Query 019814
Match_columns 335
No_of_seqs 228 out of 750
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 04:45:17 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019814.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019814hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1657 CCAAT-binding factor, 100.0 2.7E-34 5.8E-39 266.2 8.4 170 152-327 50-221 (236)
2 COG5208 HAP5 CCAAT-binding fac 100.0 1.7E-30 3.6E-35 240.5 8.0 114 145-258 76-191 (286)
3 PF00808 CBFD_NFYB_HMF: Histon 99.8 3.4E-19 7.3E-24 133.7 7.1 64 176-239 2-65 (65)
4 KOG1659 Class 2 transcription 99.8 4.1E-19 8.9E-24 163.5 6.4 85 169-253 6-90 (224)
5 COG5247 BUR6 Class 2 transcrip 99.7 5.4E-18 1.2E-22 141.8 5.8 82 175-256 22-103 (113)
6 KOG1658 DNA polymerase epsilon 99.3 6.5E-13 1.4E-17 117.9 2.3 82 172-253 55-136 (162)
7 cd00074 H2A Histone 2A; H2A is 99.2 4.7E-11 1E-15 101.2 7.5 77 174-250 18-94 (115)
8 COG5262 HTA1 Histone H2A [Chro 99.1 8.9E-11 1.9E-15 100.9 6.3 77 174-250 24-100 (132)
9 smart00414 H2A Histone 2A. 98.9 2.4E-09 5.2E-14 89.7 7.1 77 174-250 7-83 (106)
10 KOG1756 Histone 2A [Chromatin 98.9 3E-09 6.4E-14 92.3 7.2 79 174-252 25-103 (131)
11 COG2036 HHT1 Histones H3 and H 98.9 4.2E-09 9.1E-14 86.5 7.2 79 164-243 7-85 (91)
12 PLN00154 histone H2A; Provisio 98.9 3.7E-09 8.1E-14 92.4 6.5 77 174-250 36-113 (136)
13 PTZ00017 histone H2A; Provisio 98.9 4.1E-09 8.8E-14 91.9 6.6 76 174-249 25-100 (134)
14 PLN00156 histone H2AX; Provisi 98.8 2.1E-08 4.6E-13 88.0 7.2 77 174-250 27-103 (139)
15 PLN00153 histone H2A; Provisio 98.7 2E-08 4.3E-13 87.2 6.6 77 174-250 22-98 (129)
16 PLN00157 histone H2A; Provisio 98.7 2.2E-08 4.7E-13 87.2 6.5 76 174-249 24-99 (132)
17 KOG0869 CCAAT-binding factor, 98.6 5.9E-08 1.3E-12 87.0 6.8 76 175-251 31-107 (168)
18 PF00125 Histone: Core histone 98.6 3.9E-08 8.3E-13 74.8 4.8 68 174-241 6-74 (75)
19 PTZ00252 histone H2A; Provisio 98.6 8.8E-08 1.9E-12 83.7 6.9 77 174-250 23-102 (134)
20 smart00803 TAF TATA box bindin 98.5 2.7E-07 5.9E-12 71.0 7.0 64 176-240 2-65 (65)
21 KOG0870 DNA polymerase epsilon 98.5 2.1E-07 4.5E-12 84.0 6.9 76 175-250 9-86 (172)
22 PLN00035 histone H4; Provision 98.4 6.4E-07 1.4E-11 75.3 6.9 65 177-242 30-94 (103)
23 cd00076 H4 Histone H4, one of 98.4 7.5E-07 1.6E-11 72.4 6.9 66 176-242 13-78 (85)
24 PTZ00015 histone H4; Provision 98.3 2.1E-06 4.6E-11 72.0 6.9 67 175-242 29-95 (102)
25 smart00417 H4 Histone H4. 98.2 3.8E-06 8.3E-11 66.8 6.0 60 176-236 13-72 (74)
26 cd07981 TAF12 TATA Binding Pro 98.0 2.4E-05 5.1E-10 61.0 7.4 65 178-243 3-68 (72)
27 KOG0871 Class 2 transcription 98.0 1.7E-05 3.7E-10 70.8 7.1 78 174-251 10-88 (156)
28 smart00428 H3 Histone H3. 97.6 0.00028 6.1E-09 59.6 8.3 72 168-239 24-98 (105)
29 cd08048 TAF11 TATA Binding Pro 97.6 0.00018 4E-09 58.3 6.4 71 170-241 10-83 (85)
30 COG5150 Class 2 transcription 97.3 0.00055 1.2E-08 60.3 6.7 77 174-250 9-86 (148)
31 KOG1757 Histone 2A [Chromatin 97.3 0.00016 3.6E-09 62.4 2.9 76 174-249 28-104 (131)
32 KOG1658 DNA polymerase epsilon 97.3 0.00046 1E-08 62.2 5.4 75 172-251 7-81 (162)
33 cd07979 TAF9 TATA Binding Prot 97.2 0.00098 2.1E-08 56.6 6.2 69 180-249 5-73 (117)
34 smart00576 BTP Bromodomain tra 97.0 0.0027 5.8E-08 49.8 6.6 60 182-242 12-71 (77)
35 cd08050 TAF6 TATA Binding Prot 96.8 0.0032 7E-08 61.5 6.9 63 179-242 2-64 (343)
36 PLN00121 histone H3; Provision 96.8 0.0051 1.1E-07 54.3 7.3 72 167-239 56-129 (136)
37 PF02969 TAF: TATA box binding 96.8 0.0062 1.3E-07 47.7 6.9 64 176-240 3-66 (66)
38 PLN00161 histone H3; Provision 96.7 0.0058 1.3E-07 53.9 7.5 72 168-239 50-123 (135)
39 PTZ00018 histone H3; Provision 96.7 0.0057 1.2E-07 54.0 7.1 71 168-239 57-129 (136)
40 PF09415 CENP-X: CENP-S associ 96.7 0.007 1.5E-07 47.9 6.9 63 178-240 1-66 (72)
41 PF04719 TAFII28: hTAFII28-lik 96.6 0.005 1.1E-07 50.8 5.7 84 155-241 5-89 (90)
42 PLN00160 histone H3; Provision 96.4 0.0098 2.1E-07 49.8 6.6 72 168-239 16-89 (97)
43 PF15511 CENP-T: Centromere ki 96.4 0.0047 1E-07 62.1 5.4 64 171-234 346-414 (414)
44 smart00427 H2B Histone H2B. 96.2 0.015 3.3E-07 48.2 6.4 59 182-241 7-66 (89)
45 PTZ00463 histone H2B; Provisio 95.2 0.063 1.4E-06 46.6 6.4 59 182-241 34-93 (117)
46 PF03847 TFIID_20kDa: Transcri 95.0 0.092 2E-06 41.1 6.3 61 181-242 4-65 (68)
47 KOG3219 Transcription initiati 94.9 0.051 1.1E-06 50.6 5.5 89 150-242 89-178 (195)
48 PLN00158 histone H2B; Provisio 94.8 0.088 1.9E-06 45.7 6.4 60 181-241 32-92 (116)
49 PF15510 CENP-W: Centromere ki 94.6 0.077 1.7E-06 44.8 5.3 65 176-240 16-94 (102)
50 PLN00155 histone H2A; Provisio 94.4 0.044 9.5E-07 42.4 3.3 36 174-209 22-57 (58)
51 KOG3467 Histone H4 [Chromatin 94.3 0.13 2.8E-06 43.2 6.1 63 180-243 33-95 (103)
52 PF15630 CENP-S: Kinetochore c 94.2 0.12 2.7E-06 41.3 5.5 63 182-244 11-75 (76)
53 PF07524 Bromo_TP: Bromodomain 93.9 0.25 5.3E-06 38.3 6.5 60 182-242 12-71 (77)
54 PF02269 TFIID-18kDa: Transcri 93.2 0.081 1.7E-06 43.3 3.0 75 182-256 7-82 (93)
55 KOG1744 Histone H2B [Chromatin 92.9 0.29 6.3E-06 43.1 6.1 63 175-241 39-102 (127)
56 KOG1745 Histones H3 and H4 [Ch 92.1 0.13 2.9E-06 45.7 3.1 71 170-240 60-131 (137)
57 cd07978 TAF13 The TATA Binding 91.6 0.69 1.5E-05 38.1 6.5 76 180-256 6-82 (92)
58 KOG1142 Transcription initiati 91.6 0.21 4.6E-06 48.4 4.0 58 193-250 171-228 (258)
59 KOG3423 Transcription initiati 89.4 1.9 4.2E-05 39.8 8.0 81 153-242 71-165 (176)
60 PF05236 TAF4: Transcription i 88.3 0.88 1.9E-05 42.9 5.2 44 180-224 51-94 (264)
61 PF02291 TFIID-31kDa: Transcri 87.3 2.3 5E-05 37.2 6.8 68 181-249 17-84 (129)
62 cd08045 TAF4 TATA Binding Prot 83.0 2.5 5.4E-05 38.8 5.3 60 180-240 52-117 (212)
63 KOG2549 Transcription initiati 82.9 3.3 7.1E-05 44.2 6.8 63 179-242 14-76 (576)
64 PF03540 TFIID_30kDa: Transcri 70.6 17 0.00036 27.6 5.7 47 177-224 3-49 (51)
65 COG5162 Transcription initiati 69.3 28 0.00061 32.5 8.1 60 163-223 75-134 (197)
66 COG5095 TAF6 Transcription ini 63.4 17 0.00037 37.2 5.9 60 182-242 11-70 (450)
67 PF10979 DUF2786: Protein of u 56.0 13 0.00027 27.0 2.7 35 179-213 4-38 (43)
68 TIGR03015 pepcterm_ATPase puta 53.9 20 0.00043 32.3 4.3 50 194-243 215-267 (269)
69 PF13335 Mg_chelatase_2: Magne 51.9 1.3E+02 0.0029 24.6 9.8 62 172-240 27-94 (96)
70 PF12767 SAGA-Tad1: Transcript 48.4 26 0.00057 32.9 4.3 42 180-222 210-251 (252)
71 PRK00411 cdc6 cell division co 43.2 78 0.0017 30.5 6.7 49 194-242 228-282 (394)
72 TIGR00368 Mg chelatase-related 39.0 2.4E+02 0.0052 29.6 9.9 60 174-240 432-497 (499)
73 PF08637 NCA2: ATP synthase re 37.9 95 0.0021 30.4 6.4 83 148-248 28-112 (290)
74 KOG1560 Translation initiation 36.1 1.3E+02 0.0028 30.5 7.0 46 144-189 250-295 (339)
75 TIGR02928 orc1/cdc6 family rep 35.0 1.5E+02 0.0032 28.2 7.1 33 211-243 243-275 (365)
76 KOG2389 Predicted bromodomain 32.8 1.1E+02 0.0024 31.4 6.1 65 177-242 30-94 (353)
77 PTZ00469 60S ribosomal subunit 31.7 17 0.00038 34.0 0.3 89 148-237 34-127 (187)
78 TIGR00764 lon_rel lon-related 30.9 1.4E+02 0.0031 31.9 6.9 32 211-242 360-391 (608)
79 PF08250 Sperm_act_pep: Sperm- 30.7 23 0.0005 19.1 0.6 9 48-56 1-9 (10)
80 KOG4336 TBP-associated transcr 28.5 1.5E+02 0.0032 30.1 6.1 63 179-241 7-69 (323)
81 KOG1657 CCAAT-binding factor, 28.4 7.1 0.00015 37.3 -2.9 75 173-256 5-79 (236)
82 COG5248 TAF19 Transcription in 26.0 2.1E+02 0.0046 25.3 5.9 62 180-243 13-74 (126)
83 COG5251 TAF40 Transcription in 25.6 76 0.0017 29.9 3.3 69 170-241 109-180 (199)
84 PF13499 EF-hand_7: EF-hand do 25.3 2.4E+02 0.0053 20.0 5.3 47 193-239 15-66 (66)
85 PTZ00195 60S ribosomal protein 24.8 28 0.0006 33.0 0.4 89 148-237 34-135 (198)
86 KOG3901 Transcription initiati 23.1 2.8E+02 0.006 24.3 6.0 70 182-254 15-85 (109)
87 KOG3334 Transcription initiati 22.8 2.9E+02 0.0064 25.3 6.3 40 210-249 46-85 (148)
88 PRK09862 putative ATP-dependen 22.4 3.8E+02 0.0081 28.5 8.0 62 174-242 425-492 (506)
89 COG1474 CDC6 Cdc6-related prot 21.7 1.3E+02 0.0028 30.2 4.4 59 194-253 211-275 (366)
No 1
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=100.00 E-value=2.7e-34 Score=266.25 Aligned_cols=170 Identities=54% Similarity=0.739 Sum_probs=138.6
Q ss_pred HHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccC
Q 019814 152 QQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQ 231 (335)
Q Consensus 152 qq~L~~FW~~q~~EiE~~~Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLq 231 (335)
.++|.+||.++..|.|...||+++.|||+|||||||.|+||.+|++||++|++||||+||.+|+.+||.+|++++||||+
T Consensus 50 ~~~l~~fw~~~~~e~e~~~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~ 129 (236)
T KOG1657|consen 50 RQQLQSFWSKQAIEKEGQLDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQ 129 (236)
T ss_pred hHHHHhhhhccccccccccchhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccch
Confidence 78999999999877778899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCcchhhhhcCCCCcchhh--hhhcCCCCCCCCCCCCCCCCccccCCCCCcccCCCCeeecccCCCcccc
Q 019814 232 KNDIAAAITRTDIFDFLVDIVPREDLKDE--VLASIPRGTLPVGGPPDMPPYCYMPTQHASQVGSAGLIMGKPVMDPAIY 309 (335)
Q Consensus 232 y~DIA~AV~~~d~FDFL~DIVPr~~~~~e--~l~s~p~~~~~v~~p~~~~py~~~~~q~~~~~~~~g~~~g~pv~~~~~~ 309 (335)
++||+.+|.+++.||||+||||++..+++ .+.........-++-...++|.....- -+..++|+++|.|.|+.
T Consensus 130 ~sdia~av~~s~~fdFL~DivP~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~g~~~~~~--- 204 (236)
T KOG1657|consen 130 KSDIAAAVTQSETFDFLRDIVPRKILAEKYPSLAAKGPGEMREDDFVAPVTYIMDNAG--IQQIPPGLVAGQPQCIR--- 204 (236)
T ss_pred HHHHHHHhccCCCccceeccccchhccccccccccCCCcccccccccccccccccccc--ccccCchhhcCCccccc---
Confidence 99999999999999999999999998863 222222221111111234566555543 34567889999999876
Q ss_pred ccCCCCccCCCCCCCCCC
Q 019814 310 AQQSHPYMGQQMWPQGAD 327 (335)
Q Consensus 310 ~~q~~p~m~~~~w~~~~~ 327 (335)
..++.|+| +++|++...
T Consensus 205 ~~~~~~~~-q~~~~~~~~ 221 (236)
T KOG1657|consen 205 LAQPVSGT-QGQWQTLAT 221 (236)
T ss_pred ccCCCccc-cchhhhccC
Confidence 44445666 778986543
No 2
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.96 E-value=1.7e-30 Score=240.50 Aligned_cols=114 Identities=54% Similarity=0.907 Sum_probs=106.9
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHhhc--cCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHH
Q 019814 145 HQQQQQLQQQLQSFWANQYQEIEKVN--DFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHT 222 (335)
Q Consensus 145 ~~~~~~~qq~L~~FW~~q~~EiE~~~--Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~A 222 (335)
+-.-..+.+.|..||.+.++++|+.. ++|.+.||||||||+||.|+||+|||+||++||+|+||+||++||.+||.+|
T Consensus 76 qglvg~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~a 155 (286)
T COG5208 76 QGLVGLLDERISRYWQQTIKAAEEERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINA 155 (286)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHH
Confidence 34445788999999999999998754 7899999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCccCHHHHHHHHhcCCcchhhhhcCCCCcch
Q 019814 223 EENKRRTLQKNDIAAAITRTDIFDFLVDIVPREDLK 258 (335)
Q Consensus 223 qe~KRKTLqy~DIA~AV~~~d~FDFL~DIVPr~~~~ 258 (335)
++||||||+++||++||++++.||||+||||+....
T Consensus 156 e~NkRRtLQksDia~Av~kSeMfDFLidivpr~p~n 191 (286)
T COG5208 156 EENKRRTLQKSDIAAAVKKSEMFDFLIDIVPRNPFN 191 (286)
T ss_pred hHhhhhHHHHHHHHHHHHHHHHHhHHhhhccCCCcc
Confidence 999999999999999999999999999999998654
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=99.78 E-value=3.4e-19 Score=133.68 Aligned_cols=64 Identities=44% Similarity=0.590 Sum_probs=59.8
Q ss_pred CCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 019814 176 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 239 (335)
Q Consensus 176 ~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV 239 (335)
.||++|||||||.|+++.+||+||.+++++|+|+||++|+.+|+..|+.++||||+++||..||
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=4.1e-19 Score=163.50 Aligned_cols=85 Identities=32% Similarity=0.507 Sum_probs=81.1
Q ss_pred hccCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhh
Q 019814 169 VNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFL 248 (335)
Q Consensus 169 ~~Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL 248 (335)
..++.+..||.+||||||++|+||++|+...||+++||+|+|+++|+.++++.|+..+.|||+..||..||..++.||||
T Consensus 6 ~~~~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFL 85 (224)
T KOG1659|consen 6 SFKKYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFL 85 (224)
T ss_pred hhhhhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHH
Confidence 35667789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCC
Q 019814 249 VDIVP 253 (335)
Q Consensus 249 ~DIVP 253 (335)
.|+|-
T Consensus 86 k~~v~ 90 (224)
T KOG1659|consen 86 KEVVE 90 (224)
T ss_pred HHHHH
Confidence 99764
No 5
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=99.72 E-value=5.4e-18 Score=141.77 Aligned_cols=82 Identities=29% Similarity=0.502 Sum_probs=78.5
Q ss_pred CCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhhcCCC
Q 019814 175 HSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDIVPR 254 (335)
Q Consensus 175 ~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~DIVPr 254 (335)
.+||+|||||||+.|+||++|++..|++.+||+|+|+.+|...+.+.|+....|.++.++|..|+..++.||||.|++..
T Consensus 22 trFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~~~ 101 (113)
T COG5247 22 TRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNMEQF 101 (113)
T ss_pred hcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHHHh
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999999765
Q ss_pred Cc
Q 019814 255 ED 256 (335)
Q Consensus 255 ~~ 256 (335)
+.
T Consensus 102 ~~ 103 (113)
T COG5247 102 KN 103 (113)
T ss_pred cC
Confidence 43
No 6
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=99.31 E-value=6.5e-13 Score=117.93 Aligned_cols=82 Identities=37% Similarity=0.542 Sum_probs=78.4
Q ss_pred CCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhhc
Q 019814 172 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDI 251 (335)
Q Consensus 172 fk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~DI 251 (335)
-+.++|||+|||.+||.|||+.+...||.+++++|.|+||++|...++..++..+|||+++.|+..||...+.|.||.+.
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 34578999999999999999999999999999999999999999999999999999999999999999999999999977
Q ss_pred CC
Q 019814 252 VP 253 (335)
Q Consensus 252 VP 253 (335)
.+
T Consensus 135 ~d 136 (162)
T KOG1658|consen 135 LD 136 (162)
T ss_pred cc
Confidence 65
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=99.19 E-value=4.7e-11 Score=101.22 Aligned_cols=77 Identities=21% Similarity=0.348 Sum_probs=73.3
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhh
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 250 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~D 250 (335)
.+.||++||+|+||..-...+||+.|++.++..+|+++.++.+.|.+.|+.+||++|+..||..||.++++|++|..
T Consensus 18 gL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~nD~EL~~L~~ 94 (115)
T cd00074 18 GLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRNDEELNKLLK 94 (115)
T ss_pred CccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhccHHHHHHHc
Confidence 58899999999999877789999999999999999999999999999999999999999999999999999997764
No 8
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=99.13 E-value=8.9e-11 Score=100.89 Aligned_cols=77 Identities=23% Similarity=0.347 Sum_probs=74.4
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhh
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 250 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~D 250 (335)
.+.||++|||||||.+-.-++|+++|++.++..+|+++.++++-|-+.|+.+|.|.|.+.||..||.++++++||..
T Consensus 24 gl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~EL~~l~~ 100 (132)
T COG5262 24 GLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLG 100 (132)
T ss_pred CccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcCcHHHHHHhh
Confidence 47799999999999988899999999999999999999999999999999999999999999999999999999986
No 9
>smart00414 H2A Histone 2A.
Probab=98.93 E-value=2.4e-09 Score=89.66 Aligned_cols=77 Identities=22% Similarity=0.381 Sum_probs=72.5
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhh
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 250 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~D 250 (335)
.+.||++||.|+||..-...+|++.|++.++..+|+++.++.+.|.+.|..+|++.|+..||..||.++++|+.|..
T Consensus 7 gL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~nD~EL~~L~~ 83 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRNDEELNKLLK 83 (106)
T ss_pred CccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccCCHHHHHHHc
Confidence 47899999999999987788999999999999999999999999999999999999999999999999999986654
No 10
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=98.91 E-value=3e-09 Score=92.26 Aligned_cols=79 Identities=22% Similarity=0.356 Sum_probs=75.5
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhhcC
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDIV 252 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~DIV 252 (335)
.+.||++||.|+||...-..+|++.|+++++..+|+.+.++++.|-+.|+++++..|+..||..||.+++++.||.+-|
T Consensus 25 gl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~NDeEL~~lL~~v 103 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRNDEELNKLLGKV 103 (131)
T ss_pred ccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhCcHHHHHHhccc
Confidence 4789999999999998889999999999999999999999999999999999999999999999999999999999843
No 11
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.90 E-value=4.2e-09 Score=86.48 Aligned_cols=79 Identities=24% Similarity=0.357 Sum_probs=68.9
Q ss_pred HHHHhhccCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCC
Q 019814 164 QEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 243 (335)
Q Consensus 164 ~EiE~~~Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d 243 (335)
.|+..........||.+.|.||||.- ...+||.+|...+.+|.|.|+..|+++|...|.+.|||||+.+||..|++...
T Consensus 7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~-~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~ 85 (91)
T COG2036 7 KEIRRYQRSTDLLLPKAPVRRILRKA-GAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLG 85 (91)
T ss_pred HHHHhhhhhhhhhcCchHHHHHHHHH-hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 45555555566789999999999983 23399999999999999999999999999999999999999999999988754
No 12
>PLN00154 histone H2A; Provisional
Probab=98.87 E-value=3.7e-09 Score=92.37 Aligned_cols=77 Identities=21% Similarity=0.254 Sum_probs=72.4
Q ss_pred CCCCChHHHHHHHhCCc-chhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhh
Q 019814 174 NHSLPLARIKKIMKADE-DVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 250 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDp-DV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~D 250 (335)
.+.||++||.|+||..- ...+|++.|+++++..+|++..++.+.|.+.|+.+|++.|+..||..||.++++|++|..
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrnDeEL~~Ll~ 113 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 113 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccCcHHHHHHhc
Confidence 58899999999999964 457999999999999999999999999999999999999999999999999999998775
No 13
>PTZ00017 histone H2A; Provisional
Probab=98.87 E-value=4.1e-09 Score=91.91 Aligned_cols=76 Identities=22% Similarity=0.369 Sum_probs=72.6
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhh
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 249 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~ 249 (335)
.+.||++||.|+||..--..+|++.|+++++..+|+++.++.+.|.+.|..++++.|+..||..||.++++|+.|.
T Consensus 25 gL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 100 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLL 100 (134)
T ss_pred CcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccCcHHHHHHH
Confidence 5889999999999987777899999999999999999999999999999999999999999999999999999776
No 14
>PLN00156 histone H2AX; Provisional
Probab=98.75 E-value=2.1e-08 Score=87.97 Aligned_cols=77 Identities=22% Similarity=0.339 Sum_probs=72.3
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhh
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 250 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~D 250 (335)
.+.||++||.|.||..--..+|++.|+++++..+|+++.++.+.|.+.|..+|++.|+..||..||.++++|+.|..
T Consensus 27 gL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrnDeEL~~Ll~ 103 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG 103 (139)
T ss_pred CcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccCcHHHHHHHC
Confidence 47899999999999977778999999999999999999999999999999999999999999999999999996653
No 15
>PLN00153 histone H2A; Provisional
Probab=98.74 E-value=2e-08 Score=87.20 Aligned_cols=77 Identities=25% Similarity=0.332 Sum_probs=72.5
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhh
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 250 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~D 250 (335)
.+.||++||.|.||..--..+|++.|+++++..+|+++.++.+.|.+.|..+|++.|+..||..||.++++|+.|..
T Consensus 22 gL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll~ 98 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLG 98 (129)
T ss_pred CcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccCcHHHHHHHC
Confidence 58899999999999877778999999999999999999999999999999999999999999999999999996653
No 16
>PLN00157 histone H2A; Provisional
Probab=98.73 E-value=2.2e-08 Score=87.22 Aligned_cols=76 Identities=24% Similarity=0.336 Sum_probs=71.8
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhh
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 249 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~ 249 (335)
.+.||++||.|.||..--..+|++.|+++++..+|+++.++.+.|.+.|..+|++.|+..||..||.++++|+-|.
T Consensus 24 gL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~nDeEL~~Ll 99 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLL 99 (132)
T ss_pred CcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccCcHHHHHHH
Confidence 5889999999999997777899999999999999999999999999999999999999999999999999998554
No 17
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=98.64 E-value=5.9e-08 Score=86.99 Aligned_cols=76 Identities=24% Similarity=0.304 Sum_probs=68.6
Q ss_pred CCCChHHHHHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhhc
Q 019814 175 HSLPLARIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDI 251 (335)
Q Consensus 175 ~~LPLARIKKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~DI 251 (335)
..||+|.|-||||. -|...+||+||.-.+-.+...||..+|.+|.+.++..|||||+.+||.-|+.... ||-..+.
T Consensus 31 r~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG-Fe~Y~ep 107 (168)
T KOG0869|consen 31 RFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG-FENYAEP 107 (168)
T ss_pred hhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC-cHhHHHH
Confidence 45999999999997 5889999999999999999999999999999999999999999999999999875 4444443
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=98.64 E-value=3.9e-08 Score=74.85 Aligned_cols=68 Identities=24% Similarity=0.294 Sum_probs=60.9
Q ss_pred CCCCChHHHHHHHhCCcch-hccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Q 019814 174 NHSLPLARIKKIMKADEDV-RMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 241 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV-~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~ 241 (335)
...+|+.||.|.+..+-.. .+||++|..++..++|.|+.++...|...|..+||+||+..||..|++.
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 4567888888888876555 4999999999999999999999999999999999999999999999864
No 19
>PTZ00252 histone H2A; Provisional
Probab=98.61 E-value=8.8e-08 Score=83.68 Aligned_cols=77 Identities=21% Similarity=0.312 Sum_probs=70.6
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCccCHHHHHHHHhcCCcch-hhhh
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEE--NKRRTLQKNDIAAAITRTDIFD-FLVD 250 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe--~KRKTLqy~DIA~AV~~~d~FD-FL~D 250 (335)
.+.||++||.|.||..--..+|++.|+++++..+|++..++.+.|.+.|.+ +|++.|+..||..||.++++|+ +|.+
T Consensus 23 GL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDeEL~~Ll~~ 102 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDDDLGSLLKN 102 (134)
T ss_pred CccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccChHHHHHHHcC
Confidence 488999999999998777789999999999999999999999999999965 7889999999999999999998 4444
No 20
>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=98.54 E-value=2.7e-07 Score=71.03 Aligned_cols=64 Identities=28% Similarity=0.373 Sum_probs=60.5
Q ss_pred CCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHh
Q 019814 176 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAIT 240 (335)
Q Consensus 176 ~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~ 240 (335)
.||.+-|++|.+. -++.+||.|+...++..+|.|+.+++..|.+.++..|||||+.+||..|++
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 5899999999998 578899999999999999999999999999999999999999999998864
No 21
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.52 E-value=2.1e-07 Score=83.97 Aligned_cols=76 Identities=29% Similarity=0.398 Sum_probs=69.5
Q ss_pred CCCChHHHHHHHhC-Ccch-hccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhh
Q 019814 175 HSLPLARIKKIMKA-DEDV-RMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 250 (335)
Q Consensus 175 ~~LPLARIKKIMKs-DpDV-~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~D 250 (335)
+.||.|-|.||+|. -++- ..||+||..+|++|+-+||.+|+..|...|...+||||+.+||..|+...+.-.|+.-
T Consensus 9 l~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~p 86 (172)
T KOG0870|consen 9 LNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVNP 86 (172)
T ss_pred hhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhhH
Confidence 67999999999996 3555 7999999999999999999999999999999999999999999999999987777653
No 22
>PLN00035 histone H4; Provisional
Probab=98.42 E-value=6.4e-07 Score=75.27 Aligned_cols=65 Identities=18% Similarity=0.252 Sum_probs=62.4
Q ss_pred CChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 177 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 177 LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
||.+-|+||.+. -.+.+||.+|...+..++|.|+++++.+|...|+..+||||+.+||..|++..
T Consensus 30 ipk~~IrRLARr-~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 30 ITKPAIRRLARR-GGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred CCHHHHHHHHHH-cCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence 899999999998 56999999999999999999999999999999999999999999999998875
No 23
>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=7.5e-07 Score=72.36 Aligned_cols=66 Identities=18% Similarity=0.260 Sum_probs=62.6
Q ss_pred CCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 176 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 176 ~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
.||.+-|+||.+. ..+.+||.++...+..++|.|+++++.+|...|+..+||||+..||..|+++.
T Consensus 13 gi~k~~I~RLarr-~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~ 78 (85)
T cd00076 13 GITKPAIRRLARR-GGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 78 (85)
T ss_pred cCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHC
Confidence 4899999999998 46999999999999999999999999999999999999999999999998875
No 24
>PTZ00015 histone H4; Provisional
Probab=98.29 E-value=2.1e-06 Score=72.02 Aligned_cols=67 Identities=19% Similarity=0.258 Sum_probs=63.2
Q ss_pred CCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 175 HSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 175 ~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
..||.+-|+||.+. -.+.+||.++...+..++|.|+++++.+|...|+..+||||+.+||..|++..
T Consensus 29 ~gI~k~~IrRLarr-~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~ 95 (102)
T PTZ00015 29 RGITKGAIRRLARR-GGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95 (102)
T ss_pred cCCCHHHHHHHHHH-cCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhc
Confidence 35899999999998 68999999999999999999999999999999999999999999999998765
No 25
>smart00417 H4 Histone H4.
Probab=98.18 E-value=3.8e-06 Score=66.83 Aligned_cols=60 Identities=17% Similarity=0.215 Sum_probs=57.5
Q ss_pred CCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHH
Q 019814 176 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIA 236 (335)
Q Consensus 176 ~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA 236 (335)
.||.+-|+||.|. .++.+||.++...+..++|.|+++++.+|...|+..+||||+..||.
T Consensus 13 gI~k~~IrRLaRr-~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~ 72 (74)
T smart00417 13 GITKPAIRRLARR-GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVV 72 (74)
T ss_pred CCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhe
Confidence 4899999999998 68999999999999999999999999999999999999999999985
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=98.02 E-value=2.4e-05 Score=60.95 Aligned_cols=65 Identities=12% Similarity=0.268 Sum_probs=58.1
Q ss_pred ChHHHHHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCC
Q 019814 178 PLARIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 243 (335)
Q Consensus 178 PLARIKKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d 243 (335)
+-..+..++|. |+. .+++.+|..++...+|.|+..++..|...|+..||+||..+||.-++++.-
T Consensus 3 ~k~~l~~lv~~id~~-~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~ 68 (72)
T cd07981 3 TKRKLQELLKEIDPR-EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNW 68 (72)
T ss_pred cHHHHHHHHHhhCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Confidence 44567777776 665 889999999999999999999999999999999999999999999998764
No 27
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=98.00 E-value=1.7e-05 Score=70.80 Aligned_cols=78 Identities=17% Similarity=0.283 Sum_probs=69.4
Q ss_pred CCCCChHHHHHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhhc
Q 019814 174 NHSLPLARIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDI 251 (335)
Q Consensus 174 ~~~LPLARIKKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~DI 251 (335)
++.||-+-|.||+|. -|--.+|++||--+|-.+|-.||..|+.+|..++....+|||.+.||..|+.+-..=+|+...
T Consensus 10 e~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee~ 88 (156)
T KOG0871|consen 10 ELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEEA 88 (156)
T ss_pred cccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHHH
Confidence 478999999999997 454468999999999999999999999999999999999999999999999988755666543
No 28
>smart00428 H3 Histone H3.
Probab=97.64 E-value=0.00028 Score=59.59 Aligned_cols=72 Identities=21% Similarity=0.198 Sum_probs=60.0
Q ss_pred hhccCCCCCCChHHH-HHHHhCC-c-chhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 019814 168 KVNDFKNHSLPLARI-KKIMKAD-E-DVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 239 (335)
Q Consensus 168 ~~~Dfk~~~LPLARI-KKIMKsD-p-DV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV 239 (335)
...++--..+|.+|+ +.|+..- . +--+++.+|..++..|+|.|+..|.+.|...|...||+||..+||.-|.
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 356666778899885 5555542 2 1249999999999999999999999999999999999999999998774
No 29
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=97.59 E-value=0.00018 Score=58.35 Aligned_cols=71 Identities=23% Similarity=0.334 Sum_probs=62.1
Q ss_pred ccCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCccCHHHHHHHHhc
Q 019814 170 NDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENK---RRTLQKNDIAAAITR 241 (335)
Q Consensus 170 ~Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~K---RKTLqy~DIA~AV~~ 241 (335)
..|+...||-+.|||||...-+ ..++.+...+++..+.+||.+|+++|.++..+.+ +.-|+.+||..|...
T Consensus 10 e~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr 83 (85)
T cd08048 10 EMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR 83 (85)
T ss_pred HHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence 3455677999999999998655 8999999999999999999999999999987654 488999999999765
No 30
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=97.34 E-value=0.00055 Score=60.32 Aligned_cols=77 Identities=23% Similarity=0.373 Sum_probs=67.5
Q ss_pred CCCCChHHHHHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhh
Q 019814 174 NHSLPLARIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 250 (335)
Q Consensus 174 ~~~LPLARIKKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~D 250 (335)
+..||-|-|.|++-. -|---++.+||.-+|-.||=.||.-|+..|...+.+..+|||.|.||..|+++.+.=+|+..
T Consensus 9 e~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~~ 86 (148)
T COG5150 9 ENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIES 86 (148)
T ss_pred cccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHHH
Confidence 477999999999986 34446899999999999999999999999999999999999999999999998865555443
No 31
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=97.31 E-value=0.00016 Score=62.45 Aligned_cols=76 Identities=21% Similarity=0.266 Sum_probs=69.3
Q ss_pred CCCCChHHHHHHHhCC-cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhh
Q 019814 174 NHSLPLARIKKIMKAD-EDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 249 (335)
Q Consensus 174 ~~~LPLARIKKIMKsD-pDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~ 249 (335)
.+.||++||.|-+|.- ....+|.+-|.+..+..+|++..+..+.|-+.++.-|-|.|+..|+.-||..+|++|-|+
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRGDeELDtLI 104 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLI 104 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecCcHHHHHHH
Confidence 4789999999999984 666899999999999999999999888888888888999999999999999999999987
No 32
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=97.26 E-value=0.00046 Score=62.18 Aligned_cols=75 Identities=24% Similarity=0.181 Sum_probs=55.7
Q ss_pred CCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhhc
Q 019814 172 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDI 251 (335)
Q Consensus 172 fk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~DI 251 (335)
.....||++.+|||-|.||...+-+.+|....+.|+|.|++.|+..+- .+-..|...-|..+++..+.|.||.|-
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 345779999999999999999999999999999999999999998222 122234444555555555555555543
No 33
>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=97.17 E-value=0.00098 Score=56.62 Aligned_cols=69 Identities=12% Similarity=0.111 Sum_probs=62.1
Q ss_pred HHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhh
Q 019814 180 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 249 (335)
Q Consensus 180 ARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~ 249 (335)
.-|++|+|. -++..++.+++..+...++.++.++..+|...|+..+|+||+.+||..||+..-.+.|-.
T Consensus 5 ~~v~~iLk~-~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~ 73 (117)
T cd07979 5 RVIAAILKS-MGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTS 73 (117)
T ss_pred HHHHHHHHH-CCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCC
Confidence 358889997 477899999999999999999999999999999999999999999999999876666653
No 34
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=96.98 E-value=0.0027 Score=49.76 Aligned_cols=60 Identities=15% Similarity=0.189 Sum_probs=54.6
Q ss_pred HHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 182 IKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 182 IKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
|.+|+|. -+...++.+|.-.++..+|.|+.+|++.+...|+..+|++++..||..|+.+.
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 6677775 56779999999999999999999999999999999999999999999998764
No 35
>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=96.78 E-value=0.0032 Score=61.49 Aligned_cols=63 Identities=22% Similarity=0.286 Sum_probs=57.2
Q ss_pred hHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 179 LARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 179 LARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
..-||-|.++ -++..++.||...++.-.|.++.+++.+|.+.++..|||||+.+||..|++..
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 3457778876 57789999999999999999999999999999999999999999999997764
No 36
>PLN00121 histone H3; Provisional
Probab=96.77 E-value=0.0051 Score=54.25 Aligned_cols=72 Identities=22% Similarity=0.279 Sum_probs=60.3
Q ss_pred HhhccCCCCCCChHHHH-HHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 019814 167 EKVNDFKNHSLPLARIK-KIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 239 (335)
Q Consensus 167 E~~~Dfk~~~LPLARIK-KIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV 239 (335)
....++--..+|.+|+- .|+.. ..+ -.+..+|+.++..|+|.|+-.|-+.|..+|...||.||..+||.-+.
T Consensus 56 Qkst~lLI~k~pF~RLVREI~~~~~~~-~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 56 QKSTELLIRKLPFQRLVREIAQDFKTD-LRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccccccccccccHHHHHHHHHHHhCcc-ceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 34567777889998854 45544 344 49999999999999999999999999999999999999999997764
No 37
>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=96.76 E-value=0.0062 Score=47.66 Aligned_cols=64 Identities=22% Similarity=0.310 Sum_probs=49.7
Q ss_pred CCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHh
Q 019814 176 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAIT 240 (335)
Q Consensus 176 ~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~ 240 (335)
.||..-||-|-.+ =++..++.|+.-+++.-+|+-|.++...|.+.++.+||++|+.+||..|++
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 4667778777766 566789999999999999999999999999999999999999999999874
No 38
>PLN00161 histone H3; Provisional
Probab=96.74 E-value=0.0058 Score=53.93 Aligned_cols=72 Identities=25% Similarity=0.256 Sum_probs=60.3
Q ss_pred hhccCCCCCCChHHH-HHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 019814 168 KVNDFKNHSLPLARI-KKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 239 (335)
Q Consensus 168 ~~~Dfk~~~LPLARI-KKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV 239 (335)
...++--..+|.+|+ +.|+.. ..+.-++..+|+.++..|+|.|+-.|-+.|..+|...||.||..+||.-+.
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 456777788999986 445543 233358999999999999999999999999999999999999999998774
No 39
>PTZ00018 histone H3; Provisional
Probab=96.69 E-value=0.0057 Score=53.99 Aligned_cols=71 Identities=23% Similarity=0.301 Sum_probs=59.9
Q ss_pred hhccCCCCCCChHHHHH-HHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 019814 168 KVNDFKNHSLPLARIKK-IMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 239 (335)
Q Consensus 168 ~~~Dfk~~~LPLARIKK-IMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV 239 (335)
...|+--..+|.+|+-| |... ..++ ++..+|+.++..|+|.|+-.|-+.|..+|...||.||..+||.-+.
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 45677778899988644 5443 3454 9999999999999999999999999999999999999999997763
No 40
>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=96.69 E-value=0.007 Score=47.93 Aligned_cols=63 Identities=19% Similarity=0.294 Sum_probs=51.3
Q ss_pred ChHHHHHHHhC--CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-cCHHHHHHHHh
Q 019814 178 PLARIKKIMKA--DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRT-LQKNDIAAAIT 240 (335)
Q Consensus 178 PLARIKKIMKs--DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKT-Lqy~DIA~AV~ 240 (335)
|-.-|.||++. ..+-.+||+||..++++=.++|+.+-+.||...++..+... |..+||.++.-
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 44568889986 46778999999999999999999999999999999988888 99999998643
No 41
>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=96.59 E-value=0.005 Score=50.81 Aligned_cols=84 Identities=24% Similarity=0.296 Sum_probs=54.1
Q ss_pred HHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCccCHH
Q 019814 155 LQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENK-RRTLQKN 233 (335)
Q Consensus 155 L~~FW~~q~~EiE~~~Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~K-RKTLqy~ 233 (335)
|.+|=.+|++--| .|+...||-+.|||||..--+...|+....++++-.+.+|+.+|.++|.+...+.+ ..-|+++
T Consensus 5 ~~~f~~eQ~~Rye---~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~ 81 (90)
T PF04719_consen 5 LSNFDEEQLDRYE---AFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPD 81 (90)
T ss_dssp -----HHHHHHHH---HHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HH
T ss_pred HHcCCHHHHHHHH---HHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcH
Confidence 3344444443333 34456799999999999855446899999999999999999999999999987654 4589999
Q ss_pred HHHHHHhc
Q 019814 234 DIAAAITR 241 (335)
Q Consensus 234 DIA~AV~~ 241 (335)
||..|..+
T Consensus 82 hlreA~rr 89 (90)
T PF04719_consen 82 HLREAYRR 89 (90)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 99998753
No 42
>PLN00160 histone H3; Provisional
Probab=96.44 E-value=0.0098 Score=49.84 Aligned_cols=72 Identities=24% Similarity=0.230 Sum_probs=59.4
Q ss_pred hhccCCCCCCChHHHH-HHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 019814 168 KVNDFKNHSLPLARIK-KIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 239 (335)
Q Consensus 168 ~~~Dfk~~~LPLARIK-KIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV 239 (335)
...++--..+|.+|+- .|+.. ..+.-++.++|..++..|+|.|+-.|-+.|..+|...||.||..+||.-+.
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 3556666788998864 44432 234459999999999999999999999999999999999999999998774
No 43
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=96.41 E-value=0.0047 Score=62.10 Aligned_cols=64 Identities=22% Similarity=0.221 Sum_probs=46.2
Q ss_pred cCCCCCCChHHHHHHHhCC-----cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHH
Q 019814 171 DFKNHSLPLARIKKIMKAD-----EDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKND 234 (335)
Q Consensus 171 Dfk~~~LPLARIKKIMKsD-----pDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~D 234 (335)
......||-+-|||+...= ---.+|+++|.-+|.+|+++|.+.|+..=-.+|++.|||||..+|
T Consensus 346 gi~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 346 GIPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ------S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3455789999999987642 133689999999999999999999999999999999999999876
No 44
>smart00427 H2B Histone H2B.
Probab=96.22 E-value=0.015 Score=48.16 Aligned_cols=59 Identities=24% Similarity=0.269 Sum_probs=51.9
Q ss_pred HHHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Q 019814 182 IKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 241 (335)
Q Consensus 182 IKKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~ 241 (335)
|.|++|- .||. .||..|.-++.--..-+.+.++.+|...+..+||+||+..+|..||+-
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 7888885 7887 688888888887777888899999999999999999999999999863
No 45
>PTZ00463 histone H2B; Provisional
Probab=95.16 E-value=0.063 Score=46.59 Aligned_cols=59 Identities=22% Similarity=0.204 Sum_probs=51.1
Q ss_pred HHHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Q 019814 182 IKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 241 (335)
Q Consensus 182 IKKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~ 241 (335)
|.|++|. .||.+ ||..|.-++.--..-..+.++.+|...+..++|+||+..+|..||.-
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 7888885 78875 68888888887777778889999999999999999999999999863
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=94.95 E-value=0.092 Score=41.15 Aligned_cols=61 Identities=13% Similarity=0.318 Sum_probs=47.8
Q ss_pred HHHHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 181 RIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 181 RIKKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
++..++|. ||. ..+..++--++...++.||...+..|...|+..|..||..+||.-.++++
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 56666775 444 57788899999999999999999999999999999999999999988764
No 47
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=94.88 E-value=0.051 Score=50.63 Aligned_cols=89 Identities=26% Similarity=0.363 Sum_probs=71.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCC
Q 019814 150 QLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEEN-KRR 228 (335)
Q Consensus 150 ~~qq~L~~FW~~q~~EiE~~~Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~-KRK 228 (335)
..+--|.+|=.+|+.--| .|+...||-+.|||+|..--.-. |+..+.++++--.++||-+|++.|.++.... ...
T Consensus 89 r~q~L~s~fseEQl~RYE---vfRrs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~ 164 (195)
T KOG3219|consen 89 RMQTLLSNFSEEQLSRYE---VFRRSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESG 164 (195)
T ss_pred HHHHHHHhcCHHHHHHHH---HHHHhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCC
Confidence 455667777777655433 57778899999999999744433 8999999999999999999999999988654 456
Q ss_pred ccCHHHHHHHHhcC
Q 019814 229 TLQKNDIAAAITRT 242 (335)
Q Consensus 229 TLqy~DIA~AV~~~ 242 (335)
-|+.+||..|+.+.
T Consensus 165 PLqP~HIREA~rrL 178 (195)
T KOG3219|consen 165 PLQPKHIREAYRRL 178 (195)
T ss_pred CCCcHHHHHHHHHH
Confidence 79999999998764
No 48
>PLN00158 histone H2B; Provisional
Probab=94.83 E-value=0.088 Score=45.65 Aligned_cols=60 Identities=22% Similarity=0.245 Sum_probs=52.2
Q ss_pred HHHHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Q 019814 181 RIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 241 (335)
Q Consensus 181 RIKKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~ 241 (335)
=|.|++|. .||.+ ||..|.-++.--..-+.+.|+.+|...+..++|+||+..+|..||.-
T Consensus 32 YI~kVLKQVhPd~g-IS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrL 92 (116)
T PLN00158 32 YIYKVLKQVHPDTG-ISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRL 92 (116)
T ss_pred HHHHHHHHhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 38888886 78875 68888888888788888899999999999999999999999999863
No 49
>PF15510 CENP-W: Centromere kinetochore component W
Probab=94.56 E-value=0.077 Score=44.77 Aligned_cols=65 Identities=20% Similarity=0.329 Sum_probs=51.3
Q ss_pred CCChHHHHHHHhCCcchhccCccHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHh
Q 019814 176 SLPLARIKKIMKADEDVRMISAEAPVI--------------FARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAIT 240 (335)
Q Consensus 176 ~LPLARIKKIMKsDpDV~~ISaEApvL--------------IAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~ 240 (335)
.-|-+-+||++|-..---++...+-.+ +---|=+|+..|+++|-..|-++|..+|+.+||..|-+
T Consensus 16 kaPrgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred hCchHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 358888999999643333444444444 56678899999999999999999999999999988754
No 50
>PLN00155 histone H2A; Provisional
Probab=94.44 E-value=0.044 Score=42.41 Aligned_cols=36 Identities=31% Similarity=0.448 Sum_probs=33.2
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHH
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEM 209 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtEL 209 (335)
.+.||++||.|.+|..--..+|++.|++.++..+|.
T Consensus 22 gL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEY 57 (58)
T PLN00155 22 GLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEY 57 (58)
T ss_pred ccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHh
Confidence 588999999999999877889999999999999886
No 51
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=94.35 E-value=0.13 Score=43.20 Aligned_cols=63 Identities=21% Similarity=0.254 Sum_probs=56.1
Q ss_pred HHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCC
Q 019814 180 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 243 (335)
Q Consensus 180 ARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d 243 (335)
--|+||.+- ..|++|+--...-+..+...||+.....|...++..|||||+..||.-++++.-
T Consensus 33 paIRRlARr-~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G 95 (103)
T KOG3467|consen 33 PAIRRLARR-GGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 95 (103)
T ss_pred HHHHHHHHh-cCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcC
Confidence 357888776 788999988888899999999999999999999999999999999999988753
No 52
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=94.17 E-value=0.12 Score=41.33 Aligned_cols=63 Identities=14% Similarity=0.126 Sum_probs=46.8
Q ss_pred HHHHHhCC--cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCc
Q 019814 182 IKKIMKAD--EDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDI 244 (335)
Q Consensus 182 IKKIMKsD--pDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~ 244 (335)
|-||.+.. +.-..+|.++..+++..+=.++..++..-...|+..||+||+.+||.-..++++.
T Consensus 11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~ 75 (76)
T PF15630_consen 11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPS 75 (76)
T ss_dssp HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HH
T ss_pred HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCC
Confidence 34444432 2334688888888888888888899998888999999999999999999988865
No 53
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=93.87 E-value=0.25 Score=38.35 Aligned_cols=60 Identities=17% Similarity=0.189 Sum_probs=52.9
Q ss_pred HHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 182 IKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 182 IKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
|.+|++. -+...++..|.-.++-.+..||.+|+..+...|+..+|......||..|+.+.
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 5566655 56678999999999999999999999999999999999999999999998764
No 54
>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=93.21 E-value=0.081 Score=43.35 Aligned_cols=75 Identities=15% Similarity=0.240 Sum_probs=34.1
Q ss_pred HHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC-CcchhhhhcCCCCc
Q 019814 182 IKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT-DIFDFLVDIVPRED 256 (335)
Q Consensus 182 IKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~-d~FDFL~DIVPr~~ 256 (335)
|+.+|-.-.|+..-..|...++-...-.||.+|+.+|...|...++++|+.+||.-+++++ ..+.-|.+++-.+.
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 6788998899999999999999999999999999999999999999999999999999987 45666666665443
No 55
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=92.90 E-value=0.29 Score=43.10 Aligned_cols=63 Identities=19% Similarity=0.205 Sum_probs=47.4
Q ss_pred CCCChHHHHHHHhC-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Q 019814 175 HSLPLARIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 241 (335)
Q Consensus 175 ~~LPLARIKKIMKs-DpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~ 241 (335)
...++.| ++|. +||.+ |+.+|.-++.--.-.|++.++.+|...|..+||.||+-.+|..|++=
T Consensus 39 ~s~yv~k---vlk~Vhpd~g-is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 39 YSEYVYK---VLKQVHPDLG-ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred eeeehhh---hhhcccCCCC-cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 3445444 6664 78855 66666665555555558889999999999999999999999998753
No 56
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=92.13 E-value=0.13 Score=45.67 Aligned_cols=71 Identities=21% Similarity=0.216 Sum_probs=60.3
Q ss_pred ccCCCCCCChHHHHH-HHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHh
Q 019814 170 NDFKNHSLPLARIKK-IMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAIT 240 (335)
Q Consensus 170 ~Dfk~~~LPLARIKK-IMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~ 240 (335)
.|+--..+|..|.-| |++.--..-.+-+.|...|-.|.|.|+-.|-+.+..+|-..||.||-.+||.-|..
T Consensus 60 tdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr 131 (137)
T KOG1745|consen 60 TDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 131 (137)
T ss_pred hHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence 344445789999877 88775545688899999999999999999999999999999999999999987754
No 57
>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=91.64 E-value=0.69 Score=38.15 Aligned_cols=76 Identities=16% Similarity=0.249 Sum_probs=63.4
Q ss_pred HHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCC-cchhhhhcCCCCc
Q 019814 180 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD-IFDFLVDIVPRED 256 (335)
Q Consensus 180 ARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d-~FDFL~DIVPr~~ 256 (335)
.-|+.+|-.-.|+..-..|.+-++-..+-.||.+|+.+|...|. .+|..++.+||.-+|.+++ .+.-|.+++-.++
T Consensus 6 ~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL~~k~ 82 (92)
T cd07978 6 KEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPKKLARLRELLSMKD 82 (92)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 34888999888999999999999999999999999999999998 5555569999999998874 4666666665433
No 58
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.59 E-value=0.21 Score=48.37 Aligned_cols=58 Identities=14% Similarity=0.172 Sum_probs=51.0
Q ss_pred hccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhh
Q 019814 193 RMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 250 (335)
Q Consensus 193 ~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~D 250 (335)
..+-.|+--+|..-|+-||+.++.+|...|+..|..||..+||.-.++++-.+.|=.+
T Consensus 171 ~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf 228 (258)
T KOG1142|consen 171 TKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGF 228 (258)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCc
Confidence 5666778889999999999999999999999999999999999999999876665443
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.38 E-value=1.9 Score=39.82 Aligned_cols=81 Identities=19% Similarity=0.369 Sum_probs=61.1
Q ss_pred HHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh--------
Q 019814 153 QQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEE-------- 224 (335)
Q Consensus 153 q~L~~FW~~q~~EiE~~~Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe-------- 224 (335)
..|.+|-.+ ..|.. ..+|=+-+.-+|+. ..+...-.-..-|++.|+.-||.+++..|+.+++-
T Consensus 71 ~~l~efl~q-------LddYt-P~IPDavt~~yL~~-aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~ 141 (176)
T KOG3423|consen 71 THLEEFLAQ-------LDDYT-PTIPDAVTDHYLKK-AGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGK 141 (176)
T ss_pred hHHHHHHHH-------HhcCC-CCCcHHHHHHHHHh-cCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccccc
Confidence 456666442 34444 66999999999987 34444445567799999999999999999999873
Q ss_pred ------cCCCccCHHHHHHHHhcC
Q 019814 225 ------NKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 225 ------~KRKTLqy~DIA~AV~~~ 242 (335)
.|+-||+.+||..|+++.
T Consensus 142 ~k~~~kdkK~tLtmeDL~~AL~Ey 165 (176)
T KOG3423|consen 142 DKKQAKDKKYTLTMEDLSPALAEY 165 (176)
T ss_pred ccccccccceeeeHHHHHHHHHHh
Confidence 235689999999998765
No 60
>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=88.26 E-value=0.88 Score=42.92 Aligned_cols=44 Identities=18% Similarity=0.231 Sum_probs=32.9
Q ss_pred HHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 019814 180 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEE 224 (335)
Q Consensus 180 ARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe 224 (335)
.||.+|++... +..+..|.+-||+-|||..|..|..++...|+.
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 67888887755 788999999999999999999999999998864
No 61
>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=87.28 E-value=2.3 Score=37.22 Aligned_cols=68 Identities=15% Similarity=0.102 Sum_probs=42.7
Q ss_pred HHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhh
Q 019814 181 RIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 249 (335)
Q Consensus 181 RIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~ 249 (335)
-|..|+|+ -+|......++..+-.-+=.++.++...|...|...+|++|..+||..||+..-.+.|-.
T Consensus 17 ~i~~iL~~-~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ 84 (129)
T PF02291_consen 17 VIHLILKS-MGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQ 84 (129)
T ss_dssp HHHHHHHH-TT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-------
T ss_pred HHHHHHHH-cCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccC
Confidence 46667776 355555555555444445567888999999999999999999999999999775566643
No 62
>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=82.97 E-value=2.5 Score=38.84 Aligned_cols=60 Identities=17% Similarity=0.216 Sum_probs=47.1
Q ss_pred HHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCccCHHHHHHHHh
Q 019814 180 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEEN------KRRTLQKNDIAAAIT 240 (335)
Q Consensus 180 ARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~------KRKTLqy~DIA~AV~ 240 (335)
.+|.+|++. ..+..|+.|...+|+.|||.++..|.......++.. ..+....+|+...+.
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 567777776 344489999999999999999999999999988753 345666778776554
No 63
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=82.89 E-value=3.3 Score=44.21 Aligned_cols=63 Identities=19% Similarity=0.258 Sum_probs=55.4
Q ss_pred hHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 179 LARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 179 LARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
-.-+|-+.++ -.+..++.||..+++.=.|+=|++++..|.+.....||++|+-+||..|++..
T Consensus 14 ~Es~k~vAEs-lGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~ 76 (576)
T KOG2549|consen 14 KESVKVVAES-LGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSL 76 (576)
T ss_pred HHHHHHHHHH-hCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhc
Confidence 4456666665 67789999999999999999999999999999999999999999999998653
No 64
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=70.57 E-value=17 Score=27.62 Aligned_cols=47 Identities=9% Similarity=0.118 Sum_probs=33.0
Q ss_pred CChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 019814 177 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEE 224 (335)
Q Consensus 177 LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe 224 (335)
+|=+-+.-+|+. -++..--.-..-|++-|++-||.+++..|+.+++.
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 455666666664 22222333456689999999999999999998753
No 65
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.35 E-value=28 Score=32.53 Aligned_cols=60 Identities=7% Similarity=0.138 Sum_probs=43.1
Q ss_pred HHHHHhhccCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 019814 163 YQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTE 223 (335)
Q Consensus 163 ~~EiE~~~Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aq 223 (335)
++|+-+.-|--...+|=+-+.=-|.. ..+.....-..-|++.++.-||.+++..||...+
T Consensus 75 lee~l~~mDsy~PliPd~v~DYyl~k-~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsr 134 (197)
T COG5162 75 LEELLQNMDSYTPLIPDSVTDYYLEK-AGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSR 134 (197)
T ss_pred HHHHHHhcccCCCCccHHHHHHHHHh-cCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34443445555677898888877765 3344444556679999999999999999998744
No 66
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=63.44 E-value=17 Score=37.23 Aligned_cols=60 Identities=22% Similarity=0.226 Sum_probs=52.2
Q ss_pred HHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 182 IKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 182 IKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
||....+ -.+..|..|+.-+++--.|.=|.+++.+|.+.....||..|+-+||..|++..
T Consensus 11 ~KdvAes-lGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~l 70 (450)
T COG5095 11 LKDVAES-LGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSL 70 (450)
T ss_pred HHHHHHH-cCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhc
Confidence 4444443 56778999999999999999999999999999999999999999999998764
No 67
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=56.00 E-value=13 Score=26.97 Aligned_cols=35 Identities=23% Similarity=0.284 Sum_probs=28.1
Q ss_pred hHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHH
Q 019814 179 LARIKKIMKADEDVRMISAEAPVIFARACEMFILE 213 (335)
Q Consensus 179 LARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~e 213 (335)
+.||+|++..-.+..--..||-.++.+|-++..++
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 57999999987765555569999999999887654
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=53.92 E-value=20 Score=32.33 Aligned_cols=50 Identities=18% Similarity=0.111 Sum_probs=40.5
Q ss_pred ccCccHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCC
Q 019814 194 MISAEAPVIFARACEM---FILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 243 (335)
Q Consensus 194 ~ISaEApvLIAKAtEL---FI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d 243 (335)
.++.++.-.+.+.|.= .|..|+..++..|..++.++|+.++|..++....
T Consensus 215 ~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~ 267 (269)
T TIGR03015 215 VFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEID 267 (269)
T ss_pred CcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhh
Confidence 4677777777766663 6888999999998888999999999999998753
No 69
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=51.86 E-value=1.3e+02 Score=24.59 Aligned_cols=62 Identities=18% Similarity=0.222 Sum_probs=50.8
Q ss_pred CCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCHHHHHHHHh
Q 019814 172 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMF------ILELTLRSWNHTEENKRRTLQKNDIAAAIT 240 (335)
Q Consensus 172 fk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELF------I~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~ 240 (335)
..|-.||-.-|++...+++ ++..++..+.+-| +..+.+-|+.+|--++...|..+||+.|+.
T Consensus 27 ~~Na~l~~~~l~~~~~l~~-------~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 27 KCNAQLPGEELRKYCPLSS-------EAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CccccCCHHHHHhHcCCCH-------HHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 4578899999999877655 4566677777766 567888899999999999999999999985
No 70
>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=48.40 E-value=26 Score=32.91 Aligned_cols=42 Identities=14% Similarity=0.193 Sum_probs=32.4
Q ss_pred HHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHH
Q 019814 180 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHT 222 (335)
Q Consensus 180 ARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~A 222 (335)
.|+-.|... .+...|+.|+.-+|..|+|.|++.|...+...+
T Consensus 210 ~Rm~~ia~e-~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~ 251 (252)
T PF12767_consen 210 KRMEQIAWE-HGLGGVSDDCANLLNLALEVHLKNLIKSCLDLV 251 (252)
T ss_pred HHHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 344444432 445679999999999999999999999888653
No 71
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=43.24 E-value=78 Score=30.47 Aligned_cols=49 Identities=16% Similarity=0.228 Sum_probs=35.8
Q ss_pred ccCccHHHHHHHHHHH------HHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 194 MISAEAPVIFARACEM------FILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 194 ~ISaEApvLIAKAtEL------FI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
.++.++.-++++.+.- .+..|...|+..|...++.+|+.+||..|+...
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 3555666555555432 334567888888888889999999999999876
No 72
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=38.95 E-value=2.4e+02 Score=29.64 Aligned_cols=60 Identities=13% Similarity=0.148 Sum_probs=48.2
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCHHHHHHHHh
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMF------ILELTLRSWNHTEENKRRTLQKNDIAAAIT 240 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELF------I~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~ 240 (335)
|..|+-..|++..+.++ ++.-++..|.+.| ...+.+-|+..|.-+++..|..+||+.|+.
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 77889998988777655 4555566666665 567888899999999999999999999985
No 73
>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=37.93 E-value=95 Score=30.41 Aligned_cols=83 Identities=14% Similarity=0.300 Sum_probs=60.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhCC--cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 019814 148 QQQLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKAD--EDVRMISAEAPVIFARACEMFILELTLRSWNHTEEN 225 (335)
Q Consensus 148 ~~~~qq~L~~FW~~q~~EiE~~~Dfk~~~LPLARIKKIMKsD--pDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~ 225 (335)
+.+.-+.+..||.+.+- + |+-+|...++.| .++..+|++++..=...+|-.+.+++......
T Consensus 28 ~~~~~~t~~~f~~nwV~---~---------Pl~~I~~tlr~d~~s~~~i~s~~sL~~d~~SLeRMv~dF~~d~~~~---- 91 (290)
T PF08637_consen 28 QENAVETVRGFWKNWVW---E---------PLKSIWDTLRHDEKSEIAIMSKESLQSDMESLERMVVDFAKDNSPN---- 91 (290)
T ss_pred HHHHHHHHHHHHHHHHH---H---------HHHHHHHHHhCCCCCCcccccHHHHHHHHHHHHHHHHHHHhcCCCC----
Confidence 34677889999999753 2 999999999996 66789999999888888888888887754432
Q ss_pred CCCccCHHHHHHHHhcCCcchhh
Q 019814 226 KRRTLQKNDIAAAITRTDIFDFL 248 (335)
Q Consensus 226 KRKTLqy~DIA~AV~~~d~FDFL 248 (335)
.....+.|...|+.-|--.++
T Consensus 92 --~~~~~~~l~~~v~~Gdlt~Vm 112 (290)
T PF08637_consen 92 --MPADLEELRQQVREGDLTPVM 112 (290)
T ss_pred --CcchHHHHHHHHHcCCcHHHH
Confidence 125556666666665544444
No 74
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=36.14 E-value=1.3e+02 Score=30.49 Aligned_cols=46 Identities=20% Similarity=0.182 Sum_probs=34.0
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhCC
Q 019814 144 HHQQQQQLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKAD 189 (335)
Q Consensus 144 ~~~~~~~~qq~L~~FW~~q~~EiE~~~Dfk~~~LPLARIKKIMKsD 189 (335)
|+.+....++....+-+++.+|.+.-..-....||+.-+|||+|.-
T Consensus 250 yqr~~~rqq~~~~q~~aKrqaENa~R~argep~lP~dd~kr~fk~p 295 (339)
T KOG1560|consen 250 YQRQLARQQAKKHQWIAKRQAENANRAARGEPPLPEDDWKRIFKPP 295 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCCCChHHHHHHhcCC
Confidence 3444444556666667777778777677778899999999999973
No 75
>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=34.97 E-value=1.5e+02 Score=28.19 Aligned_cols=33 Identities=9% Similarity=0.169 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCC
Q 019814 211 ILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 243 (335)
Q Consensus 211 I~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d 243 (335)
+..+...|+..|..+++.+|+.+||..|+....
T Consensus 243 al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~ 275 (365)
T TIGR02928 243 AIDLLRVAGEIAEREGAERVTEDHVEKAQEKIE 275 (365)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 345667778878788888999999999987764
No 76
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=32.84 E-value=1.1e+02 Score=31.36 Aligned_cols=65 Identities=12% Similarity=0.086 Sum_probs=54.0
Q ss_pred CChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 177 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 177 LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
|=..+|+.|+.+-+. ...-..|.-.|+.-+-.||+.|.+-|..++...+|--.+..||..|+..-
T Consensus 30 la~~avaQIcqslg~-~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dl 94 (353)
T KOG2389|consen 30 LARVAVAQICQSLGY-SSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDL 94 (353)
T ss_pred HHHHHHHHHHHhcCC-cccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHh
Confidence 445678899988433 34444589999999999999999999999999999999999999998763
No 77
>PTZ00469 60S ribosomal subunit protein L18; Provisional
Probab=31.72 E-value=17 Score=34.00 Aligned_cols=89 Identities=12% Similarity=0.149 Sum_probs=54.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHH--hCCcch---hccCccHHHHHHHHHHHHHHHHHHHHHHHH
Q 019814 148 QQQLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIM--KADEDV---RMISAEAPVIFARACEMFILELTLRSWNHT 222 (335)
Q Consensus 148 ~~~~qq~L~~FW~~q~~EiE~~~Dfk~~~LPLARIKKIM--KsDpDV---~~ISaEApvLIAKAtELFI~eLT~rA~~~A 222 (335)
.......=..||...++.++.....+ ..+-|+||-|.| +.|+-+ +.|..+.-+.--...-.....+++.|...-
T Consensus 34 k~larrt~a~fwk~Va~RL~~srrnr-~pVnLSkI~r~~~~ke~~~~VVvGkVl~dgrl~~vpkvtVaAL~fS~~Ar~kI 112 (187)
T PTZ00469 34 RFLARRTNANFNKIIAKRLIMPKRFR-PPLSLSKLHRHMASYPDDVAVVVGSITDDKRLYDCKKLKVCALRFTETARKRI 112 (187)
T ss_pred HHHHHhhCChHHHHHHHHHhcccccC-CceeHHHHHHHhccCCCCEEEEEeeEccCccccccCceEEEEEecCHHHHHHH
Confidence 33344455789999988888654444 668899999999 433322 344445444311111122234566666666
Q ss_pred HhcCCCccCHHHHHH
Q 019814 223 EENKRRTLQKNDIAA 237 (335)
Q Consensus 223 qe~KRKTLqy~DIA~ 237 (335)
...+.+.|+.++|+.
T Consensus 113 ~~AGGe~lT~dqLa~ 127 (187)
T PTZ00469 113 LDAGGECLTFDQLAL 127 (187)
T ss_pred HHhCCEEEeHHHHHH
Confidence 677888898888776
No 78
>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=30.87 E-value=1.4e+02 Score=31.94 Aligned_cols=32 Identities=6% Similarity=-0.003 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 211 ILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 211 I~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
+..|.++|...|+.+++.+|+.+||..|++..
T Consensus 360 L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 360 LGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 55677778777888889999999999998754
No 79
>PF08250 Sperm_act_pep: Sperm-activating peptides; InterPro: IPR013254 The sperm-activating peptides (SAPs) are isolated in egg-conditioned media (egg jelly) of sea urchins. SAPs have several effects on sea urchin spermatozoa: stimulate sperm respiration and motility through intracellular alkalinization, transient elevation of cAMP, cGMP and Ca2+ levels in sperm cells [, ].
Probab=30.74 E-value=23 Score=19.11 Aligned_cols=9 Identities=67% Similarity=1.324 Sum_probs=7.6
Q ss_pred ccccCCCch
Q 019814 48 GFNLGEGGK 56 (335)
Q Consensus 48 ~~~~~~~~~ 56 (335)
||++|.||+
T Consensus 1 gf~l~GgGV 9 (10)
T PF08250_consen 1 GFSLGGGGV 9 (10)
T ss_pred CcccccCcC
Confidence 789998886
No 80
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=28.49 E-value=1.5e+02 Score=30.10 Aligned_cols=63 Identities=17% Similarity=0.160 Sum_probs=53.7
Q ss_pred hHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhc
Q 019814 179 LARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 241 (335)
Q Consensus 179 LARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~ 241 (335)
|+.|--+|+.+.....|++-|.--|..+..-.|.++.+.+..+++..+|...++.||+-.+.+
T Consensus 7 l~~VV~~Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~ 69 (323)
T KOG4336|consen 7 LAPVVSNLLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIE 69 (323)
T ss_pred HHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH
Confidence 455666777777888899988888888888889999999999999999999999999887554
No 81
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=28.44 E-value=7.1 Score=37.35 Aligned_cols=75 Identities=21% Similarity=0.087 Sum_probs=50.9
Q ss_pred CCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhhcC
Q 019814 173 KNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDIV 252 (335)
Q Consensus 173 k~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~DIV 252 (335)
..-..++.|+..+++ +++.+ .+++..-.|...|....+.+....+|.+|..-.+..+|...+.+||+.+++
T Consensus 5 ~~~~~~~~~~~~~~~------~~~p~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~fw~~~~~e~e~~~d~~~~~l 75 (236)
T KOG1657|consen 5 NANSDIVANIVSNRR------MKAPP---KGAKSEPEGAVCLDPEASIITGDVSRQQLQSFWSKQAIEKEGQLDFKNHIL 75 (236)
T ss_pred ccCcccccccccccc------ccCCc---cccccccccceecchhhhhcccchhhHHHHhhhhccccccccccchhhccC
Confidence 334456666666663 22222 333333334447777777776666688999889999988899999999999
Q ss_pred CCCc
Q 019814 253 PRED 256 (335)
Q Consensus 253 Pr~~ 256 (335)
|...
T Consensus 76 PlaR 79 (236)
T KOG1657|consen 76 PLAR 79 (236)
T ss_pred cHhh
Confidence 9543
No 82
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=26.01 E-value=2.1e+02 Score=25.34 Aligned_cols=62 Identities=19% Similarity=0.176 Sum_probs=46.0
Q ss_pred HHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCC
Q 019814 180 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 243 (335)
Q Consensus 180 ARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d 243 (335)
--||-+|=.-.|+..-..+..-++-.-.--++.+|+..|+..|+ .|..++.+|+.-|+++++
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 34666777666666666666666666666677888888998886 667778889999988875
No 83
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=25.58 E-value=76 Score=29.93 Aligned_cols=69 Identities=17% Similarity=0.164 Sum_probs=53.0
Q ss_pred ccCCCCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCC---CccCHHHHHHHHhc
Q 019814 170 NDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKR---RTLQKNDIAAAITR 241 (335)
Q Consensus 170 ~Dfk~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KR---KTLqy~DIA~AV~~ 241 (335)
..|+...||-+-|||+.-.- -...||....++++-....|+.++.+-|..+- +++ --|...|+..|+..
T Consensus 109 EvFrrt~lnKt~VKKlastV-~nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq--~~w~~sgpl~p~h~reayr~ 180 (199)
T COG5251 109 EVFRRTSLNKTQVKKLASTV-ANQTVSPNIRIFLQGVGKVFVGEIIELAMIVQ--NKWLTSGPLIPFHKREAYRY 180 (199)
T ss_pred HHHHhcCCCHHHHHHHHHHH-hccccCCCeeeeeechhHHHHHHHHHHHHHHH--HHhcccCCCChHHHHHHHHH
Confidence 45888999999999998762 22567788888888888999999988887653 333 34788898888654
No 84
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=25.28 E-value=2.4e+02 Score=20.04 Aligned_cols=47 Identities=9% Similarity=-0.001 Sum_probs=31.1
Q ss_pred hccCccHHHHHHHHH-----HHHHHHHHHHHHHHHHhcCCCccCHHHHHHHH
Q 019814 193 RMISAEAPVIFARAC-----EMFILELTLRSWNHTEENKRRTLQKNDIAAAI 239 (335)
Q Consensus 193 ~~ISaEApvLIAKAt-----ELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV 239 (335)
+.|+.+-...+.+.. +..+..++...+..+-.++...|+++++..++
T Consensus 15 G~i~~~el~~~~~~~~~~~~~~~~~~~~~~~~~~~D~d~dG~i~~~Ef~~~~ 66 (66)
T PF13499_consen 15 GYISKEELRRALKHLGRDMSDEESDEMIDQIFREFDTDGDGRISFDEFLNFM 66 (66)
T ss_dssp SEEEHHHHHHHHHHTTSHSTHHHHHHHHHHHHHHHTTTSSSSEEHHHHHHHH
T ss_pred CCCCHHHHHHHHHHhcccccHHHHHHHHHHHHHHhCCCCcCCCcHHHHhccC
Confidence 455544443333333 55566777777888888888899999887653
No 85
>PTZ00195 60S ribosomal protein L18; Provisional
Probab=24.83 E-value=28 Score=33.00 Aligned_cols=89 Identities=16% Similarity=0.172 Sum_probs=53.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhCCc--------c-----hhccCccHHHHHHHHHHHHHHHH
Q 019814 148 QQQLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADE--------D-----VRMISAEAPVIFARACEMFILEL 214 (335)
Q Consensus 148 ~~~~qq~L~~FW~~q~~EiE~~~Dfk~~~LPLARIKKIMKsDp--------D-----V~~ISaEApvLIAKAtELFI~eL 214 (335)
.......=..||...++.++.... ....+-|+||-|.||.++ + ++.|..|.-+.---.+-.....+
T Consensus 34 rflaRrt~a~fnk~VakRL~~sr~-nRppVsLSrI~r~~k~~d~~~~~~~~~k~~VVvGkVtdd~rl~~vPkvtVaALrf 112 (198)
T PTZ00195 34 KFLAKRTSSGFNKVVYQRLIKSRS-NRAPISLSRIAVVMKRKAVFTAKGKKAPIAVVVGDVLDDVRMARIPAMRVCALRF 112 (198)
T ss_pred HHHHHhhCCHHHHHHHHHHhcccc-cCCceeHHHHHHHHhccccccccCCCCcEEEEEeeEcCCccccccCceEEEEEec
Confidence 333444557899999888886443 346788999999999754 0 22333333221100111122345
Q ss_pred HHHHHHHHHhcCCCccCHHHHHH
Q 019814 215 TLRSWNHTEENKRRTLQKNDIAA 237 (335)
Q Consensus 215 T~rA~~~Aqe~KRKTLqy~DIA~ 237 (335)
++.|-..-...+-+.|+.++|+.
T Consensus 113 S~tAr~rI~kAGGe~lT~dQLa~ 135 (198)
T PTZ00195 113 SKSARQSIVAAGGECLTFDQLAM 135 (198)
T ss_pred CHHHHHHHHHhCCEEEeHHHHHH
Confidence 66666666667888898888776
No 86
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=23.10 E-value=2.8e+02 Score=24.30 Aligned_cols=70 Identities=14% Similarity=0.141 Sum_probs=48.0
Q ss_pred HHHHHhCCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCC-cchhhhhcCCC
Q 019814 182 IKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD-IFDFLVDIVPR 254 (335)
Q Consensus 182 IKKIMKsDpDV~~ISaEApvLIAKAtELFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d-~FDFL~DIVPr 254 (335)
++-+|=.=.|+..=-.|.+-++-.-.-.||.+|+..|.... +|..++.+||.-+|++++ .|.=..|++-.
T Consensus 15 l~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRkDpkK~~Rv~eLL~m 85 (109)
T KOG3901|consen 15 LRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRKDPKKLGRVKELLAM 85 (109)
T ss_pred HHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHhChHHHhHHHHHHHh
Confidence 34444444455555567777777777778888888777764 788889999999999885 35545555543
No 87
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=22.75 E-value=2.9e+02 Score=25.29 Aligned_cols=40 Identities=15% Similarity=0.122 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhh
Q 019814 210 FILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 249 (335)
Q Consensus 210 FI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~ 249 (335)
++..+...|...++..++.+|..+||..||...-.+.|-.
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 4667788899999999999999999999999988888866
No 88
>PRK09862 putative ATP-dependent protease; Provisional
Probab=22.36 E-value=3.8e+02 Score=28.49 Aligned_cols=62 Identities=10% Similarity=0.114 Sum_probs=43.6
Q ss_pred CCCCChHHHHHHHhCCcchhccCccHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCccCHHHHHHHHhcC
Q 019814 174 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMF------ILELTLRSWNHTEENKRRTLQKNDIAAAITRT 242 (335)
Q Consensus 174 ~~~LPLARIKKIMKsDpDV~~ISaEApvLIAKAtELF------I~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~ 242 (335)
+..++-..|++.++.+.+... ++..+.+.+ ...|.+-|+..|--.+|..|+.+||+.|+.-.
T Consensus 425 n~~l~~~~l~~~~~l~~~~~~-------~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR 492 (506)
T PRK09862 425 NAWLDSPEIRQFCKLESEDAR-------WLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYR 492 (506)
T ss_pred hcccCHHHHHHHhCCCHHHHH-------HHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhh
Confidence 556676677766665554443 333333332 45678888999999999999999999999865
No 89
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=21.74 E-value=1.3e+02 Score=30.21 Aligned_cols=59 Identities=17% Similarity=0.268 Sum_probs=42.0
Q ss_pred ccCccHHHHHHH--HHH----HHHHHHHHHHHHHHHhcCCCccCHHHHHHHHhcCCcchhhhhcCC
Q 019814 194 MISAEAPVIFAR--ACE----MFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDIVP 253 (335)
Q Consensus 194 ~ISaEApvLIAK--AtE----LFI~eLT~rA~~~Aqe~KRKTLqy~DIA~AV~~~d~FDFL~DIVP 253 (335)
.++.++.-+++. |.+ .+..+|...|...|++.++.+++.+|+..|....+ .+++.+.+-
T Consensus 211 ~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~-~~~~~~~~~ 275 (366)
T COG1474 211 VIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIE-RDVLEEVLK 275 (366)
T ss_pred CcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhh-HHHHHHHHH
Confidence 455555555552 222 25568999999999999999999999999955554 566666643
Done!