Query 028748
Match_columns 204
No_of_seqs 125 out of 561
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 16:22:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028748.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028748hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1657 CCAAT-binding factor, 99.9 9.2E-23 2E-27 178.2 4.1 94 99-192 65-159 (236)
2 COG5208 HAP5 CCAAT-binding fac 99.8 1.8E-21 4E-26 169.8 3.0 85 102-186 103-188 (286)
3 PF00808 CBFD_NFYB_HMF: Histon 99.8 7.3E-20 1.6E-24 129.1 6.2 63 108-170 2-65 (65)
4 KOG1659 Class 2 transcription 99.7 1.1E-18 2.3E-23 150.9 3.7 86 99-184 4-90 (224)
5 COG5247 BUR6 Class 2 transcrip 99.7 2.5E-17 5.4E-22 129.1 3.9 84 101-184 16-100 (113)
6 KOG1658 DNA polymerase epsilon 99.4 1.5E-13 3.3E-18 114.3 3.1 82 104-185 55-137 (162)
7 KOG0869 CCAAT-binding factor, 98.9 1.4E-09 3.1E-14 91.0 5.6 92 100-194 24-117 (168)
8 cd00074 H2A Histone 2A; H2A is 98.8 7.7E-09 1.7E-13 82.2 6.4 79 103-181 15-94 (115)
9 COG5262 HTA1 Histone H2A [Chro 98.7 1.1E-08 2.3E-13 82.6 4.1 80 102-181 20-100 (132)
10 KOG0870 DNA polymerase epsilon 98.6 5.1E-08 1.1E-12 82.3 5.8 91 104-197 6-99 (172)
11 smart00414 H2A Histone 2A. 98.4 3.1E-07 6.8E-12 72.1 5.2 76 105-180 6-82 (106)
12 COG2036 HHT1 Histones H3 and H 98.4 3.6E-07 7.9E-12 70.3 4.5 69 102-171 13-82 (91)
13 PLN00154 histone H2A; Provisio 98.4 5.7E-07 1.2E-11 73.8 4.9 77 105-181 35-113 (136)
14 PTZ00017 histone H2A; Provisio 98.3 5.3E-07 1.2E-11 73.7 4.4 77 104-180 23-100 (134)
15 PF00125 Histone: Core histone 98.3 1.4E-06 3.1E-11 62.1 4.6 67 105-171 5-73 (75)
16 KOG1756 Histone 2A [Chromatin 98.2 1.4E-06 3.1E-11 70.9 4.2 79 103-181 22-101 (131)
17 PLN00153 histone H2A; Provisio 98.1 3.4E-06 7.4E-11 68.7 4.5 77 104-180 20-97 (129)
18 PLN00157 histone H2A; Provisio 98.1 3.8E-06 8.3E-11 68.6 4.5 78 104-181 22-101 (132)
19 PLN00156 histone H2AX; Provisi 98.1 4.1E-06 8.9E-11 69.0 4.6 76 105-180 26-102 (139)
20 cd00076 H4 Histone H4, one of 98.0 1.4E-05 3.1E-10 60.7 6.5 63 108-171 13-76 (85)
21 smart00803 TAF TATA box bindin 98.0 2.2E-05 4.7E-10 56.6 6.4 62 108-170 2-64 (65)
22 PLN00035 histone H4; Provision 98.0 2.4E-05 5.2E-10 61.6 6.5 70 108-178 29-101 (103)
23 PTZ00252 histone H2A; Provisio 98.0 1.4E-05 3E-10 65.5 5.3 78 104-181 21-102 (134)
24 smart00417 H4 Histone H4. 97.7 0.00012 2.6E-09 54.5 6.4 60 108-168 13-72 (74)
25 PTZ00015 histone H4; Provision 97.7 0.00012 2.6E-09 57.5 6.5 65 106-171 28-93 (102)
26 cd07981 TAF12 TATA Binding Pro 97.6 0.00022 4.7E-09 52.0 6.4 66 110-176 3-70 (72)
27 KOG1658 DNA polymerase epsilon 97.6 5E-05 1.1E-09 63.8 3.1 75 104-183 7-82 (162)
28 KOG0871 Class 2 transcription 97.5 0.0002 4.4E-09 59.8 6.3 76 106-185 10-87 (156)
29 smart00428 H3 Histone H3. 97.3 0.00081 1.8E-08 53.0 6.7 71 100-170 24-98 (105)
30 cd08048 TAF11 TATA Binding Pro 96.9 0.0025 5.5E-08 48.3 5.8 66 105-171 13-82 (85)
31 PLN00121 histone H3; Provision 96.7 0.0045 9.7E-08 51.0 6.2 70 100-170 57-129 (136)
32 COG5150 Class 2 transcription 96.6 0.0025 5.3E-08 52.6 4.2 70 106-178 9-80 (148)
33 PTZ00018 histone H3; Provision 96.6 0.006 1.3E-07 50.3 6.0 70 100-170 57-129 (136)
34 PLN00161 histone H3; Provision 96.3 0.012 2.7E-07 48.5 6.5 71 100-170 50-123 (135)
35 PLN00160 histone H3; Provision 96.2 0.013 2.7E-07 45.9 5.7 70 101-170 17-89 (97)
36 PF15511 CENP-T: Centromere ki 96.0 0.0084 1.8E-07 56.5 4.7 63 104-166 347-414 (414)
37 cd07979 TAF9 TATA Binding Prot 95.8 0.021 4.6E-07 45.3 5.4 68 112-180 5-73 (117)
38 PF02269 TFIID-18kDa: Transcri 95.6 0.017 3.7E-07 44.1 4.0 70 114-183 7-78 (93)
39 KOG1757 Histone 2A [Chromatin 95.5 0.017 3.6E-07 46.9 3.7 76 105-180 27-104 (131)
40 PF02969 TAF: TATA box binding 95.2 0.076 1.6E-06 38.7 6.1 62 108-170 3-65 (66)
41 PF09415 CENP-X: CENP-S associ 95.2 0.034 7.3E-07 41.0 4.2 62 110-171 1-66 (72)
42 smart00576 BTP Bromodomain tra 95.0 0.066 1.4E-06 39.1 5.3 57 114-171 12-69 (77)
43 PF04719 TAFII28: hTAFII28-lik 94.8 0.053 1.2E-06 41.7 4.6 67 104-170 19-87 (90)
44 cd08050 TAF6 TATA Binding Prot 94.4 0.087 1.9E-06 48.3 5.9 60 111-171 2-62 (343)
45 cd07978 TAF13 The TATA Binding 94.3 0.14 3E-06 39.3 5.7 62 112-174 6-68 (92)
46 PF03847 TFIID_20kDa: Transcri 93.8 0.18 3.9E-06 36.8 5.4 61 113-173 4-65 (68)
47 PF15630 CENP-S: Kinetochore c 93.6 0.18 4E-06 37.5 5.2 63 114-176 11-76 (76)
48 PF05236 TAF4: Transcription i 91.9 0.26 5.6E-06 43.4 4.7 44 112-156 51-94 (264)
49 KOG1745 Histones H3 and H4 [Ch 91.7 0.3 6.4E-06 40.5 4.4 71 101-171 59-131 (137)
50 KOG3219 Transcription initiati 90.6 0.15 3.3E-06 44.4 1.9 67 104-171 108-176 (195)
51 PF15510 CENP-W: Centromere ki 89.4 0.46 9.9E-06 37.4 3.5 62 107-168 15-90 (102)
52 KOG1142 Transcription initiati 89.1 1.3 2.9E-05 40.1 6.7 77 105-181 151-228 (258)
53 smart00427 H2B Histone H2B. 88.4 1.4 3.1E-05 34.0 5.5 57 114-171 7-65 (89)
54 PLN00155 histone H2A; Provisio 86.8 0.66 1.4E-05 33.4 2.7 37 105-141 21-57 (58)
55 PLN00158 histone H2B; Provisio 85.1 2.6 5.5E-05 34.2 5.5 59 112-171 31-91 (116)
56 PF07524 Bromo_TP: Bromodomain 83.9 3.8 8.1E-05 29.5 5.6 50 122-171 19-69 (77)
57 PF03540 TFIID_30kDa: Transcri 83.7 1.9 4E-05 30.3 3.7 47 109-156 3-49 (51)
58 PTZ00463 histone H2B; Provisio 83.6 3.4 7.3E-05 33.6 5.6 57 114-171 34-92 (117)
59 KOG1744 Histone H2B [Chromatin 80.7 3.9 8.5E-05 33.6 5.1 63 105-171 37-101 (127)
60 KOG3423 Transcription initiati 76.3 4.1 9E-05 35.1 4.2 67 104-171 82-163 (176)
61 cd08045 TAF4 TATA Binding Prot 75.6 8.8 0.00019 32.9 6.1 44 112-156 52-95 (212)
62 PF10979 DUF2786: Protein of u 71.0 9.4 0.0002 25.5 4.1 35 111-145 4-38 (43)
63 PF02291 TFIID-31kDa: Transcri 65.4 17 0.00036 29.7 5.3 66 112-178 16-82 (129)
64 KOG2549 Transcription initiati 64.6 9.8 0.00021 38.1 4.5 67 111-178 14-84 (576)
65 KOG3467 Histone H4 [Chromatin 63.2 16 0.00036 28.7 4.6 59 113-172 34-93 (103)
66 PF12767 SAGA-Tad1: Transcript 48.7 43 0.00092 29.3 5.4 32 123-154 220-251 (252)
67 COG5095 TAF6 Transcription ini 41.9 38 0.00081 32.5 4.2 49 123-171 19-68 (450)
68 TIGR03015 pepcterm_ATPase puta 30.3 48 0.001 27.9 2.7 47 126-172 215-265 (269)
69 KOG2389 Predicted bromodomain 28.3 1.1E+02 0.0025 29.1 5.0 70 101-171 22-92 (353)
70 COG5248 TAF19 Transcription in 22.8 2.2E+02 0.0048 23.3 5.1 63 110-174 11-74 (126)
71 COG5162 Transcription initiati 22.3 1.2E+02 0.0025 26.5 3.6 27 129-155 108-134 (197)
72 KOG3901 Transcription initiati 21.5 2.5E+02 0.0054 22.7 5.1 58 114-174 15-73 (109)
No 1
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=99.86 E-value=9.2e-23 Score=178.17 Aligned_cols=94 Identities=30% Similarity=0.456 Sum_probs=89.8
Q ss_pred CccccccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccc
Q 028748 99 DDDEVSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYD 177 (204)
Q Consensus 99 ~~~~~~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fd 177 (204)
.+..++....|||+|||+|||.|+|+.+|+.||++++++|||+||..|+..||.++..++|++|++.||+ +|.+.+.|+
T Consensus 65 e~~~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fd 144 (236)
T KOG1657|consen 65 EGQLDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFD 144 (236)
T ss_pred ccccchhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCcc
Confidence 4567889999999999999999999999999999999999999999999999999999999999999999 999999999
Q ss_pred cccccCCCcccHHHH
Q 028748 178 FLSDYVPEKIKAEDA 192 (204)
Q Consensus 178 FL~DiVP~kI~l~d~ 192 (204)
||.||||+++.++.+
T Consensus 145 FL~DivP~~~~~~~~ 159 (236)
T KOG1657|consen 145 FLRDIVPRKILAEKY 159 (236)
T ss_pred ceeccccchhccccc
Confidence 999999999877654
No 2
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.83 E-value=1.8e-21 Score=169.81 Aligned_cols=85 Identities=31% Similarity=0.497 Sum_probs=81.9
Q ss_pred ccccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccc
Q 028748 102 EVSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLS 180 (204)
Q Consensus 102 ~~~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~ 180 (204)
-......||++|||++||.|.||.+||.||++|++++||.||..|+-+||-+|..++||||+..||+ +|...+.|+||.
T Consensus 103 ~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLi 182 (286)
T COG5208 103 ILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLI 182 (286)
T ss_pred HHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHh
Confidence 3567788999999999999999999999999999999999999999999999999999999999999 999999999999
Q ss_pred ccCCCc
Q 028748 181 DYVPEK 186 (204)
Q Consensus 181 DiVP~k 186 (204)
||||+.
T Consensus 183 divpr~ 188 (286)
T COG5208 183 DIVPRN 188 (286)
T ss_pred hhccCC
Confidence 999986
No 3
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.80 E-value=7.3e-20 Score=129.14 Aligned_cols=63 Identities=30% Similarity=0.629 Sum_probs=58.6
Q ss_pred CCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hh
Q 028748 108 NFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VV 170 (204)
Q Consensus 108 ~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV 170 (204)
.||++||+||||.+|++..||+||+++|++|+|+||++|+..|+..|..++|+||+|+||. ||
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 6999999999999999999999999999999999999999999999999999999999998 75
No 4
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=99.73 E-value=1.1e-18 Score=150.91 Aligned_cols=86 Identities=23% Similarity=0.382 Sum_probs=81.2
Q ss_pred CccccccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccc
Q 028748 99 DDDEVSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYD 177 (204)
Q Consensus 99 ~~~~~~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fd 177 (204)
+...+....+||.+|||+||++|.||+.|++.++++|++|.|||++.|+..++++++..+.+||+..||. ||...+.|+
T Consensus 4 ~~~~~~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~Fd 83 (224)
T KOG1659|consen 4 PSSFKKYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFD 83 (224)
T ss_pred cchhhhhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhH
Confidence 3456677899999999999999999999999999999999999999999999999999999999999999 999999999
Q ss_pred cccccCC
Q 028748 178 FLSDYVP 184 (204)
Q Consensus 178 FL~DiVP 184 (204)
||.++|-
T Consensus 84 FLk~~v~ 90 (224)
T KOG1659|consen 84 FLKEVVE 90 (224)
T ss_pred HHHHHHH
Confidence 9999763
No 5
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=99.68 E-value=2.5e-17 Score=129.11 Aligned_cols=84 Identities=20% Similarity=0.346 Sum_probs=79.7
Q ss_pred cccccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccccc
Q 028748 101 DEVSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFL 179 (204)
Q Consensus 101 ~~~~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL 179 (204)
.+.-..++||++|||+||++|.||+.|++.+++++++|.|+||..|+..+...|+....+.|+..+|. ++.+++.|+||
T Consensus 16 ~~~~~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL 95 (113)
T COG5247 16 SQKKKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFL 95 (113)
T ss_pred hhhhhhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHH
Confidence 34477899999999999999999999999999999999999999999999999999999999999999 99999999999
Q ss_pred cccCC
Q 028748 180 SDYVP 184 (204)
Q Consensus 180 ~DiVP 184 (204)
.+++-
T Consensus 96 ~~~~~ 100 (113)
T COG5247 96 KNMEQ 100 (113)
T ss_pred HHHHH
Confidence 98863
No 6
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=99.39 E-value=1.5e-13 Score=114.27 Aligned_cols=82 Identities=20% Similarity=0.385 Sum_probs=78.7
Q ss_pred ccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccccc
Q 028748 104 SKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLSDY 182 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~Di 182 (204)
...++|||+||+.||++|||+.+...++.++|++|+|+||+.|...+|.+++..+|+|++..|+. +|...+.|.||.+.
T Consensus 55 a~l~rLpL~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~fle~~ 134 (162)
T KOG1658|consen 55 ASLSRLPLARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAFLEGA 134 (162)
T ss_pred hhhhhccHHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHHHhhh
Confidence 55689999999999999999999999999999999999999999999999999999999999999 99999999999988
Q ss_pred CCC
Q 028748 183 VPE 185 (204)
Q Consensus 183 VP~ 185 (204)
.+.
T Consensus 135 ~d~ 137 (162)
T KOG1658|consen 135 LDT 137 (162)
T ss_pred ccc
Confidence 763
No 7
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=98.93 E-value=1.4e-09 Score=91.02 Aligned_cols=92 Identities=20% Similarity=0.267 Sum_probs=83.9
Q ss_pred ccccccCCCCChHHHHHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccc
Q 028748 100 DDEVSKVCNFPMGRIKRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYD 177 (204)
Q Consensus 100 ~~~~~~~~~LPlaRIKrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fd 177 (204)
.........|||+-|-||||. -|....||+||--.|..|+-.||..++.+|.+.|++.+||||+-+||. ++. .|.
T Consensus 24 ~~~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~---tLG 100 (168)
T KOG0869|consen 24 LSLREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMS---TLG 100 (168)
T ss_pred cccchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHH---HcC
Confidence 456677889999999999996 588999999999999999999999999999999999999999999999 998 888
Q ss_pred cccccCCCcccHHHHHH
Q 028748 178 FLSDYVPEKIKAEDALA 194 (204)
Q Consensus 178 FL~DiVP~kI~l~d~l~ 194 (204)
|-..+-|.+|.|..|.+
T Consensus 101 Fe~Y~eplkiyL~kYRe 117 (168)
T KOG0869|consen 101 FENYAEPLKIYLQKYRE 117 (168)
T ss_pred cHhHHHHHHHHHHHHHH
Confidence 98888888888777765
No 8
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=98.83 E-value=7.7e-09 Score=82.25 Aligned_cols=79 Identities=20% Similarity=0.276 Sum_probs=72.4
Q ss_pred cccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccccccc
Q 028748 103 VSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLSD 181 (204)
Q Consensus 103 ~~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~D 181 (204)
....+.||++||.|+|+..--...|+..|++.++-+.|.|...+...|...|...++++|+..||. +|.+++.|++|-.
T Consensus 15 ~ragL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~EL~~L~~ 94 (115)
T cd00074 15 ARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRNDEELNKLLK 94 (115)
T ss_pred cccCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHHHHHHHc
Confidence 445789999999999998666689999999999999999999999999999999999999999999 9999999996653
No 9
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=98.72 E-value=1.1e-08 Score=82.59 Aligned_cols=80 Identities=20% Similarity=0.307 Sum_probs=75.0
Q ss_pred ccccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccc
Q 028748 102 EVSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLS 180 (204)
Q Consensus 102 ~~~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~ 180 (204)
.....+.||++||+||||-+---+.|++.|++.++-+.|..+..++.-|-..|...+.+.|.+.||. +|.++++|+||.
T Consensus 20 sa~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~EL~~l~ 99 (132)
T COG5262 20 SAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLL 99 (132)
T ss_pred hhhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcCcHHHHHHh
Confidence 3446789999999999998888889999999999999999999999999999999999999999999 999999999997
Q ss_pred c
Q 028748 181 D 181 (204)
Q Consensus 181 D 181 (204)
.
T Consensus 100 ~ 100 (132)
T COG5262 100 G 100 (132)
T ss_pred h
Confidence 6
No 10
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.64 E-value=5.1e-08 Score=82.28 Aligned_cols=91 Identities=19% Similarity=0.254 Sum_probs=75.5
Q ss_pred ccCCCCChHHHHHHHhcC-CCc-ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccc
Q 028748 104 SKVCNFPMGRIKRIFKTQ-SSD-IGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLS 180 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~D-pDV-~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~ 180 (204)
...+.||.+-|.||+|.- |+. ..|++||..+|++|+-.||-+|+..|...|..++|+||+.+||. +....+.-.|+.
T Consensus 6 i~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~ 85 (172)
T KOG0870|consen 6 IEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVN 85 (172)
T ss_pred HHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhh
Confidence 346789999999999964 555 68999999999999999999999999999999999999999999 998655555554
Q ss_pred ccCCCcccHHHHHHHHH
Q 028748 181 DYVPEKIKAEDALAQRE 197 (204)
Q Consensus 181 DiVP~kI~l~d~l~~rk 197 (204)
|.+-.|..|....+
T Consensus 86 ---plk~~Le~yk~~~k 99 (172)
T KOG0870|consen 86 ---PLKSALEAYKKAVK 99 (172)
T ss_pred ---HHHHHHHHHHHHHH
Confidence 66666666655443
No 11
>smart00414 H2A Histone 2A.
Probab=98.44 E-value=3.1e-07 Score=72.11 Aligned_cols=76 Identities=17% Similarity=0.305 Sum_probs=69.8
Q ss_pred cCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccc
Q 028748 105 KVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLS 180 (204)
Q Consensus 105 ~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~ 180 (204)
..+.||++||.|+||..--...|+..|++.++-+.|.++.++..-|...+...+++.|+..||. +|.+++.|..|-
T Consensus 6 agL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~nD~EL~~L~ 82 (106)
T smart00414 6 AGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELNKLL 82 (106)
T ss_pred CCccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccCCHHHHHHH
Confidence 3578999999999998766779999999999999999999999999999999999999999999 999999999443
No 12
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.39 E-value=3.6e-07 Score=70.28 Aligned_cols=69 Identities=19% Similarity=0.393 Sum_probs=63.1
Q ss_pred ccccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 102 EVSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 102 ~~~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
.......||.+-|.||||.-..- .||.+|...+..|.|.|+..|+..|..+|...+|+||+..||. ++.
T Consensus 13 ~~~~~~~Lp~apv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~ 82 (91)
T COG2036 13 QRSTDLLLPKAPVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALK 82 (91)
T ss_pred hhhhhhhcCchHHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHH
Confidence 45667889999999999975443 9999999999999999999999999999999999999999999 876
No 13
>PLN00154 histone H2A; Provisional
Probab=98.35 E-value=5.7e-07 Score=73.78 Aligned_cols=77 Identities=19% Similarity=0.253 Sum_probs=70.7
Q ss_pred cCCCCChHHHHHHHhcCC-CcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccccccc
Q 028748 105 KVCNFPMGRIKRIFKTQS-SDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLSD 181 (204)
Q Consensus 105 ~~~~LPlaRIKrIMK~Dp-DV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~D 181 (204)
..+.||++||.|+||..- -...|+..|++.++-..|.+...+.+-|...|...+++.|++.||. +|.+++.|++|..
T Consensus 35 AgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrnDeEL~~Ll~ 113 (136)
T PLN00154 35 AGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 113 (136)
T ss_pred cCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccCcHHHHHHhc
Confidence 478999999999999875 3469999999999999999999999999999999999999999999 9999999996654
No 14
>PTZ00017 histone H2A; Provisional
Probab=98.34 E-value=5.3e-07 Score=73.74 Aligned_cols=77 Identities=17% Similarity=0.275 Sum_probs=70.9
Q ss_pred ccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccc
Q 028748 104 SKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLS 180 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~ 180 (204)
...+.||++||.|+|+..--...|+..|++.++-+.|.++..+.+-|...+...+++.|++.||. +|.+++.|..|.
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 34789999999999997655669999999999999999999999999999999999999999999 999999999665
No 15
>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=98.25 E-value=1.4e-06 Score=62.14 Aligned_cols=67 Identities=18% Similarity=0.313 Sum_probs=60.4
Q ss_pred cCCCCChHHHHHHHhcCCCc-ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 105 KVCNFPMGRIKRIFKTQSSD-IGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 105 ~~~~LPlaRIKrIMK~DpDV-~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
..+.+|+.||.+.+..+-.. ..|+.+|+.++..++|.|+..+...|+.+|...+|+||+..||. ++.
T Consensus 5 ~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 5 LIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 45678899998888887555 49999999999999999999999999999999999999999999 764
No 16
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=98.21 E-value=1.4e-06 Score=70.90 Aligned_cols=79 Identities=16% Similarity=0.275 Sum_probs=72.2
Q ss_pred cccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccccccc
Q 028748 103 VSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLSD 181 (204)
Q Consensus 103 ~~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~D 181 (204)
....+.||++||.|+|+.---...|+..|+++++-..|.....++.-|-..|..+++..|.+.||- +|.+++++.||.+
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 445689999999999999666778999999999999999999999998888999999999999999 9999999999976
No 17
>PLN00153 histone H2A; Provisional
Probab=98.11 E-value=3.4e-06 Score=68.69 Aligned_cols=77 Identities=18% Similarity=0.255 Sum_probs=69.8
Q ss_pred ccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccc
Q 028748 104 SKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLS 180 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~ 180 (204)
..-+.||++||.|.|+.---...|+..|++.++-..|.++..+.+-|...+...+++.|.+.||. +|.+++.|..|.
T Consensus 20 ragL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 97 (129)
T PLN00153 20 KAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLL 97 (129)
T ss_pred ccCcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccCcHHHHHHH
Confidence 34789999999999987655568999999999999999999999999999999999999999999 999999999443
No 18
>PLN00157 histone H2A; Provisional
Probab=98.09 E-value=3.8e-06 Score=68.63 Aligned_cols=78 Identities=18% Similarity=0.293 Sum_probs=70.2
Q ss_pred ccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccc-cccc
Q 028748 104 SKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYD-FLSD 181 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fd-FL~D 181 (204)
...+.||++||.|.|+.----..|+..|++.++-..|.++..+.+-|...+...+++.|...||. +|.+++.|. +|.+
T Consensus 22 ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll~~ 101 (132)
T PLN00157 22 KAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLLGG 101 (132)
T ss_pred ccCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccCcHHHHHHHcC
Confidence 34789999999999987655568999999999999999999999999999999999999999999 999999998 4444
No 19
>PLN00156 histone H2AX; Provisional
Probab=98.09 E-value=4.1e-06 Score=68.99 Aligned_cols=76 Identities=18% Similarity=0.272 Sum_probs=69.0
Q ss_pred cCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccc
Q 028748 105 KVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLS 180 (204)
Q Consensus 105 ~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~ 180 (204)
.-+.||++||.|.|+.----..|+..|++.++-..|..+..+.+-|...+...+++.|.+.||. +|.+++.|..|.
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 3678999999999987655568999999999999999999999999999999999999999999 999999999444
No 20
>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=98.05 E-value=1.4e-05 Score=60.71 Aligned_cols=63 Identities=16% Similarity=0.235 Sum_probs=59.8
Q ss_pred CCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 108 NFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 108 ~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
.||.+-|+||.+... +..||.++.-.+..+.+.|++.++.+|..+|...+|+||+..||. ++.
T Consensus 13 gi~k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alk 76 (85)
T cd00076 13 GITKPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALK 76 (85)
T ss_pred cCCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHH
Confidence 499999999999876 889999999999999999999999999999999999999999999 775
No 21
>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=98.00 E-value=2.2e-05 Score=56.60 Aligned_cols=62 Identities=13% Similarity=0.238 Sum_probs=57.8
Q ss_pred CCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hh
Q 028748 108 NFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VV 170 (204)
Q Consensus 108 ~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV 170 (204)
.||.+-|++|.+.-+ +..||.++...++..+|.|+..+++.|..++...+|+||+.+||. ++
T Consensus 2 ~~p~~~i~ria~~~G-i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Al 64 (65)
T smart00803 2 WLPKETIKDVAESLG-IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSAL 64 (65)
T ss_pred CCCHHHHHHHHHHCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHh
Confidence 589999999999764 568999999999999999999999999999999999999999997 64
No 22
>PLN00035 histone H4; Provisional
Probab=97.96 E-value=2.4e-05 Score=61.57 Aligned_cols=70 Identities=19% Similarity=0.259 Sum_probs=62.6
Q ss_pred CCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcc--cccccc
Q 028748 108 NFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSE--QSKYDF 178 (204)
Q Consensus 108 ~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~--~e~fdF 178 (204)
.||.+-|+||.+.-. +..||.++...+..+.|.|++.++.+|..+|...+|+||+..||. ++.. .+-|-|
T Consensus 29 ~ipk~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~lyGf 101 (103)
T PLN00035 29 GITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 101 (103)
T ss_pred cCCHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCCCC
Confidence 499999999999765 889999999999999999999999999999999999999999999 7753 344444
No 23
>PTZ00252 histone H2A; Provisional
Probab=97.96 E-value=1.4e-05 Score=65.54 Aligned_cols=78 Identities=14% Similarity=0.264 Sum_probs=68.3
Q ss_pred ccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCcccccccc-hhccccccc-cc
Q 028748 104 SKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAK--DRKKSLAYKHLA-VVSEQSKYD-FL 179 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~--~kRKTLqy~DLa-aV~~~e~fd-FL 179 (204)
..-+.||++||.|.|+.----..|+..|++.++-..|.....+.+-|...|.. .+++.|...||. +|.+++.|. +|
T Consensus 21 rAGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDeEL~~Ll 100 (134)
T PTZ00252 21 KAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDDDLGSLL 100 (134)
T ss_pred ccCccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccChHHHHHHH
Confidence 34689999999999997655568999999999999999999999999988865 678999999999 999999998 66
Q ss_pred cc
Q 028748 180 SD 181 (204)
Q Consensus 180 ~D 181 (204)
.+
T Consensus 101 ~~ 102 (134)
T PTZ00252 101 KN 102 (134)
T ss_pred cC
Confidence 55
No 24
>smart00417 H4 Histone H4.
Probab=97.71 E-value=0.00012 Score=54.48 Aligned_cols=60 Identities=18% Similarity=0.227 Sum_probs=56.5
Q ss_pred CCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc
Q 028748 108 NFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA 168 (204)
Q Consensus 108 ~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa 168 (204)
.||.+-|+||.+-. .+..||.++.--+..+.|.|+..++.+|..+|...+|+||+..||.
T Consensus 13 gI~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~ 72 (74)
T smart00417 13 GITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVV 72 (74)
T ss_pred CCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhe
Confidence 58999999999965 6789999999999999999999999999999999999999999985
No 25
>PTZ00015 histone H4; Provisional
Probab=97.70 E-value=0.00012 Score=57.49 Aligned_cols=65 Identities=18% Similarity=0.279 Sum_probs=60.2
Q ss_pred CCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 106 VCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 106 ~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
...+|.+-|+||.+.. .+..||.++.-.+..+.|.|+..++.+|..+|...+|+||+..||. ++.
T Consensus 28 i~gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlK 93 (102)
T PTZ00015 28 IRGITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALK 93 (102)
T ss_pred ccCCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHH
Confidence 3469999999999966 6789999999999999999999999999999999999999999999 775
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=97.61 E-value=0.00022 Score=51.96 Aligned_cols=66 Identities=14% Similarity=0.256 Sum_probs=56.2
Q ss_pred ChHHHHHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccc
Q 028748 110 PMGRIKRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKY 176 (204)
Q Consensus 110 PlaRIKrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~f 176 (204)
+-..+..+|+. ||. ..++.+|..++...+|.|+..++..|..+|...+|+||...||. ++.....+
T Consensus 3 ~k~~l~~lv~~id~~-~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~~~ 70 (72)
T cd07981 3 TKRKLQELLKEIDPR-EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNWNI 70 (72)
T ss_pred cHHHHHHHHHhhCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhcCC
Confidence 44456666664 665 68999999999999999999999999999999999999999999 88765443
No 27
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=97.58 E-value=5e-05 Score=63.83 Aligned_cols=75 Identities=19% Similarity=0.260 Sum_probs=57.6
Q ss_pred ccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccccc
Q 028748 104 SKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLSDY 182 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~Di 182 (204)
.....||++.+++|-|.||.++..+.+|...+++|+|+|++.|+.-+. .+--.|...-|. ||...|.|.||.|-
T Consensus 7 e~~p~~p~ekvkkiak~dPey~~te~~a~~etafatE~fvq~lv~~p~-----a~l~rLpL~rik~vvkl~pdl~l~~de 81 (162)
T KOG1658|consen 7 ECSPKLPMEKVKKIAKNDPEYMDTEDDAFVETAFATEQFVQVLVHLPQ-----ASLSRLPLARIKQVVKLDPDLTLLNDE 81 (162)
T ss_pred hhCccccHHHHHHhhcCCchhhhcccchHHHHHHHHHHHHhhhhhhhh-----hhhhhccHHHHHhhccCCcchhhhhhH
Confidence 356789999999999999999999999999999999999999998222 222345555566 66666666666654
Q ss_pred C
Q 028748 183 V 183 (204)
Q Consensus 183 V 183 (204)
+
T Consensus 82 a 82 (162)
T KOG1658|consen 82 A 82 (162)
T ss_pred H
Confidence 3
No 28
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=97.55 E-value=0.0002 Score=59.84 Aligned_cols=76 Identities=24% Similarity=0.460 Sum_probs=66.6
Q ss_pred CCCCChHHHHHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccccccccC
Q 028748 106 VCNFPMGRIKRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLSDYV 183 (204)
Q Consensus 106 ~~~LPlaRIKrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~DiV 183 (204)
...||-+-|-+|++. -|-...|+.||--+|--||=.||..|+.+|..+|....+|||.|.||- +.. .|.|= ++|
T Consensus 10 e~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe---~LgF~-eYi 85 (156)
T KOG0871|consen 10 ELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALE---NLGFG-EYI 85 (156)
T ss_pred cccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHH---HcchH-HHH
Confidence 468999999999995 454558999999999999999999999999999999999999999999 998 66664 555
Q ss_pred CC
Q 028748 184 PE 185 (204)
Q Consensus 184 P~ 185 (204)
+.
T Consensus 86 ee 87 (156)
T KOG0871|consen 86 EE 87 (156)
T ss_pred HH
Confidence 43
No 29
>smart00428 H3 Histone H3.
Probab=97.31 E-value=0.00081 Score=53.05 Aligned_cols=71 Identities=14% Similarity=0.274 Sum_probs=59.5
Q ss_pred ccccccCCCCChHH-HHHHHhcCCC--cccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hh
Q 028748 100 DDEVSKVCNFPMGR-IKRIFKTQSS--DIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VV 170 (204)
Q Consensus 100 ~~~~~~~~~LPlaR-IKrIMK~DpD--V~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV 170 (204)
.+.+..-..+|.+| |+.|+..-.. --.++.+|+.++..|+|.|+-.|...|+.+|...+|.||...||. +.
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ 98 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLAR 98 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHH
Confidence 34566778899887 4666665322 348999999999999999999999999999999999999999998 54
No 30
>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=96.92 E-value=0.0025 Score=48.32 Aligned_cols=66 Identities=20% Similarity=0.328 Sum_probs=57.5
Q ss_pred cCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCcccccccc-hhc
Q 028748 105 KVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDR---KKSLAYKHLA-VVS 171 (204)
Q Consensus 105 ~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~k---RKTLqy~DLa-aV~ 171 (204)
+...||-+.|||||...-+ ..++.+.+.+|+..+.+||..|+..|..+..... +.-|++.||- |..
T Consensus 13 Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~r 82 (85)
T cd08048 13 RRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYR 82 (85)
T ss_pred HHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHH
Confidence 4566999999999998766 7899999999999999999999999999877644 4889999998 754
No 31
>PLN00121 histone H3; Provisional
Probab=96.71 E-value=0.0045 Score=50.99 Aligned_cols=70 Identities=16% Similarity=0.359 Sum_probs=59.6
Q ss_pred ccccccCCCCChHHH-HHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hh
Q 028748 100 DDEVSKVCNFPMGRI-KRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VV 170 (204)
Q Consensus 100 ~~~~~~~~~LPlaRI-KrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV 170 (204)
.+.+..-..+|..|+ +.|+.. .++ -.+..+|+.++..|+|.|+-.|-..++.+|...+|-||...||. +.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~-~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTD-LRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCcc-ceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 455777888998885 556654 344 48999999999999999999999999999999999999999998 53
No 32
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.65 E-value=0.0025 Score=52.58 Aligned_cols=70 Identities=23% Similarity=0.474 Sum_probs=61.7
Q ss_pred CCCCChHHHHHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccc
Q 028748 106 VCNFPMGRIKRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDF 178 (204)
Q Consensus 106 ~~~LPlaRIKrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdF 178 (204)
...||-+-|.+++-. -|-...+++||--++--||=.||-.|+..|...|....++||.|.||. +.. .|.|
T Consensus 9 e~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALe---nLef 80 (148)
T COG5150 9 ENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALE---NLEF 80 (148)
T ss_pred cccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHH---hccH
Confidence 357999999998875 355558999999999999999999999999999999999999999999 998 4555
No 33
>PTZ00018 histone H3; Provisional
Probab=96.58 E-value=0.006 Score=50.27 Aligned_cols=70 Identities=16% Similarity=0.327 Sum_probs=59.4
Q ss_pred ccccccCCCCChHHH-HHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hh
Q 028748 100 DDEVSKVCNFPMGRI-KRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VV 170 (204)
Q Consensus 100 ~~~~~~~~~LPlaRI-KrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV 170 (204)
.+.+..-..+|..|+ +.|+.. .+++ .+..+|+.++..|+|.|+-.|-..++.+|...+|-||...||. +.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~-rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcc-eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 455677888998885 556553 3444 9999999999999999999999999999999999999999998 53
No 34
>PLN00161 histone H3; Provisional
Probab=96.34 E-value=0.012 Score=48.45 Aligned_cols=71 Identities=20% Similarity=0.359 Sum_probs=59.9
Q ss_pred ccccccCCCCChHHH-HHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hh
Q 028748 100 DDEVSKVCNFPMGRI-KRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VV 170 (204)
Q Consensus 100 ~~~~~~~~~LPlaRI-KrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV 170 (204)
.+.+..-..+|.+|+ +.|+.. .+..-.+..+|+.++..|+|.|+-.|-+.|+-+|...+|-||...||. +.
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ 123 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR 123 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH
Confidence 445677789998885 566654 233458999999999999999999999999999999999999999998 54
No 35
>PLN00160 histone H3; Provisional
Probab=96.21 E-value=0.013 Score=45.85 Aligned_cols=70 Identities=16% Similarity=0.302 Sum_probs=58.3
Q ss_pred cccccCCCCChHHH-HHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hh
Q 028748 101 DEVSKVCNFPMGRI-KRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VV 170 (204)
Q Consensus 101 ~~~~~~~~LPlaRI-KrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV 170 (204)
+.+..-..+|..|+ +.|+.. ..+.-.+..+|+.++..|+|.|+-.|-..|+.+|...+|-||...|+. +.
T Consensus 17 st~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 17 STDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred chhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 34556678898885 556553 244458999999999999999999999999999999999999999998 53
No 36
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=96.04 E-value=0.0084 Score=56.47 Aligned_cols=63 Identities=21% Similarity=0.317 Sum_probs=45.5
Q ss_pred ccCCCCChHHHHHHHhcC-----CCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccc
Q 028748 104 SKVCNFPMGRIKRIFKTQ-----SSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKH 166 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~D-----pDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~D 166 (204)
-....||-+-||++...- -.-+.|+++|+-+|.+|++.|.++|+..=-.||...+||||.-.|
T Consensus 347 i~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 347 IPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 345679999999986642 234689999999999999999999999999999999999997654
No 37
>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=95.82 E-value=0.021 Score=45.33 Aligned_cols=68 Identities=13% Similarity=0.172 Sum_probs=59.9
Q ss_pred HHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccc
Q 028748 112 GRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLS 180 (204)
Q Consensus 112 aRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~ 180 (204)
.-|.+|++.- .+..++..++..+..-++.++..++.+|..+|...+|+||+.+||. +|...-.|.|-.
T Consensus 5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~ 73 (117)
T cd07979 5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTS 73 (117)
T ss_pred HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCC
Confidence 4577888865 5678999999999999999999999999999999999999999999 998777777754
No 38
>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=95.62 E-value=0.017 Score=44.11 Aligned_cols=70 Identities=17% Similarity=0.301 Sum_probs=34.4
Q ss_pred HHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccc-ccccccccC
Q 028748 114 IKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQS-KYDFLSDYV 183 (204)
Q Consensus 114 IKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e-~fdFL~DiV 183 (204)
|+.||-.-.|+..-..|++.+|-...-.||..|+..|..+|...+++.|+.+||. ++.+++ .|.-|.+++
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~Kl~Rl~~~L 78 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKKLARLRELL 78 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHHHHHHHHHH
Confidence 6789999999999999999999999999999999999999999999999999999 777654 344444443
No 39
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=95.49 E-value=0.017 Score=46.90 Aligned_cols=76 Identities=22% Similarity=0.275 Sum_probs=54.1
Q ss_pred cCCCCChHHHHHHHhcC-CCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccccc
Q 028748 105 KVCNFPMGRIKRIFKTQ-SSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLS 180 (204)
Q Consensus 105 ~~~~LPlaRIKrIMK~D-pDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~ 180 (204)
.-+.||++||.|.+|.- -..+.|..-|.+..+-..|.......+-|-..+..-+-+.|++.||. +|..++.||-|.
T Consensus 27 aGlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRGDeELDtLI 104 (131)
T KOG1757|consen 27 AGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLI 104 (131)
T ss_pred cccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecCcHHHHHHH
Confidence 45789999999999975 34556777666666655544433333333333334467899999999 999999999885
No 40
>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=95.21 E-value=0.076 Score=38.70 Aligned_cols=62 Identities=13% Similarity=0.214 Sum_probs=47.5
Q ss_pred CCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hh
Q 028748 108 NFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VV 170 (204)
Q Consensus 108 ~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV 170 (204)
.||..-||-|-.+- .+..++.|+..+++.=+|..|..+.+.|..++...+|+.|+-+||. +.
T Consensus 3 ~~~~esvk~iAes~-Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~AL 65 (66)
T PF02969_consen 3 VFSQESVKDIAESL-GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSAL 65 (66)
T ss_dssp ---HHHHHHHHHHT-T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH
T ss_pred cCCHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHh
Confidence 46777777776654 3567999999999999999999999999999999999999999997 64
No 41
>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=95.18 E-value=0.034 Score=41.04 Aligned_cols=62 Identities=19% Similarity=0.303 Sum_probs=49.5
Q ss_pred ChHHHHHHHhc--CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-ccccccc-hhc
Q 028748 110 PMGRIKRIFKT--QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKS-LAYKHLA-VVS 171 (204)
Q Consensus 110 PlaRIKrIMK~--DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKT-Lqy~DLa-aV~ 171 (204)
|-.-|.||++. ..+-..|+.+|+-++++=.++||..-+.+|+..+...+... |..+||. +.-
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 55668889986 35677999999999999999999999999999998888888 9999998 543
No 42
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=94.99 E-value=0.066 Score=39.13 Aligned_cols=57 Identities=5% Similarity=0.119 Sum_probs=49.7
Q ss_pred HHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 114 IKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 114 IKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
|-+|++. -....++..|+-.++..++.|+..|++.+..+|...+|.+.+..||. +..
T Consensus 12 Vaqil~~-~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~ 69 (77)
T smart00576 12 VAQILES-AGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALE 69 (77)
T ss_pred HHHHHHH-cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 4455553 35668999999999999999999999999999999999999999999 765
No 43
>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=94.81 E-value=0.053 Score=41.75 Aligned_cols=67 Identities=16% Similarity=0.230 Sum_probs=47.5
Q ss_pred ccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCcccccccc-hh
Q 028748 104 SKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDR-KKSLAYKHLA-VV 170 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~k-RKTLqy~DLa-aV 170 (204)
.+...||-+-||+||..--....|+...+++|+-.+-+||.+|...|.++..... ..-|++.||. +.
T Consensus 19 fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~ 87 (90)
T PF04719_consen 19 FRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAY 87 (90)
T ss_dssp HHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHH
T ss_pred HHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHH
Confidence 4567899999999999865546899999999999999999999999999876543 3588888887 64
No 44
>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=94.44 E-value=0.087 Score=48.31 Aligned_cols=60 Identities=13% Similarity=0.189 Sum_probs=52.7
Q ss_pred hHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 111 MGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 111 laRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
..-|+-|.+.- .+..++.+|...++.-+|.++..+++.|...+...+|++|+-+||. |+.
T Consensus 2 ~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~ 62 (343)
T cd08050 2 QESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALR 62 (343)
T ss_pred hhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHH
Confidence 34566666654 5678999999999999999999999999999999999999999999 765
No 45
>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=94.26 E-value=0.14 Score=39.32 Aligned_cols=62 Identities=15% Similarity=0.255 Sum_probs=54.7
Q ss_pred HHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccc
Q 028748 112 GRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQS 174 (204)
Q Consensus 112 aRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e 174 (204)
.-|+.+|-.-.|+..-..|++-+|-..+--||..|+..|..+|+ .++..++.+||. ++.+++
T Consensus 6 ~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~ 68 (92)
T cd07978 6 KEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDP 68 (92)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCH
Confidence 45889999999999999999999999999999999999999998 444556999999 887664
No 46
>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=93.81 E-value=0.18 Score=36.76 Aligned_cols=61 Identities=11% Similarity=0.224 Sum_probs=46.0
Q ss_pred HHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccc
Q 028748 113 RIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQ 173 (204)
Q Consensus 113 RIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~ 173 (204)
++..+|+.=..-..+..++--++...++-||...+..|...|...+..||...||. +...+
T Consensus 4 ~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~ 65 (68)
T PF03847_consen 4 KLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERN 65 (68)
T ss_dssp HHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhh
Confidence 45566665333447899999999999999999999999999999999999999999 77643
No 47
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=93.63 E-value=0.18 Score=37.55 Aligned_cols=63 Identities=8% Similarity=0.213 Sum_probs=48.4
Q ss_pred HHHHHhcC--CCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccc
Q 028748 114 IKRIFKTQ--SSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKY 176 (204)
Q Consensus 114 IKrIMK~D--pDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~f 176 (204)
|-+|.... +.-..+|+..+.+++..+=.++..++.+-..+|+..+|.||+.+||. +...+|.|
T Consensus 11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~L 76 (76)
T PF15630_consen 11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPSL 76 (76)
T ss_dssp HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HHH
T ss_pred HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCCC
Confidence 45566643 33447999999999999999999999999999999999999999999 88777643
No 48
>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=91.88 E-value=0.26 Score=43.40 Aligned_cols=44 Identities=23% Similarity=0.262 Sum_probs=33.5
Q ss_pred HHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028748 112 GRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAK 156 (204)
Q Consensus 112 aRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~ 156 (204)
.+|.+|++... +..+..|.+-+|+.|||..|..|...++..+..
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 78889987776 778999999999999999999999999988865
No 49
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=91.66 E-value=0.3 Score=40.51 Aligned_cols=71 Identities=17% Similarity=0.325 Sum_probs=62.0
Q ss_pred cccccCCCCChHHHHH-HHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 101 DEVSKVCNFPMGRIKR-IFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 101 ~~~~~~~~LPlaRIKr-IMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
+.+..-..+|-.|+-+ |++.--....+.+.|+.++--|+|.|+-.|-..++-+|...+|-||-..||. +..
T Consensus 59 stdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr 131 (137)
T KOG1745|consen 59 STDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 131 (137)
T ss_pred hhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence 4455666899888777 8887666678999999999999999999999999999999999999999998 654
No 50
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=90.62 E-value=0.15 Score=44.39 Aligned_cols=67 Identities=15% Similarity=0.286 Sum_probs=56.5
Q ss_pred ccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcccccccc-hhc
Q 028748 104 SKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKD-RKKSLAYKHLA-VVS 171 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~-kRKTLqy~DLa-aV~ 171 (204)
.+...||-+.||++|..=-.-. |+..+.++|+=-+.+||-.|+..|..++... ...-|++.||- ++.
T Consensus 108 fRrs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~r 176 (195)
T KOG3219|consen 108 FRRSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYR 176 (195)
T ss_pred HHHhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence 3478999999999999754433 8889999999999999999999999987654 35789999999 775
No 51
>PF15510 CENP-W: Centromere kinetochore component W
Probab=89.42 E-value=0.46 Score=37.39 Aligned_cols=62 Identities=21% Similarity=0.360 Sum_probs=49.7
Q ss_pred CCCChHHHHHHHhcCCCcccchhHHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc
Q 028748 107 CNFPMGRIKRIFKTQSSDIGITGEAVFL--------------VNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA 168 (204)
Q Consensus 107 ~~LPlaRIKrIMK~DpDV~~IS~EA~~l--------------IaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa 168 (204)
..-|-+-+|++||--...-.+...+-.+ |---|=|||..|+++|-..|=.++-.+|..+||.
T Consensus 15 rkaPrgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~ 90 (102)
T PF15510_consen 15 RKAPRGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVL 90 (102)
T ss_pred HhCchHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHH
Confidence 4568999999999554444444444444 6667889999999999999999999999999997
No 52
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.11 E-value=1.3 Score=40.09 Aligned_cols=77 Identities=4% Similarity=0.113 Sum_probs=63.1
Q ss_pred cCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhccccccccccc
Q 028748 105 KVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDFLSD 181 (204)
Q Consensus 105 ~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdFL~D 181 (204)
....|--.+|..+|+.-.....+..|+--++..-|+-||..++..|...|...+..+|...||. .++.+-.+.|=.+
T Consensus 151 ~~~il~k~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf 228 (258)
T KOG1142|consen 151 NNPILSKRKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGF 228 (258)
T ss_pred CCccccccchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCc
Confidence 3334444566666665444568899999999999999999999999999999999999999999 9999888877543
No 53
>smart00427 H2B Histone H2B.
Probab=88.41 E-value=1.4 Score=34.04 Aligned_cols=57 Identities=19% Similarity=0.415 Sum_probs=47.2
Q ss_pred HHHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 114 IKRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 114 IKrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
|.|++|. .||. .||..|.-++.--.--+.+.++.+|...+..++|.||+-.+|. +|.
T Consensus 7 i~kvLKqVhpd~-giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvr 65 (89)
T smart00427 7 IYKVLKQVHPDT-GISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVR 65 (89)
T ss_pred HHHHHHHhCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 5666664 6887 6888888777766666778899999999999999999999999 876
No 54
>PLN00155 histone H2A; Provisional
Probab=86.85 E-value=0.66 Score=33.41 Aligned_cols=37 Identities=24% Similarity=0.298 Sum_probs=31.1
Q ss_pred cCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHH
Q 028748 105 KVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDK 141 (204)
Q Consensus 105 ~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtEL 141 (204)
.-+.||++||.+.++.----..|+..|++.++-..|.
T Consensus 21 AgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEY 57 (58)
T PLN00155 21 AGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEY 57 (58)
T ss_pred cccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHh
Confidence 4689999999999998766668999999988877663
No 55
>PLN00158 histone H2B; Provisional
Probab=85.08 E-value=2.6 Score=34.18 Aligned_cols=59 Identities=15% Similarity=0.268 Sum_probs=48.1
Q ss_pred HHHHHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 112 GRIKRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 112 aRIKrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
.-|.+++|. .||.+ ||..|.-+|.--..-+.+.|+.+|...+..++|.||+-.+|. +|.
T Consensus 31 ~YI~kVLKQVhPd~g-IS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvr 91 (116)
T PLN00158 31 IYIYKVLKQVHPDTG-ISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVR 91 (116)
T ss_pred HHHHHHHHHhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 347777775 78885 577787777766666778899999999999999999999999 886
No 56
>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=83.90 E-value=3.8 Score=29.52 Aligned_cols=50 Identities=6% Similarity=0.100 Sum_probs=45.4
Q ss_pred CCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 122 SSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 122 pDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
-.+..+++.|+-.++-.+..||+.|+..+..+|...+|....+.||. +..
T Consensus 19 ~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~ 69 (77)
T PF07524_consen 19 AGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALE 69 (77)
T ss_pred cCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 45668999999999999999999999999999999999999999998 664
No 57
>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=83.75 E-value=1.9 Score=30.27 Aligned_cols=47 Identities=19% Similarity=0.230 Sum_probs=33.1
Q ss_pred CChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028748 109 FPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAK 156 (204)
Q Consensus 109 LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~ 156 (204)
+|=+-+.-+|.... +..-..-..-||+-|++.||..++..|++++..
T Consensus 3 IPD~v~~~yL~~~G-~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 3 IPDEVTDYYLERSG-FQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCHHHHHHHHHHCC-CCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45455555565432 222344557899999999999999999999854
No 58
>PTZ00463 histone H2B; Provisional
Probab=83.57 E-value=3.4 Score=33.56 Aligned_cols=57 Identities=16% Similarity=0.327 Sum_probs=46.5
Q ss_pred HHHHHhc-CCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 114 IKRIFKT-QSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 114 IKrIMK~-DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
|.+++|. .||.+ ||..|.-+|.--..-..+.++.+|...+...+|.||+-.+|. +|.
T Consensus 34 I~KVLKqVhPd~g-IS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr 92 (117)
T PTZ00463 34 IFKVLKQVHPDTG-ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR 92 (117)
T ss_pred HHHHHHhhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh
Confidence 6676764 78885 577777777766666667899999999999999999999999 876
No 59
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=80.68 E-value=3.9 Score=33.59 Aligned_cols=63 Identities=8% Similarity=0.076 Sum_probs=45.1
Q ss_pred cCCCCChHHHHHHHh-cCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 105 KVCNFPMGRIKRIFK-TQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 105 ~~~~LPlaRIKrIMK-~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
.....++-| ++| .+||++.-+.+-.++.++.-.+ ++.++.+|...|...+|.||.-.+|. +|.
T Consensus 37 e~~s~yv~k---vlk~Vhpd~gis~~a~~vmnsf~ndi-fe~iA~ea~rla~y~krstisSreiqta~r 101 (127)
T KOG1744|consen 37 ESYSEYVYK---VLKQVHPDLGISSKAMGVMNSFVNDI-FERIASEAGRLAHYNKRSTISSREIQTAVR 101 (127)
T ss_pred Cceeeehhh---hhhcccCCCCcCHHHHHHHHHHHHHH-HHHHHHHHhhhhhhcCCCcccHHHHHHHHH
Confidence 344556655 444 4788764444444555555555 88899999999999999999999998 775
No 60
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=76.28 E-value=4.1 Score=35.08 Aligned_cols=67 Identities=18% Similarity=0.185 Sum_probs=50.3
Q ss_pred ccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--------------CCcccccccc-
Q 028748 104 SKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDR--------------KKSLAYKHLA- 168 (204)
Q Consensus 104 ~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~k--------------RKTLqy~DLa- 168 (204)
.....+|=+-+--+|+... +.....-..-||+.|+.-||..++..|+++++... +-||+..||.
T Consensus 82 dYtP~IPDavt~~yL~~aG-f~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~ 160 (176)
T KOG3423|consen 82 DYTPTIPDAVTDHYLKKAG-FQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSP 160 (176)
T ss_pred cCCCCCcHHHHHHHHHhcC-CCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHH
Confidence 4566777777777777643 33455566789999999999999999999986432 4578888888
Q ss_pred hhc
Q 028748 169 VVS 171 (204)
Q Consensus 169 aV~ 171 (204)
++.
T Consensus 161 AL~ 163 (176)
T KOG3423|consen 161 ALA 163 (176)
T ss_pred HHH
Confidence 765
No 61
>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=75.62 E-value=8.8 Score=32.86 Aligned_cols=44 Identities=18% Similarity=0.251 Sum_probs=35.9
Q ss_pred HHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 028748 112 GRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAK 156 (204)
Q Consensus 112 aRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~ 156 (204)
.+|.+||+... +..|+.+.+.+|+.|||.++..|...+...+..
T Consensus 52 ~~~~~i~~~~g-~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~h 95 (212)
T cd08045 52 KKIRKIAKKHG-LKEVDEDVLDLISLALEERLRNLLEKLIEVSEH 95 (212)
T ss_pred HHHHHHHHHcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 55566665543 338999999999999999999999999988865
No 62
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=70.96 E-value=9.4 Score=25.53 Aligned_cols=35 Identities=17% Similarity=0.156 Sum_probs=30.0
Q ss_pred hHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHH
Q 028748 111 MGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQ 145 (204)
Q Consensus 111 laRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~ 145 (204)
+.||++++.+-.+.+.-..||-.++.+|-+|..+|
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 57999999998877666679999999999998766
No 63
>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=65.45 E-value=17 Score=29.68 Aligned_cols=66 Identities=12% Similarity=0.130 Sum_probs=41.0
Q ss_pred HHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccccccc
Q 028748 112 GRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQSKYDF 178 (204)
Q Consensus 112 aRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e~fdF 178 (204)
--|..|++.- .|......++..+---+=.|+..+..+|..++...+|.+|..+||. +|+..-.+.|
T Consensus 16 ~~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f 82 (129)
T PF02291_consen 16 RVIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSF 82 (129)
T ss_dssp HHHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-----
T ss_pred HHHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhc
Confidence 3455666653 4555555555444444466788889999999999999999999999 9997666666
No 64
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=64.61 E-value=9.8 Score=38.10 Aligned_cols=67 Identities=13% Similarity=0.276 Sum_probs=54.4
Q ss_pred hHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc---ccccccc
Q 028748 111 MGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS---EQSKYDF 178 (204)
Q Consensus 111 laRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~---~~e~fdF 178 (204)
-.-||-+.++ -.+..++.|+..+++.=.|.=|..+++.|.+++...+|++++.+||. ++. ..+-|.|
T Consensus 14 ~Es~k~vAEs-lGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg~ 84 (576)
T KOG2549|consen 14 KESVKVVAES-LGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYGF 84 (576)
T ss_pred HHHHHHHHHH-hCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccCc
Confidence 4445555444 34678999999999999999999999999999999999999999999 665 3445555
No 65
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=63.18 E-value=16 Score=28.67 Aligned_cols=59 Identities=17% Similarity=0.226 Sum_probs=46.9
Q ss_pred HHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcc
Q 028748 113 RIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSE 172 (204)
Q Consensus 113 RIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~ 172 (204)
-|+||.+- ..|..|+.--.--+..+...||+.....|..++...+|+||+-.||. +...
T Consensus 34 aIRRlARr-~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR 93 (103)
T KOG3467|consen 34 AIRRLARR-GGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKR 93 (103)
T ss_pred HHHHHHHh-cCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHH
Confidence 35565553 34666666666677889999999999999999999999999999998 6653
No 66
>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=48.68 E-value=43 Score=29.32 Aligned_cols=32 Identities=16% Similarity=0.242 Sum_probs=27.9
Q ss_pred CcccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028748 123 SDIGITGEAVFLVNKATDKFLEQFCEDAYECC 154 (204)
Q Consensus 123 DV~~IS~EA~~lIaKAtELFIe~La~~A~~~A 154 (204)
....|+.+++-+|..|+|.||..|...++..+
T Consensus 220 GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~ 251 (252)
T PF12767_consen 220 GLGGVSDDCANLLNLALEVHLKNLIKSCLDLV 251 (252)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34569999999999999999999999987653
No 67
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=41.88 E-value=38 Score=32.49 Aligned_cols=49 Identities=10% Similarity=0.243 Sum_probs=45.6
Q ss_pred CcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 123 SDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 123 DV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
.+.+|..|++.+++--.|.=|...+++|.......+|..|+-+||. +..
T Consensus 19 Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr 68 (450)
T COG5095 19 GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALR 68 (450)
T ss_pred CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHH
Confidence 5778999999999999999999999999999999999999999999 654
No 68
>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=30.31 E-value=48 Score=27.86 Aligned_cols=47 Identities=11% Similarity=0.240 Sum_probs=41.0
Q ss_pred cchhHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCcccccccc-hhcc
Q 028748 126 GITGEAVFLVNKATDK---FLEQFCEDAYECCAKDRKKSLAYKHLA-VVSE 172 (204)
Q Consensus 126 ~IS~EA~~lIaKAtEL---FIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~ 172 (204)
.++.+++-.|...+.= .|..|+..++..|...+.+.|..++|. ++..
T Consensus 215 ~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~ 265 (269)
T TIGR03015 215 VFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAE 265 (269)
T ss_pred CcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 5788999888888873 799999999999988889999999999 8764
No 69
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=28.26 E-value=1.1e+02 Score=29.08 Aligned_cols=70 Identities=6% Similarity=0.098 Sum_probs=53.9
Q ss_pred cccccCCCCChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhc
Q 028748 101 DEVSKVCNFPMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVS 171 (204)
Q Consensus 101 ~~~~~~~~LPlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~ 171 (204)
........|=.-+|..|+++-+ +...-..|+-+++--+.+||+.|++.|..++...+|-.....||. +++
T Consensus 22 ~~~~ya~sla~~avaQIcqslg-~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~ 92 (353)
T KOG2389|consen 22 EEAEYAFSLARVAVAQICQSLG-YSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQ 92 (353)
T ss_pred hHHHHHHHHHHHHHHHHHHhcC-CcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHH
Confidence 3344444455567889998765 334445599999999999999999999999999999888888887 655
No 70
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=22.76 E-value=2.2e+02 Score=23.32 Aligned_cols=63 Identities=8% Similarity=0.139 Sum_probs=47.7
Q ss_pred ChHHHHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccc
Q 028748 110 PMGRIKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQS 174 (204)
Q Consensus 110 PlaRIKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e 174 (204)
=.--|+-+|=.=.|+..--.+++.++---.--++..||..|+..|+ .|..+..+|+. +...+|
T Consensus 11 F~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~Dp 74 (126)
T COG5248 11 FMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRRDP 74 (126)
T ss_pred HHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhhCh
Confidence 3445777777778887777777777777777777888999998887 46778888888 777654
No 71
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=22.35 E-value=1.2e+02 Score=26.50 Aligned_cols=27 Identities=22% Similarity=0.343 Sum_probs=22.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 028748 129 GEAVFLVNKATDKFLEQFCEDAYECCA 155 (204)
Q Consensus 129 ~EA~~lIaKAtELFIe~La~~A~~~A~ 155 (204)
.-.--|++.++.-||..++..||++.+
T Consensus 108 ~rvKkLl~L~aqKFvsDiA~dayqYsr 134 (197)
T COG5162 108 QRVKKLLSLLAQKFVSDIAVDAYQYSR 134 (197)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344478999999999999999999853
No 72
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=21.48 E-value=2.5e+02 Score=22.70 Aligned_cols=58 Identities=10% Similarity=0.237 Sum_probs=43.7
Q ss_pred HHHHHhcCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccccccc-hhcccc
Q 028748 114 IKRIFKTQSSDIGITGEAVFLVNKATDKFLEQFCEDAYECCAKDRKKSLAYKHLA-VVSEQS 174 (204)
Q Consensus 114 IKrIMK~DpDV~~IS~EA~~lIaKAtELFIe~La~~A~~~A~~~kRKTLqy~DLa-aV~~~e 174 (204)
++-+|=.=.|+..=-.+++-++---.=-||..|+..|..++ +|..++.+|+. ++..+|
T Consensus 15 l~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRkDp 73 (109)
T KOG3901|consen 15 LRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRKDP 73 (109)
T ss_pred HHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHhCh
Confidence 55566666777777778888877777777778877777665 67789999999 888764
Done!