Query 024238
Match_columns 270
No_of_seqs 192 out of 817
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 03:05:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024238.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024238hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1657 CCAAT-binding factor, 100.0 1.3E-33 2.8E-38 255.8 9.2 166 82-252 50-218 (236)
2 COG5208 HAP5 CCAAT-binding fac 100.0 3.6E-30 7.7E-35 232.2 8.4 114 76-189 77-192 (286)
3 PF00808 CBFD_NFYB_HMF: Histon 99.8 9E-20 2E-24 133.7 7.0 64 106-169 2-65 (65)
4 KOG1659 Class 2 transcription 99.8 8.1E-20 1.8E-24 163.8 6.1 87 100-186 7-93 (224)
5 COG5247 BUR6 Class 2 transcrip 99.8 8.6E-19 1.9E-23 142.4 5.4 83 104-186 21-103 (113)
6 COG5262 HTA1 Histone H2A [Chro 99.3 2.8E-12 6E-17 107.0 6.0 77 104-180 24-100 (132)
7 cd00074 H2A Histone 2A; H2A is 99.3 4.8E-12 1E-16 104.5 7.2 77 104-180 18-94 (115)
8 KOG1658 DNA polymerase epsilon 99.3 9.7E-13 2.1E-17 113.7 2.1 90 102-191 55-147 (162)
9 KOG1756 Histone 2A [Chromatin 99.1 1.3E-10 2.8E-15 97.8 6.9 77 104-180 25-101 (131)
10 smart00414 H2A Histone 2A. 99.1 1.6E-10 3.5E-15 94.2 6.7 77 104-180 7-83 (106)
11 COG2036 HHT1 Histones H3 and H 99.1 3.6E-10 7.8E-15 90.2 7.0 80 93-173 6-85 (91)
12 PTZ00017 histone H2A; Provisio 99.0 3.3E-10 7.1E-15 96.1 6.3 76 104-179 25-100 (134)
13 PLN00154 histone H2A; Provisio 99.0 3.4E-10 7.3E-15 96.2 6.2 77 104-180 36-113 (136)
14 KOG0869 CCAAT-binding factor, 99.0 3.7E-10 8E-15 98.2 6.6 69 105-173 31-100 (168)
15 PLN00156 histone H2AX; Provisi 99.0 1.3E-09 2.8E-14 92.9 6.9 77 104-180 27-103 (139)
16 PLN00153 histone H2A; Provisio 99.0 1.3E-09 2.9E-14 91.9 6.5 77 104-180 22-98 (129)
17 PLN00157 histone H2A; Provisio 98.9 1.4E-09 3E-14 92.1 6.2 76 104-179 24-99 (132)
18 PTZ00252 histone H2A; Provisio 98.8 6E-09 1.3E-13 88.4 6.5 77 104-180 23-102 (134)
19 smart00803 TAF TATA box bindin 98.8 1.3E-08 2.8E-13 76.2 7.0 64 106-170 2-65 (65)
20 PF00125 Histone: Core histone 98.8 8.3E-09 1.8E-13 76.7 5.2 69 103-171 5-74 (75)
21 KOG0870 DNA polymerase epsilon 98.7 2.4E-08 5.2E-13 87.5 6.4 76 104-179 8-85 (172)
22 cd00076 H4 Histone H4, one of 98.7 6E-08 1.3E-12 76.6 6.9 67 106-173 13-79 (85)
23 PLN00035 histone H4; Provision 98.7 6.5E-08 1.4E-12 79.0 6.9 67 106-173 29-95 (103)
24 PTZ00015 histone H4; Provision 98.6 1.5E-07 3.3E-12 76.7 7.0 68 105-173 29-96 (102)
25 smart00417 H4 Histone H4. 98.5 1.5E-07 3.2E-12 72.8 5.2 61 106-167 13-73 (74)
26 KOG0871 Class 2 transcription 98.5 3.8E-07 8.2E-12 78.9 6.6 78 103-181 9-88 (156)
27 cd07981 TAF12 TATA Binding Pro 98.1 1.4E-05 3E-10 60.6 7.2 65 108-173 3-68 (72)
28 COG5150 Class 2 transcription 98.0 1.8E-05 4E-10 67.4 6.4 78 102-180 7-86 (148)
29 cd08048 TAF11 TATA Binding Pro 97.8 6.7E-05 1.5E-09 59.2 6.6 71 100-171 10-83 (85)
30 smart00428 H3 Histone H3. 97.8 0.00013 2.8E-09 59.9 8.1 77 92-169 15-98 (105)
31 KOG1757 Histone 2A [Chromatin 97.6 4.1E-05 8.9E-10 64.1 2.5 76 104-179 28-104 (131)
32 cd07979 TAF9 TATA Binding Prot 97.5 0.00022 4.7E-09 59.0 6.3 76 110-187 5-80 (117)
33 cd08050 TAF6 TATA Binding Prot 97.4 0.00031 6.6E-09 67.0 6.9 64 109-173 2-65 (343)
34 PF02969 TAF: TATA box binding 97.4 0.00056 1.2E-08 51.9 7.0 64 106-170 3-66 (66)
35 PF04719 TAFII28: hTAFII28-lik 97.4 0.00027 5.9E-09 56.5 5.5 85 84-171 4-89 (90)
36 smart00576 BTP Bromodomain tra 97.4 0.00052 1.1E-08 52.3 6.6 60 112-172 12-71 (77)
37 PF09415 CENP-X: CENP-S associ 97.3 0.0011 2.3E-08 51.0 6.8 63 108-170 1-66 (72)
38 KOG1658 DNA polymerase epsilon 97.1 0.00073 1.6E-08 59.2 5.3 84 102-185 7-104 (162)
39 PLN00161 histone H3; Provision 97.1 0.0021 4.6E-08 55.0 7.5 74 97-170 49-124 (135)
40 PLN00121 histone H3; Provision 97.0 0.0021 4.6E-08 55.1 6.8 72 97-169 56-129 (136)
41 PTZ00018 histone H3; Provision 97.0 0.0022 4.7E-08 55.0 6.7 72 97-169 56-129 (136)
42 PF15511 CENP-T: Centromere ki 97.0 0.001 2.2E-08 65.1 5.3 64 101-164 346-414 (414)
43 PLN00160 histone H3; Provision 97.0 0.0024 5.3E-08 51.9 6.6 77 93-169 8-89 (97)
44 smart00427 H2B Histone H2B. 96.7 0.0047 1E-07 49.6 6.2 60 111-171 6-66 (89)
45 KOG3467 Histone H4 [Chromatin 96.5 0.0084 1.8E-07 48.6 6.2 63 110-173 33-95 (103)
46 KOG3219 Transcription initiati 96.3 0.0071 1.5E-07 54.6 5.1 89 80-172 89-178 (195)
47 PF02269 TFIID-18kDa: Transcri 96.2 0.0043 9.3E-08 49.4 3.0 76 112-187 7-83 (93)
48 PLN00158 histone H2B; Provisio 96.1 0.018 4E-07 48.3 6.2 62 109-171 30-92 (116)
49 PF03847 TFIID_20kDa: Transcri 95.9 0.033 7.2E-07 42.3 6.5 61 111-172 4-65 (68)
50 PTZ00463 histone H2B; Provisio 95.9 0.025 5.5E-07 47.5 6.2 60 111-171 33-93 (117)
51 PLN00155 histone H2A; Provisio 95.7 0.012 2.5E-07 44.1 3.3 36 104-139 22-57 (58)
52 cd07978 TAF13 The TATA Binding 95.7 0.029 6.2E-07 44.9 5.6 75 110-185 6-81 (92)
53 PF07524 Bromo_TP: Bromodomain 95.5 0.06 1.3E-06 40.7 6.5 60 112-172 12-71 (77)
54 PF15630 CENP-S: Kinetochore c 95.4 0.037 7.9E-07 43.1 5.3 51 124-174 25-75 (76)
55 PF15510 CENP-W: Centromere ki 95.0 0.055 1.2E-06 44.2 5.3 64 106-170 16-94 (102)
56 KOG1745 Histones H3 and H4 [Ch 94.3 0.05 1.1E-06 46.9 3.8 71 99-170 59-131 (137)
57 KOG1744 Histone H2B [Chromatin 93.8 0.18 3.8E-06 43.1 6.1 59 112-171 43-102 (127)
58 KOG1142 Transcription initiati 93.2 0.12 2.7E-06 48.5 4.5 70 110-179 158-227 (258)
59 KOG3423 Transcription initiati 92.7 0.69 1.5E-05 41.4 8.2 72 99-172 80-165 (176)
60 PF02291 TFIID-31kDa: Transcri 91.2 0.84 1.8E-05 38.8 6.9 77 110-188 16-92 (129)
61 KOG2549 Transcription initiati 91.0 0.6 1.3E-05 48.2 6.7 63 109-172 14-76 (576)
62 PF05236 TAF4: Transcription i 90.3 0.53 1.1E-05 43.3 5.2 45 109-154 50-94 (264)
63 cd08045 TAF4 TATA Binding Prot 87.3 1.2 2.5E-05 39.9 5.2 70 102-172 44-119 (212)
64 PF03540 TFIID_30kDa: Transcri 82.8 5 0.00011 29.3 5.8 48 106-154 2-49 (51)
65 COG5095 TAF6 Transcription ini 80.4 4.1 8.9E-05 40.3 6.0 62 110-172 9-70 (450)
66 COG5162 Transcription initiati 78.4 14 0.00031 33.3 8.3 62 91-153 73-134 (197)
67 TIGR03015 pepcterm_ATPase puta 64.2 11 0.00023 33.2 4.3 50 124-173 215-267 (269)
68 PF10979 DUF2786: Protein of u 63.8 7.7 0.00017 27.1 2.7 35 109-143 4-38 (43)
69 PRK00411 cdc6 cell division co 61.2 27 0.0006 32.7 6.7 64 109-172 209-282 (394)
70 PF13335 Mg_chelatase_2: Magne 57.2 79 0.0017 25.1 7.7 62 102-170 27-94 (96)
71 TIGR02928 orc1/cdc6 family rep 55.3 47 0.001 30.7 7.1 50 124-173 220-275 (365)
72 PF12767 SAGA-Tad1: Transcript 54.3 19 0.00041 32.9 4.3 42 110-152 210-251 (252)
73 COG5248 TAF19 Transcription in 53.3 43 0.00093 28.5 5.8 71 110-182 13-84 (126)
74 KOG3901 Transcription initiati 50.0 56 0.0012 27.5 5.9 69 113-184 16-85 (109)
75 KOG1560 Translation initiation 48.9 1.1E+02 0.0024 30.0 8.5 47 73-119 249-295 (339)
76 COG1474 CDC6 Cdc6-related prot 47.7 27 0.00058 34.0 4.4 71 110-181 193-273 (366)
77 TIGR00764 lon_rel lon-related 46.7 58 0.0013 33.9 6.8 63 110-172 316-391 (608)
78 COG1222 RPT1 ATP-dependent 26S 46.5 21 0.00045 35.9 3.4 51 116-172 338-392 (406)
79 KOG2680 DNA helicase TIP49, TB 45.1 53 0.0012 32.9 5.9 59 111-170 362-427 (454)
80 TIGR00368 Mg chelatase-related 43.9 81 0.0018 32.1 7.2 60 104-170 432-497 (499)
81 PF13654 AAA_32: AAA domain; P 42.9 59 0.0013 33.3 6.1 33 140-172 474-506 (509)
82 KOG3334 Transcription initiati 40.3 1.1E+02 0.0023 27.1 6.4 40 140-179 46-85 (148)
83 PTZ00195 60S ribosomal protein 39.6 11 0.00024 34.5 0.4 85 82-167 38-135 (198)
84 COG5251 TAF40 Transcription in 38.7 78 0.0017 28.9 5.5 85 84-172 96-181 (199)
85 PRK07452 DNA polymerase III su 38.5 65 0.0014 29.7 5.2 63 124-186 149-215 (326)
86 KOG1657 CCAAT-binding factor, 38.3 3.8 8.2E-05 38.1 -2.9 78 102-188 4-81 (236)
87 KOG4336 TBP-associated transcr 38.0 88 0.0019 30.7 6.1 64 109-172 7-70 (323)
88 KOG3521 Predicted guanine nucl 37.1 78 0.0017 34.3 6.0 74 73-148 288-370 (846)
89 COG1067 LonB Predicted ATP-dep 35.9 1E+02 0.0022 32.8 6.6 95 82-186 319-414 (647)
90 PF08637 NCA2: ATP synthase re 35.7 1.2E+02 0.0025 29.0 6.5 70 67-148 17-88 (290)
91 PRK09862 putative ATP-dependen 34.8 1.9E+02 0.0041 29.8 8.2 65 104-172 425-492 (506)
92 KOG2389 Predicted bromodomain 33.6 1.1E+02 0.0025 30.3 6.2 65 107-172 30-94 (353)
93 PF04157 EAP30: EAP30/Vps36 fa 33.0 13 0.00027 33.4 -0.4 84 80-175 37-148 (223)
94 KOG4811 Uncharacterized conser 32.7 84 0.0018 26.9 4.5 35 84-122 4-39 (127)
95 TIGR01242 26Sp45 26S proteasom 32.1 60 0.0013 30.8 4.0 41 131-171 318-362 (364)
96 TIGR01128 holA DNA polymerase 31.9 1.1E+02 0.0024 27.4 5.5 63 124-186 130-195 (302)
97 PRK03992 proteasome-activating 31.4 62 0.0013 31.4 4.0 33 140-172 340-372 (389)
98 PRK05574 holA DNA polymerase I 31.1 1.1E+02 0.0024 28.0 5.4 62 124-186 165-230 (340)
99 PTZ00469 60S ribosomal subunit 29.1 20 0.00043 32.6 0.2 87 80-167 36-127 (187)
100 PRK06585 holA DNA polymerase I 29.1 1E+02 0.0022 28.7 4.9 63 124-186 161-227 (343)
101 PF13499 EF-hand_7: EF-hand do 28.5 1.9E+02 0.0042 19.9 5.2 32 138-169 35-66 (66)
102 COG1224 TIP49 DNA helicase TIP 28.1 1.2E+02 0.0025 31.0 5.3 61 110-170 364-430 (450)
103 PTZ00361 26 proteosome regulat 27.8 72 0.0016 32.0 3.9 32 141-172 393-424 (438)
104 PRK13765 ATP-dependent proteas 27.1 1.2E+02 0.0026 32.0 5.5 31 141-171 369-399 (637)
105 KOG3341 RNA polymerase II tran 26.9 1.5E+02 0.0032 28.1 5.4 42 63-105 24-65 (249)
106 PTZ00454 26S protease regulato 26.4 82 0.0018 31.0 4.0 32 141-172 355-386 (398)
107 TIGR02902 spore_lonB ATP-depen 24.6 2E+02 0.0044 29.3 6.4 61 112-172 268-332 (531)
108 KOG4718 Non-SMC (structural ma 24.1 1.1E+02 0.0025 28.7 4.2 56 125-180 93-154 (235)
109 PF08369 PCP_red: Proto-chloro 24.0 1.2E+02 0.0026 21.2 3.4 24 145-168 21-44 (45)
110 PRK05907 hypothetical protein; 22.2 1.7E+02 0.0037 27.9 5.1 74 111-186 142-220 (311)
111 PF04625 DEC-1_N: DEC-1 protei 21.8 2.5E+02 0.0055 28.1 6.2 38 82-120 278-337 (407)
112 cd01106 HTH_TipAL-Mta Helix-Tu 21.6 1.7E+02 0.0038 22.8 4.3 33 88-120 39-71 (103)
113 TIGR02442 Cob-chelat-sub cobal 21.0 2.7E+02 0.0057 29.1 6.6 48 124-171 249-303 (633)
114 cd04773 HTH_TioE_rpt2 Second H 20.6 2.1E+02 0.0046 22.8 4.7 28 92-119 43-70 (108)
115 COG5094 TAF9 Transcription ini 20.5 3.4E+02 0.0073 23.7 6.0 65 112-177 20-87 (145)
No 1
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=100.00 E-value=1.3e-33 Score=255.77 Aligned_cols=166 Identities=53% Similarity=0.775 Sum_probs=134.0
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc
Q 024238 82 QQQLQMFWSNQMQEIEQTADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQ 161 (270)
Q Consensus 82 ~q~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq 161 (270)
+++|++||++...|+|...||+++.|||+|||||||.|+|+.+|+.||+++++||||+||.+|+.+||.++++++||||+
T Consensus 50 ~~~l~~fw~~~~~e~e~~~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~ 129 (236)
T KOG1657|consen 50 RQQLQSFWSKQAIEKEGQLDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQ 129 (236)
T ss_pred hHHHHhhhhccccccccccchhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccch
Confidence 78999999999877778899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCcccchhccCCCccccc--ccCCC-CcCCCCCCCCCCCCCCcccCCCCCCCCCCccccccCCccccccC
Q 024238 162 KNDIAAAISRTDVFDFLVDIIPRDELKE--EGLGV-TKGALPVVGSPGDMPLYYVPPQHPVGHTGMIMGKPVDQAALYSG 238 (270)
Q Consensus 162 ~~DIa~AI~~~e~FdFL~DIVP~~~~~~--~~~~~-~~~~~~~~~~p~~~p~~~~~~~~~~~~~g~~~g~~~~~~~~~~~ 238 (270)
++||+.+|.+++.||||.||||++...+ ..+.. .+..+...+..+.++|++...-....|+|+++|+|.++. +
T Consensus 130 ~sdia~av~~s~~fdFL~DivP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~-~--- 205 (236)
T KOG1657|consen 130 KSDIAAAVTQSETFDFLRDIVPRKILAEKYPSLAAKGPGEMREDDFVAPVTYIMDNAGIQQIPPGLVAGQPQCIR-L--- 205 (236)
T ss_pred HHHHHHHhccCCCccceeccccchhccccccccccCCCccccccccccccccccccccccccCchhhcCCccccc-c---
Confidence 9999999999999999999999998876 23332 222222122233367666554433558999999998755 2
Q ss_pred CCCCCCCCCCCCCC
Q 024238 239 QQPRPPVAFMPWPQ 252 (270)
Q Consensus 239 ~~~~p~~~~~~w~~ 252 (270)
.++.+.+..+ |++
T Consensus 206 ~~~~~~~q~~-~~~ 218 (236)
T KOG1657|consen 206 AQPVSGTQGQ-WQT 218 (236)
T ss_pred cCCCccccch-hhh
Confidence 3444444344 654
No 2
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.96 E-value=3.6e-30 Score=232.22 Aligned_cols=114 Identities=54% Similarity=0.920 Sum_probs=106.8
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHhh--hcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024238 76 QQQQQQQQQLQMFWSNQMQEIEQT--ADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTE 153 (270)
Q Consensus 76 ~~~~~~~q~l~~FW~~~~~eiE~~--~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~ 153 (270)
.+-..+.+.|..||.+.++++|.+ .++|.+.|||+||||+||.|+||++||+||++||+|+||.||.+||.+||.+|+
T Consensus 77 glvg~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae 156 (286)
T COG5208 77 GLVGLLDERISRYWQQTIKAAEEERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAE 156 (286)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHh
Confidence 344578899999999999999875 478999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCcccHHHHHHHHhcCCcccchhccCCCccccc
Q 024238 154 ENKRRTLQKNDIAAAISRTDVFDFLVDIIPRDELKE 189 (270)
Q Consensus 154 ~~KRKTLq~~DIa~AI~~~e~FdFL~DIVP~~~~~~ 189 (270)
++|||||+++||+.||++++.||||.|||||.....
T Consensus 157 ~NkRRtLQksDia~Av~kSeMfDFLidivpr~p~n~ 192 (286)
T COG5208 157 ENKRRTLQKSDIAAAVKKSEMFDFLIDIVPRNPFNH 192 (286)
T ss_pred HhhhhHHHHHHHHHHHHHHHHHhHHhhhccCCCccc
Confidence 999999999999999999999999999999986543
No 3
>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=99.80 E-value=9e-20 Score=133.72 Aligned_cols=64 Identities=45% Similarity=0.574 Sum_probs=59.7
Q ss_pred CCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024238 106 SLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAI 169 (270)
Q Consensus 106 ~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI 169 (270)
.||++|||||||.|+++.+||+||.+++++|+|+||.+|+.+|+++|+.++||||+++||..||
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 6999999999999999999999999999999999999999999999999999999999999986
No 4
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=99.79 E-value=8.1e-20 Score=163.83 Aligned_cols=87 Identities=29% Similarity=0.479 Sum_probs=82.1
Q ss_pred hcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchh
Q 024238 100 ADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLV 179 (270)
Q Consensus 100 ~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~ 179 (270)
.++.+..||.+||||||++|+||++|+...||+++||+|+|++.|+.++++.++..+-|||+..||+.||.+++.||||+
T Consensus 7 ~~~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk 86 (224)
T KOG1659|consen 7 FKKYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK 86 (224)
T ss_pred hhhhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence 35567899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCcc
Q 024238 180 DIIPRDE 186 (270)
Q Consensus 180 DIVP~~~ 186 (270)
|+|.+..
T Consensus 87 ~~v~~vp 93 (224)
T KOG1659|consen 87 EVVEKVP 93 (224)
T ss_pred HHHHhcC
Confidence 9876544
No 5
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=99.75 E-value=8.6e-19 Score=142.40 Aligned_cols=83 Identities=30% Similarity=0.481 Sum_probs=79.2
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhccCC
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVDIIP 183 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~DIVP 183 (270)
.+.||+|||||||+.|+|+++|+...|++.+||+|+|+.+|...+.+.|+....|+++.++|..|+.++++||||.|++.
T Consensus 21 ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~~ 100 (113)
T COG5247 21 KTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNMEQ 100 (113)
T ss_pred hhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHHH
Confidence 35899999999999999999999999999999999999999999999999999999999999999999999999999986
Q ss_pred Ccc
Q 024238 184 RDE 186 (270)
Q Consensus 184 ~~~ 186 (270)
.+.
T Consensus 101 ~~~ 103 (113)
T COG5247 101 FKN 103 (113)
T ss_pred hcC
Confidence 543
No 6
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=99.31 E-value=2.8e-12 Score=106.98 Aligned_cols=77 Identities=22% Similarity=0.323 Sum_probs=74.0
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhc
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVD 180 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~D 180 (270)
.+.||++|||||||.+..-.+|+++|++.++.++|+++.++++.|.+.|+.+|+|+|.++||..||+++++++||..
T Consensus 24 gl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~EL~~l~~ 100 (132)
T COG5262 24 GLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLG 100 (132)
T ss_pred CccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcCcHHHHHHhh
Confidence 46899999999999888888999999999999999999999999999999999999999999999999999999985
No 7
>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=99.31 E-value=4.8e-12 Score=104.47 Aligned_cols=77 Identities=19% Similarity=0.323 Sum_probs=73.0
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhc
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVD 180 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~D 180 (270)
.+.||++||+|+||.+-...+||++|++.|+.++|+++.++.+.|.+.|+..||++|+++||..||.++++|++|..
T Consensus 18 gL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~EL~~L~~ 94 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRNDEELNKLLK 94 (115)
T ss_pred CccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHHHHHHHc
Confidence 57899999999999877778999999999999999999999999999999999999999999999999999997764
No 8
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=99.29 E-value=9.7e-13 Score=113.71 Aligned_cols=90 Identities=37% Similarity=0.544 Sum_probs=81.7
Q ss_pred CCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhcc
Q 024238 102 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVDI 181 (270)
Q Consensus 102 fk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~DI 181 (270)
-+.++|||+|||+|||.|+|+.+...|+.+++++|+|+||++|...++.++...||||+++.|+..||+..+.|.||.+.
T Consensus 55 a~l~rLpL~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~fle~~ 134 (162)
T KOG1658|consen 55 ASLSRLPLARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAFLEGA 134 (162)
T ss_pred hhhhhccHHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHHHhhh
Confidence 45689999999999999999999999999999999999999999999999999999999999999999999999999865
Q ss_pred C---CCccccccc
Q 024238 182 I---PRDELKEEG 191 (270)
Q Consensus 182 V---P~~~~~~~~ 191 (270)
. |+..+++..
T Consensus 135 ~d~~pk~~~~~~k 147 (162)
T KOG1658|consen 135 LDTAPKPNIVEIK 147 (162)
T ss_pred cccCCccchhhhh
Confidence 5 555444433
No 9
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=99.12 E-value=1.3e-10 Score=97.79 Aligned_cols=77 Identities=19% Similarity=0.335 Sum_probs=74.6
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhc
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVD 180 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~D 180 (270)
.+.||++||.|+||..-...+|++.|+++++.++|+.+.++++.|-+.|+.+|+..|+++||..||.+++++.||.+
T Consensus 25 gl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~NDeEL~~lL~ 101 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRNDEELNKLLG 101 (131)
T ss_pred ccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhCcHHHHHHhc
Confidence 47899999999999988889999999999999999999999999999999999999999999999999999999988
No 10
>smart00414 H2A Histone 2A.
Probab=99.11 E-value=1.6e-10 Score=94.19 Aligned_cols=77 Identities=21% Similarity=0.357 Sum_probs=72.5
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhc
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVD 180 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~D 180 (270)
.+.||++||+|+||..-...+|++.|++.++.++|+++.++.+.|.+.|+.+|++.|+++||..||.++++|+.|..
T Consensus 7 gL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~nD~EL~~L~~ 83 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELNKLLK 83 (106)
T ss_pred CccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccCCHHHHHHHc
Confidence 47899999999999987788999999999999999999999999999999999999999999999999999986654
No 11
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.07 E-value=3.6e-10 Score=90.24 Aligned_cols=80 Identities=24% Similarity=0.335 Sum_probs=70.7
Q ss_pred HHHHHhhhcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 93 MQEIEQTADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 93 ~~eiE~~~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
+.|+..........||.+.|.||||..-. .+||.+|...+.+|+|.|+.+|+++|..+|.+.|||||+.+||..|++..
T Consensus 6 ~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~-~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~ 84 (91)
T COG2036 6 LKEIRRYQRSTDLLLPKAPVRRILRKAGA-ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRL 84 (91)
T ss_pred HHHHHhhhhhhhhhcCchHHHHHHHHHhH-HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHh
Confidence 34556566666788999999999998733 39999999999999999999999999999999999999999999999876
Q ss_pred C
Q 024238 173 D 173 (270)
Q Consensus 173 e 173 (270)
.
T Consensus 85 ~ 85 (91)
T COG2036 85 G 85 (91)
T ss_pred c
Confidence 4
No 12
>PTZ00017 histone H2A; Provisional
Probab=99.05 E-value=3.3e-10 Score=96.09 Aligned_cols=76 Identities=21% Similarity=0.344 Sum_probs=72.4
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchh
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLV 179 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~ 179 (270)
.+.||++||.|+||..-...+|++.|++.|+.++|+++.++.+.|.+.|+.+|++.|+++||..||.++++|+.|.
T Consensus 25 gL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 100 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLL 100 (134)
T ss_pred CcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccCcHHHHHHH
Confidence 4789999999999998777899999999999999999999999999999999999999999999999999999776
No 13
>PLN00154 histone H2A; Provisional
Probab=99.04 E-value=3.4e-10 Score=96.21 Aligned_cols=77 Identities=19% Similarity=0.230 Sum_probs=72.4
Q ss_pred CCCCChHHHHHHHhCCh-hhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhc
Q 024238 104 NHSLPLARIKKIMKADE-DVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVD 180 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDp-DV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~D 180 (270)
.+.||++||+|+||..- ...+|++.|++.++.++|++..++.+.|.+.|+.+|++.|+++||..||.++++|++|..
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrnDeEL~~Ll~ 113 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 113 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccCcHHHHHHhc
Confidence 57999999999999975 456999999999999999999999999999999999999999999999999999998875
No 14
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.04 E-value=3.7e-10 Score=98.16 Aligned_cols=69 Identities=26% Similarity=0.310 Sum_probs=65.8
Q ss_pred CCCChHHHHHHHhCC-hhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024238 105 HSLPLARIKKIMKAD-EDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD 173 (270)
Q Consensus 105 ~~LPLARIKKIMKsD-pDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e 173 (270)
..|||+.|-||||.- |...+||+||...+-+|+..||..+|.+|.+.|...|||||+.+||.-|+....
T Consensus 31 r~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 31 RFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 479999999999987 777899999999999999999999999999999999999999999999999885
No 15
>PLN00156 histone H2AX; Provisional
Probab=98.97 E-value=1.3e-09 Score=92.94 Aligned_cols=77 Identities=21% Similarity=0.315 Sum_probs=72.3
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhc
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVD 180 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~D 180 (270)
.+.||++||.|.||..-...+|++.|++.|+.++|+++.++.+.|.+.|+.+|++.|+++||..||.++++|+.|..
T Consensus 27 gL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrnDeEL~~Ll~ 103 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG 103 (139)
T ss_pred CcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccCcHHHHHHHC
Confidence 47899999999999987778999999999999999999999999999999999999999999999999999996653
No 16
>PLN00153 histone H2A; Provisional
Probab=98.95 E-value=1.3e-09 Score=91.89 Aligned_cols=77 Identities=23% Similarity=0.308 Sum_probs=72.4
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhc
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVD 180 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~D 180 (270)
.+.||++||.|.||..-...+|++.|++.++.++|+++.++.+.|.+.|+.+|++.|+++||..||.++++|+.|..
T Consensus 22 gL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll~ 98 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLG 98 (129)
T ss_pred CcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccCcHHHHHHHC
Confidence 47999999999999987788999999999999999999999999999999999999999999999999999985553
No 17
>PLN00157 histone H2A; Provisional
Probab=98.94 E-value=1.4e-09 Score=92.13 Aligned_cols=76 Identities=22% Similarity=0.312 Sum_probs=71.7
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchh
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLV 179 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~ 179 (270)
.+.||++||.|.||..-...+|++.|++.|+.++|+++.++.+.|.+.|..+|++.|+++||..||.++++|+.|.
T Consensus 24 gL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 99 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLL 99 (132)
T ss_pred CcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccCcHHHHHHH
Confidence 4799999999999998777899999999999999999999999999999999999999999999999999998554
No 18
>PTZ00252 histone H2A; Provisional
Probab=98.84 E-value=6e-09 Score=88.44 Aligned_cols=77 Identities=21% Similarity=0.304 Sum_probs=70.6
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCcccHHHHHHHHhcCCccc-chhc
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEE--NKRRTLQKNDIAAAISRTDVFD-FLVD 180 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~--~KRKTLq~~DIa~AI~~~e~Fd-FL~D 180 (270)
.+.||++||.|.||..-...+|++.|++.|+.++|++..++.+.|.+.|+. +|++.|+++||..||.++++|+ +|.+
T Consensus 23 GL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDeEL~~Ll~~ 102 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKN 102 (134)
T ss_pred CccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccChHHHHHHHcC
Confidence 479999999999999877789999999999999999999999999999965 7889999999999999999998 4444
No 19
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.82 E-value=1.3e-08 Score=76.23 Aligned_cols=64 Identities=28% Similarity=0.356 Sum_probs=61.1
Q ss_pred CCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024238 106 SLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAIS 170 (270)
Q Consensus 106 ~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~ 170 (270)
.||.+-|++|.+.. ++.+||.|+...|+..+|.|+.+++..|...++..|||||+.+||..|++
T Consensus 2 ~~p~~~i~ria~~~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 58999999999998 78899999999999999999999999999999999999999999999874
No 20
>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=98.80 E-value=8.3e-09 Score=76.75 Aligned_cols=69 Identities=22% Similarity=0.249 Sum_probs=61.8
Q ss_pred CCCCCChHHHHHHHhCChhh-hccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024238 103 KNHSLPLARIKKIMKADEDV-RMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISR 171 (270)
Q Consensus 103 k~~~LPLARIKKIMKsDpDV-~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~ 171 (270)
....+|+.||.|.+..+-.. .+||++|..+|..++|.|+.+|...|...|..+||+||+.+||..|+..
T Consensus 5 ~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 5 LIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp SSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred ccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 34578888888888887554 3899999999999999999999999999999999999999999999864
No 21
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.72 E-value=2.4e-08 Score=87.48 Aligned_cols=76 Identities=28% Similarity=0.389 Sum_probs=68.7
Q ss_pred CCCCChHHHHHHHhCC-hhh-hccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchh
Q 024238 104 NHSLPLARIKKIMKAD-EDV-RMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLV 179 (270)
Q Consensus 104 ~~~LPLARIKKIMKsD-pDV-~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~ 179 (270)
.+.||.|-|.||+|.- ++. ..||+||..+|++|+-+||.+|+..|..+|...+||||+.+||..|+...+.-.|+.
T Consensus 8 dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~ 85 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVN 85 (172)
T ss_pred HhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhh
Confidence 4679999999999975 343 579999999999999999999999999999999999999999999999988767765
No 22
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=98.68 E-value=6e-08 Score=76.61 Aligned_cols=67 Identities=18% Similarity=0.258 Sum_probs=63.8
Q ss_pred CCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024238 106 SLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD 173 (270)
Q Consensus 106 ~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e 173 (270)
.||.+-|+||.+.. .+.+||.++...+..++|.|+++++.+|...|+..+||||+.+||..|+++..
T Consensus 13 gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g 79 (85)
T cd00076 13 GITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 79 (85)
T ss_pred cCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCC
Confidence 59999999999998 69999999999999999999999999999999999999999999999998754
No 23
>PLN00035 histone H4; Provisional
Probab=98.66 E-value=6.5e-08 Score=78.99 Aligned_cols=67 Identities=18% Similarity=0.245 Sum_probs=63.8
Q ss_pred CCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024238 106 SLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD 173 (270)
Q Consensus 106 ~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e 173 (270)
.||.+-|+||.+.. .+.+||.++...+..++|.|+++++.+|...|++.+||||+.+||..|+++..
T Consensus 29 ~ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g 95 (103)
T PLN00035 29 GITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
T ss_pred cCCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcC
Confidence 39999999999988 69999999999999999999999999999999999999999999999998764
No 24
>PTZ00015 histone H4; Provisional
Probab=98.58 E-value=1.5e-07 Score=76.70 Aligned_cols=68 Identities=19% Similarity=0.256 Sum_probs=64.3
Q ss_pred CCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024238 105 HSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD 173 (270)
Q Consensus 105 ~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e 173 (270)
..||.+-|+||.+.. .+.+||.++...+..++|.|+++++.+|...|+..+||||+.+||..|+++..
T Consensus 29 ~gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g 96 (102)
T PTZ00015 29 RGITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQG 96 (102)
T ss_pred cCCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcC
Confidence 468999999999998 89999999999999999999999999999999999999999999999998654
No 25
>smart00417 H4 Histone H4.
Probab=98.52 E-value=1.5e-07 Score=72.76 Aligned_cols=61 Identities=16% Similarity=0.201 Sum_probs=58.5
Q ss_pred CCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Q 024238 106 SLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAA 167 (270)
Q Consensus 106 ~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~ 167 (270)
.||.+.|+||.+.. ++.+||.++...+..++|.|+++++.+|...|+..+||||+.+||..
T Consensus 13 gI~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 13 GITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred CCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 59999999999988 89999999999999999999999999999999999999999999864
No 26
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=98.46 E-value=3.8e-07 Score=78.90 Aligned_cols=78 Identities=19% Similarity=0.327 Sum_probs=70.0
Q ss_pred CCCCCChHHHHHHHhCC-h-hhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhc
Q 024238 103 KNHSLPLARIKKIMKAD-E-DVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVD 180 (270)
Q Consensus 103 k~~~LPLARIKKIMKsD-p-DV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~D 180 (270)
.++.||-+-|.||+|.= | |+ +|.+||.-+|-.||-.||..|+++|.++|...+||||.++||.+|+.+...=+|+..
T Consensus 9 de~sLPkAtv~KmIke~lP~d~-rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee 87 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLPKDV-RVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEE 87 (156)
T ss_pred ccccCcHHHHHHHHHHhCCccc-ccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHH
Confidence 45789999999999964 4 66 799999999999999999999999999999999999999999999999876566654
Q ss_pred c
Q 024238 181 I 181 (270)
Q Consensus 181 I 181 (270)
.
T Consensus 88 ~ 88 (156)
T KOG0871|consen 88 A 88 (156)
T ss_pred H
Confidence 3
No 27
>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=98.09 E-value=1.4e-05 Score=60.64 Aligned_cols=65 Identities=12% Similarity=0.260 Sum_probs=57.1
Q ss_pred ChHHHHHHHhC-ChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024238 108 PLARIKKIMKA-DEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD 173 (270)
Q Consensus 108 PLARIKKIMKs-DpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e 173 (270)
+-.++..++|. |+. .+++.+|..+|...+|.|+..++..|...|+..||+||+.+||.-++++.-
T Consensus 3 ~k~~l~~lv~~id~~-~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~ 68 (72)
T cd07981 3 TKRKLQELLKEIDPR-EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNW 68 (72)
T ss_pred cHHHHHHHHHhhCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Confidence 44566677764 555 689999999999999999999999999999999999999999999998764
No 28
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=97.96 E-value=1.8e-05 Score=67.40 Aligned_cols=78 Identities=24% Similarity=0.404 Sum_probs=67.8
Q ss_pred CCCCCCChHHHHHHHhC--ChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchh
Q 024238 102 FKNHSLPLARIKKIMKA--DEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLV 179 (270)
Q Consensus 102 fk~~~LPLARIKKIMKs--DpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~ 179 (270)
..+..||-+.|.|.+-. +.|. ++.+||..+|-.||-.||.-|+..|.+.|+...+|||.|+||..|+++.+.=.|+.
T Consensus 7 dDe~sLPKATVqKMvS~iLp~dl-~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 7 DDENSLPKATVQKMVSSILPKDL-VFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred cccccCcHHHHHHHHHHhccccc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 34578999999998875 3443 79999999999999999999999999999999999999999999999987555554
Q ss_pred c
Q 024238 180 D 180 (270)
Q Consensus 180 D 180 (270)
.
T Consensus 86 ~ 86 (148)
T COG5150 86 S 86 (148)
T ss_pred H
Confidence 3
No 29
>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=97.80 E-value=6.7e-05 Score=59.21 Aligned_cols=71 Identities=23% Similarity=0.301 Sum_probs=63.0
Q ss_pred hcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCcccHHHHHHHHhc
Q 024238 100 ADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENK---RRTLQKNDIAAAISR 171 (270)
Q Consensus 100 ~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~K---RKTLq~~DIa~AI~~ 171 (270)
..|+...|+-+.|||||...-+ ..++.+..++++..+.+||.+|+.+|.++..+.+ +.-|+++||..|..+
T Consensus 10 e~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr 83 (85)
T cd08048 10 EMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR 83 (85)
T ss_pred HHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence 4677778999999999998766 6799999999999999999999999999987655 489999999999865
No 30
>smart00428 H3 Histone H3.
Probab=97.77 E-value=0.00013 Score=59.90 Aligned_cols=77 Identities=22% Similarity=0.320 Sum_probs=62.7
Q ss_pred HHHHHH---hhhcCCCCCCChHHHHH-HHhCC-h--hhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHH
Q 024238 92 QMQEIE---QTADFKNHSLPLARIKK-IMKAD-E--DVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKND 164 (270)
Q Consensus 92 ~~~eiE---~~~dfk~~~LPLARIKK-IMKsD-p--DV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~D 164 (270)
.+.||. ..+++--..+|.+|+-| |+..- . ++ +++.+|..+|..|+|.|+..|.+.|..+|...||+||+.+|
T Consensus 15 aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~-R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kD 93 (105)
T smart00428 15 ALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDL-RFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKD 93 (105)
T ss_pred HHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCc-eeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhh
Confidence 345664 45677677899998654 44332 2 44 89999999999999999999999999999999999999999
Q ss_pred HHHHH
Q 024238 165 IAAAI 169 (270)
Q Consensus 165 Ia~AI 169 (270)
|.-|.
T Consensus 94 i~La~ 98 (105)
T smart00428 94 IQLAR 98 (105)
T ss_pred HHHHH
Confidence 98775
No 31
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=97.58 E-value=4.1e-05 Score=64.11 Aligned_cols=76 Identities=20% Similarity=0.242 Sum_probs=69.5
Q ss_pred CCCCChHHHHHHHhCC-hhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchh
Q 024238 104 NHSLPLARIKKIMKAD-EDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLV 179 (270)
Q Consensus 104 ~~~LPLARIKKIMKsD-pDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~ 179 (270)
-+.||++||+|.+|.. ...++|.+.+.+..+..+|++..++.+.|.+.++.-|-|+|+++|+.-||.-+|++|-|.
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRGDeELDtLI 104 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLI 104 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecCcHHHHHHH
Confidence 4689999999999976 566789999999999999999999999888888888999999999999999999999886
No 32
>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=97.54 E-value=0.00022 Score=59.00 Aligned_cols=76 Identities=16% Similarity=0.180 Sum_probs=64.5
Q ss_pred HHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhccCCCccc
Q 024238 110 ARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVDIIPRDEL 187 (270)
Q Consensus 110 ARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~DIVP~~~~ 187 (270)
.-|++|+|+- ++..++.+++..|...++.++.++..+|...|+..||+||+.+||.-||+..-.+.|-. --|++.+
T Consensus 5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~-~p~~~~l 80 (117)
T cd07979 5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTS-PPPRDFL 80 (117)
T ss_pred HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCC-CCcHHHH
Confidence 4588999986 66789999999999999999999999999999999999999999999998776566653 2344444
No 33
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=97.45 E-value=0.00031 Score=66.96 Aligned_cols=64 Identities=22% Similarity=0.276 Sum_probs=58.6
Q ss_pred hHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024238 109 LARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD 173 (270)
Q Consensus 109 LARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e 173 (270)
..-||-|.++- ++.+++.||...++.-+|.++.+++.+|.+.++..|||||+.+||..|++...
T Consensus 2 ~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n 65 (343)
T cd08050 2 QESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRN 65 (343)
T ss_pred hhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhC
Confidence 45688888877 77899999999999999999999999999999999999999999999997553
No 34
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.45 E-value=0.00056 Score=51.88 Aligned_cols=64 Identities=22% Similarity=0.293 Sum_probs=50.3
Q ss_pred CCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024238 106 SLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAIS 170 (270)
Q Consensus 106 ~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~ 170 (270)
.||..-||-|-.+- ++..++.|+..+|+.=+|+-|.++...|.++++.+||++|+.+||..|++
T Consensus 3 ~~~~esvk~iAes~-Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL-GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT-T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 57777888887765 67789999999999999999999999999999999999999999999874
No 35
>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=97.44 E-value=0.00027 Score=56.54 Aligned_cols=85 Identities=24% Similarity=0.263 Sum_probs=56.6
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCcccH
Q 024238 84 QLQMFWSNQMQEIEQTADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENK-RRTLQK 162 (270)
Q Consensus 84 ~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~K-RKTLq~ 162 (270)
-|.+|=.+|++--| .|+...|+-+.|||||+.--+-..|+....++++-.+.+||-+|.++|.++..+.+ ..-|++
T Consensus 4 L~~~f~~eQ~~Rye---~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P 80 (90)
T PF04719_consen 4 LLSNFDEEQLDRYE---AFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQP 80 (90)
T ss_dssp ------HHHHHHHH---HHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--H
T ss_pred HHHcCCHHHHHHHH---HHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCc
Confidence 45667677664444 57778899999999999865435789999999999999999999999998887654 458999
Q ss_pred HHHHHHHhc
Q 024238 163 NDIAAAISR 171 (270)
Q Consensus 163 ~DIa~AI~~ 171 (270)
+||..|..+
T Consensus 81 ~hlreA~rr 89 (90)
T PF04719_consen 81 DHLREAYRR 89 (90)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHh
Confidence 999998754
No 36
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.42 E-value=0.00052 Score=52.35 Aligned_cols=60 Identities=15% Similarity=0.178 Sum_probs=55.0
Q ss_pred HHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 112 IKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 112 IKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
|.+|+|.. +...++.+|...|+..+|.|+.+|++.+...|+..+|++.+..||..|+.+.
T Consensus 12 Vaqil~~~-Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~ 71 (77)
T smart00576 12 VAQILESA-GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENL 71 (77)
T ss_pred HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 67788866 6668999999999999999999999999999999999999999999998764
No 37
>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=97.28 E-value=0.0011 Score=51.04 Aligned_cols=63 Identities=19% Similarity=0.280 Sum_probs=51.2
Q ss_pred ChHHHHHHHhCC--hhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-ccHHHHHHHHh
Q 024238 108 PLARIKKIMKAD--EDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRT-LQKNDIAAAIS 170 (270)
Q Consensus 108 PLARIKKIMKsD--pDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKT-Lq~~DIa~AI~ 170 (270)
|-.-|.||++.. .+-.+||++|..++++-+++||.+-+.||...++..+... |..+||.++.-
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 445688899863 4667999999999999999999999999999999999888 99999998653
No 38
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=97.14 E-value=0.00073 Score=59.18 Aligned_cols=84 Identities=23% Similarity=0.196 Sum_probs=61.0
Q ss_pred CCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHH------------HHHHhcCCCcccHHHHHHHH
Q 024238 102 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSW------------IHTEENKRRTLQKNDIAAAI 169 (270)
Q Consensus 102 fk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~------------~~A~~~KRKTLq~~DIa~AI 169 (270)
.+...||++.+|||-|.||....-+.+|.+..+.++|.|++.|+..+. .+.+.+.--|+.++++...|
T Consensus 7 e~~p~~p~ekvkkiak~dPey~~te~~a~~etafatE~fvq~lv~~p~a~l~rLpL~rik~vvkl~pdl~l~~dea~~l~ 86 (162)
T KOG1658|consen 7 ECSPKLPMEKVKKIAKNDPEYMDTEDDAFVETAFATEQFVQVLVHLPQASLSRLPLARIKQVVKLDPDLTLLNDEASQLI 86 (162)
T ss_pred hhCccccHHHHHHhhcCCchhhhcccchHHHHHHHHHHHHhhhhhhhhhhhhhccHHHHHhhccCCcchhhhhhHHHHHH
Confidence 355789999999999999999888899999999999999999998221 11122333466677777777
Q ss_pred hcCC--cccchhccCCCc
Q 024238 170 SRTD--VFDFLVDIIPRD 185 (270)
Q Consensus 170 ~~~e--~FdFL~DIVP~~ 185 (270)
.+.- ...||.+..+..
T Consensus 87 a~aaelfi~~Ln~~~~~~ 104 (162)
T KOG1658|consen 87 AKAAELFIQELNDVAYTT 104 (162)
T ss_pred HHHHHHHHHHHHhccchh
Confidence 6553 345666666554
No 39
>PLN00161 histone H3; Provisional
Probab=97.09 E-value=0.0021 Score=55.04 Aligned_cols=74 Identities=22% Similarity=0.290 Sum_probs=61.1
Q ss_pred HhhhcCCCCCCChHHHHHHHhCC--hhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024238 97 EQTADFKNHSLPLARIKKIMKAD--EDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAIS 170 (270)
Q Consensus 97 E~~~dfk~~~LPLARIKKIMKsD--pDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~ 170 (270)
...+++--..+|.+|+-|-+-.+ .+.-++..+|..+|..|+|.|+-.|-+.|..+|...||-||..+||.-+..
T Consensus 49 Qkst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 49 QKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred ccccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 34567777889999975555322 222489999999999999999999999999999999999999999987753
No 40
>PLN00121 histone H3; Provisional
Probab=97.01 E-value=0.0021 Score=55.07 Aligned_cols=72 Identities=21% Similarity=0.334 Sum_probs=60.7
Q ss_pred HhhhcCCCCCCChHHHHHHHhCC--hhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024238 97 EQTADFKNHSLPLARIKKIMKAD--EDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAI 169 (270)
Q Consensus 97 E~~~dfk~~~LPLARIKKIMKsD--pDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI 169 (270)
+..+++--..+|.+|+-|-+-.+ .++ ++..+|..+|..|+|.|+-.|-+.|..+|...||.||..+||.-+.
T Consensus 56 Qkst~lLI~k~pF~RLVREI~~~~~~~~-Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 56 QKSTELLIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccccccccccccHHHHHHHHHHHhCccc-eeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 34567777789999866544432 455 8999999999999999999999999999999999999999997664
No 41
>PTZ00018 histone H3; Provisional
Probab=96.99 E-value=0.0022 Score=55.01 Aligned_cols=72 Identities=19% Similarity=0.315 Sum_probs=60.8
Q ss_pred HhhhcCCCCCCChHHHHHHHhC--ChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024238 97 EQTADFKNHSLPLARIKKIMKA--DEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAI 169 (270)
Q Consensus 97 E~~~dfk~~~LPLARIKKIMKs--DpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI 169 (270)
+..+++--..+|.+|+-|-+-. ..++ ++..+|..+|..|+|.|+-.|-+.+..+|...||.||..+||.-+.
T Consensus 56 Qkst~lLI~k~pF~RLVREI~~~~~~~~-rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 56 QKSTELLIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cccchhccccccHHHHHHHHHHHcCCcc-eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 3456777778999997665532 3555 8999999999999999999999999999999999999999997663
No 42
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=96.98 E-value=0.001 Score=65.12 Aligned_cols=64 Identities=22% Similarity=0.219 Sum_probs=46.2
Q ss_pred cCCCCCCChHHHHHHHhCC-----hhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHH
Q 024238 101 DFKNHSLPLARIKKIMKAD-----EDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKND 164 (270)
Q Consensus 101 dfk~~~LPLARIKKIMKsD-----pDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~D 164 (270)
.+....||-+-|||+...- ---.+|+++|..+|.+|++.|.+.|+..--.+|++.|||||..+|
T Consensus 346 gi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 346 GIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4556789999999987643 123589999999999999999999999999999999999999877
No 43
>PLN00160 histone H3; Provisional
Probab=96.98 E-value=0.0024 Score=51.87 Aligned_cols=77 Identities=22% Similarity=0.315 Sum_probs=62.2
Q ss_pred HHHHH---hhhcCCCCCCChHHHHHHHhCC--hhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Q 024238 93 MQEIE---QTADFKNHSLPLARIKKIMKAD--EDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAA 167 (270)
Q Consensus 93 ~~eiE---~~~dfk~~~LPLARIKKIMKsD--pDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~ 167 (270)
+.||. +.+++--.++|.+|+-|-+-.+ .+.-++.++|..++..|+|.|+-.|-+.|..+|...||.||..+||.-
T Consensus 8 LrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L 87 (97)
T PLN00160 8 LKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQL 87 (97)
T ss_pred HHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHH
Confidence 44554 4566666789999875555332 233489999999999999999999999999999999999999999976
Q ss_pred HH
Q 024238 168 AI 169 (270)
Q Consensus 168 AI 169 (270)
+.
T Consensus 88 ~~ 89 (97)
T PLN00160 88 AR 89 (97)
T ss_pred HH
Confidence 64
No 44
>smart00427 H2B Histone H2B.
Probab=96.72 E-value=0.0047 Score=49.60 Aligned_cols=60 Identities=23% Similarity=0.254 Sum_probs=52.4
Q ss_pred HHHHHHhC-ChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024238 111 RIKKIMKA-DEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISR 171 (270)
Q Consensus 111 RIKKIMKs-DpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~ 171 (270)
-|.|++|. .||.+ ||..|--++.--..-+.+.|+.+|...+..+||+||+.++|..||.-
T Consensus 6 Yi~kvLKqVhpd~g-iS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl 66 (89)
T smart00427 6 YIYKVLKQVHPDTG-ISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRL 66 (89)
T ss_pred HHHHHHHHhCCCcc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 48888885 58885 89999888887777788999999999999999999999999999863
No 45
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=96.48 E-value=0.0084 Score=48.59 Aligned_cols=63 Identities=21% Similarity=0.252 Sum_probs=57.3
Q ss_pred HHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024238 110 ARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD 173 (270)
Q Consensus 110 ARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e 173 (270)
--|+||-+.. .|++|+.-...-+..+...||++....|...++..|||||+..||..++++..
T Consensus 33 paIRRlARr~-GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G 95 (103)
T KOG3467|consen 33 PAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 95 (103)
T ss_pred HHHHHHHHhc-CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcC
Confidence 3588888877 88999999889999999999999999999999999999999999999998764
No 46
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=96.26 E-value=0.0071 Score=54.64 Aligned_cols=89 Identities=26% Similarity=0.318 Sum_probs=73.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CC
Q 024238 80 QQQQQLQMFWSNQMQEIEQTADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENK-RR 158 (270)
Q Consensus 80 ~~~q~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~K-RK 158 (270)
..+--|.+|=.+|+.--| -|+...||-+.|||+|..=-.-. |+..+.++++-..++||-+|...|.+++...+ ..
T Consensus 89 r~q~L~s~fseEQl~RYE---vfRrs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~ 164 (195)
T KOG3219|consen 89 RMQTLLSNFSEEQLSRYE---VFRRSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESG 164 (195)
T ss_pred HHHHHHHhcCHHHHHHHH---HHHHhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCC
Confidence 445567777777664444 68889999999999999764433 89999999999999999999999999987544 56
Q ss_pred cccHHHHHHHHhcC
Q 024238 159 TLQKNDIAAAISRT 172 (270)
Q Consensus 159 TLq~~DIa~AI~~~ 172 (270)
-|+++||..|+.+.
T Consensus 165 PLqP~HIREA~rrL 178 (195)
T KOG3219|consen 165 PLQPKHIREAYRRL 178 (195)
T ss_pred CCCcHHHHHHHHHH
Confidence 89999999999765
No 47
>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=96.19 E-value=0.0043 Score=49.40 Aligned_cols=76 Identities=13% Similarity=0.201 Sum_probs=33.6
Q ss_pred HHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC-cccchhccCCCccc
Q 024238 112 IKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD-VFDFLVDIIPRDEL 187 (270)
Q Consensus 112 IKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e-~FdFL~DIVP~~~~ 187 (270)
|+.+|-.-.|+..-..|+..++-..+-.||.+|+.+|..+|...++++|+.+||.-++.++. ++.-|.+++-..+.
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~Kl~Rl~~~L~~k~~ 83 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKKLARLRELLSMKDE 83 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHHHHHHHHHHHHHHH
Confidence 67888888888889999999999999999999999999999999999999999999999886 67777777755543
No 48
>PLN00158 histone H2B; Provisional
Probab=96.05 E-value=0.018 Score=48.30 Aligned_cols=62 Identities=21% Similarity=0.208 Sum_probs=53.7
Q ss_pred hHHHHHHHhC-ChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024238 109 LARIKKIMKA-DEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISR 171 (270)
Q Consensus 109 LARIKKIMKs-DpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~ 171 (270)
-.-|.|++|. .||.+ ||..|--++.--..-+.+.|+.+|...+..+||+||+.++|..||.-
T Consensus 30 ~~YI~kVLKQVhPd~g-IS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrL 92 (116)
T PLN00158 30 KIYIYKVLKQVHPDTG-ISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRL 92 (116)
T ss_pred HHHHHHHHHHhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 3458899985 69986 78888888888888888999999999999999999999999999863
No 49
>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=95.89 E-value=0.033 Score=42.33 Aligned_cols=61 Identities=13% Similarity=0.297 Sum_probs=47.7
Q ss_pred HHHHHHhC-ChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 111 RIKKIMKA-DEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 111 RIKKIMKs-DpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
++..++|. ||.. .+-.++--+|...++.||..++..|...|+..|..||..+||.-.++++
T Consensus 4 ~l~~Lv~~iDp~~-~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~ 65 (68)
T PF03847_consen 4 KLQELVKQIDPNE-KLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN 65 (68)
T ss_dssp HHHHHHHCC-SS-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence 45556664 5554 6889999999999999999999999999999999999999999998765
No 50
>PTZ00463 histone H2B; Provisional
Probab=95.85 E-value=0.025 Score=47.53 Aligned_cols=60 Identities=22% Similarity=0.177 Sum_probs=52.2
Q ss_pred HHHHHHhC-ChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024238 111 RIKKIMKA-DEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISR 171 (270)
Q Consensus 111 RIKKIMKs-DpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~ 171 (270)
-|.|++|. .||.+ ||..|--++.--..-+.+.|+.+|...+..+||+||+.++|..||.-
T Consensus 33 YI~KVLKqVhPd~g-IS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrL 93 (117)
T PTZ00463 33 YIFKVLKQVHPDTG-ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRL 93 (117)
T ss_pred HHHHHHHhhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhh
Confidence 48888885 69986 78888888887777777899999999999999999999999999863
No 51
>PLN00155 histone H2A; Provisional
Probab=95.71 E-value=0.012 Score=44.09 Aligned_cols=36 Identities=31% Similarity=0.450 Sum_probs=33.3
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHH
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEM 139 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtEl 139 (270)
.+.||++||.|.+|..-...+|++.|++.++..+|+
T Consensus 22 gL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEY 57 (58)
T PLN00155 22 GLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEY 57 (58)
T ss_pred ccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHh
Confidence 579999999999999877889999999999999986
No 52
>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=95.65 E-value=0.029 Score=44.89 Aligned_cols=75 Identities=15% Similarity=0.222 Sum_probs=63.9
Q ss_pred HHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC-cccchhccCCCc
Q 024238 110 ARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD-VFDFLVDIIPRD 185 (270)
Q Consensus 110 ARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e-~FdFL~DIVP~~ 185 (270)
.-|+.+|-.-.|+..-..|+..++-..+-.||.+|+.+|..+|. .+|..++.+||.-+|.++. ++..|..++-..
T Consensus 6 ~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL~~k 81 (92)
T cd07978 6 KEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPKKLARLRELLSMK 81 (92)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHH
Confidence 34788888888888889999999999999999999999999998 6666679999999998886 677777776543
No 53
>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=95.48 E-value=0.06 Score=40.66 Aligned_cols=60 Identities=17% Similarity=0.178 Sum_probs=53.0
Q ss_pred HHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 112 IKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 112 IKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
|.+|++.. +...++..|.-.|+..+..||.+|+..+...|+..+|......||..++.+.
T Consensus 12 va~il~~~-GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~ 71 (77)
T PF07524_consen 12 VAQILKHA-GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEM 71 (77)
T ss_pred HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 55677665 5567899999999999999999999999999999999999999999998765
No 54
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=95.43 E-value=0.037 Score=43.05 Aligned_cols=51 Identities=12% Similarity=0.074 Sum_probs=42.8
Q ss_pred ccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCc
Q 024238 124 MISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDV 174 (270)
Q Consensus 124 ~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~ 174 (270)
.+|.+...+|+..+=.++..++..-...|+..||+||+.+|+.-...+++.
T Consensus 25 ~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~ 75 (76)
T PF15630_consen 25 EVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPS 75 (76)
T ss_dssp EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HH
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCC
Confidence 588999999999998999999999999999999999999999999888764
No 55
>PF15510 CENP-W: Centromere kinetochore component W
Probab=94.98 E-value=0.055 Score=44.18 Aligned_cols=64 Identities=20% Similarity=0.357 Sum_probs=51.8
Q ss_pred CCChHHHHHHHhCC-hhhhccCccHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024238 106 SLPLARIKKIMKAD-EDVRMISAEAPVI--------------FAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAIS 170 (270)
Q Consensus 106 ~LPLARIKKIMKsD-pDV~~ISaEApvl--------------lAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~ 170 (270)
.-|-+-+||++|.. |-. ++.+.+-.+ +-.-|=+|+..|+++|-..|-++|.++|+.+||..|.+
T Consensus 16 kaPrgfLkrv~Kr~Kphl-Rl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPHL-RLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred hCchHHHHHHHHhcCCce-eecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 56889999999965 444 455544444 55678899999999999999999999999999988765
No 56
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=94.31 E-value=0.05 Score=46.86 Aligned_cols=71 Identities=23% Similarity=0.302 Sum_probs=60.7
Q ss_pred hhcCCCCCCChHHHHH-HHhCC-hhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024238 99 TADFKNHSLPLARIKK-IMKAD-EDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAIS 170 (270)
Q Consensus 99 ~~dfk~~~LPLARIKK-IMKsD-pDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~ 170 (270)
.+|.--..+|-.|+-| |++.- +|+ ++-+.|..+|-.|.|.|+-.|-..+..+|...||-||.++||.-|..
T Consensus 59 stdLlI~K~PFqRlvrei~q~f~~dL-rfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr 131 (137)
T KOG1745|consen 59 STDLLIRKLPFQRLVREIAQDFKTDL-RFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 131 (137)
T ss_pred hhHHHhhcCcHHHHhHHHHhcccccc-eehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence 4555555899999888 77765 554 79999999999999999999999999999999999999999977654
No 57
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=93.83 E-value=0.18 Score=43.10 Aligned_cols=59 Identities=20% Similarity=0.251 Sum_probs=44.8
Q ss_pred HHHHHh-CChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024238 112 IKKIMK-ADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISR 171 (270)
Q Consensus 112 IKKIMK-sDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~ 171 (270)
|.|++| .+||.+ |+.++.-++.--.-.|++.|+.+|...|..+||.||+-++|..++.-
T Consensus 43 v~kvlk~Vhpd~g-is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 43 VYKVLKQVHPDLG-ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred hhhhhhcccCCCC-cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 444666 457876 66666555554445557999999999999999999999999998763
No 58
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=93.17 E-value=0.12 Score=48.50 Aligned_cols=70 Identities=11% Similarity=0.209 Sum_probs=56.4
Q ss_pred HHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchh
Q 024238 110 ARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLV 179 (270)
Q Consensus 110 ARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~ 179 (270)
.+|..+++.=..-.+|-.|+..+|...|+-||..++..|...|+..|..||..+||.-.++++-.+.|=.
T Consensus 158 ~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPg 227 (258)
T KOG1142|consen 158 RKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPG 227 (258)
T ss_pred cchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCC
Confidence 4455555432223467788999999999999999999999999999999999999999999886555443
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.73 E-value=0.69 Score=41.40 Aligned_cols=72 Identities=17% Similarity=0.296 Sum_probs=56.3
Q ss_pred hhcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc--------------CCCcccHHH
Q 024238 99 TADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEEN--------------KRRTLQKND 164 (270)
Q Consensus 99 ~~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~--------------KRKTLq~~D 164 (270)
..|. ...||=+-+--+|+.. ++...-.-..-||+.|+.-||.+++..|+.+++-+ ||-||+-+|
T Consensus 80 LddY-tP~IPDavt~~yL~~a-Gf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeD 157 (176)
T KOG3423|consen 80 LDDY-TPTIPDAVTDHYLKKA-GFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMED 157 (176)
T ss_pred HhcC-CCCCcHHHHHHHHHhc-CCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHH
Confidence 3344 4579999999999987 33334445677999999999999999999998732 345899999
Q ss_pred HHHHHhcC
Q 024238 165 IAAAISRT 172 (270)
Q Consensus 165 Ia~AI~~~ 172 (270)
|..|+++.
T Consensus 158 L~~AL~Ey 165 (176)
T KOG3423|consen 158 LSPALAEY 165 (176)
T ss_pred HHHHHHHh
Confidence 99998765
No 60
>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=91.23 E-value=0.84 Score=38.78 Aligned_cols=77 Identities=17% Similarity=0.148 Sum_probs=43.4
Q ss_pred HHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhccCCCcccc
Q 024238 110 ARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVDIIPRDELK 188 (270)
Q Consensus 110 ARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~DIVP~~~~~ 188 (270)
--|+.|+|+- +|......++..|-.-+=.++.++...|...|...+|++|..+||.-||...-.+.|-. -.|++.+.
T Consensus 16 ~~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~-pppre~ll 92 (129)
T PF02291_consen 16 RVIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQ-PPPREFLL 92 (129)
T ss_dssp HHHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT----------------
T ss_pred HHHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccC-CCChHHHH
Confidence 4577777765 44444444444444555567889999999999999999999999999999765555533 23444433
No 61
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.97 E-value=0.6 Score=48.22 Aligned_cols=63 Identities=19% Similarity=0.241 Sum_probs=55.5
Q ss_pred hHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 109 LARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 109 LARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
..-+|-+.++= +++.|+.|+..+|+.=+|+=|.+++..|.++....||++++-+||..|+...
T Consensus 14 ~Es~k~vAEsl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~ 76 (576)
T KOG2549|consen 14 KESVKVVAESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSL 76 (576)
T ss_pred HHHHHHHHHHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhc
Confidence 55566665554 7788999999999999999999999999999999999999999999999744
No 62
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=90.32 E-value=0.53 Score=43.29 Aligned_cols=45 Identities=18% Similarity=0.254 Sum_probs=34.0
Q ss_pred hHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024238 109 LARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEE 154 (270)
Q Consensus 109 LARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~ 154 (270)
-.||.+|++... +..|..|...+|+-|||..|..|...+...|+.
T Consensus 50 ~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~h 94 (264)
T PF05236_consen 50 QKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRH 94 (264)
T ss_dssp HHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH-----
T ss_pred HHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 478999998874 678999999999999999999999999988764
No 63
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=87.34 E-value=1.2 Score=39.91 Aligned_cols=70 Identities=19% Similarity=0.167 Sum_probs=51.8
Q ss_pred CCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCcccHHHHHHHHhcC
Q 024238 102 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEEN------KRRTLQKNDIAAAISRT 172 (270)
Q Consensus 102 fk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~------KRKTLq~~DIa~AI~~~ 172 (270)
|-+...=..+|.+|++.. .++.|+.+...+|+.|||.++..|.......++.. ..+....+|+..-+...
T Consensus 44 fl~~~~l~~~~~~i~~~~-g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l 119 (212)
T cd08045 44 FLNPSPLAKKIRKIAKKH-GLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFL 119 (212)
T ss_pred ccCHHHHHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHH
Confidence 444333346788888876 44478999999999999999999999998888643 34566667777666543
No 64
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=82.84 E-value=5 Score=29.34 Aligned_cols=48 Identities=8% Similarity=0.111 Sum_probs=34.9
Q ss_pred CCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024238 106 SLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEE 154 (270)
Q Consensus 106 ~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~ 154 (270)
.+|=+-+.-+|+.. ++..--....-|++-|++-||.+++..|+.+++-
T Consensus 2 ~IPD~v~~~yL~~~-G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERS-GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHC-CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35666677777765 2222233456799999999999999999998863
No 65
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=80.42 E-value=4.1 Score=40.29 Aligned_cols=62 Identities=21% Similarity=0.197 Sum_probs=53.3
Q ss_pred HHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 110 ARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 110 ARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
..||.+-.+- +++.|..|+..+++--+|+=|.+++.+|.+....+||..|+-+||..|+...
T Consensus 9 et~KdvAesl-Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~l 70 (450)
T COG5095 9 ETLKDVAESL-GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSL 70 (450)
T ss_pred HHHHHHHHHc-CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhc
Confidence 3455544443 6678899999999999999999999999999999999999999999999754
No 66
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=78.36 E-value=14 Score=33.31 Aligned_cols=62 Identities=8% Similarity=0.167 Sum_probs=45.8
Q ss_pred HHHHHHHhhhcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024238 91 NQMQEIEQTADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTE 153 (270)
Q Consensus 91 ~~~~eiE~~~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~ 153 (270)
+.++|+-+.-|--...||=+-+.--|... .+...-.-...|++.++.-||.+++..|+...+
T Consensus 73 ktlee~l~~mDsy~PliPd~v~DYyl~k~-Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsr 134 (197)
T COG5162 73 KTLEELLQNMDSYTPLIPDSVTDYYLEKA-GFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSR 134 (197)
T ss_pred HHHHHHHHhcccCCCCccHHHHHHHHHhc-CceeccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555556666789999888888766 333444556779999999999999999987653
No 67
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=64.24 E-value=11 Score=33.22 Aligned_cols=50 Identities=16% Similarity=0.151 Sum_probs=43.4
Q ss_pred ccCccHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024238 124 MISAEAPVIFAKACE---MFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD 173 (270)
Q Consensus 124 ~ISaEApvllAKAtE---lFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e 173 (270)
.++.++...|.+.+. ..|..|+.+++..|-.++.++|+.++|..++....
T Consensus 215 ~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~ 267 (269)
T TIGR03015 215 VFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEID 267 (269)
T ss_pred CcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhh
Confidence 478888888888887 37999999999999889999999999999998653
No 68
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=63.83 E-value=7.7 Score=27.12 Aligned_cols=35 Identities=26% Similarity=0.289 Sum_probs=27.2
Q ss_pred hHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHH
Q 024238 109 LARIKKIMKADEDVRMISAEAPVIFAKACEMFILE 143 (270)
Q Consensus 109 LARIKKIMKsDpDV~~ISaEApvllAKAtElFI~e 143 (270)
+.||+|++....+.+---.||-.++.+|-++..++
T Consensus 4 l~kI~kLLalA~~~~~~~~EA~~A~~kAq~Lm~ky 38 (43)
T PF10979_consen 4 LEKIRKLLALAESTGSNEHEAEAALAKAQRLMAKY 38 (43)
T ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHHHHHHHHh
Confidence 68999999998765433359999999998876554
No 69
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=61.24 E-value=27 Score=32.72 Aligned_cols=64 Identities=17% Similarity=0.250 Sum_probs=45.5
Q ss_pred hHHHHHHHhCChh----hhccCccHHHHHHHHHHH------HHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 109 LARIKKIMKADED----VRMISAEAPVIFAKACEM------FILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 109 LARIKKIMKsDpD----V~~ISaEApvllAKAtEl------FI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
..-++.|++.--. -..++.++.-++++.+.- .+..|+.+|+..|...++.+|+.+||..|+.+.
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 3556666653211 124677777777776633 345777889989998999999999999999876
No 70
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=57.20 E-value=79 Score=25.09 Aligned_cols=62 Identities=16% Similarity=0.202 Sum_probs=48.4
Q ss_pred CCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024238 102 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMF------ILELTLRSWIHTEENKRRTLQKNDIAAAIS 170 (270)
Q Consensus 102 fk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElF------I~eLT~~A~~~A~~~KRKTLq~~DIa~AI~ 170 (270)
..|-.||-.-|++....+++. ..+|..+++-| +..|.+-|+-+|--++...|..+||..|+.
T Consensus 27 ~~Na~l~~~~l~~~~~l~~~~-------~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 27 KCNAQLPGEELRKYCPLSSEA-------KKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CccccCCHHHHHhHcCCCHHH-------HHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 346789999999987776554 55666666654 346777788888899999999999999985
No 71
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=55.34 E-value=47 Score=30.75 Aligned_cols=50 Identities=8% Similarity=0.076 Sum_probs=37.2
Q ss_pred ccCccHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024238 124 MISAEAPVIFAKACE------MFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD 173 (270)
Q Consensus 124 ~ISaEApvllAKAtE------lFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e 173 (270)
.++.++.-++++.++ ..+..++..|+..|..+++.+|+.+||..|+....
T Consensus 220 ~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~ 275 (365)
T TIGR02928 220 VLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIE 275 (365)
T ss_pred CCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 366676666655443 24556788888889888899999999999987663
No 72
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=54.25 E-value=19 Score=32.90 Aligned_cols=42 Identities=14% Similarity=0.147 Sum_probs=32.5
Q ss_pred HHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHH
Q 024238 110 ARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHT 152 (270)
Q Consensus 110 ARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A 152 (270)
.|+-.|.... +..-|+.|+.-+|..|+|.|+..|...+...+
T Consensus 210 ~Rm~~ia~e~-GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~ 251 (252)
T PF12767_consen 210 KRMEQIAWEH-GLGGVSDDCANLLNLALEVHLKNLIKSCLDLV 251 (252)
T ss_pred HHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4555555433 44569999999999999999999999887653
No 73
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=53.33 E-value=43 Score=28.51 Aligned_cols=71 Identities=15% Similarity=0.152 Sum_probs=51.0
Q ss_pred HHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC-cccchhccC
Q 024238 110 ARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD-VFDFLVDII 182 (270)
Q Consensus 110 ARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e-~FdFL~DIV 182 (270)
--||-+|=.-.|+..=..++.-++-..+--++.+|+..|...|+ .|.+++-+|+.-|+.+++ ++.-..+++
T Consensus 13 KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~DpkKlgRveeLl 84 (126)
T COG5248 13 KDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRRDPKKLGRVEELL 84 (126)
T ss_pred HHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhhChHHHhHHHHHH
Confidence 34566666555665555677777777777788888889988887 778888999999999886 344444443
No 74
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=50.02 E-value=56 Score=27.45 Aligned_cols=69 Identities=14% Similarity=0.122 Sum_probs=50.5
Q ss_pred HHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC-cccchhccCCC
Q 024238 113 KKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD-VFDFLVDIIPR 184 (270)
Q Consensus 113 KKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e-~FdFL~DIVP~ 184 (270)
|-+|=.=.|+..=-.++.-++-..+-.||.+||..|..+. +|.+++-+||.-+|.+++ +|.-.+|++.-
T Consensus 16 ~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRkDpkK~~Rv~eLL~m 85 (109)
T KOG3901|consen 16 RSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRKDPKKLGRVKELLAM 85 (109)
T ss_pred HHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHhChHHHhHHHHHHHh
Confidence 3333332344444567788888888888999988777665 888899999999999987 57777777654
No 75
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=48.93 E-value=1.1e+02 Score=30.03 Aligned_cols=47 Identities=21% Similarity=0.203 Sum_probs=33.5
Q ss_pred HhHHhHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHHhCC
Q 024238 73 FHHQQQQQQQQQLQMFWSNQMQEIEQTADFKNHSLPLARIKKIMKAD 119 (270)
Q Consensus 73 ~~~~~~~~~~q~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIMKsD 119 (270)
.|++....++.+...+-.+...|.++-..-....||..-||||.|.-
T Consensus 249 kyqr~~~rqq~~~~q~~aKrqaENa~R~argep~lP~dd~kr~fk~p 295 (339)
T KOG1560|consen 249 KYQRQLARQQAKKHQWIAKRQAENANRAARGEPPLPEDDWKRIFKPP 295 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCCCChHHHHHHhcCC
Confidence 34444445555666666677777776666677899999999999975
No 76
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=47.66 E-value=27 Score=34.04 Aligned_cols=71 Identities=15% Similarity=0.244 Sum_probs=49.7
Q ss_pred HHHHHHHhCChhh----hccCccHHHHHHH--HHH----HHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchh
Q 024238 110 ARIKKIMKADEDV----RMISAEAPVIFAK--ACE----MFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLV 179 (270)
Q Consensus 110 ARIKKIMKsDpDV----~~ISaEApvllAK--AtE----lFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~ 179 (270)
.-|..|++..-+. +.++.++.-++++ |.+ .+..+|+..|.+.|++.++.+++.+|+..|..+.+ .+++.
T Consensus 193 ~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~-~~~~~ 271 (366)
T COG1474 193 EELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIE-RDVLE 271 (366)
T ss_pred HHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhh-HHHHH
Confidence 5566666654222 2567777766662 222 36679999999999999999999999999955554 45555
Q ss_pred cc
Q 024238 180 DI 181 (270)
Q Consensus 180 DI 181 (270)
++
T Consensus 272 ~~ 273 (366)
T COG1474 272 EV 273 (366)
T ss_pred HH
Confidence 44
No 77
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=46.72 E-value=58 Score=33.85 Aligned_cols=63 Identities=8% Similarity=-0.029 Sum_probs=41.8
Q ss_pred HHHHHHHhCChhhhccCccHHHHHHHH-H------------HHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 110 ARIKKIMKADEDVRMISAEAPVIFAKA-C------------EMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 110 ARIKKIMKsDpDV~~ISaEApvllAKA-t------------ElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
..|++.++.+.....++.+|...|.+- + ..=|..|..+|..+|+.+++.+|+.+||.+|++..
T Consensus 316 ~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 316 QFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 344455554433345667666655431 1 23456778888888888899999999999998744
No 78
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=46.52 E-value=21 Score=35.91 Aligned_cols=51 Identities=18% Similarity=0.307 Sum_probs=40.1
Q ss_pred HhCChhhhccCccHHHHHHHHHHHH----HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 116 MKADEDVRMISAEAPVIFAKACEMF----ILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 116 MKsDpDV~~ISaEApvllAKAtElF----I~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
|+.++||. .-.|++.|+-| |.-++.+|...|-+..|+.++-+|+..|+.+.
T Consensus 338 M~l~~dvd------~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 338 MNLADDVD------LELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred ccCccCcC------HHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 45555553 45666766655 67889999999999999999999999999764
No 79
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=45.14 E-value=53 Score=32.90 Aligned_cols=59 Identities=24% Similarity=0.356 Sum_probs=43.3
Q ss_pred HHHHHHhC--C-hhhhccCccHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024238 111 RIKKIMKA--D-EDVRMISAEAPVIFAKACE----MFILELTLRSWIHTEENKRRTLQKNDIAAAIS 170 (270)
Q Consensus 111 RIKKIMKs--D-pDV~~ISaEApvllAKAtE----lFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~ 170 (270)
-||+|++. . +|| .++.+|..+|.+..+ .+...|...|...|...|.+++.-+||.++..
T Consensus 362 d~~~IL~iRc~EEdv-~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 362 DIKKILRIRCQEEDV-EMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred HHHHHHHhhhhhhcc-ccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 46677663 3 555 689999998887654 23445666677788888999999999999864
No 80
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=43.91 E-value=81 Score=32.15 Aligned_cols=60 Identities=13% Similarity=0.137 Sum_probs=46.1
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMF------ILELTLRSWIHTEENKRRTLQKNDIAAAIS 170 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElF------I~eLT~~A~~~A~~~KRKTLq~~DIa~AI~ 170 (270)
|-.++-..|+|+.+.+.+ +..++..+.+.| ...+.+-|+.+|.-+++.+|..+||..|+.
T Consensus 432 N~~l~~~~l~~~~~l~~~-------~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 432 NADLNSDEIEQFCKLSAI-------DANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred cccCCHHHHHhhcCCCHH-------HHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 678888889887776654 444555555554 456777788889899999999999999985
No 81
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=42.85 E-value=59 Score=33.30 Aligned_cols=33 Identities=9% Similarity=0.227 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 140 FILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 140 FI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
-|.+|..+|...|+..+++.|+.+||..||+..
T Consensus 474 ~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 474 WLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 346888899999999999999999999999864
No 82
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=40.30 E-value=1.1e+02 Score=27.10 Aligned_cols=40 Identities=15% Similarity=0.175 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchh
Q 024238 140 FILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLV 179 (270)
Q Consensus 140 FI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~ 179 (270)
++..+...|...++..++.+|..+||..||...-.+.|-.
T Consensus 46 Ytt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~ 85 (148)
T KOG3334|consen 46 YTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTP 85 (148)
T ss_pred HHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCC
Confidence 4667788899999999999999999999999887777765
No 83
>PTZ00195 60S ribosomal protein L18; Provisional
Probab=39.56 E-value=11 Score=34.49 Aligned_cols=85 Identities=14% Similarity=0.118 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHHhCChh-------------hhccCccHHHHHHHHHHHHHHHHHHHH
Q 024238 82 QQQLQMFWSNQMQEIEQTADFKNHSLPLARIKKIMKADED-------------VRMISAEAPVIFAKACEMFILELTLRS 148 (270)
Q Consensus 82 ~q~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIMKsDpD-------------V~~ISaEApvllAKAtElFI~eLT~~A 148 (270)
...=..||....+.++. .......+-||||-|.||.++. ++.|..|.-+.-.-.+-.....++..|
T Consensus 38 Rrt~a~fnk~VakRL~~-sr~nRppVsLSrI~r~~k~~d~~~~~~~~~k~~VVvGkVtdd~rl~~vPkvtVaALrfS~tA 116 (198)
T PTZ00195 38 KRTSSGFNKVVYQRLIK-SRSNRAPISLSRIAVVMKRKAVFTAKGKKAPIAVVVGDVLDDVRMARIPAMRVCALRFSKSA 116 (198)
T ss_pred HhhCCHHHHHHHHHHhc-ccccCCceeHHHHHHHHhccccccccCCCCcEEEEEeeEcCCccccccCceEEEEEecCHHH
Confidence 33446899999988874 4444567899999999997640 122333322111001111123556666
Q ss_pred HHHHHhcCCCcccHHHHHH
Q 024238 149 WIHTEENKRRTLQKNDIAA 167 (270)
Q Consensus 149 ~~~A~~~KRKTLq~~DIa~ 167 (270)
...-...+-+.|+.++|+.
T Consensus 117 r~rI~kAGGe~lT~dQLa~ 135 (198)
T PTZ00195 117 RQSIVAAGGECLTFDQLAM 135 (198)
T ss_pred HHHHHHhCCEEEeHHHHHH
Confidence 6666677778999888876
No 84
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=38.67 E-value=78 Score=28.89 Aligned_cols=85 Identities=14% Similarity=0.144 Sum_probs=59.7
Q ss_pred HHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCcccH
Q 024238 84 QLQMFWSNQMQEIEQTADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEE-NKRRTLQK 162 (270)
Q Consensus 84 ~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~-~KRKTLq~ 162 (270)
-+.+|-.+++..- ..|+...|+-+.|||+...--. .-||....+++......|+-++...|..+-.+ ...--|.+
T Consensus 96 l~~~~deeq~~Ry---EvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p 171 (199)
T COG5251 96 LVTNLDEEQTNRY---EVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIP 171 (199)
T ss_pred HHhhcCHHHHHHH---HHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCCh
Confidence 3445555544333 4699999999999999876422 35777778888888889999998888655322 12345788
Q ss_pred HHHHHHHhcC
Q 024238 163 NDIAAAISRT 172 (270)
Q Consensus 163 ~DIa~AI~~~ 172 (270)
.|+..|+...
T Consensus 172 ~h~reayr~~ 181 (199)
T COG5251 172 FHKREAYRYK 181 (199)
T ss_pred HHHHHHHHHH
Confidence 9998887643
No 85
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=38.52 E-value=65 Score=29.68 Aligned_cols=63 Identities=14% Similarity=0.120 Sum_probs=43.4
Q ss_pred ccCccHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCcccHHHHHHHHhcCC--cccchhccCCCcc
Q 024238 124 MISAEAPVIFAKACEMFILELTLRSWIHTEE--NKRRTLQKNDIAAAISRTD--VFDFLVDIIPRDE 186 (270)
Q Consensus 124 ~ISaEApvllAKAtElFI~eLT~~A~~~A~~--~KRKTLq~~DIa~AI~~~e--~FdFL~DIVP~~~ 186 (270)
.|+.+|...|...++-=+..+..+--+.+.. +++++|+.+||..+|...+ .|+++..++-++.
T Consensus 149 ~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~if~l~dai~~~~~ 215 (326)
T PRK07452 149 KLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQNSLQLADALLQGNT 215 (326)
T ss_pred CCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCcHHHHHHHHHCCCH
Confidence 5888888888888775444444444444444 5678899999999986543 5776666665553
No 86
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=38.31 E-value=3.8 Score=38.06 Aligned_cols=78 Identities=23% Similarity=0.115 Sum_probs=50.6
Q ss_pred CCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCcccchhcc
Q 024238 102 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTDVFDFLVDI 181 (270)
Q Consensus 102 fk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e~FdFL~DI 181 (270)
++.-..++.|++.+++. ++.+ .+++..-.|...|....+.+....+|.+|..-.+...|+..+.++|+.++
T Consensus 4 ~~~~~~~~~~~~~~~~~------~~p~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~fw~~~~~e~e~~~d~~~~~ 74 (236)
T KOG1657|consen 4 NNANSDIVANIVSNRRM------KAPP---KGAKSEPEGAVCLDPEASIITGDVSRQQLQSFWSKQAIEKEGQLDFKNHI 74 (236)
T ss_pred cccCccccccccccccc------cCCc---cccccccccceecchhhhhcccchhhHHHHhhhhccccccccccchhhcc
Confidence 33345556666666622 2222 33333333334677777776665668888888888888888899999999
Q ss_pred CCCcccc
Q 024238 182 IPRDELK 188 (270)
Q Consensus 182 VP~~~~~ 188 (270)
||....|
T Consensus 75 lPlaRiK 81 (236)
T KOG1657|consen 75 LPLARIK 81 (236)
T ss_pred CcHhhcc
Confidence 9986533
No 87
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=38.02 E-value=88 Score=30.73 Aligned_cols=64 Identities=16% Similarity=0.118 Sum_probs=54.3
Q ss_pred hHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 109 LARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 109 LARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
++.|--+|+.+.....|++-|..-|..++.-.|.++...+..+|+-.+|..-++.||+-.+.+.
T Consensus 7 l~~VV~~Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~m 70 (323)
T KOG4336|consen 7 LAPVVSNLLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEM 70 (323)
T ss_pred HHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHh
Confidence 4566667777767777888888888888888999999999999999999999999999887644
No 88
>KOG3521 consensus Predicted guanine nucleotide exchange factor [Signal transduction mechanisms]
Probab=37.12 E-value=78 Score=34.31 Aligned_cols=74 Identities=18% Similarity=0.322 Sum_probs=44.4
Q ss_pred HhHHhHHHHHHHHHHH--HHHHHHHHHhhhcCCCCCCChHHH-------HHHHhCChhhhccCccHHHHHHHHHHHHHHH
Q 024238 73 FHHQQQQQQQQQLQMF--WSNQMQEIEQTADFKNHSLPLARI-------KKIMKADEDVRMISAEAPVIFAKACEMFILE 143 (270)
Q Consensus 73 ~~~~~~~~~~q~l~~F--W~~~~~eiE~~~dfk~~~LPLARI-------KKIMKsDpDV~~ISaEApvllAKAtElFI~e 143 (270)
+|.+-+.+-+....+| |.+..+......=...+.-|.-|+ |-|+|.-+|++ ..||..++-.++|-|+..
T Consensus 288 ~y~rel~~~n~lFrafvtW~Ekqk~c~RqkL~D~l~kPmQRLTKY~LLLkAVlK~t~d~~--e~Eai~aMi~svEsf~~~ 365 (846)
T KOG3521|consen 288 KYIRELLKENELFRAFVTWAEKQKNCDRQKLIDTLSKPMQRLTKYPLLLKAVLKVTTDER--EREAISAMIDSVESFTAH 365 (846)
T ss_pred HHHHHHhccchHHHHHHHHHHhhhhhhhHHHHHHhhhHHHHhhhhHHHHHHHHhhCCCHH--HHHHHHHHHHHHHHHHHH
Confidence 3444344555566666 666544332211112234455554 44677666765 679999999999999988
Q ss_pred HHHHH
Q 024238 144 LTLRS 148 (270)
Q Consensus 144 LT~~A 148 (270)
+-.+-
T Consensus 366 vN~~l 370 (846)
T KOG3521|consen 366 VNKEL 370 (846)
T ss_pred HHHHH
Confidence 76543
No 89
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=35.86 E-value=1e+02 Score=32.81 Aligned_cols=95 Identities=11% Similarity=0.113 Sum_probs=56.2
Q ss_pred HHHHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc
Q 024238 82 QQQLQMFWSNQMQEIEQTADFKNHSLPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQ 161 (270)
Q Consensus 82 ~q~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq 161 (270)
+..+-.||.+ ++++. -+...|--+-|+||++....- + +--..++...-. +..|...|...|...+++-|+
T Consensus 319 r~k~~~~~~q---~v~~d--~~ip~~~~~Av~~li~~a~R~---A-g~~~~Ltl~~rd-l~~lv~~A~~ia~~~~~~~I~ 388 (647)
T COG1067 319 RSKLVQFYVQ---ELARD--GNIPHLDKDAVEELIREAARR---A-GDQNKLTLRLRD-LGNLVREAGDIAVSEGRKLIT 388 (647)
T ss_pred HHHHHHHHHH---HHHhc--CCCCCCCHHHHHHHHHHHHHh---c-cccceeccCHHH-HHHHHHHhhHHHhcCCcccCc
Confidence 3344445544 44422 233446667788888765211 1 111111111111 236667899999999999999
Q ss_pred HHHHHHHHhcCC-cccchhccCCCcc
Q 024238 162 KNDIAAAISRTD-VFDFLVDIIPRDE 186 (270)
Q Consensus 162 ~~DIa~AI~~~e-~FdFL~DIVP~~~ 186 (270)
.+||..|+++.. .-.||.+..-++.
T Consensus 389 ae~Ve~a~~~~~~~e~~l~e~~~~~~ 414 (647)
T COG1067 389 AEDVEEALQKRELREGQLAERYIEDI 414 (647)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 999999998754 4567776655444
No 90
>PF08637 NCA2: ATP synthase regulation protein NCA2; InterPro: IPR013946 NCA2 (Nuclear Control of ATPase), is one of the two nuclear genes involved in the control of mitochondrial expression of subunits 6 and 8 of the Fo-F1 ATP synthase in Saccharomyces cerevisiae (Baker's yeast). Mutations in either NCA2 or NCA3 (IPR005556 from INTERPRO) dramatically lower the level of the co-transcript encoding subunits 6 and 8 [, ].
Probab=35.72 E-value=1.2e+02 Score=28.97 Aligned_cols=70 Identities=17% Similarity=0.338 Sum_probs=55.2
Q ss_pred HHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHHhCC--hhhhccCccHHHHHHHHHHHHHHHH
Q 024238 67 YQQAQHFHHQQQQQQQQQLQMFWSNQMQEIEQTADFKNHSLPLARIKKIMKAD--EDVRMISAEAPVIFAKACEMFILEL 144 (270)
Q Consensus 67 ~~~~~~~~~~~~~~~~q~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIMKsD--pDV~~ISaEApvllAKAtElFI~eL 144 (270)
+..-..+-.-.+.+..+.+..||.+-+ .=|+-+|...++.| .++..+|+++...=...+|-.+.++
T Consensus 17 ~~~r~~i~~wi~~~~~~t~~~f~~nwV------------~~Pl~~I~~tlr~d~~s~~~i~s~~sL~~d~~SLeRMv~dF 84 (290)
T PF08637_consen 17 YNNRDEIDNWIQENAVETVRGFWKNWV------------WEPLKSIWDTLRHDEKSEIAIMSKESLQSDMESLERMVVDF 84 (290)
T ss_pred HcCHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHHHHHHhCCCCCCcccccHHHHHHHHHHHHHHHHHH
Confidence 334455555556688889999999975 34899999999996 5678899999999889999888888
Q ss_pred HHHH
Q 024238 145 TLRS 148 (270)
Q Consensus 145 T~~A 148 (270)
+.+.
T Consensus 85 ~~d~ 88 (290)
T PF08637_consen 85 AKDN 88 (290)
T ss_pred HhcC
Confidence 8764
No 91
>PRK09862 putative ATP-dependent protease; Provisional
Probab=34.80 E-value=1.9e+02 Score=29.80 Aligned_cols=65 Identities=14% Similarity=0.145 Sum_probs=43.8
Q ss_pred CCCCChHHHHHHHhCChhhhccCccHHHHH---HHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 104 NHSLPLARIKKIMKADEDVRMISAEAPVIF---AKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 104 ~~~LPLARIKKIMKsDpDV~~ISaEApvll---AKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
+..++-..|++.++.+.+..++-.++..-+ .++ ...|.+-|+.+|.-++|..|+.+||..|+.-.
T Consensus 425 n~~l~~~~l~~~~~l~~~~~~~l~~~~~~~~lS~Ra----~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR 492 (506)
T PRK09862 425 NAWLDSPEIRQFCKLESEDARWLEETLIHLGLSIRA----WQRLLKVARTIADIDQSDIITRQHLQEAVSYR 492 (506)
T ss_pred hcccCHHHHHHHhCCCHHHHHHHHHHHHHcCCCHHH----HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhh
Confidence 556777777776666655544333322211 122 24677778888989999999999999999855
No 92
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=33.57 E-value=1.1e+02 Score=30.34 Aligned_cols=65 Identities=12% Similarity=0.078 Sum_probs=54.2
Q ss_pred CChHHHHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 107 LPLARIKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 107 LPLARIKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
|=..+|+.|+.+=+. ...-..|.-.|+..+..||+.|.+.|..++.-.+|---...||..|+...
T Consensus 30 la~~avaQIcqslg~-~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dl 94 (353)
T KOG2389|consen 30 LARVAVAQICQSLGY-SSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDL 94 (353)
T ss_pred HHHHHHHHHHHhcCC-cccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHh
Confidence 445678899987633 34556699999999999999999999999999999988889999998754
No 93
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=32.99 E-value=13 Score=33.38 Aligned_cols=84 Identities=20% Similarity=0.287 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHHh---CChhhhccCccHHHHHH---HHHHHHHHHHHHHHHHHHH
Q 024238 80 QQQQQLQMFWSNQMQEIEQTADFKNHSLPLARIKKIMK---ADEDVRMISAEAPVIFA---KACEMFILELTLRSWIHTE 153 (270)
Q Consensus 80 ~~~q~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIMK---sDpDV~~ISaEApvllA---KAtElFI~eLT~~A~~~A~ 153 (270)
..+..|++|=++-..+|....+|+. .++.++. .||- ++.+ +.+ +....|-.+|+.+-.+++.
T Consensus 37 ~~~~~l~~fa~k~~~~i~~~~~~r~------~f~~~~~~lGvdp~---~s~~---~~s~~l~~~~~f~~ELa~qi~e~c~ 104 (223)
T PF04157_consen 37 DFVELLENFARKHKSEIKSDPEFRS------QFQSMCASLGVDPL---ASSK---FWSESLKGSGDFYYELAVQIAEVCL 104 (223)
T ss_dssp HHHHHHHHHHHHHCCCCCCSHHHHH------HHHHHHHHHT--CH---CCTT---CCCCCCSCHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhhccccCCchHHH------HHHHHHHHcCCCcc---cchh---hhhhccccchhHHHHHHHHHHHHHH
Confidence 5566777777666666665555554 4444443 3431 2222 111 3555666666666555554
Q ss_pred h------------------cCCC----cccHHHHHHHHhcCCcc
Q 024238 154 E------------------NKRR----TLQKNDIAAAISRTDVF 175 (270)
Q Consensus 154 ~------------------~KRK----TLq~~DIa~AI~~~e~F 175 (270)
. +++| .|+.+||.+|++..+.+
T Consensus 105 ~~~~~~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~l 148 (223)
T PF04157_consen 105 ATRSKNGGIISLSDLYCRYNRARGGSELISPEDILRACKLLEVL 148 (223)
T ss_dssp HHCCTTTSEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCC
T ss_pred HHHhcCCCEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHc
Confidence 2 2233 67777777777766544
No 94
>KOG4811 consensus Uncharacterized conserved protein [Function unknown]
Probab=32.73 E-value=84 Score=26.92 Aligned_cols=35 Identities=37% Similarity=0.671 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHhhh-cCCCCCCChHHHHHHHhCChhh
Q 024238 84 QLQMFWSNQMQEIEQTA-DFKNHSLPLARIKKIMKADEDV 122 (270)
Q Consensus 84 ~l~~FW~~~~~eiE~~~-dfk~~~LPLARIKKIMKsDpDV 122 (270)
.|.+-|.+.|..|.... +.++ ++|+|+|++.+.|+
T Consensus 4 slrSk~kR~mraikr~k~epke----~~rLkk~l~l~D~~ 39 (127)
T KOG4811|consen 4 SLRSKWKRKMRAIKRKKNEPKE----ASRLKKILKLDDDV 39 (127)
T ss_pred hhHHHHHHHHHHHHHhhcChHH----HHHHHHHHccchHH
Confidence 57788999887776543 3343 89999999999764
No 95
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=32.13 E-value=60 Score=30.80 Aligned_cols=41 Identities=15% Similarity=0.151 Sum_probs=31.8
Q ss_pred HHHHHHHHH----HHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024238 131 VIFAKACEM----FILELTLRSWIHTEENKRRTLQKNDIAAAISR 171 (270)
Q Consensus 131 vllAKAtEl----FI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~ 171 (270)
..+++.++- -|..|+.+|...|...+|+.|+.+||..|+.+
T Consensus 318 ~~la~~t~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 318 EAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 344454543 34578888888888899999999999999975
No 96
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=31.92 E-value=1.1e+02 Score=27.39 Aligned_cols=63 Identities=17% Similarity=0.192 Sum_probs=40.0
Q ss_pred ccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC---cccchhccCCCcc
Q 024238 124 MISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQKNDIAAAISRTD---VFDFLVDIIPRDE 186 (270)
Q Consensus 124 ~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~e---~FdFL~DIVP~~~ 186 (270)
.|+.+|...|...+..=+..+..+--+.+-..+.++|+.+||...+.... .|+|+..++-++.
T Consensus 130 ~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~~~~~if~l~dal~~~~~ 195 (302)
T TIGR01128 130 RIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDSARFNVFDLTDALLEGKA 195 (302)
T ss_pred CCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhhhcCCHHHHHHHHHCCCH
Confidence 58888888888777643333333333333333334799999999986443 5788887776654
No 97
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=31.36 E-value=62 Score=31.41 Aligned_cols=33 Identities=12% Similarity=0.176 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 140 FILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 140 FI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
=|..|+.+|...|..++++.|+.+||..|+.+.
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 356788889889988999999999999999876
No 98
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=31.12 E-value=1.1e+02 Score=27.96 Aligned_cols=62 Identities=23% Similarity=0.247 Sum_probs=41.1
Q ss_pred ccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcccHHHHHHHHhcC---CcccchhccCCCcc
Q 024238 124 MISAEAPVIFAKACEMFILELTLRSWIHTEEN-KRRTLQKNDIAAAISRT---DVFDFLVDIIPRDE 186 (270)
Q Consensus 124 ~ISaEApvllAKAtElFI~eLT~~A~~~A~~~-KRKTLq~~DIa~AI~~~---e~FdFL~DIVP~~~ 186 (270)
.|+.+|...|...++.=+..|..+.-..+-.. +++ |+.+||..++... ..|+|+.-++-++.
T Consensus 165 ~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~~~~~~~f~l~dai~~~~~ 230 (340)
T PRK05574 165 QIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPDSARFDVFDLVDAILAGKI 230 (340)
T ss_pred CCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhhhhcCCHHHHHHHHHCCCH
Confidence 58888888888777643344444444444333 334 9999999998654 46788888777654
No 99
>PTZ00469 60S ribosomal subunit protein L18; Provisional
Probab=29.06 E-value=20 Score=32.60 Aligned_cols=87 Identities=14% Similarity=0.142 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhhcCCCCCCChHHHHHHH--hCChhh---hccCccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024238 80 QQQQQLQMFWSNQMQEIEQTADFKNHSLPLARIKKIM--KADEDV---RMISAEAPVIFAKACEMFILELTLRSWIHTEE 154 (270)
Q Consensus 80 ~~~q~l~~FW~~~~~eiE~~~dfk~~~LPLARIKKIM--KsDpDV---~~ISaEApvllAKAtElFI~eLT~~A~~~A~~ 154 (270)
.....=..||....+.++..... ...+-||||-|.| +.|+=+ +.|..|.-+.--..+-.....++..|...-..
T Consensus 36 larrt~a~fwk~Va~RL~~srrn-r~pVnLSkI~r~~~~ke~~~~VVvGkVl~dgrl~~vpkvtVaAL~fS~~Ar~kI~~ 114 (187)
T PTZ00469 36 LARRTNANFNKIIAKRLIMPKRF-RPPLSLSKLHRHMASYPDDVAVVVGSITDDKRLYDCKKLKVCALRFTETARKRILD 114 (187)
T ss_pred HHHhhCChHHHHHHHHHhccccc-CCceeHHHHHHHhccCCCCEEEEEeeEccCccccccCceEEEEEecCHHHHHHHHH
Confidence 33444568999999888854433 4578899999999 544211 23333433321111111123556666666667
Q ss_pred cCCCcccHHHHHH
Q 024238 155 NKRRTLQKNDIAA 167 (270)
Q Consensus 155 ~KRKTLq~~DIa~ 167 (270)
.+-+.|+.++|+.
T Consensus 115 AGGe~lT~dqLa~ 127 (187)
T PTZ00469 115 AGGECLTFDQLAL 127 (187)
T ss_pred hCCEEEeHHHHHH
Confidence 7888999888876
No 100
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=29.05 E-value=1e+02 Score=28.73 Aligned_cols=63 Identities=11% Similarity=0.004 Sum_probs=41.0
Q ss_pred ccCccHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCcccHHHHHHHHhcCC---cccchhccCCCcc
Q 024238 124 MISAEAPVIFAKACEMFILELTLRSWIHTEE-NKRRTLQKNDIAAAISRTD---VFDFLVDIIPRDE 186 (270)
Q Consensus 124 ~ISaEApvllAKAtElFI~eLT~~A~~~A~~-~KRKTLq~~DIa~AI~~~e---~FdFL~DIVP~~~ 186 (270)
.|+.+|.-+|...++-=...|..+--+.+.. +++++|+.+||..++.... .|+|+.-++-++.
T Consensus 161 ~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~~e~~if~l~dai~~~~~ 227 (343)
T PRK06585 161 RITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDASALSLDDAADAALAGDL 227 (343)
T ss_pred CCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCcccccHHHHHHHHHCCCH
Confidence 5788888888777764333333333333333 4457899999999987654 5677777776654
No 101
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=28.54 E-value=1.9e+02 Score=19.94 Aligned_cols=32 Identities=3% Similarity=-0.014 Sum_probs=24.4
Q ss_pred HHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024238 138 EMFILELTLRSWIHTEENKRRTLQKNDIAAAI 169 (270)
Q Consensus 138 ElFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI 169 (270)
+..+..++...+..+-.++...|+++++..++
T Consensus 35 ~~~~~~~~~~~~~~~D~d~dG~i~~~Ef~~~~ 66 (66)
T PF13499_consen 35 DEESDEMIDQIFREFDTDGDGRISFDEFLNFM 66 (66)
T ss_dssp HHHHHHHHHHHHHHHTTTSSSSEEHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCCcCCCcHHHHhccC
Confidence 45566666777778888888999999987763
No 102
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=28.13 E-value=1.2e+02 Score=31.00 Aligned_cols=61 Identities=16% Similarity=0.249 Sum_probs=44.6
Q ss_pred HHHHHHHhC--ChhhhccCccHHHHHHHHHH----HHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024238 110 ARIKKIMKA--DEDVRMISAEAPVIFAKACE----MFILELTLRSWIHTEENKRRTLQKNDIAAAIS 170 (270)
Q Consensus 110 ARIKKIMKs--DpDV~~ISaEApvllAKAtE----lFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~ 170 (270)
.-||.|++. +++--.++.+|.-.|++.-+ .+...|..-|...|+..|+++|..+|+..|-.
T Consensus 364 ~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~ 430 (450)
T COG1224 364 EEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE 430 (450)
T ss_pred HHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH
Confidence 457777764 33333689999998886544 23345556788899999999999999998854
No 103
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=27.80 E-value=72 Score=32.04 Aligned_cols=32 Identities=13% Similarity=0.180 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 141 ILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 141 I~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
|..|+.+|...|.+.+|..|+.+|+..|+.+.
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 56788889999999999999999999999875
No 104
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=27.08 E-value=1.2e+02 Score=32.00 Aligned_cols=31 Identities=6% Similarity=-0.131 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024238 141 ILELTLRSWIHTEENKRRTLQKNDIAAAISR 171 (270)
Q Consensus 141 I~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~ 171 (270)
|..|..+|...|+..+++.|+.+|+..|+.+
T Consensus 369 l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 369 LGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred HHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 4467788888999999999999999988764
No 105
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=26.92 E-value=1.5e+02 Score=28.14 Aligned_cols=42 Identities=29% Similarity=0.383 Sum_probs=32.6
Q ss_pred hhhhHHHHHHHhHHhHHHHHHHHHHHHHHHHHHHHhhhcCCCC
Q 024238 63 HQLAYQQAQHFHHQQQQQQQQQLQMFWSNQMQEIEQTADFKNH 105 (270)
Q Consensus 63 ~~~~~~~~~~~~~~~~~~~~q~l~~FW~~~~~eiE~~~dfk~~ 105 (270)
.+++-+|.-++..|+. ..+..|.+|=++--.||.+...|++.
T Consensus 24 ~~l~e~Ql~q~~~Ql~-~f~~~LeeFA~kH~~ei~knsqFR~~ 65 (249)
T KOG3341|consen 24 TELAEQQLVQMSKQLE-VFQEALEEFARKHKTEIRKNSQFRNQ 65 (249)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHhhCHHHHHH
Confidence 3455666667776654 77889999999999999998888764
No 106
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=26.36 E-value=82 Score=31.03 Aligned_cols=32 Identities=9% Similarity=0.155 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 141 ILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 141 I~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
|..|+.+|...|..++|+.|+.+|+..|+.+.
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 67899999999999999999999999998764
No 107
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=24.55 E-value=2e+02 Score=29.30 Aligned_cols=61 Identities=15% Similarity=0.036 Sum_probs=40.5
Q ss_pred HHHHHhCC--hhhhccCccHHHHHHHHHH--HHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024238 112 IKKIMKAD--EDVRMISAEAPVIFAKACE--MFILELTLRSWIHTEENKRRTLQKNDIAAAISRT 172 (270)
Q Consensus 112 IKKIMKsD--pDV~~ISaEApvllAKAtE--lFI~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~~ 172 (270)
|++|++.- ..-..++.++..+|++.+. -.+..+...|...|..++|++|+.+||..++...
T Consensus 268 i~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~ 332 (531)
T TIGR02902 268 IKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENG 332 (531)
T ss_pred HHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCc
Confidence 55666542 1112467777777766554 2233555666667777889999999999999765
No 108
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=24.11 E-value=1.1e+02 Score=28.67 Aligned_cols=56 Identities=16% Similarity=0.179 Sum_probs=44.0
Q ss_pred cCccHHHHHHHHHHHHHHH-HHHHHHH-----HHHhcCCCcccHHHHHHHHhcCCcccchhc
Q 024238 125 ISAEAPVIFAKACEMFILE-LTLRSWI-----HTEENKRRTLQKNDIAAAISRTDVFDFLVD 180 (270)
Q Consensus 125 ISaEApvllAKAtElFI~e-LT~~A~~-----~A~~~KRKTLq~~DIa~AI~~~e~FdFL~D 180 (270)
...+-..+|.||+|.|+.. =+-.||. .....|.|.|++++|...+.+..+..||..
T Consensus 93 f~~nEielfrkalE~im~sed~~~asst~~~~~vlq~k~k~L~ks~iE~lLqkf~q~gwf~e 154 (235)
T KOG4718|consen 93 FTANEIELFRKALEKIMSSEDCHIASSTAYNDIVLQAKSKPLKKSRIEELLQKFIQMGWFME 154 (235)
T ss_pred CCHHHHHHHHHHHHHHHhhhHhhhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhchhhe
Confidence 4456788999999999987 3444443 334568899999999999999999888876
No 109
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=23.98 E-value=1.2e+02 Score=21.21 Aligned_cols=24 Identities=13% Similarity=-0.053 Sum_probs=16.5
Q ss_pred HHHHHHHHHhcCCCcccHHHHHHH
Q 024238 145 TLRSWIHTEENKRRTLQKNDIAAA 168 (270)
Q Consensus 145 T~~A~~~A~~~KRKTLq~~DIa~A 168 (270)
=..+-..|++++...|+.++|..|
T Consensus 21 r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 21 RDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHHcCCCeECHHHHHhh
Confidence 334456788999999999988765
No 110
>PRK05907 hypothetical protein; Provisional
Probab=22.22 E-value=1.7e+02 Score=27.86 Aligned_cols=74 Identities=14% Similarity=0.167 Sum_probs=45.3
Q ss_pred HHHHHHhCChhhhccCccHHHHHHHHH-HHHHHHHHHHHHHHHHh-cCCCcccHHHHHHHHhcCC---cccchhccCCCc
Q 024238 111 RIKKIMKADEDVRMISAEAPVIFAKAC-EMFILELTLRSWIHTEE-NKRRTLQKNDIAAAISRTD---VFDFLVDIIPRD 185 (270)
Q Consensus 111 RIKKIMKsDpDV~~ISaEApvllAKAt-ElFI~eLT~~A~~~A~~-~KRKTLq~~DIa~AI~~~e---~FdFL~DIVP~~ 185 (270)
.|++.++.. + ..|+.+|.-+|...+ +-=+..|..+--+.+.. +++++|+.+||...|.++. .|+...-+.-++
T Consensus 142 Wi~~~~~~~-g-~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~s~e~nIF~L~dai~~~~ 219 (311)
T PRK05907 142 LLIQRAKEL-G-ISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVKKEAASLWKLRDALLRRD 219 (311)
T ss_pred HHHHHHHHc-C-CCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcCcccccHHHHHHHHHccC
Confidence 444444443 2 357778777666655 33233444443344444 6789999999999998665 466666666554
Q ss_pred c
Q 024238 186 E 186 (270)
Q Consensus 186 ~ 186 (270)
.
T Consensus 220 ~ 220 (311)
T PRK05907 220 R 220 (311)
T ss_pred H
Confidence 3
No 111
>PF04625 DEC-1_N: DEC-1 protein, N-terminal region; InterPro: IPR006719 The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing []. Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa). This domain is present at the N-terminal of these proteins.; GO: 0005213 structural constituent of chorion, 0007304 chorion-containing eggshell formation, 0005576 extracellular region, 0042600 chorion
Probab=21.80 E-value=2.5e+02 Score=28.11 Aligned_cols=38 Identities=29% Similarity=0.542 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHH------hh--------------hcCCCCCCChHH--HHHHHhCCh
Q 024238 82 QQQLQMFWSNQMQEIE------QT--------------ADFKNHSLPLAR--IKKIMKADE 120 (270)
Q Consensus 82 ~q~l~~FW~~~~~eiE------~~--------------~dfk~~~LPLAR--IKKIMKsDp 120 (270)
+-.|+.|=+..+.|+. .. ..+| +..||+| |.||-+.|-
T Consensus 278 eakL~AFerQVI~EL~~LQqIEr~AkeMRasA~~~~~~s~yk-l~YPLsrTPvHKITRADI 337 (407)
T PF04625_consen 278 EAKLRAFERQVIAELKMLQQIERMAKEMRASATAQNGTSPYK-LRYPLSRTPVHKITRADI 337 (407)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCee-ecccccCCchhhhhHHHH
Confidence 4578899888777653 21 1122 4678876 788888773
No 112
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=21.64 E-value=1.7e+02 Score=22.81 Aligned_cols=33 Identities=18% Similarity=0.373 Sum_probs=22.8
Q ss_pred HHHHHHHHHHhhhcCCCCCCChHHHHHHHhCCh
Q 024238 88 FWSNQMQEIEQTADFKNHSLPLARIKKIMKADE 120 (270)
Q Consensus 88 FW~~~~~eiE~~~dfk~~~LPLARIKKIMKsDp 120 (270)
|=.+.+..++.....+...||++.|++++....
T Consensus 39 y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 39 YTEEDLERLQQILFLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred eCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcCc
Confidence 333444444555556678999999999998763
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=21.01 E-value=2.7e+02 Score=29.08 Aligned_cols=48 Identities=17% Similarity=0.186 Sum_probs=32.9
Q ss_pred ccCccHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024238 124 MISAEAPVIFAKACEMFI-------LELTLRSWIHTEENKRRTLQKNDIAAAISR 171 (270)
Q Consensus 124 ~ISaEApvllAKAtElFI-------~eLT~~A~~~A~~~KRKTLq~~DIa~AI~~ 171 (270)
.|+.++.-++...+.-+- ..+.+.|+.+|.-++|.+|+.+||..|+.-
T Consensus 249 ~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~l 303 (633)
T TIGR02442 249 RISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAEL 303 (633)
T ss_pred CCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence 356665555555554331 245566677888899999999999988753
No 114
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=20.63 E-value=2.1e+02 Score=22.77 Aligned_cols=28 Identities=7% Similarity=0.144 Sum_probs=20.4
Q ss_pred HHHHHHhhhcCCCCCCChHHHHHHHhCC
Q 024238 92 QMQEIEQTADFKNHSLPLARIKKIMKAD 119 (270)
Q Consensus 92 ~~~eiE~~~dfk~~~LPLARIKKIMKsD 119 (270)
.+..+.....++...|||+.|+.++...
T Consensus 43 dl~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (108)
T cd04773 43 DVRDARLIHLLRRGGYLLEQIATVVEQL 70 (108)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHHh
Confidence 3344444556667889999999999864
No 115
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=20.47 E-value=3.4e+02 Score=23.75 Aligned_cols=65 Identities=11% Similarity=0.204 Sum_probs=43.8
Q ss_pred HHHHHhCChhhhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc---HHHHHHHHhcCCcccc
Q 024238 112 IKKIMKADEDVRMISAEAPVIFAKACEMFILELTLRSWIHTEENKRRTLQ---KNDIAAAISRTDVFDF 177 (270)
Q Consensus 112 IKKIMKsDpDV~~ISaEApvllAKAtElFI~eLT~~A~~~A~~~KRKTLq---~~DIa~AI~~~e~FdF 177 (270)
|.-|+.+- .+.-.+...+.-+-.-+-.+.+.+.+.|...|+..+|-.+. -+||.-||+..-...|
T Consensus 20 ihliL~Sl-gi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F 87 (145)
T COG5094 20 IHLILRSL-GIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHF 87 (145)
T ss_pred HHHHHHhc-CchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCc
Confidence 44444443 44445555555444445567889999999999888776554 5999999987766665
Done!