIDRAMRYGLGFPMGPFELADLVGLDVVYHILEYLAAALGD----------- 68 (97)
T ss_dssp THHHHHHHHHHHHHHHHHTTS---SSHHHHHHHHHHHHTHSSTHHHHHHHHHHHHHHHHHHHHHHHHCC-----------
T ss_pred HHHHHHHHHHHHHHHHHHHcC---CCHHHHHHHHHHhCCCCCccchHHHHhCchHHHHHHHHHHHhcCC-----------
Confidence 578999999999999998643 4899999999984 56444444444443333321 111110
Q ss_pred CCCCCcccchhHHHHHHhhcCcccccCC
Q psy17765 138 SSRAGLQFPVGRIHRLLRKGNYAERVGA 165 (475)
Q Consensus 138 SsRagL~FPVsRi~r~Lke~~~~~RI~~ 165 (475)
...-|..-+++++.++++..+-+.
T Consensus 69 ----~~~~~~~~l~~mv~~g~~G~k~g~ 92 (97)
T PF00725_consen 69 ----RAFRPSPLLKEMVEEGRLGRKSGK 92 (97)
T ss_dssp ----GGGSS-HHHHHHHHTT--BGGGTB
T ss_pred ----CcCCchHHHHHHHHCCCCcCcCCC
Confidence 112246677777777777665544
No 119
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=25.79 E-value=3.1e+02 Score=28.35 Aligned_cols=66 Identities=6% Similarity=0.047 Sum_probs=44.7
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHH------HHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCc
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFV------NDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLP 102 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v------~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLP 102 (475)
...+..-++....+..++.++++.+..++ .+..-.++..|..++...++.++|..+|+.|+..+.+
T Consensus 213 ~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~ 284 (394)
T PRK00411 213 FDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEI 284 (394)
T ss_pred HHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHH
Confidence 33444444444334458888988887766 3333456677777777777788999999999988743
No 120
>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=25.33 E-value=42 Score=26.32 Aligned_cols=22 Identities=41% Similarity=0.756 Sum_probs=18.1
Q ss_pred ccHHHHhhhcCceecCCcccCCccc
Q psy17765 209 NDEELNKLLSGVTIAQGGVLPNIQA 233 (475)
Q Consensus 209 nD~EL~~Lf~~~tIa~gGV~p~i~~ 233 (475)
.|+||+.++++. ++||++.|..
T Consensus 16 s~eELd~ilGg~---g~Gv~~Tis~ 37 (51)
T PF04604_consen 16 SDEELDQILGGA---GNGVIKTISH 37 (51)
T ss_pred CHHHHHHHhCCC---CCCceeeccc
Confidence 689999999874 7899987654
No 121
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=25.17 E-value=1.8e+02 Score=29.71 Aligned_cols=71 Identities=17% Similarity=0.149 Sum_probs=56.1
Q ss_pred HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcC-CCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765 36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYN-KRSTITSREIQTAVRLLLPGELAKH 108 (475)
Q Consensus 36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~-kr~TlT~rdIqtAVrllLPgeLaKh 108 (475)
...+|.+.+++- +..|+.+|+..+-..+..=+..+..|..+|+.+. ...+||..||+..+-......+...
T Consensus 147 l~~~i~~~~~~~--g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~~e~~if~l 218 (343)
T PRK06585 147 LARLIDDELAEA--GLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDASALSLDDA 218 (343)
T ss_pred HHHHHHHHHHHC--CCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCcccccHHHH
Confidence 455677776665 4678999999999999988889999999999984 3568999999888777665555444
No 122
>KOG1745|consensus
Probab=23.92 E-value=83 Score=29.37 Aligned_cols=64 Identities=19% Similarity=0.274 Sum_probs=43.8
Q ss_pred HHHHHHHHhhccCCCCCcChHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHH
Q psy17765 36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVNDIFERIAAESSRLAHYNKRSTITSREIQTAVRL 99 (475)
Q Consensus 36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrl 99 (475)
|+.-.+-+...--||+.+.+.|+.-+..-....+.-+-+.+.-.+...++-||-+.|||-|.++
T Consensus 69 FqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArri 132 (137)
T KOG1745|consen 69 FQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 132 (137)
T ss_pred HHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhc
Confidence 4444444445557888899988887766555444444444443445678999999999999887
No 123
>PRK05907 hypothetical protein; Provisional
Probab=23.82 E-value=90 Score=32.36 Aligned_cols=70 Identities=20% Similarity=0.133 Sum_probs=52.9
Q ss_pred HHHHHHHhhccCCCCCcChHHHHHHHHHH-HHHHHHHHHHHhhhhhc-CCCCCCChHHHHHHHHHhCcHHHHHH
Q psy17765 37 AIYIYKVLKQVHPDTGVSSKAMSIMNSFV-NDIFERIAAESSRLAHY-NKRSTITSREIQTAVRLLLPGELAKH 108 (475)
Q Consensus 37 ~~yI~KVLKQVhPd~~IS~~Am~imns~v-~diferIa~EA~~L~~~-~kr~TlT~rdIqtAVrllLPgeLaKh 108 (475)
..+|.+.+++- +..|+.+|++.+...+ ..=+..|..|..+|+.| .++.+||.+||+..|-..+-..+...
T Consensus 140 ~~Wi~~~~~~~--g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~nIF~L 211 (311)
T PRK05907 140 AQLLIQRAKEL--GISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAASLWKL 211 (311)
T ss_pred HHHHHHHHHHc--CCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCcccccHHHH
Confidence 45555555554 3578999999988877 34456999999999998 66888999999988877666555444
No 124
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=23.05 E-value=79 Score=33.57 Aligned_cols=57 Identities=26% Similarity=0.382 Sum_probs=40.4
Q ss_pred hhccCCCCCcChHHHHHHHHHHHHHH---HHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765 44 LKQVHPDTGVSSKAMSIMNSFVNDIF---ERIAAESSRLAHYNKRSTITSREIQTAVRLL 100 (475)
Q Consensus 44 LKQVhPd~~IS~~Am~imns~v~dif---erIa~EA~~L~~~~kr~TlT~rdIqtAVrll 100 (475)
+|.|---+||+.=+-+.+..+..|+- ..+++||..+...++|..+|..||-.|.|-+
T Consensus 11 ~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~l 70 (450)
T COG5095 11 LKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSL 70 (450)
T ss_pred HHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhc
Confidence 34444445655444444444444544 4568999999999999999999999999987
No 125
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=21.86 E-value=2.7e+02 Score=31.60 Aligned_cols=65 Identities=9% Similarity=0.104 Sum_probs=42.1
Q ss_pred HHHHHHHHhhccCCCCCcChHHHHHHHHHHH-------------HHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHh
Q psy17765 36 YAIYIYKVLKQVHPDTGVSSKAMSIMNSFVN-------------DIFERIAAESSRLAHYNKRSTITSREIQTAVRLL 100 (475)
Q Consensus 36 f~~yI~KVLKQVhPd~~IS~~Am~imns~v~-------------diferIa~EA~~L~~~~kr~TlT~rdIqtAVrll 100 (475)
|..+|.+..+.-..--.++.+|+..+-.+.. +-+..|+++|...+...++.+++.+||+.|++.-
T Consensus 314 ~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 314 LVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 5566666555431112678888887654433 4566777777666666667788888888887654
No 126
>KOG3523|consensus
Probab=21.59 E-value=16 Score=41.43 Aligned_cols=68 Identities=13% Similarity=0.038 Sum_probs=44.5
Q ss_pred hhHHHHHHhc---ccccc-----ccccccccccccccccCCcchhhhhccccCCCCcccchhhhccccccchhhhhhhcc
Q psy17765 286 VLEEHLENAT---GLLVD-----ESGNTLDSTSTRQTTDGGLGDSLDVVTEYFPVPLGASFSESLSSLTTADLLSITMAA 357 (475)
Q Consensus 286 Vfre~l~~~~---~l~~~-----~f~n~ld~~e~~~~~~g~leD~le~~~e~~~~p~~gs~fe~la~~~~~~~~~~~m~~ 357 (475)
|+.++|.... ..+.+ .||||.|+.+.+..|+-.||.-++- |--.--|..|-++-|+- .|+||..|--.
T Consensus 278 llv~hF~~s~~l~~~Ls~~d~~~LFSni~~V~~~Serfl~dLE~r~e~---ni~i~dicDiv~~ha~~-~f~vYv~Y~tN 353 (695)
T KOG3523|consen 278 LLVDHFMNSKELRSTLSASDRHHLFSNIQDVREVSERFLCDLEARLEE---NIFIDDICDIVEDHAAK-HFSVYVKYCTN 353 (695)
T ss_pred HHHHHHhhhHHHHHhcChHHHHHHHhhhHHHHHHHHHHHHHHHHHHHh---CchhhHHHHHHHHhccc-ccceeehhccc
Confidence 7777777542 22332 9999999999999999887755432 11122244455555554 88999887543
No 127
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=21.24 E-value=53 Score=29.22 Aligned_cols=40 Identities=28% Similarity=0.442 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCCChHHHHHHHHHhCcHHHHHHHHHHh
Q psy17765 66 NDIFERIAAESSRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEG 113 (475)
Q Consensus 66 ~diferIa~EA~~L~~~~kr~TlT~rdIqtAVrllLPgeLaKhAvseG 113 (475)
.+.+++|..|.. +-+-||+..| +=|+-+.+.||+.++.+-
T Consensus 44 ~~~~~kl~kEV~------~~K~ITp~~l--serlkI~~SlAr~~Lr~L 83 (105)
T PF03297_consen 44 KETYDKLLKEVP------KMKLITPSVL--SERLKINGSLARKALREL 83 (105)
T ss_dssp CHHHHHHHHHCT------TSSCECHHHH--HHHHCCSCHHHHHHHHHH
T ss_pred HHHHHHHHHHhc------cCcEeeHHHH--HHhHhhHHHHHHHHHHHH
Confidence 345788887733 3456899988 556666899999988764
No 128
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=20.85 E-value=1.5e+02 Score=27.48 Aligned_cols=42 Identities=21% Similarity=0.403 Sum_probs=29.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHhHH-HHhcCCcccchhHHHHHHhcc
Q psy17765 167 APVYLAAVMEYLAAEVLELAGNA-ARDNKKTRIIPRHLQLAIRND 210 (475)
Q Consensus 167 A~VYLaAVLEYLtaEILELAgn~-A~~~k~~rItP~hI~lAI~nD 210 (475)
--+++-+++|++- +|..-.|. |.+-.++.|.|+|+-.|+.|=
T Consensus 36 rei~in~cieFi~--~lsseAne~ce~EaKKTIa~EHviKALenL 78 (148)
T COG5150 36 REIFINACIEFIN--MLSSEANEACEEEAKKTIAYEHVIKALENL 78 (148)
T ss_pred HHHHHHHHHHHHH--HHHHHHHHHHHHHHhccccHHHHHHHHHhc
Confidence 3578888888873 34433343 334467889999999998763
Done!