Query 045847
Match_columns 237
No_of_seqs 206 out of 636
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 06:06:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/045847.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/045847hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5208 HAP5 CCAAT-binding fac 100.0 4.1E-32 9E-37 241.0 10.0 129 57-186 78-214 (286)
2 KOG1657 CCAAT-binding factor, 100.0 5.1E-30 1.1E-34 228.3 5.7 108 62-171 50-157 (236)
3 PF00808 CBFD_NFYB_HMF: Histon 99.8 5.9E-20 1.3E-24 132.3 7.0 64 88-151 2-65 (65)
4 KOG1659 Class 2 transcription 99.8 4.2E-19 9.2E-24 156.7 6.4 81 86-166 11-91 (224)
5 COG5247 BUR6 Class 2 transcrip 99.7 4E-18 8.6E-23 136.4 6.2 83 86-168 21-103 (113)
6 KOG1658 DNA polymerase epsilon 99.4 1.4E-13 3E-18 117.0 2.1 81 86-166 57-137 (162)
7 cd00074 H2A Histone 2A; H2A is 99.1 2.1E-10 4.6E-15 93.1 7.3 78 85-162 17-94 (115)
8 COG5262 HTA1 Histone H2A [Chro 99.1 3.2E-10 6.8E-15 93.3 6.1 78 85-162 23-100 (132)
9 smart00414 H2A Histone 2A. 98.8 1.2E-08 2.5E-13 81.9 6.8 78 85-162 6-83 (106)
10 KOG1756 Histone 2A [Chromatin 98.8 1.3E-08 2.9E-13 84.4 7.0 80 83-162 22-101 (131)
11 COG2036 HHT1 Histones H3 and H 98.8 1.5E-08 3.2E-13 79.7 6.8 69 86-155 17-85 (91)
12 PLN00154 histone H2A; Provisio 98.7 2.8E-08 6.1E-13 83.2 7.3 79 84-162 34-113 (136)
13 PTZ00017 histone H2A; Provisio 98.7 2.5E-08 5.5E-13 83.2 6.3 78 84-161 23-100 (134)
14 PLN00153 histone H2A; Provisio 98.6 9.6E-08 2.1E-12 79.4 7.0 77 85-161 21-97 (129)
15 PLN00156 histone H2AX; Provisi 98.6 1.1E-07 2.4E-12 79.8 7.5 77 85-161 26-102 (139)
16 PLN00157 histone H2A; Provisio 98.6 1E-07 2.2E-12 79.5 6.8 78 84-161 22-99 (132)
17 smart00803 TAF TATA box bindin 98.6 1.6E-07 3.6E-12 69.1 7.0 64 88-152 2-65 (65)
18 PF00125 Histone: Core histone 98.6 8.1E-08 1.8E-12 70.1 5.2 68 86-153 6-74 (75)
19 KOG0869 CCAAT-binding factor, 98.5 3.9E-07 8.4E-12 78.3 6.6 70 86-155 30-100 (168)
20 KOG0870 DNA polymerase epsilon 98.4 4.2E-07 9.2E-12 78.5 6.6 76 86-161 8-85 (172)
21 PTZ00252 histone H2A; Provisio 98.4 6.7E-07 1.5E-11 74.8 7.5 78 85-162 22-102 (134)
22 cd00076 H4 Histone H4, one of 98.4 9.6E-07 2.1E-11 68.6 7.3 67 87-154 12-78 (85)
23 PLN00035 histone H4; Provision 98.4 9.5E-07 2.1E-11 71.0 7.3 66 88-154 29-94 (103)
24 PTZ00015 histone H4; Provision 98.3 3.2E-06 7E-11 67.8 7.3 68 86-154 28-95 (102)
25 smart00417 H4 Histone H4. 98.2 2E-06 4.3E-11 65.4 5.2 62 87-149 12-73 (74)
26 cd07981 TAF12 TATA Binding Pro 97.8 9.1E-05 2E-09 55.1 7.4 63 92-155 5-68 (72)
27 KOG0871 Class 2 transcription 97.7 0.00011 2.4E-09 62.8 6.7 77 86-162 10-87 (156)
28 cd08048 TAF11 TATA Binding Pro 97.6 0.00032 6.9E-09 54.4 7.8 69 83-153 12-83 (85)
29 smart00428 H3 Histone H3. 97.5 0.0005 1.1E-08 55.5 8.1 67 86-152 30-99 (105)
30 KOG1658 DNA polymerase epsilon 97.3 0.00045 9.7E-09 59.5 5.1 43 86-128 9-51 (162)
31 cd07979 TAF9 TATA Binding Prot 97.1 0.0016 3.4E-08 52.9 6.3 68 92-160 5-72 (117)
32 smart00576 BTP Bromodomain tra 97.1 0.0023 5E-08 47.9 6.7 60 94-154 12-71 (77)
33 PF02969 TAF: TATA box binding 96.9 0.0043 9.3E-08 46.3 6.9 64 88-152 3-66 (66)
34 PF09415 CENP-X: CENP-S associ 96.9 0.0033 7.3E-08 47.4 6.4 63 90-152 1-66 (72)
35 COG5150 Class 2 transcription 96.9 0.0027 5.9E-08 53.5 6.3 76 86-161 9-85 (148)
36 cd08050 TAF6 TATA Binding Prot 96.8 0.0032 6.9E-08 58.9 7.0 63 91-154 2-64 (343)
37 PF04719 TAFII28: hTAFII28-lik 96.8 0.0055 1.2E-07 48.3 7.0 85 64-153 4-89 (90)
38 KOG1757 Histone 2A [Chromatin 96.7 0.0014 3.1E-08 54.1 3.0 78 85-162 27-105 (131)
39 PLN00121 histone H3; Provision 96.5 0.0093 2E-07 50.3 6.9 65 86-151 63-129 (136)
40 PLN00161 histone H3; Provision 96.3 0.017 3.7E-07 48.7 7.3 67 86-152 56-124 (135)
41 PLN00160 histone H3; Provision 96.3 0.017 3.8E-07 46.1 6.8 67 86-152 22-90 (97)
42 PTZ00018 histone H3; Provision 96.1 0.019 4.2E-07 48.4 6.7 65 86-151 63-129 (136)
43 PF15511 CENP-T: Centromere ki 96.0 0.011 2.4E-07 56.9 5.6 61 86-146 349-414 (414)
44 KOG3219 Transcription initiati 95.5 0.037 8.1E-07 49.2 6.1 89 60-154 89-178 (195)
45 smart00427 H2B Histone H2B. 95.2 0.083 1.8E-06 41.8 6.6 59 94-153 7-66 (89)
46 PLN00158 histone H2B; Provisio 94.0 0.22 4.7E-06 41.2 6.7 59 94-153 33-92 (116)
47 PF07524 Bromo_TP: Bromodomain 93.8 0.29 6.3E-06 36.2 6.6 60 94-154 12-71 (77)
48 PF02269 TFIID-18kDa: Transcri 93.8 0.063 1.4E-06 42.0 3.1 75 94-168 7-82 (93)
49 PF15630 CENP-S: Kinetochore c 93.6 0.2 4.3E-06 38.2 5.5 52 105-156 24-75 (76)
50 PF03847 TFIID_20kDa: Transcri 93.6 0.37 8E-06 36.0 6.8 61 93-154 4-65 (68)
51 PTZ00463 histone H2B; Provisio 93.6 0.27 5.9E-06 40.7 6.6 59 94-153 34-93 (117)
52 KOG3467 Histone H4 [Chromatin 93.6 0.26 5.6E-06 39.5 6.2 62 93-155 34-95 (103)
53 PLN00155 histone H2A; Provisio 93.1 0.11 2.4E-06 38.2 3.2 38 84-121 20-57 (58)
54 KOG1745 Histones H3 and H4 [Ch 92.3 0.18 3.8E-06 42.8 3.9 66 87-152 65-131 (137)
55 cd07978 TAF13 The TATA Binding 92.0 0.73 1.6E-05 36.2 6.8 71 93-164 7-78 (92)
56 KOG3423 Transcription initiati 90.9 1.7 3.8E-05 38.2 8.6 82 62-154 70-165 (176)
57 PF15510 CENP-W: Centromere ki 90.4 0.69 1.5E-05 37.3 5.3 65 87-152 15-94 (102)
58 KOG1744 Histone H2B [Chromatin 89.4 1.1 2.3E-05 37.7 5.8 63 87-153 39-102 (127)
59 KOG1142 Transcription initiati 87.8 0.81 1.7E-05 42.4 4.5 69 93-161 159-227 (258)
60 KOG2549 Transcription initiati 86.9 1.9 4.2E-05 43.9 6.9 81 91-172 14-98 (576)
61 PF05236 TAF4: Transcription i 84.5 1.8 3.9E-05 39.0 5.0 44 92-136 51-94 (264)
62 PF02291 TFIID-31kDa: Transcri 83.3 5.1 0.00011 33.4 6.8 67 93-160 17-83 (129)
63 cd08045 TAF4 TATA Binding Prot 81.7 5 0.00011 35.2 6.5 60 92-152 52-117 (212)
64 KOG2389 Predicted bromodomain 80.4 12 0.00025 36.4 8.9 64 89-153 30-93 (353)
65 PF03540 TFIID_30kDa: Transcri 76.4 11 0.00024 27.1 5.8 47 89-136 3-49 (51)
66 COG5095 TAF6 Transcription ini 74.5 8.5 0.00018 37.5 6.2 53 102-154 18-70 (450)
67 COG5162 Transcription initiati 65.5 42 0.00091 29.9 8.1 49 86-135 86-134 (197)
68 PF10979 DUF2786: Protein of u 63.8 9.4 0.0002 26.2 3.0 35 91-125 4-38 (43)
69 TIGR03015 pepcterm_ATPase puta 51.2 24 0.00052 30.4 4.2 49 106-154 215-266 (269)
70 PF13335 Mg_chelatase_2: Magne 45.9 1.4E+02 0.0031 23.2 8.9 63 83-152 26-94 (96)
71 PRK00411 cdc6 cell division co 43.1 89 0.0019 28.7 6.8 64 91-154 209-282 (394)
72 PF12767 SAGA-Tad1: Transcript 34.6 69 0.0015 28.7 4.6 47 86-133 199-250 (252)
73 KOG4336 TBP-associated transcr 33.9 1.1E+02 0.0025 29.4 6.0 64 91-154 7-70 (323)
74 TIGR02928 orc1/cdc6 family rep 33.2 1.9E+02 0.0041 26.2 7.2 50 106-155 220-275 (365)
75 PF12162 STAT1_TAZ2bind: STAT1 32.1 13 0.00028 22.9 -0.3 8 29-36 5-12 (23)
76 COG5248 TAF19 Transcription in 31.3 1.8E+02 0.0039 24.4 6.1 62 92-155 13-74 (126)
77 TIGR00368 Mg chelatase-related 29.7 3.9E+02 0.0086 26.7 9.3 60 86-152 432-497 (499)
78 PF08637 NCA2: ATP synthase re 25.3 2E+02 0.0044 26.8 6.1 82 59-160 29-112 (290)
79 PRK09862 putative ATP-dependen 24.9 6.7E+02 0.015 25.4 10.0 62 86-154 425-492 (506)
80 TIGR01242 26Sp45 26S proteasom 24.3 99 0.0021 28.7 3.9 42 112-153 317-362 (364)
81 PLN02720 complex II 23.6 1.4E+02 0.0031 25.6 4.3 45 61-105 9-56 (140)
82 PRK03992 proteasome-activating 23.1 1.1E+02 0.0023 29.2 3.9 33 122-154 340-372 (389)
83 KOG1657 CCAAT-binding factor, 22.9 11 0.00023 34.5 -2.7 77 86-171 6-82 (236)
84 KOG3334 Transcription initiati 22.8 1.2E+02 0.0026 26.3 3.8 40 122-161 46-85 (148)
85 KOG3901 Transcription initiati 22.6 3.5E+02 0.0076 22.4 6.2 68 94-164 15-83 (109)
86 PF06752 E_Pc_C: Enhancer of P 22.1 1.4E+02 0.003 27.6 4.3 29 44-73 2-30 (230)
87 KOG1560 Translation initiation 20.9 2.6E+02 0.0057 27.0 5.9 41 59-101 255-295 (339)
88 TIGR00764 lon_rel lon-related 20.3 3.5E+02 0.0075 27.7 7.1 34 121-154 358-391 (608)
No 1
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.97 E-value=4.1e-32 Score=241.02 Aligned_cols=129 Identities=43% Similarity=0.694 Sum_probs=114.9
Q ss_pred HhHHHHHHHHHHHHHHHHHHHhhh-hhhccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHh
Q 045847 57 LMLKQRQLVQSFWEQQKSDIENAT-TESLRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTE 135 (237)
Q Consensus 57 ~~~~~~q~L~~FW~~~~~eie~~~-~~fk~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~ 135 (237)
+-..+.+.|..||.+.+.++|... ..+| .+.||||||||+||.|+||+|||+|||+|++|+||+||++||.|||.+|+
T Consensus 78 lvg~~~e~i~ryWq~ti~~~e~~~q~~~k-~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae 156 (286)
T COG5208 78 LVGLLDERISRYWQQTIKAAEEERQILLK-DHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAE 156 (286)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHhHHHHHH-hccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHh
Confidence 456789999999999999998886 4467 99999999999999999999999999999999999999999999999999
Q ss_pred hCCCCcccHHHHHHHHhcCCcccchhhcCCCCCCCC-------CcccccCCCCCCCCC
Q 045847 136 DGKRRTLQRCDIARALRLDELFDFLIDFVPYDCRQD-------DEAVEIRPANKQHFP 186 (237)
Q Consensus 136 ~~kRKTLq~~DIa~AV~~~d~fdFL~DIVP~~~~~~-------~~~~~~~p~~~~~~p 186 (237)
++||||||++||++||++++.||||+||||+..... ++....+|++++.+-
T Consensus 157 ~NkRRtLQksDia~Av~kSeMfDFLidivpr~p~n~~~~S~~~H~~~~~~~~MG~~~~ 214 (286)
T COG5208 157 ENKRRTLQKSDIAAAVKKSEMFDFLIDIVPRNPFNHLVPSKMHHGGEDFAPRMGDAYA 214 (286)
T ss_pred HhhhhHHHHHHHHHHHHHHHHHhHHhhhccCCCccccCchhhhccchhhhhhhccccc
Confidence 999999999999999999999999999999986544 344445666665543
No 2
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=99.96 E-value=5.1e-30 Score=228.28 Aligned_cols=108 Identities=56% Similarity=0.891 Sum_probs=102.5
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCc
Q 045847 62 RQLVQSFWEQQKSDIENATTESLRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRT 141 (237)
Q Consensus 62 ~q~L~~FW~~~~~eie~~~~~fk~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKT 141 (237)
+++|.+||.++..|++...+ |+ ++.|||+|||||||.|+||.+|++|||++++||||+||.+|+.+||.+|++++|||
T Consensus 50 ~~~l~~fw~~~~~e~e~~~d-~~-~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrt 127 (236)
T KOG1657|consen 50 RQQLQSFWSKQAIEKEGQLD-FK-NHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRT 127 (236)
T ss_pred hHHHHhhhhccccccccccc-hh-hccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhccccccc
Confidence 88999999999855556666 99 99999999999999999999999999999999999999999999999999999999
Q ss_pred ccHHHHHHHHhcCCcccchhhcCCCCCCCC
Q 045847 142 LQRCDIARALRLDELFDFLIDFVPYDCRQD 171 (237)
Q Consensus 142 Lq~~DIa~AV~~~d~fdFL~DIVP~~~~~~ 171 (237)
|+++||+.||.+++.||||+||||++....
T Consensus 128 l~~sdia~av~~s~~fdFL~DivP~~~~~~ 157 (236)
T KOG1657|consen 128 LQKSDIAAAVTQSETFDFLRDIVPRKILAE 157 (236)
T ss_pred chHHHHHHHhccCCCccceeccccchhccc
Confidence 999999999999999999999999997664
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=99.81 E-value=5.9e-20 Score=132.25 Aligned_cols=64 Identities=38% Similarity=0.488 Sum_probs=59.8
Q ss_pred CCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHH
Q 045847 88 LLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARAL 151 (237)
Q Consensus 88 ~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV 151 (237)
.||++|||||||.+|++.+||+||..++++|+|+||++|+.+|+..|+.++||||+++||..||
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=99.77 E-value=4.2e-19 Score=156.67 Aligned_cols=81 Identities=28% Similarity=0.457 Sum_probs=78.7
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhhcCC
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLIDFVP 165 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~DIVP 165 (237)
+.+||.+||||||++|+||++|++-+|++++||+|||++.|+..++..|+..+-|||+..||..||..++.||||.|+|-
T Consensus 11 ~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~ 90 (224)
T KOG1659|consen 11 KTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVE 90 (224)
T ss_pred hccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHH
Confidence 78999999999999999999999999999999999999999999999999999999999999999999999999999764
Q ss_pred C
Q 045847 166 Y 166 (237)
Q Consensus 166 ~ 166 (237)
.
T Consensus 91 ~ 91 (224)
T KOG1659|consen 91 K 91 (224)
T ss_pred h
Confidence 3
No 5
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=99.73 E-value=4e-18 Score=136.44 Aligned_cols=83 Identities=27% Similarity=0.436 Sum_probs=79.6
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhhcCC
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLIDFVP 165 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~DIVP 165 (237)
.++||+|||||||+.|+||+.|++-.|++.+||.|+|+.+|...+...|+.+..+.++.+.|..|+..+++||||.|++-
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 68899999999999999999999999999999999999999999999999999999999999999999999999999976
Q ss_pred CCC
Q 045847 166 YDC 168 (237)
Q Consensus 166 ~~~ 168 (237)
...
T Consensus 101 ~~~ 103 (113)
T COG5247 101 FKN 103 (113)
T ss_pred hcC
Confidence 543
No 6
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=99.38 E-value=1.4e-13 Score=117.03 Aligned_cols=81 Identities=35% Similarity=0.438 Sum_probs=78.5
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhhcCC
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLIDFVP 165 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~DIVP 165 (237)
.++|||+|||.+||.|||+.+...||.++++||.|+||++|...++.+++..+|+|++..|+..||...+.|.||.+..+
T Consensus 57 l~rLpL~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~fle~~~d 136 (162)
T KOG1658|consen 57 LSRLPLARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAFLEGALD 136 (162)
T ss_pred hhhccHHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHHHhhhcc
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999998765
Q ss_pred C
Q 045847 166 Y 166 (237)
Q Consensus 166 ~ 166 (237)
-
T Consensus 137 ~ 137 (162)
T KOG1658|consen 137 T 137 (162)
T ss_pred c
Confidence 4
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=99.11 E-value=2.1e-10 Score=93.11 Aligned_cols=78 Identities=22% Similarity=0.284 Sum_probs=73.6
Q ss_pred cCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhh
Q 045847 85 RNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLID 162 (237)
Q Consensus 85 ~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~D 162 (237)
..+.||++||.|+||..-....|++.|++.++..+|.+..++...|.+.|...+|++|+..||..||.+++.|++|..
T Consensus 17 agL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~EL~~L~~ 94 (115)
T cd00074 17 AGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRNDEELNKLLK 94 (115)
T ss_pred cCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHHHHHHHc
Confidence 468999999999999877779999999999999999999999999999999999999999999999999999997764
No 8
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=99.05 E-value=3.2e-10 Score=93.31 Aligned_cols=78 Identities=22% Similarity=0.300 Sum_probs=75.2
Q ss_pred cCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhh
Q 045847 85 RNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLID 162 (237)
Q Consensus 85 ~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~D 162 (237)
..+.||++|||||||-+..-++|+++|++.++...|..+.+++.-|-+.|..+|.+.|...||..||++++.++||..
T Consensus 23 agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~EL~~l~~ 100 (132)
T COG5262 23 AGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLG 100 (132)
T ss_pred cCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcCcHHHHHHhh
Confidence 368999999999999989899999999999999999999999999999999999999999999999999999999986
No 9
>smart00414 H2A Histone 2A.
Probab=98.81 E-value=1.2e-08 Score=81.93 Aligned_cols=78 Identities=23% Similarity=0.314 Sum_probs=72.9
Q ss_pred cCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhh
Q 045847 85 RNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLID 162 (237)
Q Consensus 85 ~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~D 162 (237)
..+.||++||.|.||..-....|++.|++.++..+|.+..++...|.+.|..++++.|+..||..||.+++.++.|..
T Consensus 6 agL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~nD~EL~~L~~ 83 (106)
T smart00414 6 AGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELNKLLK 83 (106)
T ss_pred CCccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccCCHHHHHHHc
Confidence 468999999999999987788999999999999999999999999999999999999999999999999999985554
No 10
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=98.80 E-value=1.3e-08 Score=84.40 Aligned_cols=80 Identities=21% Similarity=0.283 Sum_probs=76.1
Q ss_pred hccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhh
Q 045847 83 SLRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLID 162 (237)
Q Consensus 83 fk~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~D 162 (237)
-+..+.||++||.|+||...-...|++.||++++-..|....+++..|-+.|+.+++..|...||..||.+++++.||.+
T Consensus 22 ~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~NDeEL~~lL~ 101 (131)
T KOG1756|consen 22 SRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRNDEELNKLLG 101 (131)
T ss_pred hhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhCcHHHHHHhc
Confidence 34478999999999999988889999999999999999999999999999999999999999999999999999999988
No 11
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.79 E-value=1.5e-08 Score=79.66 Aligned_cols=69 Identities=23% Similarity=0.326 Sum_probs=63.2
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCC
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDE 155 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d 155 (237)
...||.+-|.||||.- ...+||.+|...+.+|.|.|+.+|+..|..+|.+.|||||+..||..|+....
T Consensus 17 ~~~Lp~apv~Ri~r~~-~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~ 85 (91)
T COG2036 17 DLLLPKAPVRRILRKA-GAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLG 85 (91)
T ss_pred hhhcCchHHHHHHHHH-hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 4679999999999984 33499999999999999999999999999999999999999999999998653
No 12
>PLN00154 histone H2A; Provisional
Probab=98.74 E-value=2.8e-08 Score=83.17 Aligned_cols=79 Identities=24% Similarity=0.211 Sum_probs=73.3
Q ss_pred ccCCCCChHHHHHHhhccc-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhh
Q 045847 84 LRNHLLPLARIKKVMKSRE-EVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLID 162 (237)
Q Consensus 84 k~~~~LPLARIKKIMK~Dp-DV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~D 162 (237)
+..++||++||.|++|..- ...+|++.|++.++-.+|.+..++.+.|.+.|..++++.|+..||..||.+++.|+.|..
T Consensus 34 rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrnDeEL~~Ll~ 113 (136)
T PLN00154 34 RAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 113 (136)
T ss_pred ccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccCcHHHHHHhc
Confidence 3478999999999999875 457999999999999999999999999999999999999999999999999999998775
No 13
>PTZ00017 histone H2A; Provisional
Probab=98.72 E-value=2.5e-08 Score=83.21 Aligned_cols=78 Identities=23% Similarity=0.291 Sum_probs=73.4
Q ss_pred ccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchh
Q 045847 84 LRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLI 161 (237)
Q Consensus 84 k~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~ 161 (237)
+..+.||++||.|.||..--..+|++.|++.++..+|.+..++...|.+.|..++++.|+..||..||.+++.|+.|.
T Consensus 23 ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 100 (134)
T PTZ00017 23 KAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLL 100 (134)
T ss_pred cCCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccCcHHHHHHH
Confidence 346899999999999987777899999999999999999999999999999999999999999999999999999776
No 14
>PLN00153 histone H2A; Provisional
Probab=98.62 E-value=9.6e-08 Score=79.37 Aligned_cols=77 Identities=23% Similarity=0.266 Sum_probs=72.4
Q ss_pred cCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchh
Q 045847 85 RNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLI 161 (237)
Q Consensus 85 ~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~ 161 (237)
..+.||++||.|.||..--..+|++.|++.++...|.++.++...|.+.|..++++.|+..||..||.+++.|+-|.
T Consensus 21 agL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 97 (129)
T PLN00153 21 AGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLL 97 (129)
T ss_pred cCcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccCcHHHHHHH
Confidence 36899999999999987777899999999999999999999999999999999999999999999999999998554
No 15
>PLN00156 histone H2AX; Provisional
Probab=98.62 E-value=1.1e-07 Score=79.83 Aligned_cols=77 Identities=22% Similarity=0.269 Sum_probs=72.2
Q ss_pred cCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchh
Q 045847 85 RNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLI 161 (237)
Q Consensus 85 ~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~ 161 (237)
..+.||++||.|.||..--..+|++.|+++++...|....++...|.+.|..++++.|+..||..||.+++.|+-|.
T Consensus 26 AgL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrnDeEL~~Ll 102 (139)
T PLN00156 26 AGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL 102 (139)
T ss_pred cCcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccCcHHHHHHH
Confidence 36889999999999987777899999999999999999999999999999999999999999999999999998555
No 16
>PLN00157 histone H2A; Provisional
Probab=98.61 E-value=1e-07 Score=79.51 Aligned_cols=78 Identities=23% Similarity=0.250 Sum_probs=72.3
Q ss_pred ccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchh
Q 045847 84 LRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLI 161 (237)
Q Consensus 84 k~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~ 161 (237)
+..+.||++||.|.||..--..+|++.|+++++...|.+..++...|.+.|..++++.|+..||..||.+++.|+-|.
T Consensus 22 ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 99 (132)
T PLN00157 22 KAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLL 99 (132)
T ss_pred ccCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccCcHHHHHHH
Confidence 346899999999999987777899999999999999999999999999999999999999999999999999998444
No 17
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.60 E-value=1.6e-07 Score=69.09 Aligned_cols=64 Identities=31% Similarity=0.357 Sum_probs=60.6
Q ss_pred CCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHh
Q 045847 88 LLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALR 152 (237)
Q Consensus 88 ~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~ 152 (237)
.||.+-|++|.+. -++..||.|+...++...|.|+.+++..|..+++..||+||+.+||..|++
T Consensus 2 ~~p~~~i~ria~~-~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAES-LGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHH-CCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 4899999999998 578899999999999999999999999999999999999999999998873
No 18
>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=98.59 E-value=8.1e-08 Score=70.06 Aligned_cols=68 Identities=18% Similarity=0.236 Sum_probs=61.5
Q ss_pred CCCCChHHHHHHhhccccc-ccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhc
Q 045847 86 NHLLPLARIKKVMKSREEV-KMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRL 153 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV-~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~ 153 (237)
...+|+.||.|-+..+-.. ..||++|+.++..++|.|+.++...|..+|..+||+||+..||..|+..
T Consensus 6 ~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 6 IPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp SSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred cCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 4568888888888887555 4999999999999999999999999999999999999999999999864
No 19
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=98.46 E-value=3.9e-07 Score=78.27 Aligned_cols=70 Identities=21% Similarity=0.282 Sum_probs=65.6
Q ss_pred CCCCChHHHHHHhhcc-cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCC
Q 045847 86 NHLLPLARIKKVMKSR-EEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDE 155 (237)
Q Consensus 86 ~~~LPLARIKKIMK~D-pDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d 155 (237)
..-||||-|-||||.- |.-.+||+||--.+-...-.||..+|.+|-..++..+||||+.+||.-|+....
T Consensus 30 Dr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 30 DRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 4569999999999976 778899999999999999999999999999999999999999999999998764
No 20
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.45 E-value=4.2e-07 Score=78.45 Aligned_cols=76 Identities=26% Similarity=0.305 Sum_probs=69.4
Q ss_pred CCCCChHHHHHHhhcc-ccc-ccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchh
Q 045847 86 NHLLPLARIKKVMKSR-EEV-KMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLI 161 (237)
Q Consensus 86 ~~~LPLARIKKIMK~D-pDV-~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~ 161 (237)
.+.||.|-|.||+|-- |+- ..||+||..+|++|+-+||.+|+..|...|...+||||..+||..|+...+.-.|+.
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 4679999999999954 555 699999999999999999999999999999999999999999999999988778865
No 21
>PTZ00252 histone H2A; Provisional
Probab=98.44 E-value=6.7e-07 Score=74.80 Aligned_cols=78 Identities=17% Similarity=0.243 Sum_probs=71.2
Q ss_pred cCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhh--CCCCcccHHHHHHHHhcCCccc-chh
Q 045847 85 RNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTED--GKRRTLQRCDIARALRLDELFD-FLI 161 (237)
Q Consensus 85 ~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~--~kRKTLq~~DIa~AV~~~d~fd-FL~ 161 (237)
-.+.||++||.|.||..--...|++.|++.++...|....++...|.+.|.. ++++.|+..||..||.+++.|+ +|.
T Consensus 22 AGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDeEL~~Ll~ 101 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLK 101 (134)
T ss_pred cCccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccChHHHHHHHc
Confidence 3689999999999998877789999999999999999999999999999865 7889999999999999999998 555
Q ss_pred h
Q 045847 162 D 162 (237)
Q Consensus 162 D 162 (237)
+
T Consensus 102 ~ 102 (134)
T PTZ00252 102 N 102 (134)
T ss_pred C
Confidence 5
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=98.41 E-value=9.6e-07 Score=68.59 Aligned_cols=67 Identities=18% Similarity=0.226 Sum_probs=63.2
Q ss_pred CCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 87 HLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 87 ~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
..||.+-|+||.+.. ++..||.++...+..+.|.|+++++.+|...|+..+||||+..||..|+++.
T Consensus 12 ~gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~ 78 (85)
T cd00076 12 KGITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 78 (85)
T ss_pred ccCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHC
Confidence 359999999999984 5999999999999999999999999999999999999999999999999865
No 23
>PLN00035 histone H4; Provisional
Probab=98.41 E-value=9.5e-07 Score=70.97 Aligned_cols=66 Identities=18% Similarity=0.201 Sum_probs=62.8
Q ss_pred CCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 88 LLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 88 ~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
.||.+-|+||.+. -.|..||.++...+..++|.|+++++.+|..+|+..+||||+..||..|+++.
T Consensus 29 ~ipk~~IrRLARr-~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 29 GITKPAIRRLARR-GGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred cCCHHHHHHHHHH-cCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence 4999999999998 56999999999999999999999999999999999999999999999999865
No 24
>PTZ00015 histone H4; Provisional
Probab=98.27 E-value=3.2e-06 Score=67.79 Aligned_cols=68 Identities=18% Similarity=0.200 Sum_probs=63.8
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
-..||.+-|+||.+. -.|..||.++...+..+.|.|+++++.+|..+|+..+||||+..||..|++..
T Consensus 28 i~gI~k~~IrRLarr-~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~ 95 (102)
T PTZ00015 28 IRGITKGAIRRLARR-GGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95 (102)
T ss_pred ccCCCHHHHHHHHHH-cCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhc
Confidence 356999999999998 67999999999999999999999999999999999999999999999999864
No 25
>smart00417 H4 Histone H4.
Probab=98.24 E-value=2e-06 Score=65.37 Aligned_cols=62 Identities=16% Similarity=0.169 Sum_probs=58.4
Q ss_pred CCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHH
Q 045847 87 HLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIAR 149 (237)
Q Consensus 87 ~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~ 149 (237)
..||.+-|+||.+- .++..||.++...+..+.|.|+++++.+|..+|+..+||||+..||..
T Consensus 12 ~gI~k~~IrRLaRr-~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARR-GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 45999999999998 679999999999999999999999999999999999999999999863
No 26
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=97.83 E-value=9.1e-05 Score=55.14 Aligned_cols=63 Identities=14% Similarity=0.208 Sum_probs=55.3
Q ss_pred HHHHHHhhc-ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCC
Q 045847 92 ARIKKVMKS-REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDE 155 (237)
Q Consensus 92 ARIKKIMK~-DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d 155 (237)
..+..++|. ||. ..++.+|..++...+|.|+..++..|...|...||+||..+||.-++++.-
T Consensus 5 ~~l~~lv~~id~~-~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~ 68 (72)
T cd07981 5 RKLQELLKEIDPR-EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNW 68 (72)
T ss_pred HHHHHHHHhhCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Confidence 445566654 554 789999999999999999999999999999999999999999999998764
No 27
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=97.69 E-value=0.00011 Score=62.80 Aligned_cols=77 Identities=16% Similarity=0.221 Sum_probs=68.6
Q ss_pred CCCCChHHHHHHhhcc-cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhh
Q 045847 86 NHLLPLARIKKVMKSR-EEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLID 162 (237)
Q Consensus 86 ~~~LPLARIKKIMK~D-pDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~D 162 (237)
...||-|-|-||+|.= |--.+|++||--+|--+|-.||.-|+.+|...+....+|||.+.||..|+++-..=+|+..
T Consensus 10 e~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee 87 (156)
T KOG0871|consen 10 ELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEE 87 (156)
T ss_pred cccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHH
Confidence 7889999999999954 4234899999999999999999999999999999999999999999999998765566554
No 28
>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=97.62 E-value=0.00032 Score=54.41 Aligned_cols=69 Identities=20% Similarity=0.189 Sum_probs=61.9
Q ss_pred hccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCC---CCcccHHHHHHHHhc
Q 045847 83 SLRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGK---RRTLQRCDIARALRL 153 (237)
Q Consensus 83 fk~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~k---RKTLq~~DIa~AV~~ 153 (237)
|+ ...||-+.|||||..--+ ..++.+..++++-.+.+||.+|+..|.....+.+ +.-|+.+||.+|..+
T Consensus 12 ~R-ra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr 83 (85)
T cd08048 12 FR-RSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR 83 (85)
T ss_pred HH-HhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence 77 677999999999998766 7999999999999999999999999999987644 589999999999865
No 29
>smart00428 H3 Histone H3.
Probab=97.53 E-value=0.0005 Score=55.47 Aligned_cols=67 Identities=19% Similarity=0.185 Sum_probs=56.3
Q ss_pred CCCCChHHH-HHHhhcc-c-ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHh
Q 045847 86 NHLLPLARI-KKVMKSR-E-EVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALR 152 (237)
Q Consensus 86 ~~~LPLARI-KKIMK~D-p-DV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~ 152 (237)
-..+|.+|+ +.|+..- + +--.++.+|..++..|+|.|+..|...|..+|...||.||..+||.-|..
T Consensus 30 I~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 30 IRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred cccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 467888885 5555542 2 12499999999999999999999999999999999999999999988753
No 30
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=97.26 E-value=0.00045 Score=59.49 Aligned_cols=43 Identities=30% Similarity=0.320 Sum_probs=41.3
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHH
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTL 128 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~ 128 (237)
...||++.+|||-|.||...+.+.+|-...+.|+|.|++.|+.
T Consensus 9 ~p~~p~ekvkkiak~dPey~~te~~a~~etafatE~fvq~lv~ 51 (162)
T KOG1658|consen 9 SPKLPMEKVKKIAKNDPEYMDTEDDAFVETAFATEQFVQVLVH 51 (162)
T ss_pred CccccHHHHHHhhcCCchhhhcccchHHHHHHHHHHHHhhhhh
Confidence 6789999999999999999999999999999999999999998
No 31
>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=97.08 E-value=0.0016 Score=52.93 Aligned_cols=68 Identities=12% Similarity=0.114 Sum_probs=60.7
Q ss_pred HHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccch
Q 045847 92 ARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFL 160 (237)
Q Consensus 92 ARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL 160 (237)
.-|++|+|. -++..++.+++..+...++-++.++...|...|+..||+||+.+||..||+..-.|.|-
T Consensus 5 ~~v~~iLk~-~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~ 72 (117)
T cd07979 5 RVIAAILKS-MGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFT 72 (117)
T ss_pred HHHHHHHHH-CCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCC
Confidence 347888887 47889999999999999999999999999999999999999999999999976555554
No 32
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.07 E-value=0.0023 Score=47.89 Aligned_cols=60 Identities=17% Similarity=0.134 Sum_probs=54.2
Q ss_pred HHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 94 IKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 94 IKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
|.+|+|. -+...++..|.-.++..+|.|+.+|+..+..+|+..+|++++..||..|+...
T Consensus 12 Vaqil~~-~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~ 71 (77)
T smart00576 12 VAQILES-AGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENL 71 (77)
T ss_pred HHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 5667775 46779999999999999999999999999999999999999999999998764
No 33
>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=96.92 E-value=0.0043 Score=46.27 Aligned_cols=64 Identities=22% Similarity=0.276 Sum_probs=49.5
Q ss_pred CCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHh
Q 045847 88 LLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALR 152 (237)
Q Consensus 88 ~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~ 152 (237)
.||..-||-|-.+ =++..++.|+.-+++.-+|.-|.++...|...++.+||++|+-+||..|++
T Consensus 3 ~~~~esvk~iAes-~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAES-LGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHH-TT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 4666677777766 567789999999999999999999999999999999999999999999874
No 34
>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=96.92 E-value=0.0033 Score=47.42 Aligned_cols=63 Identities=19% Similarity=0.257 Sum_probs=50.8
Q ss_pred ChHHHHHHhhc--ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCc-ccHHHHHHHHh
Q 045847 90 PLARIKKVMKS--REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRT-LQRCDIARALR 152 (237)
Q Consensus 90 PLARIKKIMK~--DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKT-Lq~~DIa~AV~ 152 (237)
|-.=|.||++. ..+-.+|+++|.-++++-.++||.+-..||+..++..+... |..+||.+..-
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 44557888885 35778999999999999999999999999999999988888 99999998653
No 35
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.89 E-value=0.0027 Score=53.51 Aligned_cols=76 Identities=24% Similarity=0.324 Sum_probs=66.3
Q ss_pred CCCCChHHHHHHhhcc-cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchh
Q 045847 86 NHLLPLARIKKVMKSR-EEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLI 161 (237)
Q Consensus 86 ~~~LPLARIKKIMK~D-pDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~ 161 (237)
...||-|-|.|.+-.= |---++.+||--++--||=.||.-|+..|...+....+|||.|.||..|+++-+.=+|+.
T Consensus 9 e~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 9 ENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred cccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 6789999999988753 333588999999999999999999999999999999999999999999999876545544
No 36
>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=96.84 E-value=0.0032 Score=58.93 Aligned_cols=63 Identities=25% Similarity=0.301 Sum_probs=56.8
Q ss_pred hHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 91 LARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 91 LARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
..-||-|.++ -++..++.||...++.-.|.++.+++..|...++..||+||+.+||..|++..
T Consensus 2 ~~~i~~ia~~-~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~ 64 (343)
T cd08050 2 QESIKLIAES-LGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLR 64 (343)
T ss_pred hhHHHHHHHH-cCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHh
Confidence 3457777776 56889999999999999999999999999999999999999999999999854
No 37
>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=96.80 E-value=0.0055 Score=48.26 Aligned_cols=85 Identities=21% Similarity=0.167 Sum_probs=55.1
Q ss_pred HHHHHHHHHHHHHHhhhhhhccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhC-CCCcc
Q 045847 64 LVQSFWEQQKSDIENATTESLRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDG-KRRTL 142 (237)
Q Consensus 64 ~L~~FW~~~~~eie~~~~~fk~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~-kRKTL 142 (237)
.|+.|=.+|++-.| .|+ ...||-+.|||||+.--+-..|+....++++-.+.+||-+|...|.....+. ...-|
T Consensus 4 L~~~f~~eQ~~Rye----~fR-Rs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl 78 (90)
T PF04719_consen 4 LLSNFDEEQLDRYE----AFR-RSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPL 78 (90)
T ss_dssp ------HHHHHHHH----HHH-H----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS-
T ss_pred HHHcCCHHHHHHHH----HHH-HccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 35556666665443 266 6779999999999986555689999999999999999999999999987653 34589
Q ss_pred cHHHHHHHHhc
Q 045847 143 QRCDIARALRL 153 (237)
Q Consensus 143 q~~DIa~AV~~ 153 (237)
++.||.+|..+
T Consensus 79 ~P~hlreA~rr 89 (90)
T PF04719_consen 79 QPDHLREAYRR 89 (90)
T ss_dssp -HHHHHHHHHH
T ss_pred CcHHHHHHHHh
Confidence 99999999764
No 38
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=96.66 E-value=0.0014 Score=54.12 Aligned_cols=78 Identities=24% Similarity=0.232 Sum_probs=68.1
Q ss_pred cCCCCChHHHHHHhhcc-cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhh
Q 045847 85 RNHLLPLARIKKVMKSR-EEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLID 162 (237)
Q Consensus 85 ~~~~LPLARIKKIMK~D-pDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~D 162 (237)
..++||++||.|-+|.- ..-+.|.+-|.+..+...|..-.+...-|-+.+..-|-|.|+..|+.-||..++.+|=|+.
T Consensus 27 aGlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRGDeELDtLIk 105 (131)
T KOG1757|consen 27 AGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 105 (131)
T ss_pred cccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecCcHHHHHHHH
Confidence 36889999999999976 5567899999999999988888888777777777778899999999999999999999874
No 39
>PLN00121 histone H3; Provisional
Probab=96.52 E-value=0.0093 Score=50.27 Aligned_cols=65 Identities=20% Similarity=0.259 Sum_probs=55.6
Q ss_pred CCCCChHHHH-HHhhc-ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHH
Q 045847 86 NHLLPLARIK-KVMKS-REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARAL 151 (237)
Q Consensus 86 ~~~LPLARIK-KIMK~-DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV 151 (237)
-..+|..|+- .|... ..++ .+..+|..++--|+|.|+-.|-..|+.+|...||.||...||.-+.
T Consensus 63 I~k~pF~RLVREI~~~~~~~~-Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 63 IRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cccccHHHHHHHHHHHhCccc-eeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 4678998854 45543 2444 9999999999999999999999999999999999999999998774
No 40
>PLN00161 histone H3; Provisional
Probab=96.30 E-value=0.017 Score=48.74 Aligned_cols=67 Identities=27% Similarity=0.261 Sum_probs=56.4
Q ss_pred CCCCChHHH-HHHhhc-ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHh
Q 045847 86 NHLLPLARI-KKVMKS-REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALR 152 (237)
Q Consensus 86 ~~~LPLARI-KKIMK~-DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~ 152 (237)
-..+|.+|+ +.|+.. .++--.+..+|..++--|+|.|+-.|-..|+.||...||.||...||.-|..
T Consensus 56 IpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~r 124 (135)
T PLN00161 56 IRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARR 124 (135)
T ss_pred cccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHH
Confidence 467999886 455543 2333589999999999999999999999999999999999999999987754
No 41
>PLN00160 histone H3; Provisional
Probab=96.27 E-value=0.017 Score=46.14 Aligned_cols=67 Identities=24% Similarity=0.251 Sum_probs=55.9
Q ss_pred CCCCChHHH-HHHhhc-ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHh
Q 045847 86 NHLLPLARI-KKVMKS-REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALR 152 (237)
Q Consensus 86 ~~~LPLARI-KKIMK~-DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~ 152 (237)
-..+|..|+ +.|+.. ..+.-...++|..++--|+|.|+-.|-..|..+|...||.||..+|+.-|..
T Consensus 22 I~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~r 90 (97)
T PLN00160 22 IRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARR 90 (97)
T ss_pred hccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHH
Confidence 467899886 445432 2343589999999999999999999999999999999999999999987753
No 42
>PTZ00018 histone H3; Provisional
Probab=96.12 E-value=0.019 Score=48.39 Aligned_cols=65 Identities=20% Similarity=0.266 Sum_probs=55.6
Q ss_pred CCCCChHHHHH-Hhhc-ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHH
Q 045847 86 NHLLPLARIKK-VMKS-REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARAL 151 (237)
Q Consensus 86 ~~~LPLARIKK-IMK~-DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV 151 (237)
-..+|..|+-| |... ..++ .+..+|..++--|+|.|+-.|-..+..||...||.||...||.-+.
T Consensus 63 I~k~pF~RLVREI~~~~~~~~-rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 63 IRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cccccHHHHHHHHHHHcCCcc-eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 46789988644 5432 3454 9999999999999999999999999999999999999999998764
No 43
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=96.03 E-value=0.011 Score=56.89 Aligned_cols=61 Identities=18% Similarity=0.204 Sum_probs=45.9
Q ss_pred CCCCChHHHHHHhhcc-----cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHH
Q 045847 86 NHLLPLARIKKVMKSR-----EEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCD 146 (237)
Q Consensus 86 ~~~LPLARIKKIMK~D-----pDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~D 146 (237)
...||-+-|||+...= ---+.|+++|.-+|.+|++-|-+.|+..=-.+|.+.|||||...|
T Consensus 349 ~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 349 YPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ---S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 5679999999986642 123699999999999999999999999998999999999998876
No 44
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=95.46 E-value=0.037 Score=49.21 Aligned_cols=89 Identities=27% Similarity=0.288 Sum_probs=71.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhhhccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhh-CC
Q 045847 60 KQRQLVQSFWEQQKSDIENATTESLRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTED-GK 138 (237)
Q Consensus 60 ~~~q~L~~FW~~~~~eie~~~~~fk~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~-~k 138 (237)
..+-.|..|=.+|++-.| .|+ ...||-+.|||+|..=-+-. |+.-+.++++--..+||-+|...|...... +.
T Consensus 89 r~q~L~s~fseEQl~RYE----vfR-rs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e 162 (195)
T KOG3219|consen 89 RMQTLLSNFSEEQLSRYE----VFR-RSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGE 162 (195)
T ss_pred HHHHHHHhcCHHHHHHHH----HHH-HhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhcc
Confidence 455667777777765443 377 78999999999999754433 889999999999999999999999998764 45
Q ss_pred CCcccHHHHHHHHhcC
Q 045847 139 RRTLQRCDIARALRLD 154 (237)
Q Consensus 139 RKTLq~~DIa~AV~~~ 154 (237)
..-|+..||.+|+.+.
T Consensus 163 ~~PLqP~HIREA~rrL 178 (195)
T KOG3219|consen 163 SGPLQPKHIREAYRRL 178 (195)
T ss_pred CCCCCcHHHHHHHHHH
Confidence 6789999999999864
No 45
>smart00427 H2B Histone H2B.
Probab=95.17 E-value=0.083 Score=41.77 Aligned_cols=59 Identities=20% Similarity=0.242 Sum_probs=49.9
Q ss_pred HHHHhhc-ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhc
Q 045847 94 IKKVMKS-REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRL 153 (237)
Q Consensus 94 IKKIMK~-DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~ 153 (237)
|.|+.|. .||. -||..|.-++.--.--+.+.++.+|...+..++|+||+..+|..||.-
T Consensus 7 i~kvLKqVhpd~-giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl 66 (89)
T smart00427 7 IYKVLKQVHPDT-GISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRL 66 (89)
T ss_pred HHHHHHHhCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 6777774 5887 588888887777777777889999999999999999999999999963
No 46
>PLN00158 histone H2B; Provisional
Probab=93.97 E-value=0.22 Score=41.23 Aligned_cols=59 Identities=19% Similarity=0.232 Sum_probs=50.3
Q ss_pred HHHHhhc-ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhc
Q 045847 94 IKKVMKS-REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRL 153 (237)
Q Consensus 94 IKKIMK~-DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~ 153 (237)
|.|++|. .||.+ ||..|.-++.--..-+.+.|+.+|...+..++|+||+..+|..||.-
T Consensus 33 I~kVLKQVhPd~g-IS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrL 92 (116)
T PLN00158 33 IYKVLKQVHPDTG-ISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRL 92 (116)
T ss_pred HHHHHHHhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 7788884 68876 58888888877777777889999999999999999999999999964
No 47
>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=93.84 E-value=0.29 Score=36.20 Aligned_cols=60 Identities=15% Similarity=0.181 Sum_probs=52.4
Q ss_pred HHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 94 IKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 94 IKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
|.+|++. -+...++..|.-.++-.+..||++|+..+..+|+..+|......||..|+...
T Consensus 12 va~il~~-~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~ 71 (77)
T PF07524_consen 12 VAQILKH-AGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEM 71 (77)
T ss_pred HHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 4556655 55668999999999999999999999999999999999999999999998654
No 48
>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=93.82 E-value=0.063 Score=41.96 Aligned_cols=75 Identities=16% Similarity=0.214 Sum_probs=34.0
Q ss_pred HHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC-CcccchhhcCCCCC
Q 045847 94 IKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD-ELFDFLIDFVPYDC 168 (237)
Q Consensus 94 IKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~-d~fdFL~DIVP~~~ 168 (237)
|+.+|-.-.|+..-..|++.++-...--||.+|+.+|..+|...|+++|+.+||.-+++++ .++.-|.+++-.++
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~Kl~Rl~~~L~~k~ 82 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKKLARLRELLSMKD 82 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 6788888899999999999999999999999999999999999999999999999999976 56666766665544
No 49
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=93.62 E-value=0.2 Score=38.24 Aligned_cols=52 Identities=12% Similarity=-0.006 Sum_probs=42.6
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCc
Q 045847 105 KMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDEL 156 (237)
Q Consensus 105 ~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~ 156 (237)
..+|.++..+++-.+=.++..++..-...|+..||+||+.+|+.-..++++.
T Consensus 24 ~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~ 75 (76)
T PF15630_consen 24 VEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPS 75 (76)
T ss_dssp SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HH
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCC
Confidence 4688888888888888899999999999999999999999999999988764
No 50
>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=93.60 E-value=0.37 Score=35.97 Aligned_cols=61 Identities=15% Similarity=0.221 Sum_probs=46.2
Q ss_pred HHHHHhhc-ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 93 RIKKVMKS-REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 93 RIKKIMK~-DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
++..+++. ||. ..+-.++--++...++-||..++..|...|+..|..||...||.-.+++.
T Consensus 4 ~l~~Lv~~iDp~-~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~ 65 (68)
T PF03847_consen 4 KLQELVKQIDPN-EKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN 65 (68)
T ss_dssp HHHHHHHCC-SS-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence 34444543 554 47788899999999999999999999999999999999999999988764
No 51
>PTZ00463 histone H2B; Provisional
Probab=93.58 E-value=0.27 Score=40.71 Aligned_cols=59 Identities=22% Similarity=0.202 Sum_probs=49.6
Q ss_pred HHHHhhc-ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhc
Q 045847 94 IKKVMKS-REEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRL 153 (237)
Q Consensus 94 IKKIMK~-DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~ 153 (237)
|.|++|. .||.+ ||..|.-++.--..-..+.|+.+|...+..++|.||+..+|..||.-
T Consensus 34 I~KVLKqVhPd~g-IS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrL 93 (117)
T PTZ00463 34 IFKVLKQVHPDTG-ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRL 93 (117)
T ss_pred HHHHHHhhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhh
Confidence 7777774 68886 58888877777677777889999999999999999999999999964
No 52
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=93.58 E-value=0.26 Score=39.48 Aligned_cols=62 Identities=21% Similarity=0.225 Sum_probs=55.1
Q ss_pred HHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCC
Q 045847 93 RIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDE 155 (237)
Q Consensus 93 RIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d 155 (237)
-|+||-+- ..|+.|+.--.--+..+...|++.....|..+++..|||||+..||..++++..
T Consensus 34 aIRRlARr-~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G 95 (103)
T KOG3467|consen 34 AIRRLARR-GGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 95 (103)
T ss_pred HHHHHHHh-cCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcC
Confidence 47777776 678899988888889999999999999999999999999999999999998653
No 53
>PLN00155 histone H2A; Provisional
Probab=93.08 E-value=0.11 Score=38.24 Aligned_cols=38 Identities=21% Similarity=0.297 Sum_probs=33.8
Q ss_pred ccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHH
Q 045847 84 LRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEM 121 (237)
Q Consensus 84 k~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtEL 121 (237)
+..++||++||.|.+|..--...|++.|++.++-..|.
T Consensus 20 rAgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEY 57 (58)
T PLN00155 20 KAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEY 57 (58)
T ss_pred ccccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHh
Confidence 33689999999999999877789999999999998875
No 54
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=92.32 E-value=0.18 Score=42.81 Aligned_cols=66 Identities=23% Similarity=0.243 Sum_probs=58.4
Q ss_pred CCCChHHHHH-HhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHh
Q 045847 87 HLLPLARIKK-VMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALR 152 (237)
Q Consensus 87 ~~LPLARIKK-IMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~ 152 (237)
..+|..|.-| |++.--..-.+-+.|..++--|.|.|+-.|=..+..||...||-||..+||.-|..
T Consensus 65 ~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr 131 (137)
T KOG1745|consen 65 RKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 131 (137)
T ss_pred hcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence 4699998877 88776555688899999999999999999999999999999999999999988764
No 55
>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=92.00 E-value=0.73 Score=36.20 Aligned_cols=71 Identities=18% Similarity=0.257 Sum_probs=59.6
Q ss_pred HHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC-CcccchhhcC
Q 045847 93 RIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD-ELFDFLIDFV 164 (237)
Q Consensus 93 RIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~-d~fdFL~DIV 164 (237)
-|+.+|-.-.|+..-..|++.++-...--||.+|+..|...|. .+|..++.+||.-++.++ .++.-|..++
T Consensus 7 ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL 78 (92)
T cd07978 7 EIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPKKLARLRELL 78 (92)
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHHHHHHHHHHH
Confidence 4788888888999999999999999999999999999999998 555556999999999877 3455555544
No 56
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.94 E-value=1.7 Score=38.22 Aligned_cols=82 Identities=16% Similarity=0.199 Sum_probs=62.5
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhh-----
Q 045847 62 RQLVQSFWEQQKSDIENATTESLRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTED----- 136 (237)
Q Consensus 62 ~q~L~~FW~~~~~eie~~~~~fk~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~----- 136 (237)
...|.+| |.++.+ ....+|=+-+--+|+. .++...-.-..-|++.|+.-||.+++..|+.+++-
T Consensus 70 d~~l~ef-------l~qLdd---YtP~IPDavt~~yL~~-aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~ 138 (176)
T KOG3423|consen 70 DTHLEEF-------LAQLDD---YTPTIPDAVTDHYLKK-AGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTA 138 (176)
T ss_pred chHHHHH-------HHHHhc---CCCCCcHHHHHHHHHh-cCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccc
Confidence 4456666 334434 3578999999999988 34445555567899999999999999999999873
Q ss_pred ---------CCCCcccHHHHHHHHhcC
Q 045847 137 ---------GKRRTLQRCDIARALRLD 154 (237)
Q Consensus 137 ---------~kRKTLq~~DIa~AV~~~ 154 (237)
.++-||+-.||..|++..
T Consensus 139 ~~~~k~~~kdkK~tLtmeDL~~AL~Ey 165 (176)
T KOG3423|consen 139 IGKDKKQAKDKKYTLTMEDLSPALAEY 165 (176)
T ss_pred cccccccccccceeeeHHHHHHHHHHh
Confidence 246789999999999764
No 57
>PF15510 CENP-W: Centromere kinetochore component W
Probab=90.43 E-value=0.69 Score=37.29 Aligned_cols=65 Identities=17% Similarity=0.263 Sum_probs=51.6
Q ss_pred CCCChHHHHHHhhcc-cccccccccHHHH--------------HHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHH
Q 045847 87 HLLPLARIKKVMKSR-EEVKMTTADSPAV--------------FAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARAL 151 (237)
Q Consensus 87 ~~LPLARIKKIMK~D-pDV~~ISaEApvl--------------iAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV 151 (237)
..-|-+-+||++|-. |-. .+.+.+=.+ +-.-|=+|+..|+++|-..|=++|-.+|+.+||..|.
T Consensus 15 rkaPrgfLkrv~Kr~Kphl-Rl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~Aaa 93 (102)
T PF15510_consen 15 RKAPRGFLKRVFKRQKPHL-RLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAA 93 (102)
T ss_pred HhCchHHHHHHHHhcCCce-eecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHH
Confidence 357888999999954 544 444444444 5667899999999999999999999999999998875
Q ss_pred h
Q 045847 152 R 152 (237)
Q Consensus 152 ~ 152 (237)
+
T Consensus 94 K 94 (102)
T PF15510_consen 94 K 94 (102)
T ss_pred H
Confidence 4
No 58
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=89.39 E-value=1.1 Score=37.73 Aligned_cols=63 Identities=16% Similarity=0.161 Sum_probs=45.9
Q ss_pred CCCChHHHHHHhh-cccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhc
Q 045847 87 HLLPLARIKKVMK-SREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRL 153 (237)
Q Consensus 87 ~~LPLARIKKIMK-~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~ 153 (237)
...++.| ++| .+||.++-+.+.-++-+..-++ .+.++.+|...|..+||.||.-.+|..||+-
T Consensus 39 ~s~yv~k---vlk~Vhpd~gis~~a~~vmnsf~ndi-fe~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 39 YSEYVYK---VLKQVHPDLGISSKAMGVMNSFVNDI-FERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred eeeehhh---hhhcccCCCCcCHHHHHHHHHHHHHH-HHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 3455544 555 4677764444444555555555 8889999999999999999999999999864
No 59
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=87.84 E-value=0.81 Score=42.43 Aligned_cols=69 Identities=12% Similarity=0.156 Sum_probs=55.3
Q ss_pred HHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchh
Q 045847 93 RIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLI 161 (237)
Q Consensus 93 RIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~ 161 (237)
+|..+++.=..-..+-.|+--+|...|+-||..++..|...|...|..||..+||.-.+++.-.+.|=.
T Consensus 159 kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPg 227 (258)
T KOG1142|consen 159 KLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPG 227 (258)
T ss_pred chhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCC
Confidence 344444422223567778899999999999999999999999999999999999999999887665543
No 60
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=86.89 E-value=1.9 Score=43.86 Aligned_cols=81 Identities=22% Similarity=0.242 Sum_probs=64.9
Q ss_pred hHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC---Ccccchh-hcCCC
Q 045847 91 LARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD---ELFDFLI-DFVPY 166 (237)
Q Consensus 91 LARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~---d~fdFL~-DIVP~ 166 (237)
-.-+|-+.++ -++..++.||..+++.=.|.=|.++++.|.+.+...||++++-+||..|+... +-|.|=. +++|.
T Consensus 14 ~Es~k~vAEs-lGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg~~s~~~i~f 92 (576)
T KOG2549|consen 14 KESVKVVAES-LGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYGFGAQEIIPF 92 (576)
T ss_pred HHHHHHHHHH-hCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccCcccCceeec
Confidence 4556666665 67889999999999999999999999999999999999999999999999743 4444433 46666
Q ss_pred CCCCCC
Q 045847 167 DCRQDD 172 (237)
Q Consensus 167 ~~~~~~ 172 (237)
....++
T Consensus 93 r~a~~~ 98 (576)
T KOG2549|consen 93 RKASGG 98 (576)
T ss_pred cccCCC
Confidence 554443
No 61
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=84.45 E-value=1.8 Score=39.00 Aligned_cols=44 Identities=23% Similarity=0.267 Sum_probs=32.2
Q ss_pred HHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 045847 92 ARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTED 136 (237)
Q Consensus 92 ARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~ 136 (237)
.+|.+|++... +..+..|.+.+|+-|||..+..|...+...++.
T Consensus 51 ~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~h 94 (264)
T PF05236_consen 51 KRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRH 94 (264)
T ss_dssp HHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH-----
T ss_pred HHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46888887655 778999999999999999999999999888763
No 62
>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=83.30 E-value=5.1 Score=33.44 Aligned_cols=67 Identities=15% Similarity=0.108 Sum_probs=41.3
Q ss_pred HHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccch
Q 045847 93 RIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFL 160 (237)
Q Consensus 93 RIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL 160 (237)
-|..|+|. -+|.-....++..+---+=.++.++...|..+|...+|++|..+||..||...-.+.|-
T Consensus 17 ~i~~iL~~-~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~ 83 (129)
T PF02291_consen 17 VIHLILKS-MGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFT 83 (129)
T ss_dssp HHHHHHHH-TT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT------
T ss_pred HHHHHHHH-cCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhcc
Confidence 35666665 35544444444444444456788888999999999999999999999999966556553
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=81.70 E-value=5 Score=35.17 Aligned_cols=60 Identities=22% Similarity=0.234 Sum_probs=46.6
Q ss_pred HHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhC------CCCcccHHHHHHHHh
Q 045847 92 ARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDG------KRRTLQRCDIARALR 152 (237)
Q Consensus 92 ARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~------kRKTLq~~DIa~AV~ 152 (237)
.+|.+|++. .+++.++.|+..+|+.|||.++..|.......++.. ..+....+|+..-+.
T Consensus 52 ~~~~~i~~~-~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~ 117 (212)
T cd08045 52 KKIRKIAKK-HGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLR 117 (212)
T ss_pred HHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHH
Confidence 456677776 345588999999999999999999999998887642 346667777776654
No 64
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=80.36 E-value=12 Score=36.37 Aligned_cols=64 Identities=16% Similarity=0.141 Sum_probs=55.0
Q ss_pred CChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhc
Q 045847 89 LPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRL 153 (237)
Q Consensus 89 LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~ 153 (237)
|=..+|+.|+.+=+ +...-.-|.-.++--+-.||+.|++-|..++...+|--....||..|+..
T Consensus 30 la~~avaQIcqslg-~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~d 93 (353)
T KOG2389|consen 30 LARVAVAQICQSLG-YSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQD 93 (353)
T ss_pred HHHHHHHHHHHhcC-CcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHH
Confidence 55677899999843 45555668999999999999999999999999999999999999999875
No 65
>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=76.38 E-value=11 Score=27.06 Aligned_cols=47 Identities=11% Similarity=0.116 Sum_probs=32.2
Q ss_pred CChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 045847 89 LPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTED 136 (237)
Q Consensus 89 LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~ 136 (237)
+|=+-+.-+|+. -++..--.-..-|++-|++.||.+++..|+.+++.
T Consensus 3 IPD~v~~~yL~~-~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 3 IPDEVTDYYLER-SGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCHHHHHHHHHH-CCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344555555554 22223333456789999999999999999998763
No 66
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=74.46 E-value=8.5 Score=37.53 Aligned_cols=53 Identities=26% Similarity=0.122 Sum_probs=49.5
Q ss_pred cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 102 EEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 102 pDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
-++..|..|+..+++--.|.=|.+++.+|.......||..|+-+||..|++..
T Consensus 18 lGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~l 70 (450)
T COG5095 18 LGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSL 70 (450)
T ss_pred cCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhc
Confidence 56789999999999999999999999999999999999999999999999753
No 67
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=65.54 E-value=42 Score=29.91 Aligned_cols=49 Identities=8% Similarity=0.203 Sum_probs=37.2
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHh
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTE 135 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~ 135 (237)
...+|=+-+-=.|-. .++...-.-.--|++.++..||.+++..||.+.+
T Consensus 86 ~PliPd~v~DYyl~k-~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsr 134 (197)
T COG5162 86 TPLIPDSVTDYYLEK-AGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSR 134 (197)
T ss_pred CCCccHHHHHHHHHh-cCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567787877777765 3344455556679999999999999999998754
No 68
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=63.79 E-value=9.4 Score=26.19 Aligned_cols=35 Identities=23% Similarity=0.309 Sum_probs=28.6
Q ss_pred hHHHHHHhhcccccccccccHHHHHHHHHHHHHHH
Q 045847 91 LARIKKVMKSREEVKMTTADSPAVFAKACEMFIME 125 (237)
Q Consensus 91 LARIKKIMK~DpDV~~ISaEApvliAKAtELFI~e 125 (237)
+.||+|++..-.+.+---.||-.++.+|-+|..++
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 57999999987776655569999999999987654
No 69
>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=51.23 E-value=24 Score=30.39 Aligned_cols=49 Identities=10% Similarity=0.022 Sum_probs=42.9
Q ss_pred cccccHHHHHHHHHHH---HHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 106 MTTADSPAVFAKACEM---FIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 106 ~ISaEApvliAKAtEL---FI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
.++.++.-.+.+.|.= .|..++.+++..|-..+.++|+.++|..++...
T Consensus 215 ~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~ 266 (269)
T TIGR03015 215 VFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEI 266 (269)
T ss_pred CcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 4788888888888874 799999999999988899999999999999764
No 70
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=45.88 E-value=1.4e+02 Score=23.18 Aligned_cols=63 Identities=21% Similarity=0.169 Sum_probs=50.5
Q ss_pred hccCCCCChHHHHHHhhcccccccccccHHHHHHHHHHHH------HHHHHHHHHHHHhhCCCCcccHHHHHHHHh
Q 045847 83 SLRNHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMF------IMELTLRAWLQTEDGKRRTLQRCDIARALR 152 (237)
Q Consensus 83 fk~~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELF------I~eLt~~A~~~A~~~kRKTLq~~DIa~AV~ 152 (237)
++.|-.||-.-|++....+++ +-.++..+++-| +..+..-|+..|--.+...|...||.+|+.
T Consensus 26 ~~~Na~l~~~~l~~~~~l~~~-------~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 26 IKCNAQLPGEELRKYCPLSSE-------AKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CCccccCCHHHHHhHcCCCHH-------HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 455889999999999877654 566666676665 456777788889999999999999999985
No 71
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=43.12 E-value=89 Score=28.68 Aligned_cols=64 Identities=20% Similarity=0.226 Sum_probs=45.4
Q ss_pred hHHHHHHhhcccc----cccccccHHHHHHHHHHH------HHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 91 LARIKKVMKSREE----VKMTTADSPAVFAKACEM------FIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 91 LARIKKIMK~DpD----V~~ISaEApvliAKAtEL------FI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
..-++.|++.--. -..++.++.-++++.+.- .+..+...|+..|...++.+|+.+||..|+...
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 3455666553211 135777887777776643 344677888888988899999999999999876
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=34.61 E-value=69 Score=28.69 Aligned_cols=47 Identities=15% Similarity=0.149 Sum_probs=34.0
Q ss_pred CCCCCh-----HHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHH
Q 045847 86 NHLLPL-----ARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQ 133 (237)
Q Consensus 86 ~~~LPL-----ARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~ 133 (237)
...||= .|+-.|... .+..-|+.|++-++..|+|.|+..|...+...
T Consensus 199 s~~LPD~~~L~~Rm~~ia~e-~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~ 250 (252)
T PF12767_consen 199 SGELPDTQSLRKRMEQIAWE-HGLGGVSDDCANLLNLALEVHLKNLIKSCLDL 250 (252)
T ss_pred hCcCCCHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 455663 344444422 34456999999999999999999999887654
No 73
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=33.86 E-value=1.1e+02 Score=29.43 Aligned_cols=64 Identities=13% Similarity=0.062 Sum_probs=54.3
Q ss_pred hHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 91 LARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 91 LARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
++-|--+|+.+.+...|+.-|.--+.-+..-.|.++...+..+++..||...++.||+..+...
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 3456666777777778898888888888888999999999999999999999999999887643
No 74
>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=33.15 E-value=1.9e+02 Score=26.19 Aligned_cols=50 Identities=12% Similarity=-0.021 Sum_probs=36.9
Q ss_pred cccccHHHHHHHHHH------HHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCC
Q 045847 106 MTTADSPAVFAKACE------MFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDE 155 (237)
Q Consensus 106 ~ISaEApvliAKAtE------LFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d 155 (237)
.++.++.-++++-++ .-+..+...|+..|...++.+|+.+||..|+....
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 466677666655443 24556777888888888889999999999987663
No 75
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=32.13 E-value=13 Score=22.92 Aligned_cols=8 Identities=63% Similarity=1.294 Sum_probs=3.5
Q ss_pred ccCCCCCC
Q 045847 29 HNFMPMTP 36 (237)
Q Consensus 29 ~~~~p~~~ 36 (237)
+|.|||+|
T Consensus 5 dnmmPMSP 12 (23)
T PF12162_consen 5 DNMMPMSP 12 (23)
T ss_dssp TS---S-H
T ss_pred hcccCCCH
Confidence 79999998
No 76
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=31.25 E-value=1.8e+02 Score=24.43 Aligned_cols=62 Identities=21% Similarity=0.179 Sum_probs=47.9
Q ss_pred HHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCC
Q 045847 92 ARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDE 155 (237)
Q Consensus 92 ARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d 155 (237)
--||-+|=.=.||..=..++.-++---.--++.+|+..|+..|+ .|..++-+|+.-|+++++
T Consensus 13 KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~Dp 74 (126)
T COG5248 13 KDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRRDP 74 (126)
T ss_pred HHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhhCh
Confidence 34677777767776666677777777677778888999999887 677788899999998774
No 77
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=29.70 E-value=3.9e+02 Score=26.74 Aligned_cols=60 Identities=15% Similarity=0.096 Sum_probs=46.8
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHH------HHHHHHHHHHHHhhCCCCcccHHHHHHHHh
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMF------IMELTLRAWLQTEDGKRRTLQRCDIARALR 152 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELF------I~eLt~~A~~~A~~~kRKTLq~~DIa~AV~ 152 (237)
+..++-..++++.+.+. ++--++..|.+.| ...+.+-||..|.-.++..|..+||++|+.
T Consensus 432 N~~l~~~~l~~~~~l~~-------~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 432 NADLNSDEIEQFCKLSA-------IDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred cccCCHHHHHhhcCCCH-------HHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 56788888888776654 4566666666665 456777788889999999999999999985
No 78
>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=25.25 E-value=2e+02 Score=26.81 Aligned_cols=82 Identities=13% Similarity=0.218 Sum_probs=57.5
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhccCCCCChHHHHHHhhcc--cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 045847 59 LKQRQLVQSFWEQQKSDIENATTESLRNHLLPLARIKKVMKSR--EEVKMTTADSPAVFAKACEMFIMELTLRAWLQTED 136 (237)
Q Consensus 59 ~~~~q~L~~FW~~~~~eie~~~~~fk~~~~LPLARIKKIMK~D--pDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~ 136 (237)
....+.+..||.+.+- =|+-+|...++.| .++.++|++++..=-...|-.|.+++......
T Consensus 29 ~~~~~t~~~f~~nwV~--------------~Pl~~I~~tlr~d~~s~~~i~s~~sL~~d~~SLeRMv~dF~~d~~~~--- 91 (290)
T PF08637_consen 29 ENAVETVRGFWKNWVW--------------EPLKSIWDTLRHDEKSEIAIMSKESLQSDMESLERMVVDFAKDNSPN--- 91 (290)
T ss_pred HHHHHHHHHHHHHHHH--------------HHHHHHHHHHhCCCCCCcccccHHHHHHHHHHHHHHHHHHHhcCCCC---
Confidence 3677788888888653 2777788889986 66789999999998888888888888764322
Q ss_pred CCCCcccHHHHHHHHhcCCcccch
Q 045847 137 GKRRTLQRCDIARALRLDELFDFL 160 (237)
Q Consensus 137 ~kRKTLq~~DIa~AV~~~d~fdFL 160 (237)
...+...|...|+.-+--.++
T Consensus 92 ---~~~~~~~l~~~v~~Gdlt~Vm 112 (290)
T PF08637_consen 92 ---MPADLEELRQQVREGDLTPVM 112 (290)
T ss_pred ---CcchHHHHHHHHHcCCcHHHH
Confidence 124555666666554433333
No 79
>PRK09862 putative ATP-dependent protease; Provisional
Probab=24.93 E-value=6.7e+02 Score=25.37 Aligned_cols=62 Identities=15% Similarity=0.096 Sum_probs=41.4
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHH------HHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMF------IMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELF------I~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
+..++-..|++.++.+.+. .-++..+.+.+ ...|.+-||..|.-.+|..|+.+||.+|+.-.
T Consensus 425 n~~l~~~~l~~~~~l~~~~-------~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR 492 (506)
T PRK09862 425 NAWLDSPEIRQFCKLESED-------ARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYR 492 (506)
T ss_pred hcccCHHHHHHHhCCCHHH-------HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhh
Confidence 3456666676666654443 33333333222 34667778888989999999999999999744
No 80
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=24.26 E-value=99 Score=28.72 Aligned_cols=42 Identities=17% Similarity=0.081 Sum_probs=32.4
Q ss_pred HHHHHHHHHHH----HHHHHHHHHHHHhhCCCCcccHHHHHHHHhc
Q 045847 112 PAVFAKACEMF----IMELTLRAWLQTEDGKRRTLQRCDIARALRL 153 (237)
Q Consensus 112 pvliAKAtELF----I~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~ 153 (237)
...+++.|+-| |..|+.+|...|...++..|+.+|+..|+.+
T Consensus 317 ~~~la~~t~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 317 LEAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 34455555433 5578888888888899999999999999975
No 81
>PLN02720 complex II
Probab=23.55 E-value=1.4e+02 Score=25.60 Aligned_cols=45 Identities=22% Similarity=0.322 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhhccCCCCCh---HHHHHHhhcccccc
Q 045847 61 QRQLVQSFWEQQKSDIENATTESLRNHLLPL---ARIKKVMKSREEVK 105 (237)
Q Consensus 61 ~~q~L~~FW~~~~~eie~~~~~fk~~~~LPL---ARIKKIMK~DpDV~ 105 (237)
.=.-+.+||++..+=+++....++|...||- +-|..-|.+||=.+
T Consensus 9 ~w~g~K~~w~e~fs~l~~y~~~~~rdkPLP~Ws~sDVeeFIaSDPVyG 56 (140)
T PLN02720 9 HWEGLKDFWRDRFSFLENYARFSKRDKPLPPWSDSDVDEFIASDPVYG 56 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCchhhHHHHHhcCCCcc
Confidence 3457889999999999888876677888886 88999999997553
No 82
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=23.13 E-value=1.1e+02 Score=29.20 Aligned_cols=33 Identities=12% Similarity=0.047 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 122 FIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 122 FI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
=|..|+.+|...|...+++.|+.+|+.+|+...
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 367788889888888899999999999999764
No 83
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=22.92 E-value=11 Score=34.48 Aligned_cols=77 Identities=21% Similarity=0.094 Sum_probs=54.5
Q ss_pred CCCCChHHHHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchhhcCC
Q 045847 86 NHLLPLARIKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLIDFVP 165 (237)
Q Consensus 86 ~~~LPLARIKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~DIVP 165 (237)
.-..+++|+..+++ +++.+ .+++..-.+...+...++.+.....|.+|+.-.+..+++..+..+|+.++||
T Consensus 6 ~~~~~~~~~~~~~~------~~~p~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~fw~~~~~e~e~~~d~~~~~lP 76 (236)
T KOG1657|consen 6 ANSDIVANIVSNRR------MKAPP---KGAKSEPEGAVCLDPEASIITGDVSRQQLQSFWSKQAIEKEGQLDFKNHILP 76 (236)
T ss_pred cCcccccccccccc------ccCCc---cccccccccceecchhhhhcccchhhHHHHhhhhccccccccccchhhccCc
Confidence 45566677776663 22222 3333333344478888888766666899999999999888899999999999
Q ss_pred CCCCCC
Q 045847 166 YDCRQD 171 (237)
Q Consensus 166 ~~~~~~ 171 (237)
...+|.
T Consensus 77 laRiKk 82 (236)
T KOG1657|consen 77 LARIKK 82 (236)
T ss_pred Hhhccc
Confidence 977665
No 84
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=22.77 E-value=1.2e+02 Score=26.27 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCCcccchh
Q 045847 122 FIMELTLRAWLQTEDGKRRTLQRCDIARALRLDELFDFLI 161 (237)
Q Consensus 122 FI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d~fdFL~ 161 (237)
++..+...|-.++...++.+|..+||..|+...-.+.|-.
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 4667778888999999999999999999999877777755
No 85
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=22.60 E-value=3.5e+02 Score=22.43 Aligned_cols=68 Identities=19% Similarity=0.200 Sum_probs=45.4
Q ss_pred HHHHhhcccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcCC-cccchhhcC
Q 045847 94 IKKVMKSREEVKMTTADSPAVFAKACEMFIMELTLRAWLQTEDGKRRTLQRCDIARALRLDE-LFDFLIDFV 164 (237)
Q Consensus 94 IKKIMK~DpDV~~ISaEApvliAKAtELFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~d-~fdFL~DIV 164 (237)
++-+|=.=.|+..=-.+++-++---.--||.+||..|... ++|..++-+||.-+|++++ +|.=..|++
T Consensus 15 l~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~---g~rgk~~veD~~f~lRkDpkK~~Rv~eLL 83 (109)
T KOG3901|consen 15 LRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEI---GKRGKVKVEDFKFLLRKDPKKLGRVKELL 83 (109)
T ss_pred HHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHh---cccCceeHHHHHHHHHhChHHHhHHHHHH
Confidence 3344444455555566777777777777788887776654 3888899999999998874 344344433
No 86
>PF06752 E_Pc_C: Enhancer of Polycomb C-terminus; InterPro: IPR009607 This entry represents the C terminus of eukaryotic enhancer of polycomb proteins, which have roles in heterochromatin formation []. This family contains several conserved motifs.
Probab=22.10 E-value=1.4e+02 Score=27.59 Aligned_cols=29 Identities=31% Similarity=0.366 Sum_probs=18.4
Q ss_pred CChHhHHHHHHHHHhHHHHHHHHHHHHHHH
Q 045847 44 PTEEDEEEAHSLALMLKQRQLVQSFWEQQK 73 (237)
Q Consensus 44 ~~~~~~~~~~~~~~~~~~~q~L~~FW~~~~ 73 (237)
+++||.|+ ||+||...++|+|...-..+.
T Consensus 2 ~T~EQyQq-HQqQL~~MQkQQLaqiqqqQ~ 30 (230)
T PF06752_consen 2 FTAEQYQQ-HQQQLVLMQKQQLAQIQQQQQ 30 (230)
T ss_pred ccHHHHHH-HHHHHHHHHHHHHHHHHHHHh
Confidence 45666654 666777777777776655544
No 87
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=20.87 E-value=2.6e+02 Score=27.03 Aligned_cols=41 Identities=15% Similarity=0.240 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhccCCCCChHHHHHHhhcc
Q 045847 59 LKQRQLVQSFWEQQKSDIENATTESLRNHLLPLARIKKVMKSR 101 (237)
Q Consensus 59 ~~~~q~L~~FW~~~~~eie~~~~~fk~~~~LPLARIKKIMK~D 101 (237)
+.+|++...+-.++.+|.++-. -++...||+.-+|||.|.-
T Consensus 255 ~rqq~~~~q~~aKrqaENa~R~--argep~lP~dd~kr~fk~p 295 (339)
T KOG1560|consen 255 ARQQAKKHQWIAKRQAENANRA--ARGEPPLPEDDWKRIFKPP 295 (339)
T ss_pred HHHHHHHHHHHHHHHHHhhhhh--hcCCCCCChHHHHHHhcCC
Confidence 3444455555556666554443 4558999999999999974
No 88
>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=20.26 E-value=3.5e+02 Score=27.73 Aligned_cols=34 Identities=12% Similarity=-0.028 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHhhCCCCcccHHHHHHHHhcC
Q 045847 121 MFIMELTLRAWLQTEDGKRRTLQRCDIARALRLD 154 (237)
Q Consensus 121 LFI~eLt~~A~~~A~~~kRKTLq~~DIa~AV~~~ 154 (237)
.=+..|...|...|...++.+|+.+||.+|++..
T Consensus 358 R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 358 RELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 3456677777777878889999999999998743
Done!