Query 026901
Match_columns 231
No_of_seqs 219 out of 774
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 14:18:52 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026901hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1657 CCAAT-binding factor, 100.0 1.3E-37 2.8E-42 276.2 12.0 181 37-224 50-236 (236)
2 COG5208 HAP5 CCAAT-binding fac 100.0 4E-31 8.8E-36 233.3 8.8 129 16-144 58-192 (286)
3 PF00808 CBFD_NFYB_HMF: Histon 99.8 3.7E-20 8E-25 133.1 7.7 64 61-124 2-65 (65)
4 KOG1659 Class 2 transcription 99.8 1.3E-19 2.9E-24 159.0 6.0 86 54-139 6-91 (224)
5 COG5247 BUR6 Class 2 transcrip 99.7 1.1E-18 2.3E-23 138.7 5.2 84 57-140 19-102 (113)
6 KOG1658 DNA polymerase epsilon 99.4 1.8E-13 4E-18 115.5 2.0 83 57-139 55-137 (162)
7 COG5262 HTA1 Histone H2A [Chro 99.3 2.4E-12 5.1E-17 104.9 5.9 78 58-135 23-100 (132)
8 cd00074 H2A Histone 2A; H2A is 99.3 4.2E-12 9.1E-17 102.6 7.1 77 59-135 18-94 (115)
9 KOG0869 CCAAT-binding factor, 99.1 2E-10 4.4E-15 97.5 6.8 70 59-128 30-100 (168)
10 COG2036 HHT1 Histones H3 and H 99.1 3.5E-10 7.6E-15 88.3 7.5 79 49-128 7-85 (91)
11 KOG1756 Histone 2A [Chromatin 99.1 2.4E-10 5.1E-15 94.1 6.7 80 58-137 24-103 (131)
12 smart00414 H2A Histone 2A. 99.1 2.5E-10 5.5E-15 91.1 6.6 77 59-135 7-83 (106)
13 PTZ00017 histone H2A; Provisio 99.0 4.3E-10 9.3E-15 93.3 6.1 76 59-134 25-100 (134)
14 PLN00154 histone H2A; Provisio 99.0 4.3E-10 9.4E-15 93.4 6.1 77 59-135 36-113 (136)
15 PLN00156 histone H2AX; Provisi 98.9 1.9E-09 4.2E-14 89.9 6.8 76 59-134 27-102 (139)
16 PLN00153 histone H2A; Provisio 98.9 1.8E-09 3.9E-14 89.1 6.1 77 59-135 22-98 (129)
17 PLN00157 histone H2A; Provisio 98.9 2.1E-09 4.5E-14 89.0 6.0 76 59-134 24-99 (132)
18 smart00803 TAF TATA box bindin 98.9 9.2E-09 2E-13 75.4 7.6 64 61-125 2-65 (65)
19 PTZ00252 histone H2A; Provisio 98.8 8.6E-09 1.9E-13 85.5 6.5 77 59-135 23-102 (134)
20 PF00125 Histone: Core histone 98.8 1.2E-08 2.7E-13 74.3 5.7 68 59-126 6-74 (75)
21 cd00076 H4 Histone H4, one of 98.7 3.5E-08 7.7E-13 76.2 7.5 66 61-127 13-78 (85)
22 PLN00035 histone H4; Provision 98.7 3.8E-08 8.1E-13 78.6 7.8 65 62-127 30-94 (103)
23 PTZ00015 histone H4; Provision 98.7 8.8E-08 1.9E-12 76.3 7.8 67 60-127 29-95 (102)
24 KOG0870 DNA polymerase epsilon 98.7 5.3E-08 1.1E-12 83.4 6.9 77 59-135 8-86 (172)
25 smart00417 H4 Histone H4. 98.6 8.9E-08 1.9E-12 72.3 5.6 61 61-122 13-73 (74)
26 KOG0871 Class 2 transcription 98.5 4.9E-07 1.1E-11 76.4 7.1 77 58-135 9-87 (156)
27 cd07981 TAF12 TATA Binding Pro 98.2 5.9E-06 1.3E-10 61.3 7.8 66 62-128 2-68 (72)
28 cd08048 TAF11 TATA Binding Pro 98.0 1.8E-05 3.9E-10 61.0 7.1 75 51-126 6-83 (85)
29 smart00428 H3 Histone H3. 98.0 4.9E-05 1.1E-09 60.9 8.9 77 47-124 15-98 (105)
30 COG5150 Class 2 transcription 97.8 6.4E-05 1.4E-09 62.6 6.7 79 57-135 7-86 (148)
31 cd07979 TAF9 TATA Binding Prot 97.7 0.0001 2.3E-09 59.5 6.8 69 65-134 5-73 (117)
32 smart00576 BTP Bromodomain tra 97.6 0.00025 5.5E-09 52.9 7.2 60 67-127 12-71 (77)
33 KOG1757 Histone 2A [Chromatin 97.6 4.3E-05 9.2E-10 62.5 2.5 76 59-134 28-104 (131)
34 PF02969 TAF: TATA box binding 97.6 0.00047 1E-08 51.1 7.6 64 61-125 3-66 (66)
35 KOG1658 DNA polymerase epsilon 97.5 0.00012 2.6E-09 62.5 5.0 74 57-135 7-80 (162)
36 cd08050 TAF6 TATA Binding Prot 97.5 0.0003 6.6E-09 65.6 7.4 65 63-128 1-65 (343)
37 PF04719 TAFII28: hTAFII28-lik 97.4 0.00038 8.3E-09 54.4 5.8 75 52-126 14-89 (90)
38 PLN00161 histone H3; Provision 97.2 0.0016 3.5E-08 54.5 8.1 77 48-124 42-123 (135)
39 PLN00160 histone H3; Provision 97.2 0.0015 3.3E-08 51.8 7.3 78 47-124 7-89 (97)
40 PF09415 CENP-X: CENP-S associ 97.1 0.0019 4.1E-08 48.5 6.8 62 63-124 1-65 (72)
41 PLN00121 histone H3; Provision 97.1 0.0016 3.5E-08 54.5 6.9 76 48-124 49-129 (136)
42 PTZ00018 histone H3; Provision 97.1 0.0017 3.6E-08 54.4 6.8 77 47-124 48-129 (136)
43 PF15511 CENP-T: Centromere ki 97.0 0.0013 2.8E-08 63.1 5.8 63 57-119 347-414 (414)
44 smart00427 H2B Histone H2B. 97.0 0.0032 6.8E-08 49.4 6.9 59 66-125 6-65 (89)
45 KOG3219 Transcription initiati 96.5 0.0034 7.4E-08 55.4 4.4 87 37-127 91-178 (195)
46 PLN00158 histone H2B; Provisio 96.4 0.012 2.5E-07 48.3 6.9 60 65-125 31-91 (116)
47 PTZ00463 histone H2B; Provisio 96.4 0.014 3E-07 47.9 6.8 58 67-125 34-92 (117)
48 PF02269 TFIID-18kDa: Transcri 96.3 0.0038 8.2E-08 48.6 3.2 77 67-143 7-84 (93)
49 KOG3467 Histone H4 [Chromatin 96.2 0.017 3.6E-07 45.7 6.5 63 65-128 33-95 (103)
50 PF03847 TFIID_20kDa: Transcri 96.2 0.028 6.1E-07 41.7 7.1 61 66-127 4-65 (68)
51 PF15630 CENP-S: Kinetochore c 96.0 0.02 4.3E-07 43.5 5.8 52 79-130 25-76 (76)
52 PF07524 Bromo_TP: Bromodomain 95.9 0.046 9.9E-07 40.4 7.1 60 67-127 12-71 (77)
53 PLN00155 histone H2A; Provisio 95.4 0.017 3.7E-07 42.1 3.2 36 59-94 22-57 (58)
54 cd07978 TAF13 The TATA Binding 95.4 0.073 1.6E-06 41.6 7.0 76 65-141 6-82 (92)
55 PF15510 CENP-W: Centromere ki 95.4 0.04 8.8E-07 43.8 5.5 64 61-125 16-94 (102)
56 KOG1744 Histone H2B [Chromatin 95.0 0.079 1.7E-06 44.1 6.4 58 67-125 43-101 (127)
57 KOG1142 Transcription initiati 94.3 0.06 1.3E-06 49.4 4.5 71 65-135 158-228 (258)
58 KOG1745 Histones H3 and H4 [Ch 94.2 0.064 1.4E-06 45.1 4.0 72 54-125 59-131 (137)
59 KOG3423 Transcription initiati 93.9 0.43 9.3E-06 41.6 8.6 68 59-127 84-165 (176)
60 PF02291 TFIID-31kDa: Transcri 93.0 0.53 1.1E-05 39.0 7.5 67 66-133 17-83 (129)
61 KOG2549 Transcription initiati 91.9 0.51 1.1E-05 47.6 7.2 63 64-127 14-76 (576)
62 PF05236 TAF4: Transcription i 90.8 0.42 9.1E-06 43.0 5.0 45 65-110 51-95 (264)
63 cd08045 TAF4 TATA Binding Prot 89.2 0.87 1.9E-05 39.8 5.5 60 65-125 52-117 (212)
64 PF03540 TFIID_30kDa: Transcri 87.0 3.1 6.8E-05 29.6 6.2 48 61-109 2-49 (51)
65 COG5162 Transcription initiati 86.0 6.3 0.00014 34.7 8.7 62 46-108 73-134 (197)
66 COG5095 TAF6 Transcription ini 84.0 2.9 6.4E-05 40.3 6.3 61 66-127 10-70 (450)
67 PF13335 Mg_chelatase_2: Magne 70.8 47 0.001 25.7 9.4 62 57-125 27-94 (96)
68 TIGR03015 pepcterm_ATPase puta 66.7 10 0.00022 32.6 4.6 50 79-128 215-267 (269)
69 PRK00411 cdc6 cell division co 64.1 28 0.0006 32.0 7.1 64 64-127 209-282 (394)
70 PF10979 DUF2786: Protein of u 60.2 12 0.00026 25.5 3.0 35 64-98 4-38 (43)
71 KOG2389 Predicted bromodomain 57.6 33 0.00071 33.2 6.5 65 62-127 30-94 (353)
72 TIGR00368 Mg chelatase-related 57.0 80 0.0017 31.4 9.4 60 59-125 432-497 (499)
73 KOG4336 TBP-associated transcr 56.9 36 0.00078 32.5 6.6 63 64-126 7-69 (323)
74 TIGR02928 orc1/cdc6 family rep 56.9 45 0.00097 30.2 7.1 63 66-128 203-275 (365)
75 KOG3334 Transcription initiati 55.8 56 0.0012 28.1 6.9 51 94-146 45-95 (148)
76 PF12767 SAGA-Tad1: Transcript 55.5 20 0.00044 32.0 4.6 41 66-107 211-251 (252)
77 COG5248 TAF19 Transcription in 54.9 49 0.0011 27.4 6.2 61 66-128 14-74 (126)
78 KOG3901 Transcription initiati 50.1 66 0.0014 26.3 6.2 68 69-139 17-85 (109)
79 TIGR00764 lon_rel lon-related 50.0 60 0.0013 33.0 7.4 63 65-127 316-391 (608)
80 PF13654 AAA_32: AAA domain; P 49.5 56 0.0012 32.6 7.0 33 95-127 474-506 (509)
81 COG1222 RPT1 ATP-dependent 26S 46.5 22 0.00047 34.9 3.5 42 85-126 346-391 (406)
82 KOG2680 DNA helicase TIP49, TB 44.6 63 0.0014 31.6 6.2 58 67-125 363-427 (454)
83 COG5251 TAF40 Transcription in 43.0 46 0.001 29.5 4.7 72 54-126 108-180 (199)
84 COG1224 TIP49 DNA helicase TIP 40.3 49 0.0011 32.8 4.8 61 65-125 364-430 (450)
85 PF08637 NCA2: ATP synthase re 38.4 1E+02 0.0022 28.6 6.4 57 35-103 30-88 (290)
86 COG5094 TAF9 Transcription ini 36.9 1.4E+02 0.0029 25.4 6.3 66 67-133 20-88 (145)
87 COG1474 CDC6 Cdc6-related prot 36.4 46 0.001 31.7 4.0 78 58-136 183-273 (366)
88 KOG1657 CCAAT-binding factor, 33.7 4.4 9.5E-05 36.8 -3.2 78 57-143 4-81 (236)
89 PRK03992 proteasome-activating 32.0 64 0.0014 30.6 4.1 33 95-127 340-372 (389)
90 TIGR01242 26Sp45 26S proteasom 31.5 66 0.0014 29.8 4.1 42 85-126 317-362 (364)
91 PRK09862 putative ATP-dependen 30.7 2.1E+02 0.0046 28.7 7.7 62 59-127 425-492 (506)
92 PRK13765 ATP-dependent proteas 30.1 1.2E+02 0.0025 31.4 5.9 60 67-126 327-399 (637)
93 TIGR02902 spore_lonB ATP-depen 30.1 1.5E+02 0.0033 29.5 6.5 61 67-127 268-332 (531)
94 PF08369 PCP_red: Proto-chloro 29.2 97 0.0021 21.1 3.6 25 99-123 20-44 (45)
95 TIGR02442 Cob-chelat-sub cobal 28.0 2.3E+02 0.005 28.8 7.6 47 79-125 249-302 (633)
96 PTZ00361 26 proteosome regulat 27.4 79 0.0017 31.0 4.0 32 96-127 393-424 (438)
97 PTZ00454 26S protease regulato 27.0 85 0.0018 30.2 4.1 31 96-126 355-385 (398)
98 cd04773 HTH_TioE_rpt2 Second H 26.2 2.4E+02 0.0053 21.9 5.9 27 48-74 44-70 (108)
99 TIGR01128 holA DNA polymerase 26.2 1.9E+02 0.0041 25.2 5.9 64 79-142 130-196 (302)
100 smart00350 MCM minichromosome 25.3 2.1E+02 0.0046 28.1 6.6 66 60-125 416-502 (509)
101 cd01106 HTH_TipAL-Mta Helix-Tu 25.1 2E+02 0.0044 21.8 5.2 28 48-75 44-71 (103)
102 TIGR02030 BchI-ChlI magnesium 24.4 1.9E+02 0.004 27.4 5.8 59 66-125 242-307 (337)
103 PRK05574 holA DNA polymerase I 23.4 2E+02 0.0043 25.7 5.5 63 79-142 165-231 (340)
104 KOG1560 Translation initiation 23.2 6.4E+02 0.014 24.3 8.9 33 42-74 262-295 (339)
105 PRK13406 bchD magnesium chelat 23.1 2.1E+02 0.0045 29.2 6.1 59 66-125 183-248 (584)
106 cd04770 HTH_HMRTR Helix-Turn-H 22.2 3.1E+02 0.0068 21.3 5.9 29 47-75 43-71 (123)
107 PF13499 EF-hand_7: EF-hand do 20.9 2.7E+02 0.0059 18.6 5.8 32 93-124 35-66 (66)
108 PRK14139 heat shock protein Gr 20.1 5.8E+02 0.013 22.4 7.6 23 79-101 68-90 (185)
No 1
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=100.00 E-value=1.3e-37 Score=276.15 Aligned_cols=181 Identities=52% Similarity=0.777 Sum_probs=153.1
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccc
Q 026901 37 QQQLQMFWSYQRQEIEQANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQ 116 (231)
Q Consensus 37 ~~~l~~fW~~~~~eie~~~d~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq 116 (231)
+++|++||.++..++|...|++++.|||+|||||||.|+|+.+|+.||+++++||||+||.+|+.+||.++++++||||+
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 78999999999866778889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCccccccccCCCccchhh--hh-ccC-Cccc-c-CCCCCccccCCCCCCCCCCCCCceeeccCCCCCCc
Q 026901 117 KNDIAAAITRTDIFDFLVDIVPRDEIKDE--AA-GLG-GMVG-A-TASGVPYYYPPMGQPTGTAGPGGMMIGRPAVDPTG 190 (231)
Q Consensus 117 ~~DIa~AI~~~d~fdFL~DIVP~~~~~~e--~~-~~~-~~~~-~-~~~~~~~~~~~~~~~~~~~~~~g~~~g~~~~~~~~ 190 (231)
++||+.+|.+++.||||.||||++.+... .. ..+ ..+. . ...+++|.....+ ...+++|+++|+|.|++
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 99999999999999999999999977752 11 111 1111 1 2445666666655 34578889999999876
Q ss_pred cccCCCCccccccccCCCCCCCCCCCCCCCCCCC
Q 026901 191 VYVQPPSQAWQSVWQTPAGTGDDGSYGSGGSGGP 224 (231)
Q Consensus 191 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 224 (231)
+|.+++.+ +..|++..+++++..+..|+++|+
T Consensus 205 ~~~~~~~~--q~~~~~~~~~~~~~~~~~g~~~~~ 236 (236)
T KOG1657|consen 205 LAQPVSGT--QGQWQTLATDAQNITGTEGQQGGQ 236 (236)
T ss_pred ccCCCccc--cchhhhccCCcccccccccCCCCC
Confidence 45544444 889999999999999999998874
No 2
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.97 E-value=4e-31 Score=233.25 Aligned_cols=129 Identities=52% Similarity=0.879 Sum_probs=117.0
Q ss_pred CCCcccccCccchhhhhhHH----HHHHHHHHHHHHHHHHHHhh--cCCCCCCChHHHHHHHhcCcchhccCchHHHHHH
Q 026901 16 PPSAAAAATATAPFHHLIQQ----QQQQLQMFWSYQRQEIEQAN--DFKNHQLPLARIKKIMKADEDVRMISAEAPILFA 89 (231)
Q Consensus 16 ~~~~~~~~~~~~~~~~~~~~----~~~~l~~fW~~~~~eie~~~--d~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllA 89 (231)
|-.+.++.-.+.+|...++. +.+.|..||.+.++++|+.. ++|.+.|||+||||+||.|+||+|||+||+++|+
T Consensus 58 h~~a~~p~e~~~~f~nv~qglvg~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFa 137 (286)
T COG5208 58 HYNASAPIEVASPFINVMQGLVGLLDERISRYWQQTIKAAEEERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFA 137 (286)
T ss_pred ccccCCchhhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHHHHHHhcccchhheecccchHHH
Confidence 44455566667888887774 57889999999999999865 7889999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccccCCCccchh
Q 026901 90 KACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVDIVPRDEIKD 144 (231)
Q Consensus 90 KAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~DIVP~~~~~~ 144 (231)
|+||+||.+||.+||.+|+++|||||+++||+.||++.+.||||.||||+..+..
T Consensus 138 k~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFLidivpr~p~n~ 192 (286)
T COG5208 138 KITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFLIDIVPRNPFNH 192 (286)
T ss_pred HHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHHhhhccCCCccc
Confidence 9999999999999999999999999999999999999999999999999985543
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=99.82 E-value=3.7e-20 Score=133.10 Aligned_cols=64 Identities=45% Similarity=0.562 Sum_probs=59.7
Q ss_pred CCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHH
Q 026901 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAI 124 (231)
Q Consensus 61 ~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI 124 (231)
.||++|||||||.+|++.+||+||.+++++|+|+||++|+.+|+.+|+.++||||+++||..||
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=99.78 E-value=1.3e-19 Score=158.98 Aligned_cols=86 Identities=28% Similarity=0.494 Sum_probs=82.0
Q ss_pred hhcCCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccc
Q 026901 54 ANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFL 133 (231)
Q Consensus 54 ~~d~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL 133 (231)
..++..+.||.+||||||++|+||++|+.-.|++++||+|+|++.|+.++++.++..+-|||+..||..||.+++.||||
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 35677899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCC
Q 026901 134 VDIVPR 139 (231)
Q Consensus 134 ~DIVP~ 139 (231)
+|+|..
T Consensus 86 k~~v~~ 91 (224)
T KOG1659|consen 86 KEVVEK 91 (224)
T ss_pred HHHHHh
Confidence 998654
No 5
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=99.75 E-value=1.1e-18 Score=138.67 Aligned_cols=84 Identities=29% Similarity=0.474 Sum_probs=80.0
Q ss_pred CCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcccccccc
Q 026901 57 FKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVDI 136 (231)
Q Consensus 57 ~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~DI 136 (231)
.+.+.||+|||||||+.|+|+++|++..|++.+||+|+|+.+|+..+...|+....|.++.++|..|+.+++.||||.++
T Consensus 19 ~~ktrFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~ 98 (113)
T COG5247 19 KKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNM 98 (113)
T ss_pred hhhhcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHH
Confidence 44678999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCc
Q 026901 137 VPRD 140 (231)
Q Consensus 137 VP~~ 140 (231)
+..+
T Consensus 99 ~~~~ 102 (113)
T COG5247 99 EQFK 102 (113)
T ss_pred HHhc
Confidence 8754
No 6
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=99.36 E-value=1.8e-13 Score=115.51 Aligned_cols=83 Identities=41% Similarity=0.552 Sum_probs=79.2
Q ss_pred CCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcccccccc
Q 026901 57 FKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVDI 136 (231)
Q Consensus 57 ~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~DI 136 (231)
-+.++|||+|||.|||.|||+.+...||.+++++|.|+||++|...++.+++..+|||++..|+..+|+..+.|.||.+.
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 55789999999999999999999999999999999999999999999999999999999999999999999999999977
Q ss_pred CCC
Q 026901 137 VPR 139 (231)
Q Consensus 137 VP~ 139 (231)
.+-
T Consensus 135 ~d~ 137 (162)
T KOG1658|consen 135 LDT 137 (162)
T ss_pred ccc
Confidence 653
No 7
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=99.32 E-value=2.4e-12 Score=104.93 Aligned_cols=78 Identities=22% Similarity=0.323 Sum_probs=74.9
Q ss_pred CCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 58 KNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 58 k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
-.+.||++|||||||.+..-++|+++|+++++.++|+++.+++..|.+.|+.+|+|.|.++||..||+++++|+||..
T Consensus 23 agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~EL~~l~~ 100 (132)
T COG5262 23 AGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLG 100 (132)
T ss_pred cCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcCcHHHHHHhh
Confidence 357899999999999888889999999999999999999999999999999999999999999999999999999986
No 8
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=99.31 E-value=4.2e-12 Score=102.58 Aligned_cols=77 Identities=21% Similarity=0.341 Sum_probs=73.2
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
.+.||++||+|+||..-...+||+.|+++++.++|+++.++...|.+.|+..||++|+.+||..||.++++|++|..
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 68899999999999877778999999999999999999999999999999999999999999999999999997764
No 9
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.09 E-value=2e-10 Score=97.53 Aligned_cols=70 Identities=24% Similarity=0.306 Sum_probs=65.5
Q ss_pred CCCCChHHHHHHHhcC-cchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC
Q 026901 59 NHQLPLARIKKIMKAD-EDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD 128 (231)
Q Consensus 59 ~~~LPLARIKRIMKsD-pDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d 128 (231)
...||||.|-||||.- |...+||+||...+.+|+..||..+|.+|.+.|++.|||||+.+||..|+....
T Consensus 30 Dr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 30 DRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 3569999999999995 777899999999999999999999999999999999999999999999998754
No 10
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.09 E-value=3.5e-10 Score=88.31 Aligned_cols=79 Identities=25% Similarity=0.334 Sum_probs=69.9
Q ss_pred HHHHHhhcCCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC
Q 026901 49 QEIEQANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD 128 (231)
Q Consensus 49 ~eie~~~d~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d 128 (231)
.++..........||.+.|.||||.-- ..+||.+|...+.+++|.|+..|+..|..+|.+.|||||+.+||..|++...
T Consensus 7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~~-~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~ 85 (91)
T COG2036 7 KEIRRYQRSTDLLLPKAPVRRILRKAG-AERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLG 85 (91)
T ss_pred HHHHhhhhhhhhhcCchHHHHHHHHHh-HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 455555566678899999999999973 3499999999999999999999999999999999999999999999998654
No 11
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=99.08 E-value=2.4e-10 Score=94.09 Aligned_cols=80 Identities=21% Similarity=0.343 Sum_probs=76.0
Q ss_pred CCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccccC
Q 026901 58 KNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVDIV 137 (231)
Q Consensus 58 k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~DIV 137 (231)
-.+.||++||.|+||......+||..|+++++.++|+.+.+++..|-+.|+.+++..|+++||..||.+++++.||.+-|
T Consensus 24 agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~NDeEL~~lL~~v 103 (131)
T KOG1756|consen 24 AGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRNDEELNKLLGKV 103 (131)
T ss_pred cccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhCcHHHHHHhccc
Confidence 36889999999999998888999999999999999999999999999999999999999999999999999999998843
No 12
>smart00414 H2A Histone 2A.
Probab=99.08 E-value=2.5e-10 Score=91.06 Aligned_cols=77 Identities=22% Similarity=0.374 Sum_probs=72.7
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
.+.||++||+|+||..-...+|++.|+++++.++|+++.++...|.+.+..+|++.|+..||..||.++++|+.|..
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 57899999999999987788999999999999999999999999999999999999999999999999999996654
No 13
>PTZ00017 histone H2A; Provisional
Probab=99.03 E-value=4.3e-10 Score=93.29 Aligned_cols=76 Identities=22% Similarity=0.362 Sum_probs=72.6
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcccccc
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLV 134 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~ 134 (231)
.+.||++||.|.||..--..+|++.|+++++.++|+++.++...|.+.+..++++.|++.||..||.++++|+.|.
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 5889999999999998777899999999999999999999999999999999999999999999999999999776
No 14
>PLN00154 histone H2A; Provisional
Probab=99.03 E-value=4.3e-10 Score=93.43 Aligned_cols=77 Identities=19% Similarity=0.238 Sum_probs=72.5
Q ss_pred CCCCChHHHHHHHhcCc-chhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 59 NHQLPLARIKKIMKADE-DVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDp-DV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
.+.||++||.|+||..- ...+|++.|+++++.++|++..++...|.+.|..+|++.|++.||..||.++++|++|..
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 68899999999999975 456999999999999999999999999999999999999999999999999999998775
No 15
>PLN00156 histone H2AX; Provisional
Probab=98.94 E-value=1.9e-09 Score=89.87 Aligned_cols=76 Identities=22% Similarity=0.336 Sum_probs=72.1
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcccccc
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLV 134 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~ 134 (231)
.+.||++||.|.||..--..+|++.|+++++.++|+++.++...|.+.|..+|++.|+++||..||.++++|+.|.
T Consensus 27 gL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrnDeEL~~Ll 102 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLL 102 (139)
T ss_pred CcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccCcHHHHHHH
Confidence 5789999999999998777899999999999999999999999999999999999999999999999999999665
No 16
>PLN00153 histone H2A; Provisional
Probab=98.93 E-value=1.8e-09 Score=89.11 Aligned_cols=77 Identities=25% Similarity=0.325 Sum_probs=72.5
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
.+.||++||.|.||..--..+|++.|+++++.++|+++.++...|.+.|..+|++.|+++||..||.++++|+.|..
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 57899999999999987788999999999999999999999999999999999999999999999999999996553
No 17
>PLN00157 histone H2A; Provisional
Probab=98.91 E-value=2.1e-09 Score=89.04 Aligned_cols=76 Identities=24% Similarity=0.329 Sum_probs=71.8
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcccccc
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLV 134 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~ 134 (231)
.+.||++||.|.||..--..+|++.|+++++.++|+++.++...|.+.|..+|++.|+.+||..||.++++|+.|.
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 18
>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=98.87 E-value=9.2e-09 Score=75.37 Aligned_cols=64 Identities=30% Similarity=0.362 Sum_probs=61.1
Q ss_pred CCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 61 ~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
.||.+-|++|.+.. ++.+||.|+...++..+|.|+.+++..|..++++.|||||+.+||..|++
T Consensus 2 ~~p~~~i~ria~~~-Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL-GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 58999999999998 78899999999999999999999999999999999999999999998864
No 19
>PTZ00252 histone H2A; Provisional
Probab=98.82 E-value=8.6e-09 Score=85.53 Aligned_cols=77 Identities=21% Similarity=0.311 Sum_probs=70.8
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHH--cCCCcccHHHHHHHHhcCCccc-cccc
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEE--NKRRTLQKNDIAAAITRTDIFD-FLVD 135 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~--~kRKTLq~~DIa~AI~~~d~fd-FL~D 135 (231)
.+.||++||.|.||..--..+|++.|+++++.++|+++.++...|.+.|.+ +|++.|+.+||..||.++++|+ +|.+
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 578999999999999877889999999999999999999999999999965 7889999999999999999998 4444
No 20
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.78 E-value=1.2e-08 Score=74.31 Aligned_cols=68 Identities=22% Similarity=0.276 Sum_probs=60.8
Q ss_pred CCCCChHHHHHHHhcCcch-hccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhc
Q 026901 59 NHQLPLARIKKIMKADEDV-RMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITR 126 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV-~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~ 126 (231)
...+|+.||.|-+..+-.. .+||++|+.++..++|.|+.+|...|..+|..+||+||+.+||..|+..
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 4567888888888887554 4999999999999999999999999999999999999999999999864
No 21
>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=98.75 E-value=3.5e-08 Score=76.15 Aligned_cols=66 Identities=17% Similarity=0.232 Sum_probs=63.3
Q ss_pred CCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 61 ~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
.||.+-|+||.+.. .+.+||.++...+..++|.|+++++.+|...|++.+||||+.+||..|+++.
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 GITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ 78 (85)
T ss_pred cCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHC
Confidence 49999999999998 6999999999999999999999999999999999999999999999999765
No 22
>PLN00035 histone H4; Provisional
Probab=98.75 E-value=3.8e-08 Score=78.57 Aligned_cols=65 Identities=17% Similarity=0.233 Sum_probs=62.9
Q ss_pred CChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 62 LPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 62 LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
||.+-|+||.+.. .+.+||.++...+..++|.|+++++.+|...|++.+||||+.+||..|+++.
T Consensus 30 ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~ 94 (103)
T PLN00035 30 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQ 94 (103)
T ss_pred CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHc
Confidence 9999999999998 6999999999999999999999999999999999999999999999999875
No 23
>PTZ00015 histone H4; Provisional
Probab=98.67 E-value=8.8e-08 Score=76.31 Aligned_cols=67 Identities=18% Similarity=0.233 Sum_probs=63.8
Q ss_pred CCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 60 HQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 60 ~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
..||.+-|+||.+.. .+.+||.++...+..++|.|+.+++.+|...|++.+||||+.+||..|+++.
T Consensus 29 ~gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~ 95 (102)
T PTZ00015 29 RGITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQ 95 (102)
T ss_pred cCCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhc
Confidence 469999999999998 8999999999999999999999999999999999999999999999998765
No 24
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.67 E-value=5.3e-08 Score=83.43 Aligned_cols=77 Identities=29% Similarity=0.394 Sum_probs=68.9
Q ss_pred CCCCChHHHHHHHhcC-cch-hccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 59 NHQLPLARIKKIMKAD-EDV-RMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 59 ~~~LPLARIKRIMKsD-pDV-~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
.+.||.|-|.||+|.- |+. ..||+||..+|++++-.||.+|+.-|...|...+||||+.+||..|+...+.-.|+.-
T Consensus 8 dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~p 86 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVNP 86 (172)
T ss_pred HhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhhH
Confidence 3569999999999984 343 5799999999999999999999999999999999999999999999998887777653
No 25
>smart00417 H4 Histone H4.
Probab=98.60 E-value=8.9e-08 Score=72.30 Aligned_cols=61 Identities=15% Similarity=0.169 Sum_probs=58.4
Q ss_pred CCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHH
Q 026901 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAA 122 (231)
Q Consensus 61 ~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~ 122 (231)
.||.+.|+||.|.. ++.+||.++...+..++|.|+.+++.+|...|++.+||||+..||..
T Consensus 13 gI~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 13 GITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred CCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 49999999999998 89999999999999999999999999999999999999999999864
No 26
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=98.46 E-value=4.9e-07 Score=76.40 Aligned_cols=77 Identities=19% Similarity=0.332 Sum_probs=69.1
Q ss_pred CCCCCChHHHHHHHhcC-c-chhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 58 KNHQLPLARIKKIMKAD-E-DVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 58 k~~~LPLARIKRIMKsD-p-DV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
.+..||-+-|.||+|.- | |+ +|.+||..+|-.||-.||..|+++|.++|....||||.++||..|+++...=+|+..
T Consensus 9 de~sLPkAtv~KmIke~lP~d~-rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee 87 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLPKDV-RVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEE 87 (156)
T ss_pred ccccCcHHHHHHHHHHhCCccc-ccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHH
Confidence 46789999999999983 4 65 799999999999999999999999999999999999999999999998765565553
No 27
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=98.24 E-value=5.9e-06 Score=61.26 Aligned_cols=66 Identities=17% Similarity=0.282 Sum_probs=57.6
Q ss_pred CChHHHHHHHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC
Q 026901 62 LPLARIKKIMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD 128 (231)
Q Consensus 62 LPLARIKRIMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d 128 (231)
++-.++..++|. ||. .+++.+|..++...+|.|+..++..|...|++.||+||..+||..++++.-
T Consensus 2 ~~k~~l~~lv~~id~~-~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~ 68 (72)
T cd07981 2 LTKRKLQELLKEIDPR-EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNW 68 (72)
T ss_pred CcHHHHHHHHHhhCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Confidence 344566677776 554 689999999999999999999999999999999999999999999998754
No 28
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=98.04 E-value=1.8e-05 Score=61.03 Aligned_cols=75 Identities=21% Similarity=0.294 Sum_probs=66.1
Q ss_pred HHHhhcCCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcC---CCcccHHHHHHHHhc
Q 026901 51 IEQANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENK---RRTLQKNDIAAAITR 126 (231)
Q Consensus 51 ie~~~d~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~k---RKTLq~~DIa~AI~~ 126 (231)
+..-..++...||-+.|||||...-+ ..++.+...+++..+.+||.+|+.+|..+..+.+ +.-|+++||..|..+
T Consensus 6 ~~Rye~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr 83 (85)
T cd08048 6 MNRYEMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR 83 (85)
T ss_pred HHHHHHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence 44556788888999999999999766 6899999999999999999999999999998755 478999999999865
No 29
>smart00428 H3 Histone H3.
Probab=97.99 E-value=4.9e-05 Score=60.95 Aligned_cols=77 Identities=25% Similarity=0.314 Sum_probs=62.3
Q ss_pred HHHHHHHh---hcCCCCCCChHHH-HHHHhcC-c--chhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHH
Q 026901 47 QRQEIEQA---NDFKNHQLPLARI-KKIMKAD-E--DVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKND 119 (231)
Q Consensus 47 ~~~eie~~---~d~k~~~LPLARI-KRIMKsD-p--DV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~D 119 (231)
.+.||... .++--..+|.+|+ +.|+..- + +. +++.+|..++..|+|.|+..|...|..+|.+.||+||+.+|
T Consensus 15 aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~-R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kD 93 (105)
T smart00428 15 ALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDL-RFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKD 93 (105)
T ss_pred HHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCc-eeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhh
Confidence 35666654 4555667888885 4455442 2 44 89999999999999999999999999999999999999999
Q ss_pred HHHHH
Q 026901 120 IAAAI 124 (231)
Q Consensus 120 Ia~AI 124 (231)
|..|.
T Consensus 94 i~La~ 98 (105)
T smart00428 94 IQLAR 98 (105)
T ss_pred HHHHH
Confidence 98775
No 30
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=97.80 E-value=6.4e-05 Score=62.64 Aligned_cols=79 Identities=20% Similarity=0.320 Sum_probs=67.8
Q ss_pred CCCCCCChHHHHHHHhcC-cchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 57 FKNHQLPLARIKKIMKAD-EDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 57 ~k~~~LPLARIKRIMKsD-pDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
-.+..||-+-|.|++-.- |---++++||..+|-.||=.||.-|+.+|.+.|....+|||.|+||-.|+++.+.=+|+..
T Consensus 7 dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~~ 86 (148)
T COG5150 7 DDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIES 86 (148)
T ss_pred cccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHHH
Confidence 346789999999998773 2234799999999999999999999999999999999999999999999998775555543
No 31
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=97.73 E-value=0.0001 Score=59.53 Aligned_cols=69 Identities=12% Similarity=0.125 Sum_probs=62.4
Q ss_pred HHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcccccc
Q 026901 65 ARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLV 134 (231)
Q Consensus 65 ARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~ 134 (231)
.-|++|+|+- ++..++.+++..+...++.++.++...|...|++.+|+||+.+||..||+..-.+.|-.
T Consensus 5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~ 73 (117)
T cd07979 5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTS 73 (117)
T ss_pred HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCC
Confidence 3588999986 67789999999999999999999999999999999999999999999998876666664
No 32
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.63 E-value=0.00025 Score=52.88 Aligned_cols=60 Identities=17% Similarity=0.171 Sum_probs=55.3
Q ss_pred HHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 67 IKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 67 IKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
|.+|+|.. +...++.+|...++..+|.|+.+|++.+..+|+..+|++.+..||..|+.+.
T Consensus 12 Vaqil~~~-Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~ 71 (77)
T smart00576 12 VAQILESA-GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENL 71 (77)
T ss_pred HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 67788876 6779999999999999999999999999999999999999999999998764
No 33
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=97.57 E-value=4.3e-05 Score=62.50 Aligned_cols=76 Identities=20% Similarity=0.249 Sum_probs=69.9
Q ss_pred CCCCChHHHHHHHhcC-cchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcccccc
Q 026901 59 NHQLPLARIKKIMKAD-EDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLV 134 (231)
Q Consensus 59 ~~~LPLARIKRIMKsD-pDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~ 134 (231)
-+.||+.||+|-+|.. ...++|.+-|.+..+..+|++..++...|.+.++.-|-|.|+++|+..||.-+++||-|.
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRGDeELDtLI 104 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLI 104 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecCcHHHHHHH
Confidence 5789999999999985 456789999999999999999999999999988888999999999999999999999886
No 34
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.55 E-value=0.00047 Score=51.07 Aligned_cols=64 Identities=22% Similarity=0.285 Sum_probs=50.9
Q ss_pred CCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 61 ~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
.||..-||-|-.+- ++..++.|+..+++.=+|+-|.++...|...++++||++|+.+||..|++
T Consensus 3 ~~~~esvk~iAes~-Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL-GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT-T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 47778888888776 67789999999999999999999999999999999999999999999874
No 35
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=97.55 E-value=0.00012 Score=62.50 Aligned_cols=74 Identities=23% Similarity=0.195 Sum_probs=53.6
Q ss_pred CCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 57 FKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 57 ~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
.+...||++.+|||-|.||...+-+.+|....+.++|.|++.|+..+. .+-..|...-|..+++..+.|.||.|
T Consensus 7 e~~p~~p~ekvkkiak~dPey~~te~~a~~etafatE~fvq~lv~~p~-----a~l~rLpL~rik~vvkl~pdl~l~~d 80 (162)
T KOG1658|consen 7 ECSPKLPMEKVKKIAKNDPEYMDTEDDAFVETAFATEQFVQVLVHLPQ-----ASLSRLPLARIKQVVKLDPDLTLLND 80 (162)
T ss_pred hhCccccHHHHHHhhcCCchhhhcccchHHHHHHHHHHHHhhhhhhhh-----hhhhhccHHHHHhhccCCcchhhhhh
Confidence 356789999999999999999999999999999999999999998322 11123333444455555555544443
No 36
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=97.50 E-value=0.0003 Score=65.59 Aligned_cols=65 Identities=25% Similarity=0.314 Sum_probs=59.1
Q ss_pred ChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC
Q 026901 63 PLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD 128 (231)
Q Consensus 63 PLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d 128 (231)
|..-||-|.++- ++.++|.||...++.-+|.++.+++.+|.+.+++.|||||+.+||..|++...
T Consensus 1 ~~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n 65 (343)
T cd08050 1 PQESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRN 65 (343)
T ss_pred ChhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhC
Confidence 345688888887 78899999999999999999999999999999999999999999999987653
No 37
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.41 E-value=0.00038 Score=54.42 Aligned_cols=75 Identities=21% Similarity=0.245 Sum_probs=54.5
Q ss_pred HHhhcCCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcC-CCcccHHHHHHHHhc
Q 026901 52 EQANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENK-RRTLQKNDIAAAITR 126 (231)
Q Consensus 52 e~~~d~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~k-RKTLq~~DIa~AI~~ 126 (231)
+...-|+...||-+.|||||..--+-..||....++++-.+.+||-+|..+|.++..+.+ ..-|+++||..|..+
T Consensus 14 ~Rye~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rr 89 (90)
T PF04719_consen 14 DRYEAFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRR 89 (90)
T ss_dssp HHHHHHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHH
T ss_pred HHHHHHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHh
Confidence 444557788899999999999965445799999999999999999999999999988654 348999999999764
No 38
>PLN00161 histone H3; Provisional
Probab=97.24 E-value=0.0016 Score=54.46 Aligned_cols=77 Identities=27% Similarity=0.307 Sum_probs=61.8
Q ss_pred HHHHHH---hhcCCCCCCChHHHHH-HHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHH
Q 026901 48 RQEIEQ---ANDFKNHQLPLARIKK-IMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAA 122 (231)
Q Consensus 48 ~~eie~---~~d~k~~~LPLARIKR-IMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~ 122 (231)
+.||.. ..++--..+|.+|+-| |+.. .++.-++..+|+.++..|+|.|+-.|-..|+.+|.+.||-||..+||..
T Consensus 42 LrEIR~yQkst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~L 121 (135)
T PLN00161 42 LREIRKYQKSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQL 121 (135)
T ss_pred HHHHHHHccccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHH
Confidence 455655 4456667889888644 4433 2223489999999999999999999999999999999999999999987
Q ss_pred HH
Q 026901 123 AI 124 (231)
Q Consensus 123 AI 124 (231)
+.
T Consensus 122 a~ 123 (135)
T PLN00161 122 AR 123 (135)
T ss_pred HH
Confidence 74
No 39
>PLN00160 histone H3; Provisional
Probab=97.21 E-value=0.0015 Score=51.81 Aligned_cols=78 Identities=26% Similarity=0.278 Sum_probs=61.6
Q ss_pred HHHHHHHh---hcCCCCCCChHHHHH-HHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHH
Q 026901 47 QRQEIEQA---NDFKNHQLPLARIKK-IMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIA 121 (231)
Q Consensus 47 ~~~eie~~---~d~k~~~LPLARIKR-IMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa 121 (231)
.+.||... .+.--..+|-+|+-| |+.. ..+.-++..+|+.++..|+|.|+-.|-..|..+|.+.||.||..+||.
T Consensus 7 aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~ 86 (97)
T PLN00160 7 ALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQ 86 (97)
T ss_pred HHHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHH
Confidence 35566653 455556788888644 4432 223348999999999999999999999999999999999999999998
Q ss_pred HHH
Q 026901 122 AAI 124 (231)
Q Consensus 122 ~AI 124 (231)
-+.
T Consensus 87 L~~ 89 (97)
T PLN00160 87 LAR 89 (97)
T ss_pred HHH
Confidence 774
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=97.14 E-value=0.0019 Score=48.46 Aligned_cols=62 Identities=23% Similarity=0.300 Sum_probs=50.5
Q ss_pred ChHHHHHHHhc--CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCc-ccHHHHHHHH
Q 026901 63 PLARIKKIMKA--DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRT-LQKNDIAAAI 124 (231)
Q Consensus 63 PLARIKRIMKs--DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKT-Lq~~DIa~AI 124 (231)
|-.-|.||++. ..+-.+||.+|..++++-.++||.+-+.||...++..+... |..+||.++.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~ 65 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKIL 65 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence 45568899987 24667999999999999999999999999999999888888 9999998864
No 41
>PLN00121 histone H3; Provisional
Probab=97.13 E-value=0.0016 Score=54.51 Aligned_cols=76 Identities=25% Similarity=0.364 Sum_probs=61.8
Q ss_pred HHHHHH---hhcCCCCCCChHHHHH-HHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHH
Q 026901 48 RQEIEQ---ANDFKNHQLPLARIKK-IMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAA 122 (231)
Q Consensus 48 ~~eie~---~~d~k~~~LPLARIKR-IMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~ 122 (231)
+.||.. ..++--..+|.+|+-| |+.. ..++ ++..+|+.++..|+|.|+-.|-..++.+|.+.||.||..+||..
T Consensus 49 LrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~-Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L 127 (136)
T PLN00121 49 LREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 127 (136)
T ss_pred HHHHHHhccccccccccccHHHHHHHHHHHhCccc-eeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHH
Confidence 456665 4466667788888654 4443 2444 89999999999999999999999999999999999999999977
Q ss_pred HH
Q 026901 123 AI 124 (231)
Q Consensus 123 AI 124 (231)
+.
T Consensus 128 ~~ 129 (136)
T PLN00121 128 AR 129 (136)
T ss_pred HH
Confidence 64
No 42
>PTZ00018 histone H3; Provisional
Probab=97.10 E-value=0.0017 Score=54.39 Aligned_cols=77 Identities=25% Similarity=0.344 Sum_probs=62.2
Q ss_pred HHHHHHHh---hcCCCCCCChHHHHH-HHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHH
Q 026901 47 QRQEIEQA---NDFKNHQLPLARIKK-IMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIA 121 (231)
Q Consensus 47 ~~~eie~~---~d~k~~~LPLARIKR-IMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa 121 (231)
.+.||... .|.--..+|.+|+-| |+.. ..++ ++..+|+.++..|+|.|+-.|-..++.+|.+.||.||..+||.
T Consensus 48 aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~-rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~ 126 (136)
T PTZ00018 48 ALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQ 126 (136)
T ss_pred HHHHHHHHcccchhccccccHHHHHHHHHHHcCCcc-eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHH
Confidence 35566653 456667788888655 4433 3455 8999999999999999999999999999999999999999997
Q ss_pred HHH
Q 026901 122 AAI 124 (231)
Q Consensus 122 ~AI 124 (231)
.+.
T Consensus 127 L~~ 129 (136)
T PTZ00018 127 LAR 129 (136)
T ss_pred HHH
Confidence 764
No 43
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=96.98 E-value=0.0013 Score=63.12 Aligned_cols=63 Identities=22% Similarity=0.215 Sum_probs=46.2
Q ss_pred CCCCCCChHHHHHHHhcC-----cchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHH
Q 026901 57 FKNHQLPLARIKKIMKAD-----EDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKND 119 (231)
Q Consensus 57 ~k~~~LPLARIKRIMKsD-----pDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~D 119 (231)
.....||-+-|||+...- -.-++|+++|+-+|.+|++.|.+.|+..=-.+|++.|||||..+|
T Consensus 347 i~~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 347 IPYPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp -----S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 345679999999987653 123689999999999999999999999999999999999999876
No 44
>smart00427 H2B Histone H2B.
Probab=96.97 E-value=0.0032 Score=49.38 Aligned_cols=59 Identities=24% Similarity=0.252 Sum_probs=52.8
Q ss_pred HHHHHHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 66 RIKKIMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 66 RIKRIMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
-|.|++|. .||. .||..|.-++.--.-.+.+.++.+|...+..+||+||+.++|..||+
T Consensus 6 Yi~kvLKqVhpd~-giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvr 65 (89)
T smart00427 6 YIYKVLKQVHPDT-GISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVR 65 (89)
T ss_pred HHHHHHHHhCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 47888887 6887 59999998888888888899999999999999999999999999986
No 45
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=96.50 E-value=0.0034 Score=55.37 Aligned_cols=87 Identities=26% Similarity=0.293 Sum_probs=70.2
Q ss_pred HHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcC-CCcc
Q 026901 37 QQQLQMFWSYQRQEIEQANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENK-RRTL 115 (231)
Q Consensus 37 ~~~l~~fW~~~~~eie~~~d~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~k-RKTL 115 (231)
+--|.+|=.+| +....-|+...||-+.|||+|..--.-. ||..+.++++-...+||-+|+..|..++...+ ..-|
T Consensus 91 q~L~s~fseEQ---l~RYEvfRrs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PL 166 (195)
T KOG3219|consen 91 QTLLSNFSEEQ---LSRYEVFRRSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPL 166 (195)
T ss_pred HHHHHhcCHHH---HHHHHHHHHhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCC
Confidence 33455555544 4555568899999999999999865444 89999999999999999999999999997644 4579
Q ss_pred cHHHHHHHHhcC
Q 026901 116 QKNDIAAAITRT 127 (231)
Q Consensus 116 q~~DIa~AI~~~ 127 (231)
+++||..|+.+.
T Consensus 167 qP~HIREA~rrL 178 (195)
T KOG3219|consen 167 QPKHIREAYRRL 178 (195)
T ss_pred CcHHHHHHHHHH
Confidence 999999999764
No 46
>PLN00158 histone H2B; Provisional
Probab=96.45 E-value=0.012 Score=48.31 Aligned_cols=60 Identities=22% Similarity=0.236 Sum_probs=53.5
Q ss_pred HHHHHHHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 65 ARIKKIMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 65 ARIKRIMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
.-|.|++|. .||.+ ||..|.-++.--...+.+.|+.+|...+..++|+||+.++|..||.
T Consensus 31 ~YI~kVLKQVhPd~g-IS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvr 91 (116)
T PLN00158 31 IYIYKVLKQVHPDTG-ISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVR 91 (116)
T ss_pred HHHHHHHHHhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 348888887 68885 7999998888888888899999999999999999999999999986
No 47
>PTZ00463 histone H2B; Provisional
Probab=96.36 E-value=0.014 Score=47.92 Aligned_cols=58 Identities=21% Similarity=0.201 Sum_probs=52.2
Q ss_pred HHHHHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 67 IKKIMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 67 IKRIMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
|.|++|. .||.+ ||..|.-++.--..-..+.|+.+|...+..++|+||+.++|..||.
T Consensus 34 I~KVLKqVhPd~g-IS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr 92 (117)
T PTZ00463 34 IFKVLKQVHPDTG-ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR 92 (117)
T ss_pred HHHHHHhhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh
Confidence 8888887 78885 7999998888888888889999999999999999999999999986
No 48
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=96.31 E-value=0.0038 Score=48.58 Aligned_cols=77 Identities=16% Similarity=0.188 Sum_probs=34.2
Q ss_pred HHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC-ccccccccCCCccch
Q 026901 67 IKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD-IFDFLVDIVPRDEIK 143 (231)
Q Consensus 67 IKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d-~fdFL~DIVP~~~~~ 143 (231)
|+.+|-.-.|+..-..|+..++-..+-.||.+|+.+|..+|...++++|+.+||.-++++++ .+.-|.+++-.++..
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~Kl~Rl~~~L~~k~~~ 84 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKKLARLRELLSMKDEI 84 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHHHHHHHHHHHHHHHH
Confidence 67889998899999999999999999999999999999999999999999999999999884 678888877765443
No 49
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=96.24 E-value=0.017 Score=45.72 Aligned_cols=63 Identities=19% Similarity=0.234 Sum_probs=57.0
Q ss_pred HHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC
Q 026901 65 ARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD 128 (231)
Q Consensus 65 ARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d 128 (231)
--|+||.+.. .|++|+--...-+..+...|++.....|...+++.|||||+..||..++++.-
T Consensus 33 paIRRlARr~-GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G 95 (103)
T KOG3467|consen 33 PAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 95 (103)
T ss_pred HHHHHHHHhc-CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcC
Confidence 3588888877 79999999999999999999999999999999999999999999999988653
No 50
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=96.18 E-value=0.028 Score=41.71 Aligned_cols=61 Identities=16% Similarity=0.317 Sum_probs=47.7
Q ss_pred HHHHHHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 66 RIKKIMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 66 RIKRIMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
++..++|. ||. ..+..++-.++...++.||..++..|...|+++|-.||..+||...+++.
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 45566666 554 46889999999999999999999999999999999999999999988764
No 51
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=96.03 E-value=0.02 Score=43.45 Aligned_cols=52 Identities=13% Similarity=0.077 Sum_probs=43.9
Q ss_pred ccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcc
Q 026901 79 MISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIF 130 (231)
Q Consensus 79 ~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~f 130 (231)
.+|..+..+++..+=.++..++..-...|++.||+||+.+||.....+++.|
T Consensus 25 ~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~L 76 (76)
T PF15630_consen 25 EVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPSL 76 (76)
T ss_dssp EE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HHH
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCCC
Confidence 5899999999999999999999999999999999999999999999887653
No 52
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=95.88 E-value=0.046 Score=40.37 Aligned_cols=60 Identities=18% Similarity=0.175 Sum_probs=53.2
Q ss_pred HHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 67 IKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 67 IKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
|.+|++.. +...++..|+..|+..+..||.+|+..+..+|+..+|......||..++.+.
T Consensus 12 va~il~~~-GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~ 71 (77)
T PF07524_consen 12 VAQILKHA-GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEM 71 (77)
T ss_pred HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 56677665 5668999999999999999999999999999999999999999999998654
No 53
>PLN00155 histone H2A; Provisional
Probab=95.43 E-value=0.017 Score=42.14 Aligned_cols=36 Identities=31% Similarity=0.479 Sum_probs=33.5
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHH
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACEL 94 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtEl 94 (231)
.+.||++||.|.+|..--..+|++.|++.++..+|+
T Consensus 22 gL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEY 57 (58)
T PLN00155 22 GLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEY 57 (58)
T ss_pred ccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHh
Confidence 578999999999999888889999999999999986
No 54
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=95.41 E-value=0.073 Score=41.59 Aligned_cols=76 Identities=17% Similarity=0.229 Sum_probs=65.1
Q ss_pred HHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC-ccccccccCCCcc
Q 026901 65 ARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD-IFDFLVDIVPRDE 141 (231)
Q Consensus 65 ARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d-~fdFL~DIVP~~~ 141 (231)
.-|+.+|-.-.|+..-..|++.++-..+-.||.+|+.+|..+|. .+|..++.+||.-+|.+++ .|..|..++-..+
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 34888999988998899999999999999999999999999998 5556679999999998885 6777777776443
No 55
>PF15510 CENP-W: Centromere kinetochore component W
Probab=95.38 E-value=0.04 Score=43.82 Aligned_cols=64 Identities=25% Similarity=0.388 Sum_probs=50.1
Q ss_pred CCChHHHHHHHhcC-cchhccCchHHHH--------------HHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 61 QLPLARIKKIMKAD-EDVRMISAEAPIL--------------FAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 61 ~LPLARIKRIMKsD-pDV~~ISaEA~vl--------------lAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
.-|-+-+||++|.. |-. ++...+=.+ +---|=+|++.|+.+|-..|-++|.++|+.+||..|-+
T Consensus 16 kaPrgfLkrv~Kr~Kphl-Rl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPHL-RLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred hCchHHHHHHHHhcCCce-eecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 46889999999954 433 344433334 45567899999999999999999999999999988754
No 56
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=95.01 E-value=0.079 Score=44.07 Aligned_cols=58 Identities=22% Similarity=0.259 Sum_probs=46.1
Q ss_pred HHHHHhc-CcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 67 IKKIMKA-DEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 67 IKRIMKs-DpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
|.|++|. +||.+ ||.+|.-++.--.-.|++.++.+|...|..+||.||+-++|..++.
T Consensus 43 v~kvlk~Vhpd~g-is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~r 101 (127)
T KOG1744|consen 43 VYKVLKQVHPDLG-ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVR 101 (127)
T ss_pred hhhhhhcccCCCC-cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHH
Confidence 4446665 67865 7777766665555666899999999999999999999999999885
No 57
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.32 E-value=0.06 Score=49.43 Aligned_cols=71 Identities=14% Similarity=0.185 Sum_probs=58.3
Q ss_pred HHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccc
Q 026901 65 ARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVD 135 (231)
Q Consensus 65 ARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~D 135 (231)
.+|..+|+.-..-..+-.|+-.+|...|+-||..++..|-..|+++|..||..+||...++++-.+.|=.+
T Consensus 158 ~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf 228 (258)
T KOG1142|consen 158 RKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGF 228 (258)
T ss_pred cchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCc
Confidence 44555555433345788889999999999999999999999999999999999999999998876665443
No 58
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=94.16 E-value=0.064 Score=45.14 Aligned_cols=72 Identities=24% Similarity=0.261 Sum_probs=61.1
Q ss_pred hhcCCCCCCChHHHHH-HHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 54 ANDFKNHQLPLARIKK-IMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 54 ~~d~k~~~LPLARIKR-IMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
..|.--..+|-.|+-| |++.--..-++-+.|..+|-.|.|.|+..|-..+..+|-+.||-||..+||.-|..
T Consensus 59 stdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr 131 (137)
T KOG1745|consen 59 STDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 131 (137)
T ss_pred hhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence 3455556899999887 87775434479999999999999999999999999999999999999999987753
No 59
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=93.89 E-value=0.43 Score=41.62 Aligned_cols=68 Identities=18% Similarity=0.264 Sum_probs=55.5
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHc--------------CCCcccHHHHHHHH
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEEN--------------KRRTLQKNDIAAAI 124 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~--------------kRKTLq~~DIa~AI 124 (231)
...+|=+-+--+|+.. ++...-.-...||+.|+..||.+++..|+.+++-+ ||-||+.+||..|+
T Consensus 84 tP~IPDavt~~yL~~a-Gf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL 162 (176)
T KOG3423|consen 84 TPTIPDAVTDHYLKKA-GFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPAL 162 (176)
T ss_pred CCCCcHHHHHHHHHhc-CCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHH
Confidence 4569999999999987 34444455788999999999999999999999743 34489999999998
Q ss_pred hcC
Q 026901 125 TRT 127 (231)
Q Consensus 125 ~~~ 127 (231)
++.
T Consensus 163 ~Ey 165 (176)
T KOG3423|consen 163 AEY 165 (176)
T ss_pred HHh
Confidence 764
No 60
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=93.00 E-value=0.53 Score=39.05 Aligned_cols=67 Identities=16% Similarity=0.135 Sum_probs=44.6
Q ss_pred HHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccc
Q 026901 66 RIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFL 133 (231)
Q Consensus 66 RIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL 133 (231)
-|..|+|+- +|......++..+-..+=.++.++...|..+|.+.+|++|..+||..||+..-.+.|-
T Consensus 17 ~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~ 83 (129)
T PF02291_consen 17 VIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFT 83 (129)
T ss_dssp HHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT------
T ss_pred HHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhcc
Confidence 466677765 5555555566666666667889999999999999999999999999999976556553
No 61
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=91.90 E-value=0.51 Score=47.59 Aligned_cols=63 Identities=21% Similarity=0.251 Sum_probs=56.5
Q ss_pred hHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 64 LARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 64 LARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
-.-+|-+.++- ++..++.|+..+++.=.|+=|.+++..|.++..+.||++++-+||..|+...
T Consensus 14 ~Es~k~vAEsl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~ 76 (576)
T KOG2549|consen 14 KESVKVVAESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSL 76 (576)
T ss_pred HHHHHHHHHHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhc
Confidence 55666666665 7889999999999999999999999999999999999999999999998654
No 62
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=90.83 E-value=0.42 Score=42.96 Aligned_cols=45 Identities=20% Similarity=0.254 Sum_probs=33.4
Q ss_pred HHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHc
Q 026901 65 ARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEEN 110 (231)
Q Consensus 65 ARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~ 110 (231)
.||.+|++... +..|..|.+.+|+-|||..+..|...+...|++.
T Consensus 51 ~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR 95 (264)
T PF05236_consen 51 KRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHR 95 (264)
T ss_dssp HHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH------
T ss_pred HHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 68889998875 7789999999999999999999999999988753
No 63
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=89.21 E-value=0.87 Score=39.79 Aligned_cols=60 Identities=18% Similarity=0.192 Sum_probs=47.8
Q ss_pred HHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHc------CCCcccHHHHHHHHh
Q 026901 65 ARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEEN------KRRTLQKNDIAAAIT 125 (231)
Q Consensus 65 ARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~------kRKTLq~~DIa~AI~ 125 (231)
.+|.+|++.. .+..|+.|.+.+|+.|||.++..|.......++.. ..++...+|+..-+.
T Consensus 52 ~~~~~i~~~~-g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~ 117 (212)
T cd08045 52 KKIRKIAKKH-GLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLR 117 (212)
T ss_pred HHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHH
Confidence 5677777766 45589999999999999999999999999999754 345666778876654
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=86.99 E-value=3.1 Score=29.61 Aligned_cols=48 Identities=10% Similarity=0.112 Sum_probs=36.4
Q ss_pred CCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026901 61 QLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEE 109 (231)
Q Consensus 61 ~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~ 109 (231)
.+|=+-+.-+|+.. ++..--.-...+++-|++.||.+++..|+.+++-
T Consensus 2 ~IPD~v~~~yL~~~-G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERS-GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHC-CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35667777777775 3333333467899999999999999999999864
No 65
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=85.98 E-value=6.3 Score=34.65 Aligned_cols=62 Identities=10% Similarity=0.122 Sum_probs=48.6
Q ss_pred HHHHHHHHhhcCCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026901 46 YQRQEIEQANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAE 108 (231)
Q Consensus 46 ~~~~eie~~~d~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~ 108 (231)
+.++||.+..|.-...||=+-+.=-|-.. .+...-.-..-|++.++..||.+++..||.+.+
T Consensus 73 ktlee~l~~mDsy~PliPd~v~DYyl~k~-Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsr 134 (197)
T COG5162 73 KTLEELLQNMDSYTPLIPDSVTDYYLEKA-GFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSR 134 (197)
T ss_pred HHHHHHHHhcccCCCCccHHHHHHHHHhc-CceeccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566666677778889999888888776 444455567789999999999999999998764
No 66
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=83.96 E-value=2.9 Score=40.28 Aligned_cols=61 Identities=21% Similarity=0.195 Sum_probs=52.9
Q ss_pred HHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 66 RIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 66 RIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
.||-+-.+- ++.+|..|+..+++--+|+=|.+++.+|.+...++||..|+-+||..|++..
T Consensus 10 t~KdvAesl-Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~l 70 (450)
T COG5095 10 TLKDVAESL-GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSL 70 (450)
T ss_pred HHHHHHHHc-CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhc
Confidence 344444443 6778999999999999999999999999999999999999999999998754
No 67
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=70.76 E-value=47 Score=25.71 Aligned_cols=62 Identities=21% Similarity=0.230 Sum_probs=50.9
Q ss_pred CCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHH------HHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 57 FKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELF------ILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 57 ~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElF------I~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
..|..||-.-|++....+++ +..++..+++.| +..|.+-|+.+|.-.+...|..+||..|+.
T Consensus 27 ~~Na~l~~~~l~~~~~l~~~-------~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 27 KCNAQLPGEELRKYCPLSSE-------AKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CccccCCHHHHHhHcCCCHH-------HHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 45789999999998777655 566677776655 567888899999999999999999999985
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=66.73 E-value=10 Score=32.65 Aligned_cols=50 Identities=20% Similarity=0.157 Sum_probs=43.9
Q ss_pred ccCchHHHHHHHHHH---HHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC
Q 026901 79 MISAEAPILFAKACE---LFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD 128 (231)
Q Consensus 79 ~ISaEA~vllAKAtE---lFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d 128 (231)
.++.++...+.+.+. ..|..|+..++..|..++.++|+.++|..++....
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 588899988888887 37999999999999889999999999999998643
No 69
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=64.10 E-value=28 Score=31.98 Aligned_cols=64 Identities=22% Similarity=0.262 Sum_probs=46.7
Q ss_pred hHHHHHHHhcCcc----hhccCchHHHHHHHHHHH------HHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 64 LARIKKIMKADED----VRMISAEAPILFAKACEL------FILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 64 LARIKRIMKsDpD----V~~ISaEA~vllAKAtEl------FI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
..-++.|++.--. -..++.++..++++.+.- .+..|+..|+..|...++.+|+.+||..|+...
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 4556666664211 125788888888776643 445777889999998899999999999999876
No 70
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=60.21 E-value=12 Score=25.46 Aligned_cols=35 Identities=29% Similarity=0.288 Sum_probs=27.3
Q ss_pred hHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHH
Q 026901 64 LARIKKIMKADEDVRMISAEAPILFAKACELFILE 98 (231)
Q Consensus 64 LARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~ 98 (231)
+.||+|++....+..--..||-.++.+|-++..++
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 57999999998765434459999999998886654
No 71
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=57.57 E-value=33 Score=33.17 Aligned_cols=65 Identities=12% Similarity=0.074 Sum_probs=55.7
Q ss_pred CChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 62 LPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 62 LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
|=..+|+.|+.+-+ +...-..|...|+-.+..||+.|.+-|..++...+|---...||..|++..
T Consensus 30 la~~avaQIcqslg-~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dl 94 (353)
T KOG2389|consen 30 LARVAVAQICQSLG-YSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDL 94 (353)
T ss_pred HHHHHHHHHHHhcC-CcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHh
Confidence 44567899999874 445666699999999999999999999999999999988999999998764
No 72
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=56.99 E-value=80 Score=31.41 Aligned_cols=60 Identities=15% Similarity=0.135 Sum_probs=48.1
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHH------HHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELF------ILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElF------I~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
|..++...|+++.+.+.+ +..++..+.+.| ...+.+-|+.+|.-.++..|..+||..|+.
T Consensus 432 N~~l~~~~l~~~~~l~~~-------~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 432 NADLNSDEIEQFCKLSAI-------DANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred cccCCHHHHHhhcCCCHH-------HHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 778899999887766544 555666666655 667888899999999999999999999985
No 73
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=56.93 E-value=36 Score=32.48 Aligned_cols=63 Identities=16% Similarity=0.121 Sum_probs=55.0
Q ss_pred hHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhc
Q 026901 64 LARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITR 126 (231)
Q Consensus 64 LARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~ 126 (231)
++.|--+|+.+-....|++-|..-|..++.-.|.++.+.+..+|+..+|...++.||.....+
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 456667777777778899999999999999999999999999999999999999999887644
No 74
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=56.89 E-value=45 Score=30.21 Aligned_cols=63 Identities=11% Similarity=0.133 Sum_probs=43.8
Q ss_pred HHHHHHhcCcc----hhccCchHHHHHHHHHH------HHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC
Q 026901 66 RIKKIMKADED----VRMISAEAPILFAKACE------LFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD 128 (231)
Q Consensus 66 RIKRIMKsDpD----V~~ISaEA~vllAKAtE------lFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d 128 (231)
-+..|++.--+ -..++.++..++++.+. ..+..++..|+..|..+++.+|+.+||..|+....
T Consensus 203 e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~ 275 (365)
T TIGR02928 203 ELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIE 275 (365)
T ss_pred HHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 35666654211 12477777777666554 34566788888889888889999999999987663
No 75
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=55.76 E-value=56 Score=28.09 Aligned_cols=51 Identities=18% Similarity=0.143 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCccccccccCCCccchhhh
Q 026901 94 LFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVDIVPRDEIKDEA 146 (231)
Q Consensus 94 lFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~DIVP~~~~~~e~ 146 (231)
.++..+...|.-.+++.++.+|..+||..||...-.+.|-- -|.++..-+=
T Consensus 45 rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~--pPpRe~lL~l 95 (148)
T KOG3334|consen 45 RYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTP--PPPREFLLEL 95 (148)
T ss_pred HHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCC--CCchHHHHHH
Confidence 45677788899999999999999999999999988888876 4444444433
No 76
>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=55.51 E-value=20 Score=31.97 Aligned_cols=41 Identities=17% Similarity=0.159 Sum_probs=31.8
Q ss_pred HHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHH
Q 026901 66 RIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHA 107 (231)
Q Consensus 66 RIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A 107 (231)
|+-.|.... +..-||.|++.++..|+|.|+..|...+...+
T Consensus 211 Rm~~ia~e~-GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~ 251 (252)
T PF12767_consen 211 RMEQIAWEH-GLGGVSDDCANLLNLALEVHLKNLIKSCLDLV 251 (252)
T ss_pred HHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 444444333 45569999999999999999999999887643
No 77
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=54.88 E-value=49 Score=27.44 Aligned_cols=61 Identities=20% Similarity=0.150 Sum_probs=47.4
Q ss_pred HHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC
Q 026901 66 RIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD 128 (231)
Q Consensus 66 RIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d 128 (231)
-||-+|=.-.|+..=-.++..++-..+--++..|+..|...|+ .|..++-+|+.-|+++++
T Consensus 14 DikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~Dp 74 (126)
T COG5248 14 DIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRRDP 74 (126)
T ss_pred HHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhhCh
Confidence 4666666666666666677777777777888889999999887 566778899999998875
No 78
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=50.14 E-value=66 Score=26.35 Aligned_cols=68 Identities=16% Similarity=0.108 Sum_probs=48.8
Q ss_pred HHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCC-ccccccccCCC
Q 026901 69 KIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTD-IFDFLVDIVPR 139 (231)
Q Consensus 69 RIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d-~fdFL~DIVP~ 139 (231)
-+|=.=.|+..=-.+++.++-..+-.||.+|+..|..+. +|..++-+||.-+|++++ .|.-.++++--
T Consensus 17 ~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRkDpkK~~Rv~eLL~m 85 (109)
T KOG3901|consen 17 SMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRKDPKKLGRVKELLAM 85 (109)
T ss_pred HHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHhChHHHhHHHHHHHh
Confidence 333333444445567778888888888888888777765 777889999999999885 56666666654
No 79
>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=49.98 E-value=60 Score=32.99 Aligned_cols=63 Identities=10% Similarity=-0.029 Sum_probs=43.2
Q ss_pred HHHHHHHhcCcchhccCchHHHHHHHH-H------------HHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 65 ARIKKIMKADEDVRMISAEAPILFAKA-C------------ELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 65 ARIKRIMKsDpDV~~ISaEA~vllAKA-t------------ElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
..|++.++.+.....+|.+|...+.+- + ..=+..|.++|..+|..+++.+|+.+||..|++..
T Consensus 316 ~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 316 QFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 345555555534446777776666431 1 34567788888888888889999999999987644
No 80
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=49.46 E-value=56 Score=32.64 Aligned_cols=33 Identities=12% Similarity=0.247 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 95 FILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 95 FI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
-|..|..+|...|+.++++.|+.+||..||+..
T Consensus 474 ~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 474 WLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 457888999999999999999999999999764
No 81
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=46.50 E-value=22 Score=34.92 Aligned_cols=42 Identities=19% Similarity=0.277 Sum_probs=36.5
Q ss_pred HHHHHHHHHHH----HHHHHHHHHHHHHHcCCCcccHHHHHHHHhc
Q 026901 85 PILFAKACELF----ILELTIRSWLHAEENKRRTLQKNDIAAAITR 126 (231)
Q Consensus 85 ~vllAKAtElF----I~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~ 126 (231)
...+++.|+-| |..++.+|...|-+..|+.++.+|+..|+.+
T Consensus 346 ~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~K 391 (406)
T COG1222 346 LELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEK 391 (406)
T ss_pred HHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHH
Confidence 56777777766 7788999999999999999999999999875
No 82
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=44.59 E-value=63 Score=31.61 Aligned_cols=58 Identities=28% Similarity=0.389 Sum_probs=42.8
Q ss_pred HHHHHhc---CcchhccCchHHHHHHHHHH----HHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 67 IKKIMKA---DEDVRMISAEAPILFAKACE----LFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 67 IKRIMKs---DpDV~~ISaEA~vllAKAtE----lFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
||+|++. .+|| .++.+|..++++.-+ .+...|...|...|.++|-+++.-+||..+..
T Consensus 363 ~~~IL~iRc~EEdv-~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 363 IKKILRIRCQEEDV-EMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred HHHHHHhhhhhhcc-ccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 5666654 3455 689999999887654 34556666677778888889999999999864
No 83
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=43.03 E-value=46 Score=29.52 Aligned_cols=72 Identities=14% Similarity=0.164 Sum_probs=54.7
Q ss_pred hhcCCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCcccHHHHHHHHhc
Q 026901 54 ANDFKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEE-NKRRTLQKNDIAAAITR 126 (231)
Q Consensus 54 ~~d~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~-~kRKTLq~~DIa~AI~~ 126 (231)
..-|+.+.||-+.|||+.-.--. ..||....++++-....|+-++...|..+-.+ .-.--|...|+..|+..
T Consensus 108 yEvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reayr~ 180 (199)
T COG5251 108 YEVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAYRY 180 (199)
T ss_pred HHHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHHHH
Confidence 45689999999999999887522 35778888888888899999998888665432 22235888999888753
No 84
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=40.34 E-value=49 Score=32.76 Aligned_cols=61 Identities=16% Similarity=0.251 Sum_probs=45.5
Q ss_pred HHHHHHHhc--CcchhccCchHHHHHHHHHH----HHHHHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 65 ARIKKIMKA--DEDVRMISAEAPILFAKACE----LFILELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 65 ARIKRIMKs--DpDV~~ISaEA~vllAKAtE----lFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
.-||.|++. +++--.+|.+|...+++.-+ .+...|..-|...|+++++++|..+||..|-+
T Consensus 364 ~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~ 430 (450)
T COG1224 364 EEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE 430 (450)
T ss_pred HHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH
Confidence 456777765 33333689999999987644 34556666788899999999999999988853
No 85
>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=38.35 E-value=1e+02 Score=28.65 Aligned_cols=57 Identities=16% Similarity=0.288 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHhcC--cchhccCchHHHHHHHHHHHHHHHHHHHH
Q 026901 35 QQQQQLQMFWSYQRQEIEQANDFKNHQLPLARIKKIMKAD--EDVRMISAEAPILFAKACELFILELTIRS 103 (231)
Q Consensus 35 ~~~~~l~~fW~~~~~eie~~~d~k~~~LPLARIKRIMKsD--pDV~~ISaEA~vllAKAtElFI~~Lt~~A 103 (231)
...+.+.+||.+-+. =|+-+|...++.| .++..+|++++..=-..+|..+.+++...
T Consensus 30 ~~~~t~~~f~~nwV~------------~Pl~~I~~tlr~d~~s~~~i~s~~sL~~d~~SLeRMv~dF~~d~ 88 (290)
T PF08637_consen 30 NAVETVRGFWKNWVW------------EPLKSIWDTLRHDEKSEIAIMSKESLQSDMESLERMVVDFAKDN 88 (290)
T ss_pred HHHHHHHHHHHHHHH------------HHHHHHHHHHhCCCCCCcccccHHHHHHHHHHHHHHHHHHHhcC
Confidence 666777888886542 2788899999996 56788999999999889998888888755
No 86
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=36.92 E-value=1.4e+02 Score=25.42 Aligned_cols=66 Identities=12% Similarity=0.205 Sum_probs=47.4
Q ss_pred HHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcc---cHHHHHHHHhcCCccccc
Q 026901 67 IKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTL---QKNDIAAAITRTDIFDFL 133 (231)
Q Consensus 67 IKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTL---q~~DIa~AI~~~d~fdFL 133 (231)
|.-|+.+- .+.-.+.-.+.-+-.-+-.+.+.+.+.|.-.|+..+|-.+ .-+||.-||...-...|-
T Consensus 20 ihliL~Sl-gi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~ 88 (145)
T COG5094 20 IHLILRSL-GIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFV 88 (145)
T ss_pred HHHHHHhc-CchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcC
Confidence 33344443 5556666666655555667788999999999998877654 459999999887777773
No 87
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=36.37 E-value=46 Score=31.68 Aligned_cols=78 Identities=17% Similarity=0.233 Sum_probs=55.2
Q ss_pred CCCCCCh---HHHHHHHhcCcch----hccCchHHHHHHHH--HH----HHHHHHHHHHHHHHHHcCCCcccHHHHHHHH
Q 026901 58 KNHQLPL---ARIKKIMKADEDV----RMISAEAPILFAKA--CE----LFILELTIRSWLHAEENKRRTLQKNDIAAAI 124 (231)
Q Consensus 58 k~~~LPL---ARIKRIMKsDpDV----~~ISaEA~vllAKA--tE----lFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI 124 (231)
....||- .-|+.|++.--+. +.++.++.-+++.- .+ .+..+|.+.|.+.|++.++.+++.+|+..|.
T Consensus 183 ~~I~F~pY~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~ 262 (366)
T COG1474 183 SEIVFPPYTAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQ 262 (366)
T ss_pred ceeeeCCCCHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHH
Confidence 3345654 6778887764322 35778888777632 22 4677999999999999999999999999995
Q ss_pred hcCCcccccccc
Q 026901 125 TRTDIFDFLVDI 136 (231)
Q Consensus 125 ~~~d~fdFL~DI 136 (231)
...+ .+++.++
T Consensus 263 ~~~~-~~~~~~~ 273 (366)
T COG1474 263 EEIE-RDVLEEV 273 (366)
T ss_pred HHhh-HHHHHHH
Confidence 4443 4555544
No 88
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=33.73 E-value=4.4 Score=36.79 Aligned_cols=78 Identities=21% Similarity=0.086 Sum_probs=51.2
Q ss_pred CCCCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcCCcccccccc
Q 026901 57 FKNHQLPLARIKKIMKADEDVRMISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRTDIFDFLVDI 136 (231)
Q Consensus 57 ~k~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~d~fdFL~DI 136 (231)
++.-..++.|+..+++. ++.+ .+++..-.+...|....+.+....+|.+|..-.+...|+..+.++|+.++
T Consensus 4 ~~~~~~~~~~~~~~~~~------~~p~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~fw~~~~~e~e~~~d~~~~~ 74 (236)
T KOG1657|consen 4 NNANSDIVANIVSNRRM------KAPP---KGAKSEPEGAVCLDPEASIITGDVSRQQLQSFWSKQAIEKEGQLDFKNHI 74 (236)
T ss_pred cccCccccccccccccc------cCCc---cccccccccceecchhhhhcccchhhHHHHhhhhccccccccccchhhcc
Confidence 34445566666666632 2222 33333333344677777776655568889888888888889999999999
Q ss_pred CCCccch
Q 026901 137 VPRDEIK 143 (231)
Q Consensus 137 VP~~~~~ 143 (231)
||...+|
T Consensus 75 lPlaRiK 81 (236)
T KOG1657|consen 75 LPLARIK 81 (236)
T ss_pred CcHhhcc
Confidence 9975444
No 89
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=31.95 E-value=64 Score=30.57 Aligned_cols=33 Identities=15% Similarity=0.201 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 95 FILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 95 FI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
=|..|+.+|...|-+++++.|+.+|+..|+.+.
T Consensus 340 dl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 340 DLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 466788889999988999999999999999763
No 90
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=31.54 E-value=66 Score=29.80 Aligned_cols=42 Identities=17% Similarity=0.150 Sum_probs=32.4
Q ss_pred HHHHHHHHHHH----HHHHHHHHHHHHHHcCCCcccHHHHHHHHhc
Q 026901 85 PILFAKACELF----ILELTIRSWLHAEENKRRTLQKNDIAAAITR 126 (231)
Q Consensus 85 ~vllAKAtElF----I~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~ 126 (231)
...+++.|+-| |..|+.+|...|-+++|+.|+.+|+..|+.+
T Consensus 317 ~~~la~~t~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~ 362 (364)
T TIGR01242 317 LEAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEK 362 (364)
T ss_pred HHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHH
Confidence 34455555433 5578888989898899999999999999875
No 91
>PRK09862 putative ATP-dependent protease; Provisional
Probab=30.71 E-value=2.1e+02 Score=28.73 Aligned_cols=62 Identities=11% Similarity=0.125 Sum_probs=43.1
Q ss_pred CCCCChHHHHHHHhcCcchhccCchHHHHHHHHHHHH------HHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 59 NHQLPLARIKKIMKADEDVRMISAEAPILFAKACELF------ILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 59 ~~~LPLARIKRIMKsDpDV~~ISaEA~vllAKAtElF------I~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
+..++-..|++.++.+.+. ..++..+.+.+ ...|.+-|+..|.-.+|..|+.+||..|+.=.
T Consensus 425 n~~l~~~~l~~~~~l~~~~-------~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR 492 (506)
T PRK09862 425 NAWLDSPEIRQFCKLESED-------ARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYR 492 (506)
T ss_pred hcccCHHHHHHHhCCCHHH-------HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhh
Confidence 5667767777666655443 33333333322 45777888899999999999999999999633
No 92
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=30.12 E-value=1.2e+02 Score=31.39 Aligned_cols=60 Identities=10% Similarity=-0.039 Sum_probs=39.1
Q ss_pred HHHHHhcCcchhccCchHHHHHHHHH-------------HHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhc
Q 026901 67 IKKIMKADEDVRMISAEAPILFAKAC-------------ELFILELTIRSWLHAEENKRRTLQKNDIAAAITR 126 (231)
Q Consensus 67 IKRIMKsDpDV~~ISaEA~vllAKAt-------------ElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~ 126 (231)
|.+.++.+.....++.+|...+-+-. ..=+..|.++|...|+..+++.+..+||..|+..
T Consensus 327 iaqe~~~~G~l~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 327 VAQEVKRDGKIPHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred HHHHhhhccCCCCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 44444433233456666655543321 2234568888999999999999999999988754
No 93
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=30.09 E-value=1.5e+02 Score=29.50 Aligned_cols=61 Identities=18% Similarity=0.043 Sum_probs=40.4
Q ss_pred HHHHHhcC--cchhccCchHHHHHHHHHH--HHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 67 IKKIMKAD--EDVRMISAEAPILFAKACE--LFILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 67 IKRIMKsD--pDV~~ISaEA~vllAKAtE--lFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
|++|++.- ..-..++.++..++.+.+. ..+..+...|...|...+|++|+.+||..++...
T Consensus 268 i~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~~ 332 (531)
T TIGR02902 268 IKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAENG 332 (531)
T ss_pred HHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCCc
Confidence 55555542 1112577888887766654 2234455566667777788999999999999754
No 94
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=29.18 E-value=97 Score=21.08 Aligned_cols=25 Identities=20% Similarity=0.029 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHcCCCcccHHHHHHH
Q 026901 99 LTIRSWLHAEENKRRTLQKNDIAAA 123 (231)
Q Consensus 99 Lt~~A~~~A~~~kRKTLq~~DIa~A 123 (231)
+=..+-..|.+++...|+.++|..|
T Consensus 20 ~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 20 LRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHHHcCCCeECHHHHHhh
Confidence 3334556678899999999998765
No 95
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=28.03 E-value=2.3e+02 Score=28.80 Aligned_cols=47 Identities=19% Similarity=0.210 Sum_probs=35.2
Q ss_pred ccCchHHHHHHHHHHHHH-------HHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 79 MISAEAPILFAKACELFI-------LELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 79 ~ISaEA~vllAKAtElFI-------~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
.|+.++..++..++..+- ..+.+.|..+|.-++|.+|+.+||..|+.
T Consensus 249 ~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~ 302 (633)
T TIGR02442 249 RISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAE 302 (633)
T ss_pred CCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHH
Confidence 467777777666665442 34666777888889999999999999875
No 96
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=27.40 E-value=79 Score=31.01 Aligned_cols=32 Identities=19% Similarity=0.215 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC
Q 026901 96 ILELTIRSWLHAEENKRRTLQKNDIAAAITRT 127 (231)
Q Consensus 96 I~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~ 127 (231)
|..++.+|...|.+.+|..|+.+|+..|+.+.
T Consensus 393 I~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 393 IKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred HHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 56788899999999999999999999999763
No 97
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=27.02 E-value=85 Score=30.22 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHcCCCcccHHHHHHHHhc
Q 026901 96 ILELTIRSWLHAEENKRRTLQKNDIAAAITR 126 (231)
Q Consensus 96 I~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~ 126 (231)
|..|+.+|...|-+++|+.|+.+|+..|+.+
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~ 385 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKT 385 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHH
Confidence 7789999999999999999999999999876
No 98
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=26.21 E-value=2.4e+02 Score=21.86 Aligned_cols=27 Identities=7% Similarity=0.098 Sum_probs=20.4
Q ss_pred HHHHHHhhcCCCCCCChHHHHHHHhcC
Q 026901 48 RQEIEQANDFKNHQLPLARIKKIMKAD 74 (231)
Q Consensus 48 ~~eie~~~d~k~~~LPLARIKRIMKsD 74 (231)
+..+..+...+...||++.|++++...
T Consensus 44 l~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (108)
T cd04773 44 VRDARLIHLLRRGGYLLEQIATVVEQL 70 (108)
T ss_pred HHHHHHHHHHHHCCCCHHHHHHHHHHh
Confidence 344555556677889999999999874
No 99
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=26.17 E-value=1.9e+02 Score=25.24 Aligned_cols=64 Identities=17% Similarity=0.195 Sum_probs=41.0
Q ss_pred ccCchHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHhcC---CccccccccCCCccc
Q 026901 79 MISAEAPILFAKACELFILELTIRSWLHAEENKRRTLQKNDIAAAITRT---DIFDFLVDIVPRDEI 142 (231)
Q Consensus 79 ~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~~~---d~fdFL~DIVP~~~~ 142 (231)
.|+.+|...+...+..=+..+..+--..+...+.++|+.+||...+... ..|+|+..++-++..
T Consensus 130 ~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~~~~~if~l~dal~~~~~~ 196 (302)
T TIGR01128 130 RIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDSARFNVFDLTDALLEGKAA 196 (302)
T ss_pred CCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhhhcCCHHHHHHHHHCCCHH
Confidence 5899998888887764333333333333333333479999999887544 467888877776543
No 100
>smart00350 MCM minichromosome maintenance proteins.
Probab=25.33 E-value=2.1e+02 Score=28.14 Aligned_cols=66 Identities=18% Similarity=0.159 Sum_probs=47.8
Q ss_pred CCCChHHHHHHHhcCcc-h-hccCchHHHHHHHHHHH-------------------HHHHHHHHHHHHHHHcCCCcccHH
Q 026901 60 HQLPLARIKKIMKADED-V-RMISAEAPILFAKACEL-------------------FILELTIRSWLHAEENKRRTLQKN 118 (231)
Q Consensus 60 ~~LPLARIKRIMKsDpD-V-~~ISaEA~vllAKAtEl-------------------FI~~Lt~~A~~~A~~~kRKTLq~~ 118 (231)
..++..-+++.+..-.. + -.+|.++..++...... .++.|.+.|-.+|+-+.|.+|+.+
T Consensus 416 ~~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~ 495 (509)
T smart00350 416 VPISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEA 495 (509)
T ss_pred ccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHH
Confidence 35778888887765543 2 24788777766443322 236677888888999999999999
Q ss_pred HHHHHHh
Q 026901 119 DIAAAIT 125 (231)
Q Consensus 119 DIa~AI~ 125 (231)
|+..||+
T Consensus 496 Dv~~ai~ 502 (509)
T smart00350 496 DVEEAIR 502 (509)
T ss_pred HHHHHHH
Confidence 9999986
No 101
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=25.13 E-value=2e+02 Score=21.84 Aligned_cols=28 Identities=21% Similarity=0.297 Sum_probs=20.8
Q ss_pred HHHHHHhhcCCCCCCChHHHHHHHhcCc
Q 026901 48 RQEIEQANDFKNHQLPLARIKKIMKADE 75 (231)
Q Consensus 48 ~~eie~~~d~k~~~LPLARIKRIMKsDp 75 (231)
+..+..+...+...||++.|++++....
T Consensus 44 i~~l~~i~~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 44 LERLQQILFLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHcCc
Confidence 4444555556778899999999998763
No 102
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=24.36 E-value=1.9e+02 Score=27.36 Aligned_cols=59 Identities=17% Similarity=0.146 Sum_probs=37.0
Q ss_pred HHHHHHhcCcchhccCchHHHHHHHHHHHHHH-------HHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 66 RIKKIMKADEDVRMISAEAPILFAKACELFIL-------ELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 66 RIKRIMKsDpDV~~ISaEA~vllAKAtElFI~-------~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
+|....+.-++| .|+.+....++..+..+=. .|.+.|-.+|.-++|..|+.+||..++.
T Consensus 242 ~I~~a~~~~~~V-~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 242 KIVNAQNLLPQV-TIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred HHHHHHHHhccC-cCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 333333333444 3666666665555544321 2556666677789999999999998763
No 103
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=23.38 E-value=2e+02 Score=25.69 Aligned_cols=63 Identities=24% Similarity=0.212 Sum_probs=42.4
Q ss_pred ccCchHHHHHHHHHHHHHHHHHHHHHHHHHHc-CCCcccHHHHHHHHhc---CCccccccccCCCccc
Q 026901 79 MISAEAPILFAKACELFILELTIRSWLHAEEN-KRRTLQKNDIAAAITR---TDIFDFLVDIVPRDEI 142 (231)
Q Consensus 79 ~ISaEA~vllAKAtElFI~~Lt~~A~~~A~~~-kRKTLq~~DIa~AI~~---~d~fdFL~DIVP~~~~ 142 (231)
.|+.+|...+...+.-=+..+..+--..+-.. +++ |+.+||..++.. ...|+|+.-++-++..
T Consensus 165 ~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~~~~~~~f~l~dai~~~~~~ 231 (340)
T PRK05574 165 QIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPDSARFDVFDLVDAILAGKIK 231 (340)
T ss_pred CCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhhhhcCCHHHHHHHHHCCCHH
Confidence 68899998888887644444444444444332 334 999999988755 4677888888876543
No 104
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=23.19 E-value=6.4e+02 Score=24.28 Aligned_cols=33 Identities=21% Similarity=0.259 Sum_probs=21.6
Q ss_pred HHHH-HHHHHHHHhhcCCCCCCChHHHHHHHhcC
Q 026901 42 MFWS-YQRQEIEQANDFKNHQLPLARIKKIMKAD 74 (231)
Q Consensus 42 ~fW~-~~~~eie~~~d~k~~~LPLARIKRIMKsD 74 (231)
--|. ++.+|=++-.......||..-+|||.|.-
T Consensus 262 ~q~~aKrqaENa~R~argep~lP~dd~kr~fk~p 295 (339)
T KOG1560|consen 262 HQWIAKRQAENANRAARGEPPLPEDDWKRIFKPP 295 (339)
T ss_pred HHHHHHHHHHhhhhhhcCCCCCChHHHHHHhcCC
Confidence 3343 33333333345567889999999999984
No 105
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=23.11 E-value=2.1e+02 Score=29.24 Aligned_cols=59 Identities=19% Similarity=0.045 Sum_probs=40.1
Q ss_pred HHHHHHhcCcchhccCchHHHHHHHHHHHHH-------HHHHHHHHHHHHHcCCCcccHHHHHHHHh
Q 026901 66 RIKKIMKADEDVRMISAEAPILFAKACELFI-------LELTIRSWLHAEENKRRTLQKNDIAAAIT 125 (231)
Q Consensus 66 RIKRIMKsDpDV~~ISaEA~vllAKAtElFI-------~~Lt~~A~~~A~~~kRKTLq~~DIa~AI~ 125 (231)
+|.+.-+.-++| .|+.+....++.+|..|- ..|++-|..+|.-++|..|+.+||..|+.
T Consensus 183 ~I~~AR~rl~~v-~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 183 DIAAARARLPAV-GPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred HHHHHHHHHccC-CCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 444443332343 466666666666555553 35677788888899999999999999974
No 106
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.22 E-value=3.1e+02 Score=21.33 Aligned_cols=29 Identities=10% Similarity=0.217 Sum_probs=22.1
Q ss_pred HHHHHHHhhcCCCCCCChHHHHHHHhcCc
Q 026901 47 QRQEIEQANDFKNHQLPLARIKKIMKADE 75 (231)
Q Consensus 47 ~~~eie~~~d~k~~~LPLARIKRIMKsDp 75 (231)
.+..++.+...+...|||..||.+++...
T Consensus 43 ~i~~l~~I~~lr~~G~sl~eI~~~l~~~~ 71 (123)
T cd04770 43 DLARLRFIRRAQALGFSLAEIRELLSLRD 71 (123)
T ss_pred HHHHHHHHHHHHHCCCCHHHHHHHHHhhh
Confidence 34445666667888999999999998753
No 107
>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=20.91 E-value=2.7e+02 Score=18.64 Aligned_cols=32 Identities=3% Similarity=-0.019 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcccHHHHHHHH
Q 026901 93 ELFILELTIRSWLHAEENKRRTLQKNDIAAAI 124 (231)
Q Consensus 93 ElFI~~Lt~~A~~~A~~~kRKTLq~~DIa~AI 124 (231)
+..+..++...+..+-.++...|+++++..++
T Consensus 35 ~~~~~~~~~~~~~~~D~d~dG~i~~~Ef~~~~ 66 (66)
T PF13499_consen 35 DEESDEMIDQIFREFDTDGDGRISFDEFLNFM 66 (66)
T ss_dssp HHHHHHHHHHHHHHHTTTSSSSEEHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCCCcCCCcHHHHhccC
Confidence 55566677777888888888899999987653
No 108
>PRK14139 heat shock protein GrpE; Provisional
Probab=20.07 E-value=5.8e+02 Score=22.38 Aligned_cols=23 Identities=17% Similarity=0.005 Sum_probs=14.5
Q ss_pred ccCchHHHHHHHHHHHHHHHHHH
Q 026901 79 MISAEAPILFAKACELFILELTI 101 (231)
Q Consensus 79 ~ISaEA~vllAKAtElFI~~Lt~ 101 (231)
++.+|.-.+...+.+-|+.+|.-
T Consensus 68 R~~kE~e~~~~~a~~~~~~~LLp 90 (185)
T PRK14139 68 RAQEDVAKAHKFAIESFAESLLP 90 (185)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhh
Confidence 34445556667777777777754
Done!