Query 024740
Match_columns 263
No_of_seqs 212 out of 828
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 07:02:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024740.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024740hhsearch_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 3.2E-35 7E-40 265.4 8.4 170 80-255 50-221 (236)
2 COG5208 HAP5 CCAAT-binding fac 100.0 3.7E-32 8.1E-37 244.0 8.0 112 75-186 78-191 (286)
3 PF00808 CBFD_NFYB_HMF: Histon 99.8 7.4E-20 1.6E-24 133.8 7.3 64 104-167 2-65 (65)
4 KOG1659 Class 2 transcription 99.8 7.6E-20 1.6E-24 163.4 6.3 85 98-182 7-91 (224)
5 COG5247 BUR6 Class 2 transcrip 99.7 1.3E-18 2.9E-23 140.7 5.6 82 103-184 22-103 (113)
6 KOG1658 DNA polymerase epsilon 99.3 3.2E-13 7E-18 116.2 2.3 83 100-182 55-137 (162)
7 COG5262 HTA1 Histone H2A [Chro 99.3 3.2E-12 6.9E-17 106.1 6.2 77 102-178 24-100 (132)
8 cd00074 H2A Histone 2A; H2A is 99.3 5.3E-12 1.2E-16 103.9 7.4 77 102-178 18-94 (115)
9 KOG1756 Histone 2A [Chromatin 99.1 1.9E-10 4.1E-15 96.4 7.0 78 102-179 25-102 (131)
10 smart00414 H2A Histone 2A. 99.1 2.1E-10 4.6E-15 93.2 6.9 77 102-178 7-83 (106)
11 KOG0869 CCAAT-binding factor, 99.1 2.4E-10 5.2E-15 98.9 6.9 69 103-171 31-100 (168)
12 PTZ00017 histone H2A; Provisio 99.0 4.7E-10 1E-14 94.8 6.4 76 102-177 25-100 (134)
13 PLN00154 histone H2A; Provisio 99.0 4.7E-10 1E-14 94.9 6.4 77 102-178 36-113 (136)
14 COG2036 HHT1 Histones H3 and H 99.0 1.5E-09 3.2E-14 86.4 7.1 79 92-171 7-85 (91)
15 PLN00156 histone H2AX; Provisi 98.9 2.2E-09 4.8E-14 91.2 7.0 77 102-178 27-103 (139)
16 PLN00153 histone H2A; Provisio 98.9 2.3E-09 5.1E-14 90.1 6.6 77 102-178 22-98 (129)
17 PLN00157 histone H2A; Provisio 98.9 2.7E-09 5.8E-14 90.0 6.5 76 102-177 24-99 (132)
18 PF00125 Histone: Core histone 98.8 1.1E-08 2.4E-13 75.9 5.4 68 102-169 6-74 (75)
19 PTZ00252 histone H2A; Provisio 98.7 2.4E-08 5.2E-13 84.5 6.8 76 102-177 23-100 (134)
20 smart00803 TAF TATA box bindin 98.7 5.9E-08 1.3E-12 72.5 7.3 64 104-168 2-65 (65)
21 KOG0870 DNA polymerase epsilon 98.7 4.2E-08 9E-13 85.6 6.8 77 103-179 9-87 (172)
22 cd00076 H4 Histone H4, one of 98.5 2.5E-07 5.5E-12 72.8 7.2 66 104-170 13-78 (85)
23 PLN00035 histone H4; Provision 98.5 3E-07 6.4E-12 74.9 7.1 66 105-171 30-95 (103)
24 PTZ00015 histone H4; Provision 98.4 6.9E-07 1.5E-11 72.6 7.2 67 103-170 29-95 (102)
25 KOG0871 Class 2 transcription 98.4 1.1E-06 2.4E-11 75.8 7.2 76 102-178 10-87 (156)
26 smart00417 H4 Histone H4. 98.3 8.1E-07 1.8E-11 68.4 5.3 61 104-165 13-73 (74)
27 cd07981 TAF12 TATA Binding Pro 98.1 1.7E-05 3.7E-10 59.9 7.4 65 106-171 3-68 (72)
28 cd08048 TAF11 TATA Binding Pro 97.9 4.1E-05 8.9E-10 60.2 6.4 71 98-169 10-83 (85)
29 smart00428 H3 Histone H3. 97.8 0.00012 2.5E-09 59.9 8.5 76 91-167 16-98 (105)
30 COG5150 Class 2 transcription 97.8 7.3E-05 1.6E-09 63.5 6.5 77 102-178 9-86 (148)
31 KOG1757 Histone 2A [Chromatin 97.7 2.7E-05 5.9E-10 64.9 2.6 77 102-178 28-105 (131)
32 cd07979 TAF9 TATA Binding Prot 97.4 0.00042 9.2E-09 57.1 6.5 69 108-177 5-73 (117)
33 smart00576 BTP Bromodomain tra 97.3 0.0011 2.4E-08 50.4 6.8 60 110-170 12-71 (77)
34 PF02969 TAF: TATA box binding 97.2 0.0016 3.5E-08 49.2 7.2 64 104-168 3-66 (66)
35 PF04719 TAFII28: hTAFII28-lik 97.2 0.00091 2E-08 53.3 5.9 83 84-169 6-89 (90)
36 cd08050 TAF6 TATA Binding Prot 97.2 0.00098 2.1E-08 63.4 7.1 64 107-171 2-65 (343)
37 PTZ00018 histone H3; Provision 97.1 0.0016 3.5E-08 55.5 7.0 71 96-167 57-129 (136)
38 PF09415 CENP-X: CENP-S associ 97.1 0.0021 4.6E-08 49.2 6.7 63 106-168 1-66 (72)
39 PLN00121 histone H3; Provision 97.1 0.0022 4.7E-08 54.8 7.2 71 96-167 57-129 (136)
40 PLN00161 histone H3; Provision 97.0 0.003 6.5E-08 53.9 7.4 72 96-167 50-123 (135)
41 KOG1658 DNA polymerase epsilon 96.9 0.0017 3.7E-08 56.7 5.3 45 100-144 7-51 (162)
42 PLN00160 histone H3; Provision 96.8 0.0049 1.1E-07 49.9 6.6 71 97-167 17-89 (97)
43 PF15511 CENP-T: Centromere ki 96.7 0.0024 5.2E-08 62.5 5.5 63 100-162 347-414 (414)
44 smart00427 H2B Histone H2B. 96.7 0.0059 1.3E-07 48.8 6.7 59 110-169 7-66 (89)
45 KOG3219 Transcription initiati 96.4 0.0078 1.7E-07 54.2 5.9 89 78-170 89-178 (195)
46 PF03847 TFIID_20kDa: Transcri 96.2 0.021 4.6E-07 43.2 6.6 61 109-170 4-65 (68)
47 PTZ00463 histone H2B; Provisio 96.0 0.022 4.8E-07 47.7 6.6 59 110-169 34-93 (117)
48 PLN00158 histone H2B; Provisio 95.9 0.03 6.5E-07 46.8 6.7 60 109-169 32-92 (116)
49 KOG3467 Histone H4 [Chromatin 95.6 0.04 8.7E-07 44.5 6.3 62 109-171 34-95 (103)
50 PF15630 CENP-S: Kinetochore c 95.3 0.05 1.1E-06 42.1 5.6 52 121-172 24-75 (76)
51 PF07524 Bromo_TP: Bromodomain 95.2 0.086 1.9E-06 39.6 6.7 60 110-170 12-71 (77)
52 PLN00155 histone H2A; Provisio 95.2 0.021 4.6E-07 42.5 3.3 36 102-137 22-57 (58)
53 PF02269 TFIID-18kDa: Transcri 94.7 0.028 6.1E-07 44.6 3.0 75 110-184 7-82 (93)
54 PF15510 CENP-W: Centromere ki 94.7 0.073 1.6E-06 43.2 5.3 65 104-168 16-94 (102)
55 KOG1744 Histone H2B [Chromatin 94.7 0.093 2E-06 44.5 6.2 63 103-169 39-102 (127)
56 cd07978 TAF13 The TATA Binding 94.3 0.096 2.1E-06 41.7 5.2 75 109-184 7-82 (92)
57 KOG1142 Transcription initiati 94.3 0.053 1.1E-06 50.7 4.1 70 108-177 158-227 (258)
58 KOG1745 Histones H3 and H4 [Ch 94.1 0.058 1.3E-06 46.3 3.7 72 97-168 59-131 (137)
59 PF05236 TAF4: Transcription i 91.2 0.39 8.4E-06 44.0 5.2 61 108-169 51-117 (264)
60 PF02291 TFIID-31kDa: Transcri 91.0 1 2.2E-05 38.1 7.1 69 108-177 16-84 (129)
61 KOG3423 Transcription initiati 90.9 1.7 3.7E-05 38.8 8.6 72 97-170 80-165 (176)
62 KOG2549 Transcription initiati 89.0 1.1 2.5E-05 46.0 6.9 63 107-170 14-76 (576)
63 cd08045 TAF4 TATA Binding Prot 88.4 0.99 2.1E-05 40.2 5.4 63 107-170 51-119 (212)
64 PF03540 TFIID_30kDa: Transcri 77.4 11 0.00023 27.5 6.0 47 105-152 3-49 (51)
65 COG5095 TAF6 Transcription ini 77.2 4.7 0.0001 39.7 5.3 61 109-170 10-70 (450)
66 PF13335 Mg_chelatase_2: Magne 70.9 50 0.0011 26.1 9.6 62 100-168 27-94 (96)
67 PRK00411 cdc6 cell division co 66.8 20 0.00043 33.6 6.9 65 107-171 209-283 (394)
68 COG5162 Transcription initiati 66.4 42 0.00092 30.2 8.3 60 91-151 75-134 (197)
69 TIGR03015 pepcterm_ATPase puta 65.6 10 0.00022 33.3 4.4 50 122-171 215-267 (269)
70 PF10979 DUF2786: Protein of u 61.3 9.8 0.00021 26.5 2.8 35 107-141 4-38 (43)
71 KOG1657 CCAAT-binding factor, 59.6 1.1 2.3E-05 41.5 -2.9 77 99-184 3-79 (236)
72 TIGR02928 orc1/cdc6 family rep 57.1 38 0.00083 31.2 6.8 50 122-171 220-275 (365)
73 COG1474 CDC6 Cdc6-related prot 55.0 19 0.00041 35.0 4.6 73 108-181 193-275 (366)
74 TIGR00764 lon_rel lon-related 50.0 52 0.0011 34.1 7.0 62 109-170 317-391 (608)
75 PF12767 SAGA-Tad1: Transcript 47.7 19 0.00041 32.8 3.2 41 109-150 211-251 (252)
76 TIGR00368 Mg chelatase-related 46.0 70 0.0015 32.5 7.1 60 102-168 432-497 (499)
77 KOG4336 TBP-associated transcr 44.1 67 0.0014 31.4 6.3 64 107-170 7-70 (323)
78 PF13654 AAA_32: AAA domain; P 44.0 63 0.0014 33.0 6.5 32 139-170 475-506 (509)
79 KOG3334 Transcription initiati 40.4 1.1E+02 0.0024 26.9 6.5 40 138-177 46-85 (148)
80 PF08637 NCA2: ATP synthase re 39.3 74 0.0016 30.1 5.8 82 76-175 28-111 (290)
81 KOG2680 DNA helicase TIP49, TB 38.5 77 0.0017 31.7 5.8 60 109-168 362-427 (454)
82 PF11348 DUF3150: Protein of u 36.1 1.4E+02 0.0031 27.7 7.1 116 78-196 107-236 (257)
83 COG5248 TAF19 Transcription in 36.0 1.2E+02 0.0027 25.7 5.9 61 109-171 14-74 (126)
84 COG5251 TAF40 Transcription in 35.4 1.1E+02 0.0025 27.7 6.0 71 98-169 109-180 (199)
85 COG1222 RPT1 ATP-dependent 26S 35.3 44 0.00095 33.5 3.7 43 128-170 346-392 (406)
86 PTZ00195 60S ribosomal protein 34.9 15 0.00032 33.5 0.4 86 79-165 37-135 (198)
87 PRK09862 putative ATP-dependen 32.6 2.1E+02 0.0045 29.4 8.1 62 102-170 425-492 (506)
88 KOG3901 Transcription initiati 32.0 1.7E+02 0.0036 24.6 6.0 62 118-182 23-85 (109)
89 KOG2389 Predicted bromodomain 31.8 1.3E+02 0.0029 29.7 6.3 65 105-170 30-94 (353)
90 PTZ00469 60S ribosomal subunit 31.2 18 0.00038 32.8 0.3 89 76-165 34-127 (187)
91 TIGR02902 spore_lonB ATP-depen 30.9 1E+02 0.0022 31.3 5.6 61 110-170 268-332 (531)
92 PRK13765 ATP-dependent proteas 29.9 1.1E+02 0.0023 32.3 5.7 31 139-169 369-399 (637)
93 KOG4718 Non-SMC (structural ma 29.7 88 0.0019 29.3 4.5 56 123-178 93-154 (235)
94 COG1224 TIP49 DNA helicase TIP 29.3 1.1E+02 0.0023 31.1 5.3 61 108-168 364-430 (450)
95 TIGR01242 26Sp45 26S proteasom 29.2 74 0.0016 30.1 4.1 42 128-169 317-362 (364)
96 KOG1560 Translation initiation 29.1 3E+02 0.0065 27.0 8.0 47 71-117 249-295 (339)
97 PRK03992 proteasome-activating 28.7 76 0.0016 30.7 4.1 42 129-170 327-372 (389)
98 TIGR02442 Cob-chelat-sub cobal 28.6 1.9E+02 0.0042 30.0 7.2 48 122-169 249-303 (633)
99 PTZ00361 26 proteosome regulat 25.8 85 0.0018 31.4 4.0 32 139-170 393-424 (438)
100 smart00350 MCM minichromosome 25.6 1.8E+02 0.0039 29.2 6.3 66 104-169 417-503 (509)
101 cd01106 HTH_TipAL-Mta Helix-Tu 25.6 1.5E+02 0.0033 23.1 4.6 28 91-118 44-71 (103)
102 PF13499 EF-hand_7: EF-hand do 25.2 2.3E+02 0.005 19.4 5.6 32 136-167 35-66 (66)
103 PHA00687 hypothetical protein 25.2 29 0.00064 25.2 0.5 20 103-122 29-48 (56)
104 cd04773 HTH_TioE_rpt2 Second H 24.8 2E+02 0.0042 22.9 5.2 24 94-117 47-70 (108)
105 TIGR02030 BchI-ChlI magnesium 24.7 2.7E+02 0.0059 26.8 7.1 47 122-168 254-307 (337)
106 PTZ00454 26S protease regulato 23.8 1E+02 0.0022 30.3 4.0 32 139-170 355-386 (398)
107 PF08369 PCP_red: Proto-chloro 22.6 1.4E+02 0.003 20.8 3.4 26 141-166 19-44 (45)
108 PRK07452 DNA polymerase III su 22.3 2.2E+02 0.0047 26.2 5.7 64 121-184 148-215 (326)
109 COG1067 LonB Predicted ATP-dep 22.2 2.6E+02 0.0056 29.7 6.8 46 139-184 368-414 (647)
110 PRK13407 bchI magnesium chelat 21.8 3.4E+02 0.0073 26.2 7.1 62 105-167 235-303 (334)
111 PRK13406 bchD magnesium chelat 21.4 2E+02 0.0043 30.0 5.7 47 122-168 195-248 (584)
112 PRK05574 holA DNA polymerase I 21.2 2.9E+02 0.0062 25.1 6.2 64 121-185 164-231 (340)
113 COG5094 TAF9 Transcription ini 21.0 3.3E+02 0.0072 23.6 6.1 66 110-176 20-88 (145)
114 PRK14955 DNA polymerase III su 20.8 1.7E+02 0.0036 28.3 4.8 51 122-172 205-259 (397)
115 KOG2623 Tyrosyl-tRNA synthetas 20.2 4.7E+02 0.01 26.9 7.8 94 65-178 292-396 (467)
116 COG1239 ChlI Mg-chelatase subu 20.2 4.6E+02 0.01 26.6 7.8 77 81-170 239-322 (423)
No 1
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=100.00 E-value=3.2e-35 Score=265.44 Aligned_cols=170 Identities=54% Similarity=0.736 Sum_probs=137.9
Q ss_pred HHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccc
Q 024740 80 QQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQ 159 (263)
Q Consensus 80 ~q~L~~FW~~~~~eiE~~~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq 159 (263)
.++|++||.+...|+|...||+++.|||+|||||||.|+|+++|+.||+++++||||+||.+|+.+||.++++++||||+
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 78999999999866778899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCccchhhhcCCCccchh--HHhhcCCCCCCCCCCCCCCCCccccCCCCCcccCCCCeeecccCCCcccc
Q 024740 160 KNDIAAAITRTDIFDFLVDIVPREDLKD--EVLASIPRGTLPVGGPPDMPPYCYMPTQHASQVGSAGLIMGKPVMDPAIY 237 (263)
Q Consensus 160 ~~DIa~AI~~~d~FDFL~DIVP~~~~~~--e~l~~~p~~~~~~~~p~~~~~y~~~~~~~~~~~~~~g~~~g~p~~~~~~~ 237 (263)
++||+.||.+++.||||+||||++.+.. ..+....+.....++-...++|.....- -...++|+++|.|.|+.
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 9999999999999999999999998875 2333222222211112334566555443 34567889999999876
Q ss_pred ccCCCCccCCCCCCCCCC
Q 024740 238 AQQSHPYMGQQMWPQGAD 255 (263)
Q Consensus 238 ~~~~~p~~~~~~w~~~~~ 255 (263)
..++.++| +++|++...
T Consensus 205 ~~~~~~~~-q~~~~~~~~ 221 (236)
T KOG1657|consen 205 LAQPVSGT-QGQWQTLAT 221 (236)
T ss_pred ccCCCccc-cchhhhccC
Confidence 44445666 678976443
No 2
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=99.97 E-value=3.7e-32 Score=244.01 Aligned_cols=112 Identities=54% Similarity=0.923 Sum_probs=105.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHhhc--cCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024740 75 QQQQLQQQLQSFWANQYQEIEKVN--DFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEE 152 (263)
Q Consensus 75 ~~~~~~q~L~~FW~~~~~eiE~~~--d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~ 152 (263)
+-..+.+.|..||.+.++++|++. ++|.+.||||||||+||.|+||+|||+||+++|+|+||+||.+||.|||.+|++
T Consensus 78 lvg~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~ 157 (286)
T COG5208 78 LVGLLDERISRYWQQTIKAAEEERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEE 157 (286)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhH
Confidence 345688999999999999998765 699999999999999999999999999999999999999999999999999999
Q ss_pred cCCCcccHHHHHHHHhcCCccchhhhcCCCccch
Q 024740 153 NKRRTLQKNDIAAAITRTDIFDFLVDIVPREDLK 186 (263)
Q Consensus 153 ~KRKTLq~~DIa~AI~~~d~FDFL~DIVP~~~~~ 186 (263)
||||||+++||+.||++++.||||+||||+....
T Consensus 158 NkRRtLQksDia~Av~kSeMfDFLidivpr~p~n 191 (286)
T COG5208 158 NKRRTLQKSDIAAAVKKSEMFDFLIDIVPRNPFN 191 (286)
T ss_pred hhhhHHHHHHHHHHHHHHHHHhHHhhhccCCCcc
Confidence 9999999999999999999999999999998654
No 3
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.81 E-value=7.4e-20 Score=133.84 Aligned_cols=64 Identities=44% Similarity=0.590 Sum_probs=59.8
Q ss_pred CCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024740 104 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 167 (263)
Q Consensus 104 ~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI 167 (263)
.||++|||||||.|+++.+||+||.+++++|+|+||.+|+.+|+++|+.++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 6999999999999999999999999999999999999999999999999999999999999986
No 4
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=99.79 E-value=7.6e-20 Score=163.38 Aligned_cols=85 Identities=32% Similarity=0.521 Sum_probs=81.1
Q ss_pred ccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhh
Q 024740 98 NDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 177 (263)
Q Consensus 98 ~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~ 177 (263)
.++.+..||.+||||||++|+||++|+.-+|++++||+|+|+++|+.++++.++..+.|||+..||..||..++.||||.
T Consensus 7 ~~~~~trfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk 86 (224)
T KOG1659|consen 7 FKKYKTRFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLK 86 (224)
T ss_pred hhhhhccCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHH
Confidence 45667899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCC
Q 024740 178 DIVPR 182 (263)
Q Consensus 178 DIVP~ 182 (263)
|+|-.
T Consensus 87 ~~v~~ 91 (224)
T KOG1659|consen 87 EVVEK 91 (224)
T ss_pred HHHHh
Confidence 97754
No 5
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=99.75 E-value=1.3e-18 Score=140.66 Aligned_cols=82 Identities=29% Similarity=0.502 Sum_probs=78.4
Q ss_pred CCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhhcCCC
Q 024740 103 HSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDIVPR 182 (263)
Q Consensus 103 ~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~DIVP~ 182 (263)
..||+|||||||+.|+||++|++..|++.+||+|+|+.+|...+.+.|+....|.++.++|..|+..++.||||.|++..
T Consensus 22 trFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~~~ 101 (113)
T COG5247 22 TRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNMEQF 101 (113)
T ss_pred hcCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHHHh
Confidence 56999999999999999999999999999999999999999999999999999999999999999999999999999866
Q ss_pred cc
Q 024740 183 ED 184 (263)
Q Consensus 183 ~~ 184 (263)
+.
T Consensus 102 ~~ 103 (113)
T COG5247 102 KN 103 (113)
T ss_pred cC
Confidence 43
No 6
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=99.34 E-value=3.2e-13 Score=116.17 Aligned_cols=83 Identities=36% Similarity=0.535 Sum_probs=78.7
Q ss_pred CCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhhc
Q 024740 100 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDI 179 (263)
Q Consensus 100 ~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~DI 179 (263)
-+-++|||+|||+|||.|+|+.+...||.+++++|+|+||.+|...++..++..||||+++.|+..||+..+.|.||.+.
T Consensus 55 a~l~rLpL~rik~vvkl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~fle~~ 134 (162)
T KOG1658|consen 55 ASLSRLPLARIKQVVKLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAFLEGA 134 (162)
T ss_pred hhhhhccHHHHHhhccCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHHHhhh
Confidence 34578999999999999999999999999999999999999999999999999999999999999999999999999977
Q ss_pred CCC
Q 024740 180 VPR 182 (263)
Q Consensus 180 VP~ 182 (263)
.+-
T Consensus 135 ~d~ 137 (162)
T KOG1658|consen 135 LDT 137 (162)
T ss_pred ccc
Confidence 654
No 7
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=99.31 E-value=3.2e-12 Score=106.13 Aligned_cols=77 Identities=23% Similarity=0.347 Sum_probs=74.1
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
.+.||++|||||||.+..-++|+++|++.++.++|+++.|++.-|-+.|+.+|.|.|.++||..||+.+++++||..
T Consensus 24 gl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrnD~EL~~l~~ 100 (132)
T COG5262 24 GLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLG 100 (132)
T ss_pred CccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcCcHHHHHHhh
Confidence 47799999999999888889999999999999999999999999999999999999999999999999999999986
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=5.3e-12 Score=103.87 Aligned_cols=77 Identities=21% Similarity=0.348 Sum_probs=73.1
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
.+.||++||+|+||..-...+||++|++.++.++|+++.++.+.|.+.|+.+||++|++.||..||.++++|++|..
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 58899999999999877778999999999999999999999999999999999999999999999999999997764
No 9
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=99.10 E-value=1.9e-10 Score=96.45 Aligned_cols=78 Identities=21% Similarity=0.346 Sum_probs=74.9
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhhc
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDI 179 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~DI 179 (263)
.+.||++||+|+||...-..+|++.|+++++..+|+++.++++.|-+.|+++|+..|+++||..||.+++++.||.+-
T Consensus 25 gl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~NDeEL~~lL~~ 102 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRNDEELNKLLGK 102 (131)
T ss_pred ccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhCcHHHHHHhcc
Confidence 478999999999999888899999999999999999999999999999999999999999999999999999999983
No 10
>smart00414 H2A Histone 2A.
Probab=99.09 E-value=2.1e-10 Score=93.19 Aligned_cols=77 Identities=22% Similarity=0.381 Sum_probs=72.6
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
.+.||++||+|+||......+|++.|++.++.++|+++.|+.+.|.+.|+.+|++.|++.||..||.++++|+.|..
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 47899999999999987788999999999999999999999999999999999999999999999999999996654
No 11
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=99.08 E-value=2.4e-10 Score=98.89 Aligned_cols=69 Identities=25% Similarity=0.320 Sum_probs=65.2
Q ss_pred CCCChHHHHHHHhcC-cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 103 HSLPLARIKKIMKAD-EDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 103 ~~LPLARIKKIMK~D-pdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
..||||.|-||||.- |...+||+||...+.+++..||..+|.+|.+.|++.|||||+.+||..|+....
T Consensus 31 r~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 31 RFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 469999999999975 778899999999999999999999999999999999999999999999999854
No 12
>PTZ00017 histone H2A; Provisional
Probab=99.03 E-value=4.7e-10 Score=94.77 Aligned_cols=76 Identities=22% Similarity=0.369 Sum_probs=72.5
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhh
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 177 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~ 177 (263)
.+.||++||+|.||..--..+|++.|++.++.++|+++.|+.+.|.+.++.+|++.|++.||..||.++++|+.|.
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 4889999999999987777899999999999999999999999999999999999999999999999999999777
No 13
>PLN00154 histone H2A; Provisional
Probab=99.03 E-value=4.7e-10 Score=94.94 Aligned_cols=77 Identities=21% Similarity=0.254 Sum_probs=72.3
Q ss_pred CCCCChHHHHHHHhcCc-chhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 102 NHSLPLARIKKIMKADE-DVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 102 ~~~LPLARIKKIMK~Dp-dV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
.+.||++||+|+||..- ...+|++.|++.++.++|++..|+.+-|.+.|+.+|++.|++.||..||.++++|++|..
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 48899999999999974 456999999999999999999999999999999999999999999999999999998875
No 14
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.97 E-value=1.5e-09 Score=86.41 Aligned_cols=79 Identities=24% Similarity=0.352 Sum_probs=69.5
Q ss_pred HHHHhhccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 92 QEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 92 ~eiE~~~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
.|++.........||.+.|.||||.--. .+||.+|...+.+|+|.|+.+|+..|..+|...|||||+..||..|++...
T Consensus 7 ~~~r~~~~~~~~~Lp~apv~Ri~r~~~~-~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~ 85 (91)
T COG2036 7 KEIRRYQRSTDLLLPKAPVRRILRKAGA-ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLG 85 (91)
T ss_pred HHHHhhhhhhhhhcCchHHHHHHHHHhH-HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhc
Confidence 4555555566678999999999998532 399999999999999999999999999999999999999999999998754
No 15
>PLN00156 histone H2AX; Provisional
Probab=98.93 E-value=2.2e-09 Score=91.19 Aligned_cols=77 Identities=22% Similarity=0.339 Sum_probs=72.3
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
.+.||++||+|.||..--..+|++.|+++++.++|+++.|+.+.|.+.|..+|++.|+++||..||.++++|+.|..
T Consensus 27 gL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrnDeEL~~Ll~ 103 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLG 103 (139)
T ss_pred CcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccCcHHHHHHHC
Confidence 47899999999999976778999999999999999999999999999999999999999999999999999996653
No 16
>PLN00153 histone H2A; Provisional
Probab=98.92 E-value=2.3e-09 Score=90.08 Aligned_cols=77 Identities=25% Similarity=0.332 Sum_probs=72.4
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
.+.||++||.|.||..--..+|++.|++.++.++|+++.|+.+.|.+.|..+|++.|++.||..||.++++|+.|..
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 48899999999999877778999999999999999999999999999999999999999999999999999996653
No 17
>PLN00157 histone H2A; Provisional
Probab=98.91 E-value=2.7e-09 Score=90.03 Aligned_cols=76 Identities=24% Similarity=0.336 Sum_probs=71.7
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhh
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 177 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~ 177 (263)
.+.||++||+|.||..--..+|++.|++.++..+|+++.|+.+.|.+.|..+|++.|++.||..||.++++|+.|.
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 4889999999999997677899999999999999999999999999999999999999999999999999998555
No 18
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.78 E-value=1.1e-08 Score=75.88 Aligned_cols=68 Identities=24% Similarity=0.294 Sum_probs=61.2
Q ss_pred CCCCChHHHHHHHhcCcch-hccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024740 102 NHSLPLARIKKIMKADEDV-RMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 169 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV-~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~ 169 (263)
...+|+.||.|.+..+-.. .+||++|..++..++|.|+.+|...|...|..+||+||+..||..|+..
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 4567888888888877555 4999999999999999999999999999999999999999999999864
No 19
>PTZ00252 histone H2A; Provisional
Probab=98.73 E-value=2.4e-08 Score=84.45 Aligned_cols=76 Identities=21% Similarity=0.301 Sum_probs=70.0
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCcccHHHHHHHHhcCCccchhh
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEE--NKRRTLQKNDIAAAITRTDIFDFLV 177 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~--~KRKTLq~~DIa~AI~~~d~FDFL~ 177 (263)
.+.||++||.|.||..--..+|++.|++.++..+|++..|+.+.|.+.|.+ +|++.|++.||..||.++++|+-|.
T Consensus 23 GL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrNDeEL~~Ll 100 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRHDDDLGSLL 100 (134)
T ss_pred CccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccChHHHHHHH
Confidence 478999999999998877789999999999999999999999999999965 7889999999999999999998444
No 20
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.70 E-value=5.9e-08 Score=72.46 Aligned_cols=64 Identities=28% Similarity=0.367 Sum_probs=60.7
Q ss_pred CCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 104 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 104 ~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
.||.+-|++|.+.. ++.+||.|+...++..+|.|+.+++..|.+.++..|||||+.+||..|++
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 58999999999986 77899999999999999999999999999999999999999999999874
No 21
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.68 E-value=4.2e-08 Score=85.63 Aligned_cols=77 Identities=29% Similarity=0.410 Sum_probs=69.4
Q ss_pred CCCChHHHHHHHhcC-cch-hccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhhc
Q 024740 103 HSLPLARIKKIMKAD-EDV-RMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVDI 179 (263)
Q Consensus 103 ~~LPLARIKKIMK~D-pdV-~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~DI 179 (263)
+.||.|-|.||+|.- ++- ..||+||..+|++|+-+|+.+|+..|..+|...+||||+.+||..|+.+.+.-.|+.-+
T Consensus 9 l~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~pl 87 (172)
T KOG0870|consen 9 LNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVNPL 87 (172)
T ss_pred hhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhhHH
Confidence 679999999999963 343 68999999999999999999999999999999999999999999999999877776543
No 22
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=98.55 E-value=2.5e-07 Score=72.77 Aligned_cols=66 Identities=18% Similarity=0.265 Sum_probs=62.9
Q ss_pred CCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 104 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 104 ~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
.||.+-|+||.+.. .+++||.++...+..++|.|+++++..|...|+..+||||+..||..|+++.
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 49999999999987 6999999999999999999999999999999999999999999999999875
No 23
>PLN00035 histone H4; Provisional
Probab=98.52 E-value=3e-07 Score=74.87 Aligned_cols=66 Identities=18% Similarity=0.253 Sum_probs=62.9
Q ss_pred CChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 105 LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
||.+-|+||.+.. .+++||.++...+..++|.|+++++.+|...|+..+||||+..||..|+++.-
T Consensus 30 ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g 95 (103)
T PLN00035 30 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQG 95 (103)
T ss_pred CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcC
Confidence 9999999999986 69999999999999999999999999999999999999999999999998753
No 24
>PTZ00015 histone H4; Provisional
Probab=98.43 E-value=6.9e-07 Score=72.60 Aligned_cols=67 Identities=19% Similarity=0.262 Sum_probs=63.3
Q ss_pred CCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 103 HSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 103 ~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
..||.+-|+||.+.. .+++||.++-..+..++|.|+++++.+|...|+..+||||+..||..|+++.
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 358999999999986 8899999999999999999999999999999999999999999999998765
No 25
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=98.37 E-value=1.1e-06 Score=75.76 Aligned_cols=76 Identities=20% Similarity=0.353 Sum_probs=68.4
Q ss_pred CCCCChHHHHHHHhcC-c-chhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 102 NHSLPLARIKKIMKAD-E-DVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 102 ~~~LPLARIKKIMK~D-p-dV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
+..||-+-|-||+|.- | |+ +|.+||-.+|-.||-.||.-|+..|.++|....||||.+.||.+|+++...=+|+..
T Consensus 10 e~sLPkAtv~KmIke~lP~d~-rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee 87 (156)
T KOG0871|consen 10 ELSLPKATVNKMIKEMLPKDV-RVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEE 87 (156)
T ss_pred cccCcHHHHHHHHHHhCCccc-ccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHH
Confidence 4789999999999963 4 65 999999999999999999999999999999999999999999999999776566553
No 26
>smart00417 H4 Histone H4.
Probab=98.35 E-value=8.1e-07 Score=68.40 Aligned_cols=61 Identities=16% Similarity=0.205 Sum_probs=57.9
Q ss_pred CCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Q 024740 104 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAA 165 (263)
Q Consensus 104 ~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~ 165 (263)
.||.+-|+||.|.. .+++||.++-..+..++|.|+++++..|...|+..+||||+..||..
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 49999999999986 88999999999999999999999999999999999999999999863
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=98.07 E-value=1.7e-05 Score=59.91 Aligned_cols=65 Identities=12% Similarity=0.268 Sum_probs=57.3
Q ss_pred ChHHHHHHHhc-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 106 PLARIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 106 PLARIKKIMK~-DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
+-.++..++|. |+. .+++.+|..+|...+|.|+..++..|...|+..||+||..+||.-++++.-
T Consensus 3 ~k~~l~~lv~~id~~-~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~ 68 (72)
T cd07981 3 TKRKLQELLKEIDPR-EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNW 68 (72)
T ss_pred cHHHHHHHHHhhCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhc
Confidence 34566777775 554 689999999999999999999999999999999999999999999998864
No 28
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=97.87 E-value=4.1e-05 Score=60.19 Aligned_cols=71 Identities=23% Similarity=0.334 Sum_probs=62.6
Q ss_pred ccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCcccHHHHHHHHhc
Q 024740 98 NDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENK---RRTLQKNDIAAAITR 169 (263)
Q Consensus 98 ~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~K---RKTLq~~DIa~AI~~ 169 (263)
..|+...|+-+.|||||...-+ ..++.+...+++..+.+||.+|+.+|.++.++.+ +.-|+++||..|..+
T Consensus 10 e~~Rra~f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr 83 (85)
T cd08048 10 EMFRRSSFPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR 83 (85)
T ss_pred HHHHHhhccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence 3456677999999999998766 7999999999999999999999999999987654 589999999999765
No 29
>smart00428 H3 Histone H3.
Probab=97.82 E-value=0.00012 Score=59.92 Aligned_cols=76 Identities=24% Similarity=0.292 Sum_probs=62.4
Q ss_pred HHHHHh---hccCCCCCCChHHH-HHHHhcC-c--chhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHH
Q 024740 91 YQEIEK---VNDFKNHSLPLARI-KKIMKAD-E--DVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDI 163 (263)
Q Consensus 91 ~~eiE~---~~d~k~~~LPLARI-KKIMK~D-p--dV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DI 163 (263)
+.||.. ..++--..+|.+|+ +.|+..- . ++ +++.+|..++..|+|.|+..|...|..+|...||.||+.+||
T Consensus 16 LrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~-R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi 94 (105)
T smart00428 16 LREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDL-RFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDI 94 (105)
T ss_pred HHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCc-eeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhH
Confidence 445543 55666678899885 5565542 2 44 999999999999999999999999999999999999999999
Q ss_pred HHHH
Q 024740 164 AAAI 167 (263)
Q Consensus 164 a~AI 167 (263)
.-|.
T Consensus 95 ~La~ 98 (105)
T smart00428 95 QLAR 98 (105)
T ss_pred HHHH
Confidence 8774
No 30
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=97.75 E-value=7.3e-05 Score=63.50 Aligned_cols=77 Identities=23% Similarity=0.374 Sum_probs=67.1
Q ss_pred CCCCChHHHHHHHhcC-cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 102 NHSLPLARIKKIMKAD-EDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 102 ~~~LPLARIKKIMK~D-pdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
+..||-|.|.|++-.- |---++.+||..+|-.||-.||.-|+..|.+.|++..+|||.+.||.+|+++.+.-.|+..
T Consensus 9 e~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~~ 86 (148)
T COG5150 9 ENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIES 86 (148)
T ss_pred cccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHHH
Confidence 4679999999998853 3335899999999999999999999999999999999999999999999999775555543
No 31
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=97.67 E-value=2.7e-05 Score=64.87 Aligned_cols=77 Identities=21% Similarity=0.265 Sum_probs=70.4
Q ss_pred CCCCChHHHHHHHhcC-cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 102 NHSLPLARIKKIMKAD-EDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 102 ~~~LPLARIKKIMK~D-pdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
.+.||++||+|-+|.. ...++|.+.|.+..+..+|++..+...-|-+.++.-|-|.|+++|+.-||..+|++|-|+.
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiRGDeELDtLIk 105 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIK 105 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeeecCcHHHHHHHH
Confidence 3789999999999975 5668999999999999999999999999999888889999999999999999999998873
No 32
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=97.41 E-value=0.00042 Score=57.09 Aligned_cols=69 Identities=12% Similarity=0.107 Sum_probs=62.0
Q ss_pred HHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhh
Q 024740 108 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 177 (263)
Q Consensus 108 ARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~ 177 (263)
.-|++|+|.- ++..++.+++..|...++.++.++...|...|+..+|+||+.+||..||+..-.+.|-.
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 3588999975 67789999999999999999999999999999999999999999999999876666653
No 33
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.27 E-value=0.0011 Score=50.40 Aligned_cols=60 Identities=15% Similarity=0.187 Sum_probs=54.7
Q ss_pred HHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 110 IKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 110 IKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
|.+|+|.. +...++.+|...|+..+|.|+.+|++.+...++..+|++.+..||..|+.+.
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 66777764 6679999999999999999999999999999999999999999999998764
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=97.22 E-value=0.0016 Score=49.15 Aligned_cols=64 Identities=22% Similarity=0.304 Sum_probs=49.8
Q ss_pred CCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 104 SLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 104 ~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
.||..-||-|-.+- ++..++.|+...|+.=+|+-|.++...|.+.++.+||++|+.+||..|++
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 46677788777664 67789999999999999999999999999999999999999999999974
No 35
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=97.19 E-value=0.00091 Score=53.35 Aligned_cols=83 Identities=23% Similarity=0.284 Sum_probs=54.7
Q ss_pred HHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCcccHHH
Q 024740 84 QSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENK-RRTLQKND 162 (263)
Q Consensus 84 ~~FW~~~~~eiE~~~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~K-RKTLq~~D 162 (263)
.+|=.+|++.-| .|+...|+-+.|||||+.--+...|+....++++-.+.+|+.||..+|.++.++.+ ..-|+++|
T Consensus 6 ~~f~~eQ~~Rye---~fRRs~~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~h 82 (90)
T PF04719_consen 6 SNFDEEQLDRYE---AFRRSSFNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDH 82 (90)
T ss_dssp ----HHHHHHHH---HHHH----HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHH
T ss_pred HcCCHHHHHHHH---HHHHccCCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHH
Confidence 344444443333 35557799999999999865546899999999999999999999999999987654 45899999
Q ss_pred HHHHHhc
Q 024740 163 IAAAITR 169 (263)
Q Consensus 163 Ia~AI~~ 169 (263)
|..|..+
T Consensus 83 lreA~rr 89 (90)
T PF04719_consen 83 LREAYRR 89 (90)
T ss_dssp HHHHHHH
T ss_pred HHHHHHh
Confidence 9998754
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=97.18 E-value=0.00098 Score=63.38 Aligned_cols=64 Identities=22% Similarity=0.287 Sum_probs=57.9
Q ss_pred hHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 107 LARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 107 LARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
..-||-|.++- ++..++.||...++.-+|.++.+++..|.+.++..|||||+.+||..|++...
T Consensus 2 ~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n 65 (343)
T cd08050 2 QESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRN 65 (343)
T ss_pred hhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhC
Confidence 45678888875 77899999999999999999999999999999999999999999999987653
No 37
>PTZ00018 histone H3; Provisional
Probab=97.12 E-value=0.0016 Score=55.54 Aligned_cols=71 Identities=23% Similarity=0.294 Sum_probs=59.7
Q ss_pred hhccCCCCCCChHHHH-HHHhc-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024740 96 KVNDFKNHSLPLARIK-KIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 167 (263)
Q Consensus 96 ~~~d~k~~~LPLARIK-KIMK~-DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI 167 (263)
...|+--..+|.+|+- .|+.. ..++ .+..+|+.+|..|+|.|+..|-..+..+|...||.||..+||.-+.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~-rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcc-eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 4566666789998854 45543 3555 9999999999999999999999999999999999999999997663
No 38
>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=97.09 E-value=0.0021 Score=49.19 Aligned_cols=63 Identities=19% Similarity=0.294 Sum_probs=50.6
Q ss_pred ChHHHHHHHhc--CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCc-ccHHHHHHHHh
Q 024740 106 PLARIKKIMKA--DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRT-LQKNDIAAAIT 168 (263)
Q Consensus 106 PLARIKKIMK~--DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKT-Lq~~DIa~AI~ 168 (263)
|-.-|.||++. ..+-.+||+||..++++-.++|+.+-..||...++..+... |.-.||.+..-
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 34558888886 34668999999999999999999999999999999988888 99999998643
No 39
>PLN00121 histone H3; Provisional
Probab=97.05 E-value=0.0022 Score=54.78 Aligned_cols=71 Identities=23% Similarity=0.315 Sum_probs=59.9
Q ss_pred hhccCCCCCCChHHH-HHHHhc-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024740 96 KVNDFKNHSLPLARI-KKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 167 (263)
Q Consensus 96 ~~~d~k~~~LPLARI-KKIMK~-DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI 167 (263)
...++--..+|.+|+ +.|+.. ..++ .+..+|+.+|..|+|.|+..|-..+..+|...||.||..+||.-+.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~-Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccc-eeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 456666678999885 455544 3454 9999999999999999999999999999999999999999997663
No 40
>PLN00161 histone H3; Provisional
Probab=96.99 E-value=0.003 Score=53.93 Aligned_cols=72 Identities=25% Similarity=0.256 Sum_probs=59.9
Q ss_pred hhccCCCCCCChHHH-HHHHhc-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024740 96 KVNDFKNHSLPLARI-KKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 167 (263)
Q Consensus 96 ~~~d~k~~~LPLARI-KKIMK~-DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI 167 (263)
...++--..+|.+|+ +.|+.. ..+.-++..+|+.++..|+|.|+..|-..|..+|...||-||..+||.-|.
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ 123 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR 123 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH
Confidence 456666778999886 555543 222249999999999999999999999999999999999999999998774
No 41
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=96.90 E-value=0.0017 Score=56.69 Aligned_cols=45 Identities=31% Similarity=0.287 Sum_probs=41.2
Q ss_pred CCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHH
Q 024740 100 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTL 144 (263)
Q Consensus 100 ~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~ 144 (263)
.+...||++.+|||-|.||+..+-+.+|....+.|+|.|++.|+.
T Consensus 7 e~~p~~p~ekvkkiak~dPey~~te~~a~~etafatE~fvq~lv~ 51 (162)
T KOG1658|consen 7 ECSPKLPMEKVKKIAKNDPEYMDTEDDAFVETAFATEQFVQVLVH 51 (162)
T ss_pred hhCccccHHHHHHhhcCCchhhhcccchHHHHHHHHHHHHhhhhh
Confidence 345689999999999999999888999999999999999999998
No 42
>PLN00160 histone H3; Provisional
Probab=96.76 E-value=0.0049 Score=49.92 Aligned_cols=71 Identities=23% Similarity=0.238 Sum_probs=58.6
Q ss_pred hccCCCCCCChHHH-HHHHhc-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024740 97 VNDFKNHSLPLARI-KKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAI 167 (263)
Q Consensus 97 ~~d~k~~~LPLARI-KKIMK~-DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI 167 (263)
..++--.++|.+|+ +.|+.. ..+.-++..+|..++..|+|.|+..|-..|..+|...||.||..+||.-|.
T Consensus 17 st~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 17 STDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred chhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 45666678899885 455542 223349999999999999999999999999999999999999999998764
No 43
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=96.72 E-value=0.0024 Score=62.45 Aligned_cols=63 Identities=22% Similarity=0.224 Sum_probs=46.2
Q ss_pred CCCCCCChHHHHHHHhcC-----cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHH
Q 024740 100 FKNHSLPLARIKKIMKAD-----EDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKND 162 (263)
Q Consensus 100 ~k~~~LPLARIKKIMK~D-----pdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~D 162 (263)
.....||-+-|||+...- -.-++|+++|..+|.+|+++|.+.|+..--.+|+..|||||..+|
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 445789999999987642 133699999999999999999999999999999999999999877
No 44
>smart00427 H2B Histone H2B.
Probab=96.71 E-value=0.0059 Score=48.84 Aligned_cols=59 Identities=24% Similarity=0.269 Sum_probs=51.7
Q ss_pred HHHHHhc-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024740 110 IKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 169 (263)
Q Consensus 110 IKKIMK~-DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~ 169 (263)
|.|++|. .||. .||..|.-++.--..-+.+.|+.+|...+..+||+||+.++|..|+.-
T Consensus 7 i~kvLKqVhpd~-giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl 66 (89)
T smart00427 7 IYKVLKQVHPDT-GISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRL 66 (89)
T ss_pred HHHHHHHhCCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 7888885 6887 689999888887777778889999999999999999999999999864
No 45
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=96.36 E-value=0.0078 Score=54.16 Aligned_cols=89 Identities=26% Similarity=0.363 Sum_probs=72.6
Q ss_pred HHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCC
Q 024740 78 QLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEEN-KRR 156 (263)
Q Consensus 78 ~~~q~L~~FW~~~~~eiE~~~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~-KRK 156 (263)
+.+--|.+|=.+|+..-| .|+...||-+.|||+|..-..-. |+..+.++++-.+++|+-+|...|.++.... +..
T Consensus 89 r~q~L~s~fseEQl~RYE---vfRrs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~ 164 (195)
T KOG3219|consen 89 RMQTLLSNFSEEQLSRYE---VFRRSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESG 164 (195)
T ss_pred HHHHHHHhcCHHHHHHHH---HHHHhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCC
Confidence 555566666666655433 47888999999999999865544 9999999999999999999999999998754 467
Q ss_pred cccHHHHHHHHhcC
Q 024740 157 TLQKNDIAAAITRT 170 (263)
Q Consensus 157 TLq~~DIa~AI~~~ 170 (263)
-|+++||..|+.+.
T Consensus 165 PLqP~HIREA~rrL 178 (195)
T KOG3219|consen 165 PLQPKHIREAYRRL 178 (195)
T ss_pred CCCcHHHHHHHHHH
Confidence 89999999998764
No 46
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=96.18 E-value=0.021 Score=43.20 Aligned_cols=61 Identities=13% Similarity=0.318 Sum_probs=48.0
Q ss_pred HHHHHHhc-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 109 RIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 109 RIKKIMK~-DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
++..++|. ||. ..+-.++-.++...++.||..++..|...|+.+|..||..+||.-.++++
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 56666665 554 58889999999999999999999999999999999999999999988764
No 47
>PTZ00463 histone H2B; Provisional
Probab=96.04 E-value=0.022 Score=47.68 Aligned_cols=59 Identities=22% Similarity=0.204 Sum_probs=50.7
Q ss_pred HHHHHhc-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024740 110 IKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 169 (263)
Q Consensus 110 IKKIMK~-DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~ 169 (263)
|.|++|. .||.+ ||..|.-++.--..-..+.|+.+|...+..+||+||+.+||..||.-
T Consensus 34 I~KVLKqVhPd~g-IS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrL 93 (117)
T PTZ00463 34 IFKVLKQVHPDTG-ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRL 93 (117)
T ss_pred HHHHHHhhCCCCC-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhh
Confidence 8888885 68874 68888888887777777889999999999999999999999999864
No 48
>PLN00158 histone H2B; Provisional
Probab=95.86 E-value=0.03 Score=46.83 Aligned_cols=60 Identities=22% Similarity=0.231 Sum_probs=51.8
Q ss_pred HHHHHHhc-CcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024740 109 RIKKIMKA-DEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 169 (263)
Q Consensus 109 RIKKIMK~-DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~ 169 (263)
=|.|++|. .||. -||..|.-++.--..-+.+.|+.+|...+..+||+||+.++|..||.-
T Consensus 32 YI~kVLKQVhPd~-gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrL 92 (116)
T PLN00158 32 YIYKVLKQVHPDT-GISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRL 92 (116)
T ss_pred HHHHHHHHhCCCC-CccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 38888885 6887 468888888887777778889999999999999999999999999864
No 49
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=95.61 E-value=0.04 Score=44.47 Aligned_cols=62 Identities=21% Similarity=0.261 Sum_probs=55.3
Q ss_pred HHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 109 RIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 109 RIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
-|+||-+-. .|++|+--.-.-+..++..||+.....|...++..|||||+..||.-++++.-
T Consensus 34 aIRRlARr~-GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G 95 (103)
T KOG3467|consen 34 AIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQG 95 (103)
T ss_pred HHHHHHHhc-CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcC
Confidence 478887764 78899988888889999999999999999999999999999999999988753
No 50
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=95.27 E-value=0.05 Score=42.11 Aligned_cols=52 Identities=12% Similarity=0.053 Sum_probs=43.9
Q ss_pred hccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCc
Q 024740 121 RMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDI 172 (263)
Q Consensus 121 ~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~ 172 (263)
..+|.++..+++..+=.++..++..-...|+..||+||+.+||.-...+++.
T Consensus 24 ~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn~~ 75 (76)
T PF15630_consen 24 VEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRNPS 75 (76)
T ss_dssp SEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-HH
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcCCC
Confidence 4689999999999999999999999999999999999999999999888765
No 51
>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=95.24 E-value=0.086 Score=39.64 Aligned_cols=60 Identities=17% Similarity=0.187 Sum_probs=52.9
Q ss_pred HHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 110 IKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 110 IKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
|.+|++.. +...++..|+-.|+..+..||.+|+..+...|+..+|......||..|+.+.
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 55666653 5668999999999999999999999999999999999999999999998764
No 52
>PLN00155 histone H2A; Provisional
Probab=95.22 E-value=0.021 Score=42.49 Aligned_cols=36 Identities=31% Similarity=0.448 Sum_probs=33.1
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHH
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEM 137 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~El 137 (263)
.+.||++||+|.+|..--..+|++.|++.++..+|+
T Consensus 22 gL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEY 57 (58)
T PLN00155 22 GLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEY 57 (58)
T ss_pred ccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHh
Confidence 478999999999999877789999999999999886
No 53
>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=94.74 E-value=0.028 Score=44.56 Aligned_cols=75 Identities=15% Similarity=0.240 Sum_probs=34.0
Q ss_pred HHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC-CccchhhhcCCCcc
Q 024740 110 IKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT-DIFDFLVDIVPRED 184 (263)
Q Consensus 110 IKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~-d~FDFL~DIVP~~~ 184 (263)
|+.+|-.-.|+..-..|+..++-..+-.||.+|+.+|..+|...++++|+-+||.-++.++ ..+.-|.+++-.+.
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~~Kl~Rl~~~L~~k~ 82 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDPKKLARLRELLSMKD 82 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-------------------------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 6788988888889999999999999999999999999999999999999999999999988 45666666665544
No 54
>PF15510 CENP-W: Centromere kinetochore component W
Probab=94.72 E-value=0.073 Score=43.23 Aligned_cols=65 Identities=20% Similarity=0.329 Sum_probs=51.4
Q ss_pred CCChHHHHHHHhcCcchhccCccHHHH--------------HHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 104 SLPLARIKKIMKADEDVRMISAEAPVI--------------FARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 104 ~LPLARIKKIMK~DpdV~~ISaEApvl--------------lAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
.-|-+-+||++|...-.-++.+.+=++ +---|=+|+..|+++|-..|=++|.++|+++||..|-+
T Consensus 16 kaPrgfLkrv~Kr~KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred hCchHHHHHHHHhcCCceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 468889999999543333444444444 56678899999999999999999999999999988754
No 55
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=94.71 E-value=0.093 Score=44.53 Aligned_cols=63 Identities=19% Similarity=0.207 Sum_probs=47.0
Q ss_pred CCCChHHHHHHHh-cCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024740 103 HSLPLARIKKIMK-ADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITR 169 (263)
Q Consensus 103 ~~LPLARIKKIMK-~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~ 169 (263)
....+.| ++| .+||.+ |+.+|.-++.--.-.|++.|+.+|...|..+||.||+-++|..|+.-
T Consensus 39 ~s~yv~k---vlk~Vhpd~g-is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 39 YSEYVYK---VLKQVHPDLG-ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred eeeehhh---hhhcccCCCC-cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 3445444 666 367765 66666655555555558889999999999999999999999998764
No 56
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=94.33 E-value=0.096 Score=41.73 Aligned_cols=75 Identities=16% Similarity=0.254 Sum_probs=63.0
Q ss_pred HHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC-ccchhhhcCCCcc
Q 024740 109 RIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD-IFDFLVDIVPRED 184 (263)
Q Consensus 109 RIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d-~FDFL~DIVP~~~ 184 (263)
-|+.+|-.-.|+..-..|...++-..+-.||.+|+.+|...|. .+|..++.+||.-+|.++. .+.-|.+++--++
T Consensus 7 ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~Kl~Rl~~lL~~k~ 82 (92)
T cd07978 7 EIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPKKLARLRELLSMKD 82 (92)
T ss_pred HHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHHHHHHHHHHHHHHH
Confidence 4888999888888889999999999999999999999999998 5666669999999998884 4666666665433
No 57
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.27 E-value=0.053 Score=50.74 Aligned_cols=70 Identities=11% Similarity=0.215 Sum_probs=57.8
Q ss_pred HHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhh
Q 024740 108 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 177 (263)
Q Consensus 108 ARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~ 177 (263)
.+|..+||.-..-.+|-.|+..+|...|+-||..++.+|...|+.+|..||..+||.-.++++-.+.|=.
T Consensus 158 ~kl~dLvqqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPg 227 (258)
T KOG1142|consen 158 RKLDDLVQQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPG 227 (258)
T ss_pred cchhHHHHhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCC
Confidence 4555555543333678888999999999999999999999999999999999999999999976555443
No 58
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=94.08 E-value=0.058 Score=46.28 Aligned_cols=72 Identities=21% Similarity=0.208 Sum_probs=60.4
Q ss_pred hccCCCCCCChHHHHH-HHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 97 VNDFKNHSLPLARIKK-IMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 97 ~~d~k~~~LPLARIKK-IMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
.+|+--..+|..|+-| |++.--..-.+-+.|..+|..|.|.|+..|-..+..+|-..||-||.++||.-|..
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 3444445799988877 88765434589999999999999999999999999999999999999999987753
No 59
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=91.17 E-value=0.39 Score=44.03 Aligned_cols=61 Identities=16% Similarity=0.224 Sum_probs=33.3
Q ss_pred HHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCC------CcccHHHHHHHHhc
Q 024740 108 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKR------RTLQKNDIAAAITR 169 (263)
Q Consensus 108 ARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KR------KTLq~~DIa~AI~~ 169 (263)
.||.+|++... +..|..|.+.+|+-|||..|..|...+...|+.... ++...+||...+..
T Consensus 51 ~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~ 117 (264)
T PF05236_consen 51 KRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRF 117 (264)
T ss_dssp HHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH----------------------------
T ss_pred HHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHH
Confidence 68889998764 778999999999999999999999999998854221 23335565554443
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=90.97 E-value=1 Score=38.10 Aligned_cols=69 Identities=14% Similarity=0.093 Sum_probs=45.2
Q ss_pred HHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhh
Q 024740 108 ARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 177 (263)
Q Consensus 108 ARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~ 177 (263)
.-|+.|+|+- +|......++..|-.-+=.++.++...|...|+..+|++|..+||..||+..-.+.|-.
T Consensus 16 ~~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ 84 (129)
T PF02291_consen 16 RVIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQ 84 (129)
T ss_dssp HHHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-------
T ss_pred HHHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccC
Confidence 4467777764 55555555666666666678899999999999999999999999999999775566643
No 61
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.86 E-value=1.7 Score=38.76 Aligned_cols=72 Identities=17% Similarity=0.329 Sum_probs=56.1
Q ss_pred hccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc--------------CCCcccHHH
Q 024740 97 VNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEEN--------------KRRTLQKND 162 (263)
Q Consensus 97 ~~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~--------------KRKTLq~~D 162 (263)
..|.. ..+|=+-+--+|+.. .+...-.-...+++.|+.-||.+++..|+.+++-+ |+-||+..|
T Consensus 80 LddYt-P~IPDavt~~yL~~a-Gf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeD 157 (176)
T KOG3423|consen 80 LDDYT-PTIPDAVTDHYLKKA-GFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMED 157 (176)
T ss_pred HhcCC-CCCcHHHHHHHHHhc-CCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHH
Confidence 44554 559999999999975 33344445578999999999999999999998743 356788999
Q ss_pred HHHHHhcC
Q 024740 163 IAAAITRT 170 (263)
Q Consensus 163 Ia~AI~~~ 170 (263)
|..|+++.
T Consensus 158 L~~AL~Ey 165 (176)
T KOG3423|consen 158 LSPALAEY 165 (176)
T ss_pred HHHHHHHh
Confidence 99988764
No 62
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=88.99 E-value=1.1 Score=46.05 Aligned_cols=63 Identities=19% Similarity=0.258 Sum_probs=55.5
Q ss_pred hHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 107 LARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 107 LARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
-.-+|-+.++ -.++.|+.|+..+|+.=.|+=|.+++..|.+.....||++++-+||..|+.-.
T Consensus 14 ~Es~k~vAEs-lGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~ 76 (576)
T KOG2549|consen 14 KESVKVVAES-LGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSL 76 (576)
T ss_pred HHHHHHHHHH-hCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhc
Confidence 4456666665 47789999999999999999999999999999999999999999999998754
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=88.37 E-value=0.99 Score=40.22 Aligned_cols=63 Identities=16% Similarity=0.176 Sum_probs=49.7
Q ss_pred hHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc------CCCcccHHHHHHHHhcC
Q 024740 107 LARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEEN------KRRTLQKNDIAAAITRT 170 (263)
Q Consensus 107 LARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~------KRKTLq~~DIa~AI~~~ 170 (263)
..+|.+|++.. .++.|+.|+..+|+.|||.++..|.......++.. ..++...+|+..-+...
T Consensus 51 ~~~~~~i~~~~-g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l 119 (212)
T cd08045 51 AKKIRKIAKKH-GLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFL 119 (212)
T ss_pred HHHHHHHHHHc-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHH
Confidence 36777777764 44589999999999999999999999999988643 44667778888766543
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=77.36 E-value=11 Score=27.50 Aligned_cols=47 Identities=9% Similarity=0.121 Sum_probs=33.4
Q ss_pred CChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024740 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEE 152 (263)
Q Consensus 105 LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~ 152 (263)
+|=+-+.-+|+.. ++..--.-..-+++-|++-||.+++..|+.+++-
T Consensus 3 IPD~v~~~yL~~~-G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 3 IPDEVTDYYLERS-GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCHHHHHHHHHHC-CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5556666677653 2222223446789999999999999999998764
No 65
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=77.17 E-value=4.7 Score=39.72 Aligned_cols=61 Identities=21% Similarity=0.221 Sum_probs=52.7
Q ss_pred HHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 109 RIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 109 RIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
.||..-.+ -.+.+|..|+..+++--+|+=|.+++.+|.+....+||..|+-+||..|+...
T Consensus 10 t~KdvAes-lGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~l 70 (450)
T COG5095 10 TLKDVAES-LGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSL 70 (450)
T ss_pred HHHHHHHH-cCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhc
Confidence 34444433 36778999999999999999999999999999999999999999999998764
No 66
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=70.94 E-value=50 Score=26.11 Aligned_cols=62 Identities=16% Similarity=0.217 Sum_probs=50.9
Q ss_pred CCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 100 FKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMF------ILELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 100 ~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElF------I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
..|..||-.-|++....+++ +..++..+++-| +..|.+-|+-+|.-++...|...||..|+.
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 45788999999988777654 566777777766 566888899999999999999999999985
No 67
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=66.76 E-value=20 Score=33.56 Aligned_cols=65 Identities=17% Similarity=0.225 Sum_probs=47.4
Q ss_pred hHHHHHHHhcCcc----hhccCccHHHHHHHHHHH------HHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 107 LARIKKIMKADED----VRMISAEAPVIFARACEM------FILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 107 LARIKKIMK~Dpd----V~~ISaEApvllAKA~El------FI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
..-++.|++.--+ -..++.++.-.+++.+.- .+..++.+|+..|...++.+|+.+||..|+.+..
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~ 283 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSE 283 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHH
Confidence 4556666663211 135788888888776643 4457788999999988999999999999998863
No 68
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=66.36 E-value=42 Score=30.23 Aligned_cols=60 Identities=7% Similarity=0.136 Sum_probs=43.1
Q ss_pred HHHHHhhccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024740 91 YQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTE 151 (263)
Q Consensus 91 ~~eiE~~~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~ 151 (263)
++|+-+.-|.-...||=+-+-=-|... .+...-.-..-|++.++.-||.+++..|+...+
T Consensus 75 lee~l~~mDsy~PliPd~v~DYyl~k~-Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsr 134 (197)
T COG5162 75 LEELLQNMDSYTPLIPDSVTDYYLEKA-GFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSR 134 (197)
T ss_pred HHHHHHhcccCCCCccHHHHHHHHHhc-CceeccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444455556678988888777664 334444556779999999999999999998754
No 69
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=65.58 E-value=10 Score=33.31 Aligned_cols=50 Identities=18% Similarity=0.111 Sum_probs=43.6
Q ss_pred ccCccHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 122 MISAEAPVIFARACEM---FILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 122 ~ISaEApvllAKA~El---FI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
.++.++...+.+.+.= .|..++.+++..|-.++.++|+.++|..++....
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 5788888888888873 6999999999999889999999999999998754
No 70
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=61.35 E-value=9.8 Score=26.45 Aligned_cols=35 Identities=23% Similarity=0.284 Sum_probs=27.5
Q ss_pred hHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHH
Q 024740 107 LARIKKIMKADEDVRMISAEAPVIFARACEMFILE 141 (263)
Q Consensus 107 LARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~e 141 (263)
+.||+|++....+.+---.||-.++.+|-++...+
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 57999999987765444459999999998887654
No 71
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=59.62 E-value=1.1 Score=41.49 Aligned_cols=77 Identities=21% Similarity=0.083 Sum_probs=55.2
Q ss_pred cCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 99 DFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 99 d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
+++.-..++.|+..+++ +++.+ .+++..-.+..+|....+.+....+|.+|..-.+..+|+..+.+||+.+
T Consensus 3 ~~~~~~~~~~~~~~~~~------~~~p~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~fw~~~~~e~e~~~d~~~~ 73 (236)
T KOG1657|consen 3 ENNANSDIVANIVSNRR------MKAPP---KGAKSEPEGAVCLDPEASIITGDVSRQQLQSFWSKQAIEKEGQLDFKNH 73 (236)
T ss_pred ccccCcccccccccccc------ccCCc---cccccccccceecchhhhhcccchhhHHHHhhhhccccccccccchhhc
Confidence 34445567777777773 33333 4444444445588888888777777999999999999998999999999
Q ss_pred cCCCcc
Q 024740 179 IVPRED 184 (263)
Q Consensus 179 IVP~~~ 184 (263)
++|...
T Consensus 74 ~lPlaR 79 (236)
T KOG1657|consen 74 ILPLAR 79 (236)
T ss_pred cCcHhh
Confidence 999643
No 72
>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=57.15 E-value=38 Score=31.24 Aligned_cols=50 Identities=8% Similarity=0.096 Sum_probs=38.2
Q ss_pred ccCccHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 122 MISAEAPVIFARACE------MFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 122 ~ISaEApvllAKA~E------lFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
.++.++.-++++.++ ..+..++.+|+..|..+++.+|+.+||..|+....
T Consensus 220 ~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~ 275 (365)
T TIGR02928 220 VLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIE 275 (365)
T ss_pred CCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 467777766665443 24556888888889888899999999999988764
No 73
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=55.05 E-value=19 Score=34.98 Aligned_cols=73 Identities=15% Similarity=0.256 Sum_probs=52.9
Q ss_pred HHHHHHHhcCcch----hccCccHHHHHHH--HHH----HHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhh
Q 024740 108 ARIKKIMKADEDV----RMISAEAPVIFAR--ACE----MFILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 177 (263)
Q Consensus 108 ARIKKIMK~DpdV----~~ISaEApvllAK--A~E----lFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~ 177 (263)
.-|+.|++.--+. +.++.++.-++++ |.+ .+..+|+++|.+.|+++++.+++.+|+..|..+.+ .+++.
T Consensus 193 ~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a~~~~~-~~~~~ 271 (366)
T COG1474 193 EELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREAQEEIE-RDVLE 271 (366)
T ss_pred HHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHHHHHhh-HHHHH
Confidence 5567777653222 3677777777763 322 36789999999999999999999999999955554 56666
Q ss_pred hcCC
Q 024740 178 DIVP 181 (263)
Q Consensus 178 DIVP 181 (263)
+.+-
T Consensus 272 ~~~~ 275 (366)
T COG1474 272 EVLK 275 (366)
T ss_pred HHHH
Confidence 6543
No 74
>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=49.96 E-value=52 Score=34.12 Aligned_cols=62 Identities=10% Similarity=0.015 Sum_probs=41.3
Q ss_pred HHHHHHhcCcchhccCccHHHHHHHH-H------------HHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 109 RIKKIMKADEDVRMISAEAPVIFARA-C------------EMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 109 RIKKIMK~DpdV~~ISaEApvllAKA-~------------ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
.|++.++.+.....++.+|...+.+- + ..=+..|.++|...|+.+++.+|+.+||.+||+..
T Consensus 317 ~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 317 FVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 34444444433445666666655431 1 23466778888778888889999999999998754
No 75
>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=47.72 E-value=19 Score=32.79 Aligned_cols=41 Identities=15% Similarity=0.201 Sum_probs=31.4
Q ss_pred HHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHH
Q 024740 109 RIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHT 150 (263)
Q Consensus 109 RIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A 150 (263)
|+-.|... .+..-|+.|++-++..|+|.|+..|...+...+
T Consensus 211 Rm~~ia~e-~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~ 251 (252)
T PF12767_consen 211 RMEQIAWE-HGLGGVSDDCANLLNLALEVHLKNLIKSCLDLV 251 (252)
T ss_pred HHHHHHHH-cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 44444432 344569999999999999999999999888653
No 76
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=45.95 E-value=70 Score=32.45 Aligned_cols=60 Identities=13% Similarity=0.148 Sum_probs=47.9
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMF------ILELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElF------I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
|..++-..|+|..+.+. ++..++..|++.| ...+.+-|+.+|.-+++..|..+||+.|+.
T Consensus 432 N~~l~~~~l~~~~~l~~-------~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 432 NADLNSDEIEQFCKLSA-------IDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred cccCCHHHHHhhcCCCH-------HHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 77888888888776655 4555666666665 566888888999999999999999999985
No 77
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=44.12 E-value=67 Score=31.37 Aligned_cols=64 Identities=17% Similarity=0.154 Sum_probs=55.5
Q ss_pred hHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 107 LARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 107 LARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
|+.|--+|+.+-....|++-|..-|..++.-.|.++.+.+..+|+-.+|...+..||...+.+.
T Consensus 7 l~~VV~~Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~m 70 (323)
T KOG4336|consen 7 LAPVVSNLLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEM 70 (323)
T ss_pred HHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHh
Confidence 4566677777777788999999999999999999999999999999999999999999886553
No 78
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=44.02 E-value=63 Score=32.96 Aligned_cols=32 Identities=9% Similarity=0.186 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 139 ILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 139 I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
|.+|..+|...|+.++++.|+..||.+||+..
T Consensus 475 l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 475 LADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 56888999999999999999999999999864
No 79
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=40.40 E-value=1.1e+02 Score=26.88 Aligned_cols=40 Identities=15% Similarity=0.122 Sum_probs=35.8
Q ss_pred HHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCCccchhh
Q 024740 138 FILELTLRSWNHTEENKRRTLQKNDIAAAITRTDIFDFLV 177 (263)
Q Consensus 138 FI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d~FDFL~ 177 (263)
++..+...|...++..++.+|..+||..||...-.+.|--
T Consensus 46 Ytt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~ 85 (148)
T KOG3334|consen 46 YTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTP 85 (148)
T ss_pred HHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCC
Confidence 5677888899999999999999999999999988888876
No 80
>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=39.32 E-value=74 Score=30.13 Aligned_cols=82 Identities=15% Similarity=0.276 Sum_probs=58.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcC--cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 024740 76 QQQLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKAD--EDVRMISAEAPVIFARACEMFILELTLRSWNHTEEN 153 (263)
Q Consensus 76 ~~~~~q~L~~FW~~~~~eiE~~~d~k~~~LPLARIKKIMK~D--pdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~ 153 (263)
+.+.-+.+..||.+.+- =|+-+|...++.| .++..+|++++..=...+|-.+.+++......
T Consensus 28 ~~~~~~t~~~f~~nwV~------------~Pl~~I~~tlr~d~~s~~~i~s~~sL~~d~~SLeRMv~dF~~d~~~~---- 91 (290)
T PF08637_consen 28 QENAVETVRGFWKNWVW------------EPLKSIWDTLRHDEKSEIAIMSKESLQSDMESLERMVVDFAKDNSPN---- 91 (290)
T ss_pred HHHHHHHHHHHHHHHHH------------HHHHHHHHHHhCCCCCCcccccHHHHHHHHHHHHHHHHHHHhcCCCC----
Confidence 44677888999998753 3899999999996 66789999999988888888888887754322
Q ss_pred CCCcccHHHHHHHHhcCCccch
Q 024740 154 KRRTLQKNDIAAAITRTDIFDF 175 (263)
Q Consensus 154 KRKTLq~~DIa~AI~~~d~FDF 175 (263)
.......|...|+.-|--.+
T Consensus 92 --~~~~~~~l~~~v~~Gdlt~V 111 (290)
T PF08637_consen 92 --MPADLEELRQQVREGDLTPV 111 (290)
T ss_pred --CcchHHHHHHHHHcCCcHHH
Confidence 12444555555555444333
No 81
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=38.51 E-value=77 Score=31.67 Aligned_cols=60 Identities=18% Similarity=0.263 Sum_probs=43.3
Q ss_pred HHHHHHhc--CcchhccCccHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 109 RIKKIMKA--DEDVRMISAEAPVIFARACEM----FILELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 109 RIKKIMK~--DpdV~~ISaEApvllAKA~El----FI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
-||+|++. +++--.++.+|.-++.+..+. +...|...|...|.++|.+++.-+||.++-.
T Consensus 362 d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~ 427 (454)
T KOG2680|consen 362 DIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYR 427 (454)
T ss_pred HHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHH
Confidence 36677663 333347888998888776542 4445666677788889999999999999864
No 82
>PF11348 DUF3150: Protein of unknown function (DUF3150); InterPro: IPR021496 This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=36.12 E-value=1.4e+02 Score=27.69 Aligned_cols=116 Identities=13% Similarity=0.193 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcCcchhccCcc--------HHHHHHHHHHHHHHHHHHHHHHH
Q 024740 78 QLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAE--------APVIFARACEMFILELTLRSWNH 149 (263)
Q Consensus 78 ~~~q~L~~FW~~~~~eiE~~~d~k~~~LPLARIKKIMK~DpdV~~ISaE--------ApvllAKA~ElFI~eLt~~A~~~ 149 (263)
.+++.+.+ |.+..-|.+. -++....|.+.|++-+..+=.+-+|+.. .-..+.-..+-.+.|++..|.+.
T Consensus 107 ~Yd~~i~~-w~~~~pew~~--~Ir~~~~~~~~v~~r~~F~~~~~~v~~~~~~~~~~~l~~~v~~L~~~l~~Eia~~A~~~ 183 (257)
T PF11348_consen 107 NYDQAIEE-WIDRHPEWAD--IIRRAAPPAEDVRSRFSFSWQAIKVQPPSDDGQADGLEEEVDGLGGQLFDEIAQEARDI 183 (257)
T ss_pred HHHHHHHH-HHHHChHHHH--HHHhcCCCHHHHHhhccceeEEEEecCcccccccchHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555 6666544443 2344567888888888775333333332 12233444445555666655554
Q ss_pred HHhc--CCCcccHHH---HHHHHhcCCccchhhhcCCCc-cchhHHhhcCCCC
Q 024740 150 TEEN--KRRTLQKND---IAAAITRTDIFDFLVDIVPRE-DLKDEVLASIPRG 196 (263)
Q Consensus 150 A~~~--KRKTLq~~D---Ia~AI~~~d~FDFL~DIVP~~-~~~~e~l~~~p~~ 196 (263)
-++. +|..|+.+- |.+...+...|.||.+-|-.- ..-++.|.++|..
T Consensus 184 ~~~~~~gk~~v~~kal~~lr~i~~Kl~~lsFld~~v~~l~~~i~~~L~~lP~~ 236 (257)
T PF11348_consen 184 LEKSFAGKDQVSQKALSPLRRIRDKLAGLSFLDPRVAPLVDMIDAVLNSLPKS 236 (257)
T ss_pred HHhhhcCcccccHhHHHHHHHHHHHHhhhcccchhhHHHHHHHHHHHHhCCCC
Confidence 3332 444444332 666777889999999866543 3446788888765
No 83
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=36.05 E-value=1.2e+02 Score=25.66 Aligned_cols=61 Identities=20% Similarity=0.181 Sum_probs=45.1
Q ss_pred HHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC
Q 024740 109 RIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD 171 (263)
Q Consensus 109 RIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d 171 (263)
-||-+|=.-.|+..=..+...++-.-.--++.+|+..|...|+ .|..++-+|+.-|+.+++
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 3566666555655556677777777777778889999999886 666777789999988875
No 84
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=35.37 E-value=1.1e+02 Score=27.70 Aligned_cols=71 Identities=14% Similarity=0.151 Sum_probs=54.0
Q ss_pred ccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHh-cCCCcccHHHHHHHHhc
Q 024740 98 NDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEE-NKRRTLQKNDIAAAITR 169 (263)
Q Consensus 98 ~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~-~KRKTLq~~DIa~AI~~ 169 (263)
..|+...|+-+.|||+.-.--+ .-||....++++-....|+.++..-|-.+-.+ ...--|.+.|+..|+..
T Consensus 109 EvFrrt~lnKt~VKKlastV~n-QtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~sgpl~p~h~reayr~ 180 (199)
T COG5251 109 EVFRRTSLNKTQVKKLASTVAN-QTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTSGPLIPFHKREAYRY 180 (199)
T ss_pred HHHHhcCCCHHHHHHHHHHHhc-cccCCCeeeeeechhHHHHHHHHHHHHHHHHHhcccCCCChHHHHHHHHH
Confidence 4589999999999999876422 46777888888888999999998888776422 22345788899888754
No 85
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=35.33 E-value=44 Score=33.53 Aligned_cols=43 Identities=16% Similarity=0.232 Sum_probs=36.9
Q ss_pred HHHHHHHHHHH----HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 128 PVIFARACEMF----ILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 128 pvllAKA~ElF----I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
.-.+++.|+-| |..++.+|-..|-+..|+.|+.+|+..|+.+-
T Consensus 346 ~e~la~~~~g~sGAdlkaictEAGm~AiR~~R~~Vt~~DF~~Av~KV 392 (406)
T COG1222 346 LELLARLTEGFSGADLKAICTEAGMFAIRERRDEVTMEDFLKAVEKV 392 (406)
T ss_pred HHHHHHhcCCCchHHHHHHHHHHhHHHHHhccCeecHHHHHHHHHHH
Confidence 45677777777 77899999999999999999999999998763
No 86
>PTZ00195 60S ribosomal protein L18; Provisional
Probab=34.90 E-value=15 Score=33.54 Aligned_cols=86 Identities=16% Similarity=0.171 Sum_probs=50.4
Q ss_pred HHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcCc-------------chhccCccHHHHHHHHHHHHHHHHHHH
Q 024740 79 LQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADE-------------DVRMISAEAPVIFARACEMFILELTLR 145 (263)
Q Consensus 79 ~~q~L~~FW~~~~~eiE~~~d~k~~~LPLARIKKIMK~Dp-------------dV~~ISaEApvllAKA~ElFI~eLt~~ 145 (263)
....=..||+..++.++. .......+-||||-|.||.++ =++.|..|.-+.-.-.+-.....++..
T Consensus 37 aRrt~a~fnk~VakRL~~-sr~nRppVsLSrI~r~~k~~d~~~~~~~~~k~~VVvGkVtdd~rl~~vPkvtVaALrfS~t 115 (198)
T PTZ00195 37 AKRTSSGFNKVVYQRLIK-SRSNRAPISLSRIAVVMKRKAVFTAKGKKAPIAVVVGDVLDDVRMARIPAMRVCALRFSKS 115 (198)
T ss_pred HHhhCCHHHHHHHHHHhc-ccccCCceeHHHHHHHHhccccccccCCCCcEEEEEeeEcCCccccccCceEEEEEecCHH
Confidence 334456899999888875 344446788999999999754 012333332221100111112345555
Q ss_pred HHHHHHhcCCCcccHHHHHH
Q 024740 146 SWNHTEENKRRTLQKNDIAA 165 (263)
Q Consensus 146 A~~~A~~~KRKTLq~~DIa~ 165 (263)
|-+.-...+-+.|+-++|+.
T Consensus 116 Ar~rI~kAGGe~lT~dQLa~ 135 (198)
T PTZ00195 116 ARQSIVAAGGECLTFDQLAM 135 (198)
T ss_pred HHHHHHHhCCEEEeHHHHHH
Confidence 66555667778888777665
No 87
>PRK09862 putative ATP-dependent protease; Provisional
Probab=32.58 E-value=2.1e+02 Score=29.37 Aligned_cols=62 Identities=10% Similarity=0.117 Sum_probs=43.4
Q ss_pred CCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHH------HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 102 NHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMF------ILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 102 ~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElF------I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
|..++-..|++..+.+.+. ..++..+.+.+ ...|.+-|+..|.-++|..|+.+||+.|+.-.
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 5566666677666655444 33344333333 45677888888989999999999999999865
No 88
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=31.97 E-value=1.7e+02 Score=24.59 Aligned_cols=62 Identities=15% Similarity=0.125 Sum_probs=44.5
Q ss_pred cchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcCC-ccchhhhcCCC
Q 024740 118 EDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRTD-IFDFLVDIVPR 182 (263)
Q Consensus 118 pdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~d-~FDFL~DIVP~ 182 (263)
.|+..=-.|.+-++-..+-.||.+||..|..+. +|..++-+||.-+|.+++ .|.=..|++--
T Consensus 23 GDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRkDpkK~~Rv~eLL~m 85 (109)
T KOG3901|consen 23 GDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRKDPKKLGRVKELLAM 85 (109)
T ss_pred CCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHhChHHHhHHHHHHHh
Confidence 344445567777888888888889988887764 788888899999999885 34444455443
No 89
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=31.83 E-value=1.3e+02 Score=29.72 Aligned_cols=65 Identities=12% Similarity=0.095 Sum_probs=54.2
Q ss_pred CChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 105 LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
|=..+|++|..+-+ +...-..|.-.|+-.+..||+.|.+-|..++.-.+|---.-.||..|+...
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 44567889998863 345555699999999999999999999999999999888889999998754
No 90
>PTZ00469 60S ribosomal subunit protein L18; Provisional
Probab=31.21 E-value=18 Score=32.78 Aligned_cols=89 Identities=11% Similarity=0.101 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHH--hcCcch---hccCccHHHHHHHHHHHHHHHHHHHHHHHH
Q 024740 76 QQQLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIM--KADEDV---RMISAEAPVIFARACEMFILELTLRSWNHT 150 (263)
Q Consensus 76 ~~~~~q~L~~FW~~~~~eiE~~~d~k~~~LPLARIKKIM--K~DpdV---~~ISaEApvllAKA~ElFI~eLt~~A~~~A 150 (263)
.......=..||+...+.++.... ....+-|+||-|.| |.|+=+ +.|..|.-+.--..+-.....++..|.+.-
T Consensus 34 k~larrt~a~fwk~Va~RL~~srr-nr~pVnLSkI~r~~~~ke~~~~VVvGkVl~dgrl~~vpkvtVaAL~fS~~Ar~kI 112 (187)
T PTZ00469 34 RFLARRTNANFNKIIAKRLIMPKR-FRPPLSLSKLHRHMASYPDDVAVVVGSITDDKRLYDCKKLKVCALRFTETARKRI 112 (187)
T ss_pred HHHHHhhCChHHHHHHHHHhcccc-cCCceeHHHHHHHhccCCCCEEEEEeeEccCccccccCceEEEEEecCHHHHHHH
Confidence 333344456899999888876443 34678899999999 444221 344444433211111112234555666655
Q ss_pred HhcCCCcccHHHHHH
Q 024740 151 EENKRRTLQKNDIAA 165 (263)
Q Consensus 151 ~~~KRKTLq~~DIa~ 165 (263)
.+.+-+.|+-++|+.
T Consensus 113 ~~AGGe~lT~dqLa~ 127 (187)
T PTZ00469 113 LDAGGECLTFDQLAL 127 (187)
T ss_pred HHhCCEEEeHHHHHH
Confidence 667778888777665
No 91
>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=30.86 E-value=1e+02 Score=31.28 Aligned_cols=61 Identities=13% Similarity=0.056 Sum_probs=40.6
Q ss_pred HHHHHhcC--cchhccCccHHHHHHHHHHH--HHHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 110 IKKIMKAD--EDVRMISAEAPVIFARACEM--FILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 110 IKKIMK~D--pdV~~ISaEApvllAKA~El--FI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
|++|++.- ..-..++.++..++++-+.- .+..+...|...|..++|++|+.+||..++...
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 56666542 11135677777777665542 233456666667777889999999999999765
No 92
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=29.85 E-value=1.1e+02 Score=32.28 Aligned_cols=31 Identities=6% Similarity=-0.067 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024740 139 ILELTLRSWNHTEENKRRTLQKNDIAAAITR 169 (263)
Q Consensus 139 I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~ 169 (263)
+..|.+.|...|+..+++.++.+|+..|+..
T Consensus 369 l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~~ 399 (637)
T PRK13765 369 LGGLVRVAGDIARSEGAELTTAEHVLEAKKI 399 (637)
T ss_pred HHHHHHHHHHHHHhhccceecHHHHHHHHHh
Confidence 4557888888899999999999999988754
No 93
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=29.68 E-value=88 Score=29.26 Aligned_cols=56 Identities=14% Similarity=0.203 Sum_probs=44.7
Q ss_pred cCccHHHHHHHHHHHHHHH-HHHHHHHHH-----HhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 123 ISAEAPVIFARACEMFILE-LTLRSWNHT-----EENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 123 ISaEApvllAKA~ElFI~e-Lt~~A~~~A-----~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
..++-..+|.||.|.|+.. =+-.+|.-+ ...|-|.|++++|...+.+..+..||..
T Consensus 93 f~~nEielfrkalE~im~sed~~~asst~~~~~vlq~k~k~L~ks~iE~lLqkf~q~gwf~e 154 (235)
T KOG4718|consen 93 FTANEIELFRKALEKIMSSEDCHIASSTAYNDIVLQAKSKPLKKSRIEELLQKFIQMGWFME 154 (235)
T ss_pred CCHHHHHHHHHHHHHHHhhhHhhhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHhchhhe
Confidence 4457788999999999988 444444332 3568899999999999999999999987
No 94
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=29.31 E-value=1.1e+02 Score=31.12 Aligned_cols=61 Identities=15% Similarity=0.205 Sum_probs=45.6
Q ss_pred HHHHHHHhc--CcchhccCccHHHHHHHHHHH----HHHHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 108 ARIKKIMKA--DEDVRMISAEAPVIFARACEM----FILELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 108 ARIKKIMK~--DpdV~~ISaEApvllAKA~El----FI~eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
.-||.|++. +++--.++.||.-.|++.-+. +...|..-|...|+.+++++|..+||..|-.
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 347777774 344447889999888876543 4445667788899999999999999998854
No 95
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=29.25 E-value=74 Score=30.09 Aligned_cols=42 Identities=12% Similarity=0.103 Sum_probs=32.3
Q ss_pred HHHHHHHHHHH----HHHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024740 128 PVIFARACEMF----ILELTLRSWNHTEENKRRTLQKNDIAAAITR 169 (263)
Q Consensus 128 pvllAKA~ElF----I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~ 169 (263)
...+++.++-| |..|+.+|...|-+++|+.|+.+|+.+|+.+
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 33455555433 5578888888888899999999999999976
No 96
>KOG1560 consensus Translation initiation factor 3, subunit h (eIF-3h) [Translation, ribosomal structure and biogenesis]
Probab=29.13 E-value=3e+02 Score=26.97 Aligned_cols=47 Identities=19% Similarity=0.163 Sum_probs=30.2
Q ss_pred hHHHhHHHHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcC
Q 024740 71 IHHQQQQQLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKAD 117 (263)
Q Consensus 71 ~~~~~~~~~~q~L~~FW~~~~~eiE~~~d~k~~~LPLARIKKIMK~D 117 (263)
.|++...+.+.+...+-.++.+|.+.-..-....||..-||||.|.-
T Consensus 249 kyqr~~~rqq~~~~q~~aKrqaENa~R~argep~lP~dd~kr~fk~p 295 (339)
T KOG1560|consen 249 KYQRQLARQQAKKHQWIAKRQAENANRAARGEPPLPEDDWKRIFKPP 295 (339)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCCCChHHHHHHhcCC
Confidence 34444444555566644455555555445566889999999999974
No 97
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=28.68 E-value=76 Score=30.69 Aligned_cols=42 Identities=14% Similarity=0.105 Sum_probs=32.7
Q ss_pred HHHHHHHHHH----HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 129 VIFARACEMF----ILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 129 vllAKA~ElF----I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
..+++.++-| |..|+.+|...|-+++++.|+.+|+..|+.+.
T Consensus 327 ~~la~~t~g~sgadl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 327 EELAELTEGASGADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 3444444433 66788888888888899999999999999875
No 98
>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=28.65 E-value=1.9e+02 Score=29.96 Aligned_cols=48 Identities=17% Similarity=0.182 Sum_probs=35.6
Q ss_pred ccCccHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCcccHHHHHHHHhc
Q 024740 122 MISAEAPVIFARACEMFI-------LELTLRSWNHTEENKRRTLQKNDIAAAITR 169 (263)
Q Consensus 122 ~ISaEApvllAKA~ElFI-------~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~ 169 (263)
.|+.++..++..+|.-+- ..+.+.|+.+|.-++|.+|+.+||..|+.-
T Consensus 249 ~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~l 303 (633)
T TIGR02442 249 RISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAEL 303 (633)
T ss_pred CCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence 556677666666665552 346677778888899999999999988753
No 99
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=25.83 E-value=85 Score=31.43 Aligned_cols=32 Identities=13% Similarity=0.117 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 139 ILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 139 I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
|..++.+|...|.+.+|..|+.+|+..|+.+.
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 55788889999999999999999999999874
No 100
>smart00350 MCM minichromosome maintenance proteins.
Probab=25.65 E-value=1.8e+02 Score=29.23 Aligned_cols=66 Identities=15% Similarity=0.164 Sum_probs=47.5
Q ss_pred CCChHHHHHHHhcCcc-h-hccCccHHHHHHHHHHH-------------------HHHHHHHHHHHHHHhcCCCcccHHH
Q 024740 104 SLPLARIKKIMKADED-V-RMISAEAPVIFARACEM-------------------FILELTLRSWNHTEENKRRTLQKND 162 (263)
Q Consensus 104 ~LPLARIKKIMK~Dpd-V-~~ISaEApvllAKA~El-------------------FI~eLt~~A~~~A~~~KRKTLq~~D 162 (263)
.++..-+|+.+..-.. + -.+|.++..++...... .++.|.+.|-.+|+-+.|.+|+.+|
T Consensus 417 ~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~~D 496 (509)
T smart00350 417 PISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEEAD 496 (509)
T ss_pred cCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCHHH
Confidence 5777888887765443 2 24677777666544332 2356778888889999999999999
Q ss_pred HHHHHhc
Q 024740 163 IAAAITR 169 (263)
Q Consensus 163 Ia~AI~~ 169 (263)
+..||.=
T Consensus 497 v~~ai~l 503 (509)
T smart00350 497 VEEAIRL 503 (509)
T ss_pred HHHHHHH
Confidence 9999864
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=25.59 E-value=1.5e+02 Score=23.06 Aligned_cols=28 Identities=18% Similarity=0.371 Sum_probs=19.6
Q ss_pred HHHHHhhccCCCCCCChHHHHHHHhcCc
Q 024740 91 YQEIEKVNDFKNHSLPLARIKKIMKADE 118 (263)
Q Consensus 91 ~~eiE~~~d~k~~~LPLARIKKIMK~Dp 118 (263)
+..++....++...|||+.|++++....
T Consensus 44 i~~l~~i~~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 44 LERLQQILFLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHcCc
Confidence 3334444455667899999999998753
No 102
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=25.22 E-value=2.3e+02 Score=19.42 Aligned_cols=32 Identities=3% Similarity=0.014 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024740 136 EMFILELTLRSWNHTEENKRRTLQKNDIAAAI 167 (263)
Q Consensus 136 ElFI~eLt~~A~~~A~~~KRKTLq~~DIa~AI 167 (263)
+..+.+++...+..+-.++...|+.+++..++
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 55666777777888888999999999887763
No 103
>PHA00687 hypothetical protein
Probab=25.18 E-value=29 Score=25.24 Aligned_cols=20 Identities=50% Similarity=0.627 Sum_probs=15.5
Q ss_pred CCCChHHHHHHHhcCcchhc
Q 024740 103 HSLPLARIKKIMKADEDVRM 122 (263)
Q Consensus 103 ~~LPLARIKKIMK~DpdV~~ 122 (263)
..=||+|||.|-|..+.|++
T Consensus 29 radplarvkaiekatervkr 48 (56)
T PHA00687 29 RADPLARVKAIEKATERVKR 48 (56)
T ss_pred ccChHHHHHHHHHHHHHHHH
Confidence 45699999999888776653
No 104
>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=24.76 E-value=2e+02 Score=22.88 Aligned_cols=24 Identities=8% Similarity=0.146 Sum_probs=17.5
Q ss_pred HHhhccCCCCCCChHHHHHHHhcC
Q 024740 94 IEKVNDFKNHSLPLARIKKIMKAD 117 (263)
Q Consensus 94 iE~~~d~k~~~LPLARIKKIMK~D 117 (263)
+.....++...|||+.|++++...
T Consensus 47 l~~I~~lr~~G~~l~~I~~~l~~~ 70 (108)
T cd04773 47 ARLIHLLRRGGYLLEQIATVVEQL 70 (108)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHh
Confidence 333444555789999999999864
No 105
>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=24.67 E-value=2.7e+02 Score=26.78 Aligned_cols=47 Identities=17% Similarity=0.155 Sum_probs=30.9
Q ss_pred ccCccHHHHHHHHHHHHHH-------HHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 122 MISAEAPVIFARACEMFIL-------ELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 122 ~ISaEApvllAKA~ElFI~-------eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
.|+.+..-.++..|.-+-. .|.+.|-.+|.-++|..|+.+||..++.
T Consensus 254 ~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~ 307 (337)
T TIGR02030 254 TIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAV 307 (337)
T ss_pred cCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3555555555554444422 2556666677789999999999998754
No 106
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=23.79 E-value=1e+02 Score=30.28 Aligned_cols=32 Identities=9% Similarity=0.106 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC
Q 024740 139 ILELTLRSWNHTEENKRRTLQKNDIAAAITRT 170 (263)
Q Consensus 139 I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~ 170 (263)
|..|+.+|...|-+++|+.|+.+|+..|+.+.
T Consensus 355 I~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v 386 (398)
T PTZ00454 355 IAAICQEAGMQAVRKNRYVILPKDFEKGYKTV 386 (398)
T ss_pred HHHHHHHHHHHHHHcCCCccCHHHHHHHHHHH
Confidence 67899999999989999999999999998763
No 107
>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=22.58 E-value=1.4e+02 Score=20.79 Aligned_cols=26 Identities=15% Similarity=0.055 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHhcCCCcccHHHHHHH
Q 024740 141 ELTLRSWNHTEENKRRTLQKNDIAAA 166 (263)
Q Consensus 141 eLt~~A~~~A~~~KRKTLq~~DIa~A 166 (263)
.+=..+-..|.+++...|+..+|..|
T Consensus 19 ~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 19 KLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 34445556678899999999888765
No 108
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=22.33 E-value=2.2e+02 Score=26.16 Aligned_cols=64 Identities=13% Similarity=0.111 Sum_probs=43.2
Q ss_pred hccCccHHHHHHHHHHHHHHHHHHHHHHHHHh--cCCCcccHHHHHHHHhcC--CccchhhhcCCCcc
Q 024740 121 RMISAEAPVIFARACEMFILELTLRSWNHTEE--NKRRTLQKNDIAAAITRT--DIFDFLVDIVPRED 184 (263)
Q Consensus 121 ~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~--~KRKTLq~~DIa~AI~~~--d~FDFL~DIVP~~~ 184 (263)
..|+.+|...|...++-=+..+..+--+.+-. .++++|+.+||..+|... ..|+++..++-++.
T Consensus 148 ~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~~~~~if~l~dai~~~~~ 215 (326)
T PRK07452 148 VKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSNTTQNSLQLADALLQGNT 215 (326)
T ss_pred CCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhccCcCcHHHHHHHHHCCCH
Confidence 47888888888887765344444444444444 567889999999986554 56776666666554
No 109
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=22.24 E-value=2.6e+02 Score=29.70 Aligned_cols=46 Identities=11% Similarity=0.070 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHhcCCCcccHHHHHHHHhcC-CccchhhhcCCCcc
Q 024740 139 ILELTLRSWNHTEENKRRTLQKNDIAAAITRT-DIFDFLVDIVPRED 184 (263)
Q Consensus 139 I~eLt~~A~~~A~~~KRKTLq~~DIa~AI~~~-d~FDFL~DIVP~~~ 184 (263)
+..|...|...|+..+++-|+..||..|+++. ..-+||.+......
T Consensus 368 l~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~~~~e~~l~e~~~~~~ 414 (647)
T COG1067 368 LGNLVREAGDIAVSEGRKLITAEDVEEALQKRELREGQLAERYIEDI 414 (647)
T ss_pred HHHHHHHhhHHHhcCCcccCcHHHHHHHHHhhhhHHHHHHHHHHHHH
Confidence 34566788889999999999999999999885 33466666554433
No 110
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=21.76 E-value=3.4e+02 Score=26.17 Aligned_cols=62 Identities=8% Similarity=-0.055 Sum_probs=42.9
Q ss_pred CChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHH-------HHHHHHHHHHHhcCCCcccHHHHHHHH
Q 024740 105 LPLARIKKIMKADEDVRMISAEAPVIFARACEMFIL-------ELTLRSWNHTEENKRRTLQKNDIAAAI 167 (263)
Q Consensus 105 LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~-------eLt~~A~~~A~~~KRKTLq~~DIa~AI 167 (263)
+-..+|.+.-+.-++| .|+.+....+...|.-+-. .|.+.|-..|-.++|..|+.+||..++
T Consensus 235 ~~~~~i~~a~~~~~~V-~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~ 303 (334)
T PRK13407 235 QLRGRILGARARLPQL-KTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVA 303 (334)
T ss_pred CCHHHHHHHHHhcCCc-ccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHH
Confidence 4446666666655565 4566666666666655431 266777777888999999999998776
No 111
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=21.43 E-value=2e+02 Score=29.98 Aligned_cols=47 Identities=17% Similarity=0.076 Sum_probs=35.3
Q ss_pred ccCccHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCcccHHHHHHHHh
Q 024740 122 MISAEAPVIFARACEMFI-------LELTLRSWNHTEENKRRTLQKNDIAAAIT 168 (263)
Q Consensus 122 ~ISaEApvllAKA~ElFI-------~eLt~~A~~~A~~~KRKTLq~~DIa~AI~ 168 (263)
.|+.+....++.+|..|- ..|++.|+.+|.-++|..|+.+||..|+.
T Consensus 195 ~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~ 248 (584)
T PRK13406 195 GPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAAR 248 (584)
T ss_pred CCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 456666666666666553 35677788888889999999999999975
No 112
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=21.18 E-value=2.9e+02 Score=25.15 Aligned_cols=64 Identities=20% Similarity=0.199 Sum_probs=41.3
Q ss_pred hccCccHHHHHHHHHHHHHHHHHHHHHHHHHhc-CCCcccHHHHHHHHhc---CCccchhhhcCCCccc
Q 024740 121 RMISAEAPVIFARACEMFILELTLRSWNHTEEN-KRRTLQKNDIAAAITR---TDIFDFLVDIVPREDL 185 (263)
Q Consensus 121 ~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~-KRKTLq~~DIa~AI~~---~d~FDFL~DIVP~~~~ 185 (263)
..|+.+|...|...++-=+..+..+..+.+-.. +++ |+.+||..++.. ...|+|+.-++-++..
T Consensus 164 ~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~~~~~~~f~l~dai~~~~~~ 231 (340)
T PRK05574 164 LQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPDSARFDVFDLVDAILAGKIK 231 (340)
T ss_pred CCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhhhhcCCHHHHHHHHHCCCHH
Confidence 368888888888776532333333333333222 334 999999988665 4677888888887653
No 113
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=21.04 E-value=3.3e+02 Score=23.65 Aligned_cols=66 Identities=11% Similarity=0.186 Sum_probs=48.1
Q ss_pred HHHHHhcCcchhccCccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccH---HHHHHHHhcCCccchh
Q 024740 110 IKKIMKADEDVRMISAEAPVIFARACEMFILELTLRSWNHTEENKRRTLQK---NDIAAAITRTDIFDFL 176 (263)
Q Consensus 110 IKKIMK~DpdV~~ISaEApvllAKA~ElFI~eLt~~A~~~A~~~KRKTLq~---~DIa~AI~~~d~FDFL 176 (263)
|.-|+.+ -.|.-.+...++-+-.-+-.+.+.+.+.|...|+..+|-.+.. +||.-||+..-...|.
T Consensus 20 ihliL~S-lgi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~ 88 (145)
T COG5094 20 IHLILRS-LGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFV 88 (145)
T ss_pred HHHHHHh-cCchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcC
Confidence 4444444 3555666666766666667788999999999998877765555 9999999988777763
No 114
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=20.76 E-value=1.7e+02 Score=28.33 Aligned_cols=51 Identities=10% Similarity=0.092 Sum_probs=27.8
Q ss_pred ccCccHHHHHHHHHHH---HHHHHHHHHHHHHH-hcCCCcccHHHHHHHHhcCCc
Q 024740 122 MISAEAPVIFARACEM---FILELTLRSWNHTE-ENKRRTLQKNDIAAAITRTDI 172 (263)
Q Consensus 122 ~ISaEApvllAKA~El---FI~eLt~~A~~~A~-~~KRKTLq~~DIa~AI~~~d~ 172 (263)
.|+.++..+|...+.- .+..+..+....+. .+.+++|+.+||..+|.....
T Consensus 205 ~i~~~al~~l~~~s~g~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v~~~~~ 259 (397)
T PRK14955 205 SVDADALQLIGRKAQGSMRDAQSILDQVIAFSVESEGEGSIRYDKVAELLNYIDD 259 (397)
T ss_pred CCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccccCCCCccCHHHHHHHHCCCCH
Confidence 3666666665555432 12222222222332 245679999999988866554
No 115
>KOG2623 consensus Tyrosyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.19 E-value=4.7e+02 Score=26.86 Aligned_cols=94 Identities=18% Similarity=0.262 Sum_probs=54.7
Q ss_pred hHHHHHhHHHhHHHHHHHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcC---cchhccCccHHHHHHHHHHHHHH-
Q 024740 65 QLAYQQIHHQQQQQLQQQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKAD---EDVRMISAEAPVIFARACEMFIL- 140 (263)
Q Consensus 65 ~~~~q~~~~~~~~~~~q~L~~FW~~~~~eiE~~~d~k~~~LPLARIKKIMK~D---pdV~~ISaEApvllAKA~ElFI~- 140 (263)
-..||-+...........|+-| +-|||.-||+||+.. | ..++. -..+|+=.-.|+.
T Consensus 292 y~lYQfF~~~pDd~v~k~Lklf----------------Tfl~l~eI~~I~~~H~k~P-~~r~a---Q~~LA~eVTr~VHG 351 (467)
T KOG2623|consen 292 YHLYQFFASLPDDDVEKFLKLF----------------TFLPLEEIKQILEEHRKEP-SQRIA---QKLLAAEVTRMVHG 351 (467)
T ss_pred HHHHHHHHhCchhHHHHHHHHH----------------hcCCHHHHHHHHHHHhcCh-hhhhH---HHHHHHHHHHHHcc
Confidence 3467766665555555555544 458999999999974 3 22222 2222222222221
Q ss_pred ----HHHHHHHHH---HHhcCCCcccHHHHHHHHhcCCccchhhh
Q 024740 141 ----ELTLRSWNH---TEENKRRTLQKNDIAAAITRTDIFDFLVD 178 (263)
Q Consensus 141 ----eLt~~A~~~---A~~~KRKTLq~~DIa~AI~~~d~FDFL~D 178 (263)
+.+.++.+. ++...--++..+.|.+..+.....+++.|
T Consensus 352 ~egL~~A~r~T~al~g~~~~~~~~ls~~ei~~lfk~a~~~~l~~~ 396 (467)
T KOG2623|consen 352 KEGLEVAERCTKALFGAKKAGLSGLSLSEILQLFKDATFIDLKDE 396 (467)
T ss_pred cchHHHHHHHHHHhhcccccccccCCHHHHHHHHhcCCceecccC
Confidence 222222222 22335678899999999998888888888
No 116
>COG1239 ChlI Mg-chelatase subunit ChlI [Coenzyme metabolism]
Probab=20.18 E-value=4.6e+02 Score=26.64 Aligned_cols=77 Identities=16% Similarity=0.212 Sum_probs=47.5
Q ss_pred HHHHHHHHHHHHHHHhhccCCCCCCChHHHHHHHhcCcchhccCccHHHHHHHHHHHHHHH-------HHHHHHHHHHhc
Q 024740 81 QQLQSFWANQYQEIEKVNDFKNHSLPLARIKKIMKADEDVRMISAEAPVIFARACEMFILE-------LTLRSWNHTEEN 153 (263)
Q Consensus 81 q~L~~FW~~~~~eiE~~~d~k~~~LPLARIKKIMK~DpdV~~ISaEApvllAKA~ElFI~e-------Lt~~A~~~A~~~ 153 (263)
+.+.++|.....++. +||-.--+.-++| .++.++...++.+|-.+-.. +++.|..+|.-+
T Consensus 239 e~f~~~~~~~~~~lR------------~~ii~ar~~l~~V-~l~~~~~~~ia~~~~~~~v~g~radi~~~r~a~a~aa~~ 305 (423)
T COG1239 239 EAFLEKYADAQRALR------------ARIIAARSLLSEV-ELDDDAETKIAELCARLAVDGHRADIVVVRAAKALAALR 305 (423)
T ss_pred HHHHHHHHHHHHHHH------------HHHHHHHhccccc-cCcHHHHHHHHHHHHHhccCCCchhhHHHHHHHHHHHhc
Confidence 345666777655544 2222222223444 55666677777666555332 555566667779
Q ss_pred CCCcccHHHHHHHHhcC
Q 024740 154 KRRTLQKNDIAAAITRT 170 (263)
Q Consensus 154 KRKTLq~~DIa~AI~~~ 170 (263)
+|.+++..||..|+.-.
T Consensus 306 Gr~~v~~~Di~~a~~l~ 322 (423)
T COG1239 306 GRTEVEEEDIREAAELA 322 (423)
T ss_pred CceeeehhhHHHHHhhh
Confidence 99999999999987643
Done!