Query 017508
Match_columns 370
No_of_seqs 184 out of 347
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 09:11:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017508.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017508hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2389 Predicted bromodomain 100.0 3.7E-46 8.1E-51 362.3 17.3 347 3-369 2-352 (353)
2 KOG4336 TBP-associated transcr 100.0 2.9E-35 6.2E-40 281.9 16.1 204 32-258 6-221 (323)
3 PF10406 TAF8_C: Transcription 99.8 3.8E-21 8.3E-26 141.9 6.3 50 162-211 1-50 (51)
4 cd08049 TAF8 TATA Binding Prot 99.8 1.2E-20 2.6E-25 140.7 6.3 53 162-214 1-53 (54)
5 smart00576 BTP Bromodomain tra 99.8 7.2E-20 1.6E-24 145.6 10.0 74 26-99 1-74 (77)
6 PF07524 Bromo_TP: Bromodomain 99.8 9.9E-20 2.1E-24 144.3 10.0 74 26-99 1-74 (77)
7 PLN00035 histone H4; Provision 98.8 1.5E-08 3.2E-13 85.1 8.2 79 24-102 22-101 (103)
8 PTZ00015 histone H4; Provision 98.8 1.4E-08 3E-13 85.2 7.9 74 26-99 25-98 (102)
9 cd00076 H4 Histone H4, one of 98.7 7.8E-08 1.7E-12 78.3 8.0 73 27-99 9-81 (85)
10 cd07979 TAF9 TATA Binding Prot 98.5 1.1E-06 2.4E-11 75.5 11.6 64 35-98 5-68 (117)
11 smart00803 TAF TATA box bindin 98.4 2E-06 4.3E-11 66.6 8.1 61 34-94 5-65 (65)
12 COG2036 HHT1 Histones H3 and H 98.3 1.5E-06 3.3E-11 71.6 7.0 66 34-99 22-87 (91)
13 PF02291 TFIID-31kDa: Transcri 98.2 5.5E-06 1.2E-10 72.4 8.3 61 35-95 16-76 (129)
14 smart00417 H4 Histone H4. 98.2 3.6E-06 7.8E-11 66.9 5.4 66 27-92 9-74 (74)
15 PF15630 CENP-S: Kinetochore c 98.1 1.1E-05 2.5E-10 64.4 8.0 66 30-95 4-72 (76)
16 KOG3467 Histone H4 [Chromatin 98.0 2.1E-05 4.5E-10 64.0 6.4 76 24-99 22-97 (103)
17 KOG3334 Transcription initiati 97.9 0.00014 3E-09 64.3 11.0 62 35-96 17-78 (148)
18 PF02969 TAF: TATA box binding 97.6 0.0003 6.6E-09 54.8 8.1 61 34-94 6-66 (66)
19 cd07981 TAF12 TATA Binding Pro 97.3 0.0023 4.9E-08 50.4 8.8 50 46-95 17-66 (72)
20 PF00125 Histone: Core histone 97.2 0.0023 5E-08 49.9 7.7 60 35-94 13-73 (75)
21 cd08050 TAF6 TATA Binding Prot 97.1 0.0021 4.7E-08 64.5 8.9 65 35-99 3-67 (343)
22 COG5094 TAF9 Transcription ini 96.8 0.0042 9E-08 53.9 6.7 61 35-95 18-81 (145)
23 PF00808 CBFD_NFYB_HMF: Histon 96.8 0.0076 1.6E-07 46.0 7.5 57 37-93 8-65 (65)
24 PF15511 CENP-T: Centromere ki 96.0 0.017 3.8E-07 59.5 7.1 61 28-88 352-414 (414)
25 smart00428 H3 Histone H3. 95.9 0.047 1E-06 46.3 8.4 52 45-97 51-102 (105)
26 cd07978 TAF13 The TATA Binding 95.5 0.09 1.9E-06 43.5 8.1 65 34-99 5-70 (92)
27 KOG3423 Transcription initiati 95.4 0.067 1.5E-06 48.7 7.8 66 34-99 89-168 (176)
28 PLN00161 histone H3; Provision 95.0 0.098 2.1E-06 46.3 7.4 54 45-99 76-129 (135)
29 PLN00160 histone H3; Provision 94.7 0.14 3.1E-06 42.9 7.1 50 48-97 44-93 (97)
30 PTZ00018 histone H3; Provision 94.1 0.2 4.3E-06 44.5 7.1 61 36-97 71-133 (136)
31 PF02269 TFIID-18kDa: Transcri 94.1 0.06 1.3E-06 44.5 3.7 61 37-97 7-68 (93)
32 KOG2549 Transcription initiati 93.9 0.23 5.1E-06 52.8 8.5 65 35-99 15-79 (576)
33 KOG0870 DNA polymerase epsilon 93.8 0.27 5.8E-06 44.8 7.6 73 26-99 9-81 (172)
34 PLN00121 histone H3; Provision 93.7 0.29 6.3E-06 43.4 7.5 52 45-97 82-133 (136)
35 PF03540 TFIID_30kDa: Transcri 93.6 0.33 7.2E-06 36.1 6.4 44 35-78 6-49 (51)
36 cd00074 H2A Histone 2A; H2A is 92.7 0.41 8.8E-06 41.3 6.7 58 38-95 27-85 (115)
37 KOG0869 CCAAT-binding factor, 90.1 1.3 2.8E-05 40.3 7.3 64 36-99 37-102 (168)
38 KOG1142 Transcription initiati 90.1 1 2.2E-05 43.8 7.2 56 44-99 168-224 (258)
39 PF03847 TFIID_20kDa: Transcri 88.0 1.8 4E-05 33.8 6.1 48 48-95 17-64 (68)
40 COG5095 TAF6 Transcription ini 87.8 2 4.4E-05 43.2 7.7 69 36-104 10-80 (450)
41 COG5162 Transcription initiati 85.3 1.9 4.2E-05 39.4 5.5 45 34-78 91-135 (197)
42 KOG3901 Transcription initiati 85.3 2.5 5.4E-05 36.0 5.8 67 29-98 7-74 (109)
43 KOG0871 Class 2 transcription 83.6 3.7 8.1E-05 36.9 6.5 67 30-99 15-82 (156)
44 COG5248 TAF19 Transcription in 75.8 8.4 0.00018 33.1 5.9 65 33-99 11-76 (126)
45 KOG1745 Histones H3 and H4 [Ch 72.3 2.1 4.5E-05 38.0 1.5 49 49-97 86-134 (137)
46 cd08045 TAF4 TATA Binding Prot 72.2 12 0.00027 35.0 6.8 75 24-98 41-121 (212)
47 smart00427 H2B Histone H2B. 67.7 40 0.00087 27.9 8.0 49 48-96 19-67 (89)
48 PTZ00463 histone H2B; Provisio 66.6 39 0.00085 29.4 8.0 48 49-96 47-94 (117)
49 KOG1744 Histone H2B [Chromatin 66.4 15 0.00032 32.4 5.5 69 24-96 35-103 (127)
50 PF13654 AAA_32: AAA domain; P 65.6 42 0.00091 35.9 9.8 69 26-95 426-505 (509)
51 PLN00158 histone H2B; Provisio 64.1 47 0.001 28.9 8.0 56 38-96 38-93 (116)
52 COG5150 Class 2 transcription 63.0 39 0.00085 29.9 7.4 68 30-99 14-81 (148)
53 PLN00154 histone H2A; Provisio 59.2 29 0.00064 30.9 6.1 58 38-95 45-104 (136)
54 TIGR03015 pepcterm_ATPase puta 58.6 42 0.00091 31.4 7.6 65 33-97 197-267 (269)
55 PF09415 CENP-X: CENP-S associ 55.7 26 0.00057 27.7 4.7 58 36-94 4-66 (72)
56 PF05236 TAF4: Transcription i 53.3 23 0.00049 34.3 4.9 54 29-82 45-98 (264)
57 cd08048 TAF11 TATA Binding Pro 52.0 90 0.002 25.4 7.4 65 28-96 17-84 (85)
58 PRK00411 cdc6 cell division co 45.6 1.5E+02 0.0032 29.6 9.5 51 48-98 228-284 (394)
59 smart00414 H2A Histone 2A. 35.9 1.1E+02 0.0024 25.9 5.9 49 47-95 26-74 (106)
60 KOG2389 Predicted bromodomain 34.9 11 0.00025 38.2 -0.3 61 275-335 276-337 (353)
61 TIGR00764 lon_rel lon-related 33.3 3E+02 0.0064 30.1 10.1 63 34-96 315-391 (608)
62 PF12767 SAGA-Tad1: Transcript 32.8 1.2E+02 0.0027 29.0 6.4 43 32-74 207-249 (252)
63 PRK06585 holA DNA polymerase I 30.1 1.7E+02 0.0036 28.9 7.0 63 32-95 146-209 (343)
64 PLN00156 histone H2AX; Provisi 28.9 1.3E+02 0.0029 26.9 5.4 57 39-95 37-94 (139)
65 PRK09087 hypothetical protein; 27.4 4.5E+02 0.0099 24.6 9.1 63 33-97 158-223 (226)
66 PLN00153 histone H2A; Provisio 25.0 2.7E+02 0.006 24.6 6.5 57 39-95 32-89 (129)
67 PRK05574 holA DNA polymerase I 24.6 3.1E+02 0.0068 26.5 7.8 63 33-96 151-213 (340)
68 PTZ00017 histone H2A; Provisio 23.9 1.8E+02 0.004 25.8 5.3 48 48-95 45-92 (134)
69 TIGR02928 orc1/cdc6 family rep 23.8 4.6E+02 0.01 25.7 8.8 52 48-99 220-277 (365)
70 PRK07452 DNA polymerase III su 23.4 2.9E+02 0.0063 26.9 7.2 62 33-95 135-198 (326)
71 PRK05907 hypothetical protein; 22.9 2.3E+02 0.005 28.2 6.5 64 31-95 137-202 (311)
72 PRK12402 replication factor C 22.8 2.8E+02 0.0061 26.7 7.0 63 32-97 188-250 (337)
73 COG1224 TIP49 DNA helicase TIP 22.2 2E+02 0.0043 30.2 5.8 70 26-96 359-432 (450)
74 TIGR01128 holA DNA polymerase 21.1 4.4E+02 0.0095 24.9 7.9 65 30-95 113-177 (302)
75 CHL00081 chlI Mg-protoporyphyr 21.0 2.7E+02 0.0058 28.4 6.6 48 48-95 267-321 (350)
76 TIGR02442 Cob-chelat-sub cobal 20.9 5.3E+02 0.012 28.2 9.3 49 48-96 249-304 (633)
77 TIGR02902 spore_lonB ATP-depen 20.6 3.4E+02 0.0073 29.1 7.5 61 34-95 269-331 (531)
78 PRK00080 ruvB Holliday junctio 20.3 5E+02 0.011 25.4 8.3 65 34-99 186-253 (328)
79 COG0299 PurN Folate-dependent 20.1 34 0.00074 32.3 -0.0 15 165-179 109-123 (200)
No 1
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=100.00 E-value=3.7e-46 Score=362.30 Aligned_cols=347 Identities=24% Similarity=0.358 Sum_probs=283.8
Q ss_pred CCCCCCCCCccccCCCCCCCCCchHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Q 017508 3 HGGGESTSRSESRTDTSSDRPKAEDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRT 82 (370)
Q Consensus 3 ~g~~~~~~~~~~~~~~~~~~~~~ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT 82 (370)
|+++.+ |.++.+..+.++..++++|++++++++|||||+++||++...+||++|+++++.||++||+.||.|+|++||+
T Consensus 2 n~~r~~-~~~q~~~~~~~~~~~~~~ya~sla~~avaQIcqslg~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~ 80 (353)
T KOG2389|consen 2 NTYRRN-ENQQAEEESERSESEEAEYAFSLARVAVAQICQSLGYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRT 80 (353)
T ss_pred cccccc-hhhhhhhhcCccchhHHHHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCC
Confidence 344443 4466668999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCHHHHHHHHHhccccccccccccccccccCcchhHHHHHhhhhcCCCCCCCCCCCCCCccc-CCCCCccccCCCCCCC
Q 017508 83 ECNLFDIIRGIEDLEVLKGFMGAAEIGKCLVGSGIVKEIIDFVESKEEIPFAQPIPQYPVIRS-RRLIPSFEEMNETPPG 161 (370)
Q Consensus 83 ~p~~~DV~~AL~~mGi~~gf~~~~~~~~~l~~S~~l~eL~~yv~~~~~ipf~~~lP~fPv~~~-~~~~psfl~~G~~~~p 161 (370)
+||++|+++||.+++++.|+.+.+.-.|||++|+++++|+.|+...++|||.+++|+||+.+. ..+.|+|...|.++++
T Consensus 81 epnl~Div~Al~dls~s~~~~~~~~~s~~L~ds~v~rdii~~~g~~eevpF~~~lP~Fp~s~s~~k~~l~~~~~g~~pp~ 160 (353)
T KOG2389|consen 81 EPNLFDIVLALQDLSASLGASGSSGESHCLLDSKVLRDIIIFNGKAEEVPFKDDLPRFPVSKSVNKPFLKFGSVGAEPPG 160 (353)
T ss_pred CccHHHHHHHHHHhhhhcccccccchhHHHhhhhhHHHHHhhccccccCCCCCCCCccccccccccCCCCccccCCCCCC
Confidence 999999999999999998888888889999999999999999999999999999999999987 6678999999999999
Q ss_pred CCCCCCCC-CCCCCCccccCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCCCCCCcHHhhhhcCC
Q 017508 162 KHIPSWLP-AFPDPHTYIYTPMWNERKSDPRADKIELARQRRKAEMALLSLQQRLVCNGETGTSASRPANDEEELLKTGS 240 (370)
Q Consensus 162 ~hIP~~LP-~FP~~HTY~~TPiy~~~~tD~~~iR~k~aeq~R~~EkAL~~L~~r~~~~g~~~~~~~~~~~~~~~~~~~~~ 240 (370)
.|||.||| +||+.|+|..+|.++....+++.--.+.+.+.+.++.+.....+...+--. .+........++
T Consensus 161 ~~Ip~wLP~~fp~~~~~~~s~e~~~~~~~~~~~~~~~~s~~~~~~ls~~~~~r~~v~k~~--------~~~~~~~~~s~g 232 (353)
T KOG2389|consen 161 ESIPIWLPPAFPDLEGCSKSPEGNVTVPKPEGRPPEKASLELRASLSEDSGGRLQVKKDS--------EEKEKPEWTSKG 232 (353)
T ss_pred ccccccCCCCCCCcccCCCCccccccccCcccCchhhhhhhhhhhhhhhccccchhhhhh--------hhhcCcccccCC
Confidence 99999999 999999999999999888887766666666655555554444111110000 111111122288
Q ss_pred CCCCCCCCCCCcccccc--ccCCcccccccCCCCCcchhhhhhhHHHHhhhcCCccCCCCCcccCCCCCCceeeeeecCc
Q 017508 241 NPFFAKPLQSGEKDISP--VGLPAKLKDKMSGGNHMSVMEAFAPAIEAVKVSGFSDDADGDRRYLPEKRPAVHFKFRAGK 318 (370)
Q Consensus 241 npfl~~p~~~~ek~vs~--v~~~~~~~~~~~~~~~~~~~e~fa~a~~~~~~~~~~~~~~~~~~~~~~~r~~~~~k~~~~k 318 (370)
|+|+.++.++|+++||. +|.+.. .-.++|-.++.||.+.+. ..+.-+. -+.+-+..|.|.-+..|.|
T Consensus 233 ~~~~~~~~~~~~~~vs~~~kV~~~~-------~~~~~i~t~~~Pa~~~~~-p~l~~~a---~~e~~~~k~v~~~t~d~ek 301 (353)
T KOG2389|consen 233 PKKLTRAEEIRDQLVSAKSKVVLLN-------RVGAPIQTTLPPAQQPAT-PILVPQA---SMEPATNKPVVGATVDIEK 301 (353)
T ss_pred Chhhhcchhcccccccccccccccc-------cCCceeeccCCCcccCCc-ccccccc---ccccccCcccccchhhhhh
Confidence 99999999999999996 777776 447788889999988877 5554444 3345566677777778888
Q ss_pred chhhhhhhhhhhhhCCCCCccccccccchHHHHHHHHHHHHHhhCcccccc
Q 017508 319 KFLGEILDSSLQKKGGRRSASFWRDEEKDDKKRRAEFILKQSIENPQELSQ 369 (370)
Q Consensus 319 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~k~ra~~il~~~~~np~~l~~ 369 (370)
+.++.+....++.+....-.|.-....+||+.+|+++++|+.|.|+-++.+
T Consensus 302 ~~~~~~~~~l~~~k~~~~~~s~~~~~~~ed~~kr~k~~~r~~~~e~~d~~~ 352 (353)
T KOG2389|consen 302 APFLLAEPALLVEKKTERQFSEGPSSSREDQEKRPKKEKRDKSSEEYDEYK 352 (353)
T ss_pred chhhcccchhhhhhhcccccccccccchhhhhcchhhhhhhccchhhhhhc
Confidence 888888888777766666566665666699999999999999999987654
No 2
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=100.00 E-value=2.9e-35 Score=281.88 Aligned_cols=204 Identities=24% Similarity=0.329 Sum_probs=157.7
Q ss_pred HHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccccccccccccccc
Q 017508 32 VSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVLKGFMGAAEIGKC 111 (370)
Q Consensus 32 lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~~gf~~~~~~~~~ 111 (370)
+|..+|+++|..+||+.++..|+++|+++++.||.+||+.+|.||+|+|||+|+..||.++|..|||.
T Consensus 6 vl~~VV~~Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~------------ 73 (323)
T KOG4336|consen 6 VLAPVVSNLLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK------------ 73 (323)
T ss_pred HHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC------------
Confidence 89999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCcchhHHHHHhhhhcCCCC--CCCCCCCCCCccc---CCCC-CccccCC-CCCCCCCCCCCCCCCCCCCccccCCCCC
Q 017508 112 LVGSGIVKEIIDFVESKEEIP--FAQPIPQYPVIRS---RRLI-PSFEEMN-ETPPGKHIPSWLPAFPDPHTYIYTPMWN 184 (370)
Q Consensus 112 l~~S~~l~eL~~yv~~~~~ip--f~~~lP~fPv~~~---~~~~-psfl~~G-~~~~p~hIP~~LP~FP~~HTY~~TPiy~ 184 (370)
+.+|..|.+....+- ....+|. .... .... ...+..| +.++|.|||+|||+||++|||++||+|.
T Consensus 74 ------v~sL~~~~q~~~~sl~~~~~~aP~--~~~q~~ds~~~~~~~l~~gv~~php~yIpshLPpfPdpHTYi~Tpi~~ 145 (323)
T KOG4336|consen 74 ------VSSLYAYFQKQEFSLWSVLIAAPE--NQEQEEDSEQQPELLLTLGVSRPHPKYIPSHLPPFPDPHTYIKTPIYK 145 (323)
T ss_pred ------hhhhHHHHHhccchhhhccccCCC--cCCccccccccchHhhhcCCCCCCCccccccCCCCCCCcccccCCccC
Confidence 677888875432210 1123442 2211 0112 2234455 3689999999999999999999999999
Q ss_pred CCCCChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCC---CCC--CCCCCCcHHhhhhcCCCCCCCCCCCCCccccccc
Q 017508 185 ERKSDPRADKIELARQRRKAEMALLSLQQRLVCNGET---GTS--ASRPANDEEELLKTGSNPFFAKPLQSGEKDISPV 258 (370)
Q Consensus 185 ~~~tD~~~iR~k~aeq~R~~EkAL~~L~~r~~~~g~~---~~~--~~~~~~~~~~~~~~~~npfl~~p~~~~ek~vs~v 258 (370)
.++|||++||+++++|+|.+|+||.++ +.+++.. -+. ...+.++.......++|..+.....+-++.++..
T Consensus 146 ~p~tsyk~iRe~aaqe~r~~e~AL~~~---~~r~~p~~slf~~~~~~~~e~a~~p~~~py~~almp~~~v~~~d~~~~~ 221 (323)
T KOG4336|consen 146 VPDTSYKAIREKAAQESRNSEKALTNY---LKRNSPTSSLFPTDPSLFPEDACKPFNLPYSNALMPRKQVFDEDELEEN 221 (323)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHH---HHhcCcchhccCCCCCcCHHHhcCccccchHHhhCccccchhhhhhhhh
Confidence 999999999999999999999999999 5555544 211 1111122222233377877777777777777755
No 3
>PF10406 TAF8_C: Transcription factor TFIID complex subunit 8 C-term ; InterPro: IPR019473 This entry represents the C-terminal region of subunit 8 (also known as TAF8) of the transcription factor TFIID []. The adjacent N-terminal region generally contains a histone fold domain (IPR006565 from INTERPRO). This subunit is one of the key subunits of TFIID, being one of several general cofactors which are typically involved in gene activation to bring about the communication between gene-specific transcription factors and components of the general transcription machinery [].
Probab=99.84 E-value=3.8e-21 Score=141.88 Aligned_cols=50 Identities=54% Similarity=0.941 Sum_probs=49.2
Q ss_pred CCCCCCCCCCCCCCccccCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHH
Q 017508 162 KHIPSWLPAFPDPHTYIYTPMWNERKSDPRADKIELARQRRKAEMALLSL 211 (370)
Q Consensus 162 ~hIP~~LP~FP~~HTY~~TPiy~~~~tD~~~iR~k~aeq~R~~EkAL~~L 211 (370)
+|||+|||+||++|||++||+|+++++|++++|+++++|+|++|+||++|
T Consensus 1 ~~IP~~lP~fP~~HTY~~Tp~~~~~~~d~~~~r~~~~~~~r~~e~aL~~l 50 (51)
T PF10406_consen 1 SHIPDWLPPFPPPHTYKRTPIYNERETDPKKIREKAAEQSRLAEKALRKL 50 (51)
T ss_pred CCCcccCCCCCCCcccccCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 59999999999999999999999999999999999999999999999998
No 4
>cd08049 TAF8 TATA Binding Protein (TBP) Associated Factor 8. The TATA Binding Protein (TBP) Associated Factor 8 (TAF8) 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 the assembly of the preinitiation 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 TAF orthologs and paralogs. Several hypotheses are proposed for TAFs' functions, such as serving as activator-binding sites, involvement in the core-promo
Probab=99.82 E-value=1.2e-20 Score=140.72 Aligned_cols=53 Identities=64% Similarity=1.053 Sum_probs=51.2
Q ss_pred CCCCCCCCCCCCCCccccCCCCCCCCCChHHHHHHHHHHHHHHHHHHHHHHHH
Q 017508 162 KHIPSWLPAFPDPHTYIYTPMWNERKSDPRADKIELARQRRKAEMALLSLQQR 214 (370)
Q Consensus 162 ~hIP~~LP~FP~~HTY~~TPiy~~~~tD~~~iR~k~aeq~R~~EkAL~~L~~r 214 (370)
.|||+|||+||++|||++||+|.++++|++++|+++++|+|++|+||.+|+++
T Consensus 1 ~hIP~~LP~FP~~HTY~~Tp~~~~~~~d~~~~r~~~~~~~r~~e~aL~~l~~~ 53 (54)
T cd08049 1 AHIPSWLPPFPDPHTYKRTPTYSERETDPKKLREELASQRRLAEKALLRLQQK 53 (54)
T ss_pred CCCCcCCCCCCCchhhccCCCCCCCccCHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 49999999999999999999999999999999999999999999999999764
No 5
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=99.82 E-value=7.2e-20 Score=145.56 Aligned_cols=74 Identities=45% Similarity=0.646 Sum_probs=72.8
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 26 EDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 26 ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
++|++++|+++|+|||++.||++++++|+|+|+|++++||.+|++.++.||+|+||++|++.||.+||++||++
T Consensus 1 ~~~~~~ll~~~Vaqil~~~Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 1 NELAFALLRIAVAQILESAGFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred CHHHHHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999997
No 6
>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=99.81 E-value=9.9e-20 Score=144.31 Aligned_cols=74 Identities=39% Similarity=0.594 Sum_probs=72.9
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 26 EDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 26 ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
|+|++.+|+++|++||+++||++++++|||.|+|++.+||++|++.++.|||++|||+|++.||.+||++||++
T Consensus 1 ~e~~~~~l~~~va~il~~~GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 1 DEFARSLLRRSVAQILKHAGFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred CHHHHHHHHHHHHHHHHHcCccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999997
No 7
>PLN00035 histone H4; Provisional
Probab=98.82 E-value=1.5e-08 Score=85.11 Aligned_cols=79 Identities=11% Similarity=0.185 Sum_probs=70.9
Q ss_pred CchHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc-ccc
Q 017508 24 KAEDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL-KGF 102 (370)
Q Consensus 24 ~~ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~-~gf 102 (370)
..-|....|-..+|..+++..|-..++.+|.+.|.+++..|+.+|++.+..||+|++|.+++..||.+||+.+|-+ .||
T Consensus 22 ~~~d~i~~ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~lyGf 101 (103)
T PLN00035 22 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 101 (103)
T ss_pred HHHhhhccCCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCCCC
Confidence 3344455577778899999999999999999999999999999999999999999999999999999999999987 444
No 8
>PTZ00015 histone H4; Provisional
Probab=98.82 E-value=1.4e-08 Score=85.21 Aligned_cols=74 Identities=12% Similarity=0.231 Sum_probs=69.9
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 26 EDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 26 ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
-|..+.|...+|..|++..|-..++.+|.+.+.+++..|+.+|++.+..||+|++|.+++..||.+||+..|-+
T Consensus 25 r~~i~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~ 98 (102)
T PTZ00015 25 RDNIRGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRT 98 (102)
T ss_pred hhcccCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCC
Confidence 45566788999999999999999999999999999999999999999999999999999999999999998876
No 9
>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=98.68 E-value=7.8e-08 Score=78.30 Aligned_cols=73 Identities=14% Similarity=0.243 Sum_probs=68.0
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 27 DFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 27 df~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
|....+...+|..+++..|-..++..|.+.+.+++..|+.++++.+..||+|++|.+++..||.+||+.+|-+
T Consensus 9 ~~~~gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~ 81 (85)
T cd00076 9 DNIKGITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 81 (85)
T ss_pred HhhccCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCC
Confidence 4444577889999999999999999999999999999999999999999999999999999999999999966
No 10
>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=98.54 E-value=1.1e-06 Score=75.53 Aligned_cols=64 Identities=19% Similarity=0.275 Sum_probs=60.7
Q ss_pred HHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhccc
Q 017508 35 MAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEV 98 (370)
Q Consensus 35 ~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi 98 (370)
++|.+||++.|-+.+++.+...|.|++.+|..+++..+..||+|+||.+++..||.+|+...+-
T Consensus 5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 5 RVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 4789999999999999999999999999999999999999999999999999999999987554
No 11
>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=98.37 E-value=2e-06 Score=66.64 Aligned_cols=61 Identities=20% Similarity=0.183 Sum_probs=57.8
Q ss_pred HHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHH
Q 017508 34 KMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIE 94 (370)
Q Consensus 34 r~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~ 94 (370)
...|..++++.|.+.++..|.+.|.+.+..|+.++++.+..|++|++|++.+..||.+||+
T Consensus 5 ~~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 5 KETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred HHHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 3468889999999999999999999999999999999999999999999999999999984
No 12
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.33 E-value=1.5e-06 Score=71.58 Aligned_cols=66 Identities=21% Similarity=0.239 Sum_probs=62.3
Q ss_pred HHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 34 KMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 34 r~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
...|..|++.+|=+.++.+|.+.|.++++.|+.+|+..+..||.|++|.++...||.+|+..+|..
T Consensus 22 ~apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~ 87 (91)
T COG2036 22 KAPVRRILRKAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRR 87 (91)
T ss_pred chHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhccc
Confidence 456888999999999999999999999999999999999999999999999999999999998876
No 13
>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=98.21 E-value=5.5e-06 Score=72.43 Aligned_cols=61 Identities=21% Similarity=0.322 Sum_probs=52.9
Q ss_pred HHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 35 MAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 35 ~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
++|.+||++.|.+..++.+...|.|++.+|..++...|+.||+||+|+.++..||.+|...
T Consensus 16 ~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~ 76 (129)
T PF02291_consen 16 RVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQS 76 (129)
T ss_dssp HHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHH
T ss_pred HHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHH
Confidence 4889999999999999999999999999999999999999999999999999999999984
No 14
>smart00417 H4 Histone H4.
Probab=98.16 E-value=3.6e-06 Score=66.90 Aligned_cols=66 Identities=12% Similarity=0.223 Sum_probs=60.8
Q ss_pred HHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHH
Q 017508 27 DFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRG 92 (370)
Q Consensus 27 df~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~A 92 (370)
|....|...+|..|++..|-..++..+.+.+.+++..|+.++++.+-.||+|++|.+++..||..|
T Consensus 9 d~i~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 9 DNIQGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred hhhcCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 444557788999999999999999999999999999999999999999999999999999999753
No 15
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.14 E-value=1.1e-05 Score=64.36 Aligned_cols=66 Identities=20% Similarity=0.170 Sum_probs=56.1
Q ss_pred HHHHHHHHHHHHHHcCCC---cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 30 RAVSKMAVAQICESVGFQ---GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 30 r~lLr~aVaqIL~~~GF~---s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
.+-+.-.|++||++.+=. .+++.++..|++++-.|+.+++..+..||.||||+.++..||.+..+.
T Consensus 4 Kaal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rr 72 (76)
T PF15630_consen 4 KAALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARR 72 (76)
T ss_dssp HHHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT
T ss_pred HHHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhc
Confidence 455778899999998533 288999999999999999999999999999999999999999988765
No 16
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=97.96 E-value=2.1e-05 Score=64.03 Aligned_cols=76 Identities=9% Similarity=0.141 Sum_probs=70.4
Q ss_pred CchHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 24 KAEDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 24 ~~ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
+..|-...+.+.+|-.+.+..|...+.--..+....++..||+++...+..|++||.|..++..||+.+|..+|+.
T Consensus 22 ~LsDnIqgitKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 22 VLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred HHHhhccccchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 4455556666888999999999999999999999999999999999999999999999999999999999999998
No 17
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.90 E-value=0.00014 Score=64.34 Aligned_cols=62 Identities=19% Similarity=0.275 Sum_probs=59.3
Q ss_pred HHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhc
Q 017508 35 MAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDL 96 (370)
Q Consensus 35 ~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~m 96 (370)
++|++||++.|.+-.++-....|.|+..+|.+.+...|.-|++||+++.+...||.+|..-.
T Consensus 17 ~~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~ 78 (148)
T KOG3334|consen 17 RVIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMR 78 (148)
T ss_pred HHHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHH
Confidence 48899999999999999999999999999999999999999999999999999999998753
No 18
>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=97.65 E-value=0.0003 Score=54.79 Aligned_cols=61 Identities=21% Similarity=0.203 Sum_probs=51.1
Q ss_pred HHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHH
Q 017508 34 KMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIE 94 (370)
Q Consensus 34 r~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~ 94 (370)
..+|-.+.++.|+...+..+...|.+-+.--|.+|...+..|+.|++|+..+..||..||+
T Consensus 6 ~esvk~iAes~Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 6 QESVKDIAESLGISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHHHHTT---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 3467788999999999999999999999999999999999999999999999999999985
No 19
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=97.26 E-value=0.0023 Score=50.40 Aligned_cols=50 Identities=14% Similarity=0.104 Sum_probs=47.9
Q ss_pred CCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 46 FQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 46 F~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
-..++++|.+.|.+++..|+.+++..+..+|.|++|.++...||.++|+.
T Consensus 17 ~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 17 REQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred CCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 36789999999999999999999999999999999999999999999987
No 20
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=97.15 E-value=0.0023 Score=49.86 Aligned_cols=60 Identities=18% Similarity=0.121 Sum_probs=52.6
Q ss_pred HHHHHHHHHcCCC-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHH
Q 017508 35 MAVAQICESVGFQ-GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIE 94 (370)
Q Consensus 35 ~aVaqIL~~~GF~-s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~ 94 (370)
+++-.+....+.+ .++..|++.|..+++.|+.+|...|..+|.+++|.+.+..||..|++
T Consensus 13 r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 13 RLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp HHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred eeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 3445555555654 79999999999999999999999999999999999999999999975
No 21
>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=97.10 E-value=0.0021 Score=64.51 Aligned_cols=65 Identities=14% Similarity=0.131 Sum_probs=62.3
Q ss_pred HHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 35 MAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 35 ~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
..|-.|++++|.+..+..|...|.+.++.++.++++.|..|+.|++|+..+..||.+||+..++.
T Consensus 3 ~~i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 3 ESIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred hHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 36778899999999999999999999999999999999999999999999999999999999987
No 22
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.77 E-value=0.0042 Score=53.93 Aligned_cols=61 Identities=18% Similarity=0.178 Sum_probs=56.6
Q ss_pred HHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCH---HHHHHHHHh
Q 017508 35 MAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNL---FDIIRGIED 95 (370)
Q Consensus 35 ~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~---~DV~~AL~~ 95 (370)
+.|..||.+.|.+..++..--.|.+.+.+|-+++...+.-|++|+||++.+. .||.+|+.-
T Consensus 18 rlihliL~Slgi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 18 RLIHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred hHHHHHHHhcCchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 3678899999999999999999999999999999999999999999999886 999998864
No 23
>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=96.76 E-value=0.0076 Score=46.00 Aligned_cols=57 Identities=21% Similarity=0.231 Sum_probs=49.1
Q ss_pred HHHHHHHc-CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHH
Q 017508 37 VAQICESV-GFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGI 93 (370)
Q Consensus 37 VaqIL~~~-GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL 93 (370)
|-.|++.. +...++..|.+.|+..++.|+..|+..+...|+..+|...+..||..|+
T Consensus 8 vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 8 VKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 44566666 6667999999999999999999999999999999999999999999885
No 24
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=95.98 E-value=0.017 Score=59.54 Aligned_cols=61 Identities=23% Similarity=0.220 Sum_probs=43.7
Q ss_pred HHHHHHHHHHHHHHHHcCCC--cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHH
Q 017508 28 FSRAVSKMAVAQICESVGFQ--GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFD 88 (370)
Q Consensus 28 f~r~lLr~aVaqIL~~~GF~--s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~D 88 (370)
+...+.++.+...++..||. -++..||+.|...+..|+++||..+..||.||||.++...|
T Consensus 352 lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 352 LPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 34445566666677764554 48999999999999999999999999999999999998877
No 25
>smart00428 H3 Histone H3.
Probab=95.95 E-value=0.047 Score=46.32 Aligned_cols=52 Identities=25% Similarity=0.162 Sum_probs=47.4
Q ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcc
Q 017508 45 GFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLE 97 (370)
Q Consensus 45 GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mG 97 (370)
+| .++.+|++.|.+.++.|+.++...+...|.|++|.+....|+.++..--|
T Consensus 51 ~~-R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir~ 102 (105)
T smart00428 51 DL-RFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIRG 102 (105)
T ss_pred Cc-eeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHhc
Confidence 45 58899999999999999999999999999999999999999998875444
No 26
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=95.48 E-value=0.09 Score=43.52 Aligned_cols=65 Identities=20% Similarity=0.188 Sum_probs=55.3
Q ss_pred HHHHHHHHHHcCCC-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 34 KMAVAQICESVGFQ-GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 34 r~aVaqIL~~~GF~-s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
..-|.+|+-..|=. .-.+.....|.+++..||.+|+..|...|. ++|..+.+.|+..+|+.--..
T Consensus 5 ~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D~~K 70 (92)
T cd07978 5 TKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKDPKK 70 (92)
T ss_pred HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcCHHH
Confidence 34578888888876 356788999999999999999999999998 899999999999999874443
No 27
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.42 E-value=0.067 Score=48.75 Aligned_cols=66 Identities=11% Similarity=0.193 Sum_probs=58.9
Q ss_pred HHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC--------------CCCCCHHHHHHHHHhcccc
Q 017508 34 KMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLAC--------------RTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 34 r~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~ag--------------RT~p~~~DV~~AL~~mGi~ 99 (370)
..++-..|...||++..+.....+.-.++.||.+|+..|-.||..-+ +...+..|+.-||.++||+
T Consensus 89 Davt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~EyGin 168 (176)
T KOG3423|consen 89 DAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALAEYGIN 168 (176)
T ss_pred HHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHHHhCcc
Confidence 46788999999999999999888899999999999999999998754 3456789999999999998
No 28
>PLN00161 histone H3; Provisional
Probab=95.04 E-value=0.098 Score=46.25 Aligned_cols=54 Identities=19% Similarity=0.090 Sum_probs=48.6
Q ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 45 GFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 45 GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
+| .++.+||..|.+..+.||..+...+...|.|++|.+....|+.++.+--|..
T Consensus 76 ~~-Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~ 129 (135)
T PLN00161 76 PF-RWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPI 129 (135)
T ss_pred Cc-EeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhcccc
Confidence 45 4789999999999999999999999999999999999999999998655554
No 29
>PLN00160 histone H3; Provisional
Probab=94.68 E-value=0.14 Score=42.90 Aligned_cols=50 Identities=20% Similarity=0.032 Sum_probs=45.9
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcc
Q 017508 48 GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLE 97 (370)
Q Consensus 48 s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mG 97 (370)
.++.+|++.|.+..+.||..+...+...|.|++|.+..+.|+.++.+--|
T Consensus 44 Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~rirg 93 (97)
T PLN00160 44 RWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRIRG 93 (97)
T ss_pred EeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHhhc
Confidence 58899999999999999999999999999999999999999988875433
No 30
>PTZ00018 histone H3; Provisional
Probab=94.09 E-value=0.2 Score=44.46 Aligned_cols=61 Identities=25% Similarity=0.177 Sum_probs=51.1
Q ss_pred HHHHHHHH--cCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcc
Q 017508 36 AVAQICES--VGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLE 97 (370)
Q Consensus 36 aVaqIL~~--~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mG 97 (370)
.|-.|+.. .+| .++.+||+.|.+..+.||..+...+...|.|+.|.+....|+.++.+--|
T Consensus 71 LVREI~~~~~~~~-rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg 133 (136)
T PTZ00018 71 LVREIAQDFKTDL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
T ss_pred HHHHHHHHcCCcc-eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhcc
Confidence 34444443 355 68899999999999999999999999999999999999999988875433
No 31
>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=94.07 E-value=0.06 Score=44.51 Aligned_cols=61 Identities=16% Similarity=0.126 Sum_probs=30.1
Q ss_pred HHHHHHHcCCC-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcc
Q 017508 37 VAQICESVGFQ-GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLE 97 (370)
Q Consensus 37 VaqIL~~~GF~-s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mG 97 (370)
|.+|+-..|=. .-.+.....+.+++..||.+++..|..+|...||..+.+.|+..+|+.-.
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D~ 68 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKDP 68 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC-----------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcCH
Confidence 56777766653 46678888999999999999999999999999999999999999998743
No 32
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=93.91 E-value=0.23 Score=52.76 Aligned_cols=65 Identities=20% Similarity=0.169 Sum_probs=60.0
Q ss_pred HHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 35 MAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 35 ~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
..+--+.++.|...+...|...|++-+..-|.+|++.+..|+.|+-|+..++.||..||+-.++.
T Consensus 15 Es~k~vAEslGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVe 79 (576)
T KOG2549|consen 15 ESVKVVAESLGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVE 79 (576)
T ss_pred HHHHHHHHHhCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccc
Confidence 34556678899999999999999999999999999999999999999999999999999998776
No 33
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=93.85 E-value=0.27 Score=44.85 Aligned_cols=73 Identities=15% Similarity=0.160 Sum_probs=64.0
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 26 EDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 26 ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
..|..+++.+.|-..|.... -+++..|+..|..-+.=|+..|...+..+|.-+.|..++..||..||.+|+.+
T Consensus 9 l~lP~AiI~rlvke~l~E~~-vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs 81 (172)
T KOG0870|consen 9 LNLPNAIITRLVKEVLPESN-VSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFS 81 (172)
T ss_pred hhccHHHHHHHHHHhCcccc-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchH
Confidence 45667778888888887752 35889999999999999999999999999999999999999999999999987
No 34
>PLN00121 histone H3; Provisional
Probab=93.75 E-value=0.29 Score=43.41 Aligned_cols=52 Identities=25% Similarity=0.144 Sum_probs=47.3
Q ss_pred CCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcc
Q 017508 45 GFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLE 97 (370)
Q Consensus 45 GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mG 97 (370)
+| .++.+||+.|.+..+.||..+...+...|.|+.|.+....|+.++.+--|
T Consensus 82 ~~-Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg 133 (136)
T PLN00121 82 DL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
T ss_pred cc-eeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHhcc
Confidence 55 68899999999999999999999999999999999999999988875433
No 35
>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=93.59 E-value=0.33 Score=36.12 Aligned_cols=44 Identities=18% Similarity=0.189 Sum_probs=40.1
Q ss_pred HHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 017508 35 MAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANL 78 (370)
Q Consensus 35 ~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~ 78 (370)
.++..+|+.+||++..+.....+.-.++.||.+++..+..||.+
T Consensus 6 ~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 6 EVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred HHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46788999999999999999999999999999999999999865
No 36
>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=92.66 E-value=0.41 Score=41.29 Aligned_cols=58 Identities=5% Similarity=-0.086 Sum_probs=51.8
Q ss_pred HHHHHH-cCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 38 AQICES-VGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 38 aqIL~~-~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
-.+|+. .+...++.+|.-.|+.+++.+..+|...+-.+|.+.+|..+++.||.+|+..
T Consensus 27 ~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 27 HRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred HHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 445555 6778899999999999999999999999999999999999999999988865
No 37
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=90.10 E-value=1.3 Score=40.26 Aligned_cols=64 Identities=14% Similarity=0.119 Sum_probs=54.9
Q ss_pred HHHHHHHHcC-C-CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 36 AVAQICESVG-F-QGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 36 aVaqIL~~~G-F-~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
-|+.|.+..= = --+...|-|++.+.+.+||.=+...|..-|+.-.|.++|-.||..||..+|+.
T Consensus 37 NV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe 102 (168)
T KOG0869|consen 37 NVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFE 102 (168)
T ss_pred HHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcH
Confidence 4666666421 1 12678999999999999999999999999999999999999999999999987
No 38
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.08 E-value=1 Score=43.83 Aligned_cols=56 Identities=20% Similarity=0.173 Sum_probs=49.5
Q ss_pred cCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh-cccc
Q 017508 44 VGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED-LEVL 99 (370)
Q Consensus 44 ~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~-mGi~ 99 (370)
.|=....+.+-|.|.+++..|+.+|...+...|-|-.-..+-+.||.+.|+. ++|.
T Consensus 168 d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~ 224 (258)
T KOG1142|consen 168 DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNME 224 (258)
T ss_pred cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeecccccc
Confidence 4455678899999999999999999999999999988888899999999987 5666
No 39
>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=88.00 E-value=1.8 Score=33.85 Aligned_cols=48 Identities=13% Similarity=0.097 Sum_probs=41.0
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 48 GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 48 s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
...+.+-+.|.+++..|+.++...+...|-|-+=.++.+.||.+.|+.
T Consensus 17 ~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 17 KLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 467899999999999999999999999999988888999999999986
No 40
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=87.85 E-value=2 Score=43.19 Aligned_cols=69 Identities=25% Similarity=0.227 Sum_probs=61.2
Q ss_pred HHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc--ccccc
Q 017508 36 AVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL--KGFMG 104 (370)
Q Consensus 36 aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~--~gf~~ 104 (370)
.|-...++.|...+...++..|.-=++--|.+++..+..|+-|+.||..+..||..||+-+++. .|+.+
T Consensus 10 t~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVePLyGyd~ 80 (450)
T COG5095 10 TLKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVEPLYGYDP 80 (450)
T ss_pred HHHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCCcccCCCC
Confidence 4556677889999999999999888888899999999999999999999999999999999987 35444
No 41
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=85.28 E-value=1.9 Score=39.39 Aligned_cols=45 Identities=16% Similarity=0.205 Sum_probs=39.0
Q ss_pred HHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 017508 34 KMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANL 78 (370)
Q Consensus 34 r~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~ 78 (370)
..++--.|...||.++....-..|.-+++.|+.+|+..+-.|..+
T Consensus 91 d~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrI 135 (197)
T COG5162 91 DSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRI 135 (197)
T ss_pred HHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667789999999999888888889999999999999998766
No 42
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=85.26 E-value=2.5 Score=35.96 Aligned_cols=67 Identities=15% Similarity=0.162 Sum_probs=49.1
Q ss_pred HHHHHHHHHHHHHHHcCCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhccc
Q 017508 29 SRAVSKMAVAQICESVGFQG-FKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEV 98 (370)
Q Consensus 29 ~r~lLr~aVaqIL~~~GF~s-~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi 98 (370)
...+...-+..|+-..|=+. --+..++.|.+++..||.++...+ .+...|...-+.|+..+|+.=-.
T Consensus 7 rk~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a---~~~g~rgk~~veD~~f~lRkDpk 74 (109)
T KOG3901|consen 7 RKHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAA---MEIGKRGKVKVEDFKFLLRKDPK 74 (109)
T ss_pred HHHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHH---HHhcccCceeHHHHHHHHHhChH
Confidence 44566666666766555442 235688999999999999995544 45568889999999999987433
No 43
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=83.62 E-value=3.7 Score=36.94 Aligned_cols=67 Identities=12% Similarity=0.188 Sum_probs=56.7
Q ss_pred HHHHHHHHHHHHH-HcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 30 RAVSKMAVAQICE-SVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 30 r~lLr~aVaqIL~-~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
++-+...|.-||- .+ .+...|-|.|.+....||..|++.+...|+-..+.++.+..|..||+.+|..
T Consensus 15 kAtv~KmIke~lP~d~---rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~ 82 (156)
T KOG0871|consen 15 KATVNKMIKEMLPKDV---RVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFG 82 (156)
T ss_pred HHHHHHHHHHhCCccc---ccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchH
Confidence 4445556666655 22 3557899999999999999999999999999999999999999999999987
No 44
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=75.85 E-value=8.4 Score=33.14 Aligned_cols=65 Identities=12% Similarity=0.049 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHcCCCc-ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 33 SKMAVAQICESVGFQG-FKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 33 Lr~aVaqIL~~~GF~s-~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
.-.-|..++-..|=.. -.+...+.|-+++..||..++..++..|. .|...-..|+..||++=-+.
T Consensus 11 F~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~DpkK 76 (126)
T COG5248 11 FMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRRDPKK 76 (126)
T ss_pred HHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhhChHH
Confidence 3445666777666443 33567788999999999999999999987 68888999999999985554
No 45
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=72.30 E-value=2.1 Score=38.05 Aligned_cols=49 Identities=27% Similarity=0.177 Sum_probs=45.3
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcc
Q 017508 49 FKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLE 97 (370)
Q Consensus 49 ~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mG 97 (370)
++..|+.+|.+..+.||..|...+...|-||.|.++-+.|+.+|.+-.|
T Consensus 86 fqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 86 FQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred ehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 6789999999999999999999999999999999999999998876544
No 46
>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=72.20 E-value=12 Score=34.98 Aligned_cols=75 Identities=12% Similarity=0.053 Sum_probs=58.9
Q ss_pred CchHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC------CCCHHHHHHHHHhcc
Q 017508 24 KAEDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRT------ECNLFDIIRGIEDLE 97 (370)
Q Consensus 24 ~~ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT------~p~~~DV~~AL~~mG 97 (370)
...-|-...|..-|..|+...|+..+.+..++.|...++.||.+|...+...|+|-... .....||...|..+.
T Consensus 41 ~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~ 120 (212)
T cd08045 41 DPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLE 120 (212)
T ss_pred hhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHH
Confidence 33445566888899999999999899999999999999999999999999999984222 233566666665554
Q ss_pred c
Q 017508 98 V 98 (370)
Q Consensus 98 i 98 (370)
.
T Consensus 121 ~ 121 (212)
T cd08045 121 Q 121 (212)
T ss_pred H
Confidence 4
No 47
>smart00427 H2B Histone H2B.
Probab=67.70 E-value=40 Score=27.93 Aligned_cols=49 Identities=10% Similarity=0.130 Sum_probs=44.4
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhc
Q 017508 48 GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDL 96 (370)
Q Consensus 48 s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~m 96 (370)
+++..|+..+..++...++.|+..+...+....|.+.+..+|..|.+.+
T Consensus 19 giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 19 GISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 3678899999999999999999999999999999999999999998764
No 48
>PTZ00463 histone H2B; Provisional
Probab=66.61 E-value=39 Score=29.37 Aligned_cols=48 Identities=8% Similarity=0.121 Sum_probs=44.0
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhc
Q 017508 49 FKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDL 96 (370)
Q Consensus 49 ~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~m 96 (370)
++..|+..+..++...++.|+..+...|....|.+.+..||..|.+.+
T Consensus 47 IS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 47 ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 678899999999999999999999999999999999999999998754
No 49
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=66.44 E-value=15 Score=32.37 Aligned_cols=69 Identities=16% Similarity=0.229 Sum_probs=54.1
Q ss_pred CchHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhc
Q 017508 24 KAEDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDL 96 (370)
Q Consensus 24 ~~ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~m 96 (370)
..+.|...+-+ +.-|.+-..| +...|+..+...+-..+..|+..+.+++..-+|...+..++..|++.+
T Consensus 35 ~~e~~s~yv~k-vlk~Vhpd~g---is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 35 RKESYSEYVYK-VLKQVHPDLG---ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ccCceeeehhh-hhhcccCCCC---cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 34444444433 4445555555 778899999888888999999999999999999999999999999875
No 50
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=65.64 E-value=42 Score=35.90 Aligned_cols=69 Identities=23% Similarity=0.359 Sum_probs=55.1
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhCCCCCCHHHHHHHHH
Q 017508 26 EDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIR-----------YICDLGKTSSFQANLACRTECNLFDIIRGIE 94 (370)
Q Consensus 26 ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~-----------YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~ 94 (370)
++-....+ ..|+.+|+..|.-..+.+|+..|.+...+ .|.+|.+.|..||...+...++..||..|++
T Consensus 426 ~e~~~~~~-~~i~~~~~~~~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~ 504 (509)
T PF13654_consen 426 EENIRQYA-RFIASICQKEGLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIE 504 (509)
T ss_dssp HHHHHHHH-HHHHHHHHHHSS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHH
T ss_pred HHHHHHHH-HHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Confidence 44444444 48999999999999999999999887765 6889999999999999999999999999997
Q ss_pred h
Q 017508 95 D 95 (370)
Q Consensus 95 ~ 95 (370)
.
T Consensus 505 ~ 505 (509)
T PF13654_consen 505 E 505 (509)
T ss_dssp H
T ss_pred c
Confidence 5
No 51
>PLN00158 histone H2B; Provisional
Probab=64.14 E-value=47 Score=28.85 Aligned_cols=56 Identities=9% Similarity=0.128 Sum_probs=47.8
Q ss_pred HHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhc
Q 017508 38 AQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDL 96 (370)
Q Consensus 38 aqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~m 96 (370)
-|+.-..| ++..|+..+..++...++.|+..+...+....|.+.+..+|..|.+.+
T Consensus 38 KQVhPd~g---IS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 38 KQVHPDTG---ISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred HHhCCCCC---ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 35555555 467899999999999999999999999999999999999999998764
No 52
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=62.96 E-value=39 Score=29.87 Aligned_cols=68 Identities=18% Similarity=0.243 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 30 RAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 30 r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
.+-.+..|..||-. . -.++..|-|.|.+..+.||.-|...|...|+--...++....|+.||+.++..
T Consensus 14 KATVqKMvS~iLp~-d-l~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~ 81 (148)
T COG5150 14 KATVQKMVSSILPK-D-LVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFE 81 (148)
T ss_pred HHHHHHHHHHhccc-c-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHH
Confidence 44556777888764 2 23567899999999999999999999999999999999999999999999887
No 53
>PLN00154 histone H2A; Provisional
Probab=59.25 E-value=29 Score=30.87 Aligned_cols=58 Identities=5% Similarity=-0.160 Sum_probs=47.6
Q ss_pred HHHHHHcC-C-CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 38 AQICESVG-F-QGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 38 aqIL~~~G-F-~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
..+|++-. + ..+..+|.-.|+.+++-...+|...+-.+|.-.+++.+++.+|.+|++.
T Consensus 45 ~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 45 HRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred HHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 44577655 3 4788889999999887777799999999999999999999999888754
No 54
>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=58.62 E-value=42 Score=31.40 Aligned_cols=65 Identities=18% Similarity=0.192 Sum_probs=51.9
Q ss_pred HHHHHHHHHHHcCCC---cccHHHHHHHHHHHHH---HHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcc
Q 017508 33 SKMAVAQICESVGFQ---GFKDSALDALSDIAIR---YICDLGKTSSFQANLACRTECNLFDIIRGIEDLE 97 (370)
Q Consensus 33 Lr~aVaqIL~~~GF~---s~~~sALe~Ltdl~~~---YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mG 97 (370)
++..+...+...|+. .+++.+++.|.++..- +|+.++..+-..+-..+-..++..||..++.++.
T Consensus 197 ~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~ 267 (269)
T TIGR03015 197 TREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEID 267 (269)
T ss_pred HHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhh
Confidence 344556667777862 4788999999988875 8889999988887778888999999999998754
No 55
>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=55.69 E-value=26 Score=27.72 Aligned_cols=58 Identities=10% Similarity=0.095 Sum_probs=47.2
Q ss_pred HHHHHHHHcCCC----cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCC-CCHHHHHHHHH
Q 017508 36 AVAQICESVGFQ----GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTE-CNLFDIIRGIE 94 (370)
Q Consensus 36 aVaqIL~~~GF~----s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~-p~~~DV~~AL~ 94 (370)
.|+.||+ ..|. .++..|+..+++.+.-|+.+-...+..-++..|.+. ..+.|+...+-
T Consensus 4 li~rll~-~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 4 LIARLLH-EHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp HHHHHHC-TTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred HHHHHHH-HHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 5788888 7786 588899999999999999999999999899999888 88899876543
No 56
>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=53.28 E-value=23 Score=34.28 Aligned_cols=54 Identities=11% Similarity=0.138 Sum_probs=38.2
Q ss_pred HHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCC
Q 017508 29 SRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRT 82 (370)
Q Consensus 29 ~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT 82 (370)
-..+|..-|..|+...|-..+.+..++.|...++.||.+|...+...|.|-..+
T Consensus 45 ~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 45 NPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp -HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred CHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 355788889999999998889999999999999999999999999999884444
No 57
>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=52.01 E-value=90 Score=25.43 Aligned_cols=65 Identities=14% Similarity=0.120 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCC--CCC-CHHHHHHHHHhc
Q 017508 28 FSRAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACR--TEC-NLFDIIRGIEDL 96 (370)
Q Consensus 28 f~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agR--T~p-~~~DV~~AL~~m 96 (370)
|....+++.|.+++. .++++.....|.-+..-|+.+|...|....+.-+. +.| .+..|..|++.+
T Consensus 17 f~k~~iKr~~~~~~~----~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 17 FPKAAIKRLIQSVTG----QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred ccHHHHHHHHHHHcC----CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 444455555555543 67889999999999999999999999998888776 344 477788877654
No 58
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=45.62 E-value=1.5e+02 Score=29.61 Aligned_cols=51 Identities=22% Similarity=0.272 Sum_probs=43.3
Q ss_pred cccHHHHHHHHHHH------HHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhccc
Q 017508 48 GFKDSALDALSDIA------IRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEV 98 (370)
Q Consensus 48 s~~~sALe~Ltdl~------~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi 98 (370)
.+...+++.+...+ .+++.+++..|..+|...++..++..||..|+..+..
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~ 284 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEI 284 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHH
Confidence 57889999999988 5667788888888888888999999999999998743
No 59
>smart00414 H2A Histone 2A.
Probab=35.89 E-value=1.1e+02 Score=25.92 Aligned_cols=49 Identities=8% Similarity=-0.041 Sum_probs=42.7
Q ss_pred CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 47 QGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 47 ~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
..+..+|.-.|+.+++-...+|...+-.+|.-.++...++.|+.+|...
T Consensus 26 ~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 26 KRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred cccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 3688889999999998888899998888999999999999999888754
No 60
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=34.89 E-value=11 Score=38.17 Aligned_cols=61 Identities=13% Similarity=0.025 Sum_probs=51.2
Q ss_pred chhhhhhhHHHHhhhcCCccCCCCCcc-cCCCCCCceeeeeecCcchhhhhhhhhhhhhCCC
Q 017508 275 SVMEAFAPAIEAVKVSGFSDDADGDRR-YLPEKRPAVHFKFRAGKKFLGEILDSSLQKKGGR 335 (370)
Q Consensus 275 ~~~e~fa~a~~~~~~~~~~~~~~~~~~-~~~~~r~~~~~k~~~~k~~~~~~~~~~~~~~~~~ 335 (370)
++|++.|+.-.+.++.......+-+|+ ++..+-.+++|||++.+.+.|++.+.-.++|...
T Consensus 276 p~l~~~a~~e~~~~k~v~~~t~d~ek~~~~~~~~~l~~~k~~~~~~s~~~~~~~ed~~kr~k 337 (353)
T KOG2389|consen 276 PILVPQASMEPATNKPVVGATVDIEKAPFLLAEPALLVEKKTERQFSEGPSSSREDQEKRPK 337 (353)
T ss_pred cccccccccccccCcccccchhhhhhchhhcccchhhhhhhcccccccccccchhhhhcchh
Confidence 889999999888887888777776666 6889999999999999999999999966555543
No 61
>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=33.33 E-value=3e+02 Score=30.13 Aligned_cols=63 Identities=16% Similarity=0.106 Sum_probs=50.9
Q ss_pred HHHHHHHHHHcC-CCcccHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhc
Q 017508 34 KMAVAQICESVG-FQGFKDSALDALSDIAI-------------RYICDLGKTSSFQANLACRTECNLFDIIRGIEDL 96 (370)
Q Consensus 34 r~aVaqIL~~~G-F~s~~~sALe~Ltdl~~-------------~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~m 96 (370)
-..|++.|+..| +..++.+|++.|.+-.. +.|.+|.+.+..+|...+...++..||..|++..
T Consensus 315 ~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 315 VQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 447778777774 77789999999976444 5677888888888888899999999999998864
No 62
>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=32.77 E-value=1.2e+02 Score=29.01 Aligned_cols=43 Identities=19% Similarity=0.096 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHH
Q 017508 32 VSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSF 74 (370)
Q Consensus 32 lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~ 74 (370)
.|+.=+-.||...|.++++..|.+.|.-.++.||.+|...+-.
T Consensus 207 ~L~~Rm~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~ 249 (252)
T PF12767_consen 207 SLRKRMEQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLD 249 (252)
T ss_pred HHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5666677899999999999999999999999999999988754
No 63
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=30.10 E-value=1.7e+02 Score=28.87 Aligned_cols=63 Identities=14% Similarity=-0.012 Sum_probs=47.7
Q ss_pred HHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC-CCCCCHHHHHHHHHh
Q 017508 32 VSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLAC-RTECNLFDIIRGIED 95 (370)
Q Consensus 32 lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~ag-RT~p~~~DV~~AL~~ 95 (370)
-+...|.+.|+..|.. +++.|++.|.+.+..=+..+.......+-.++ ...++..||...+..
T Consensus 146 ~l~~~i~~~~~~~g~~-i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~ 209 (343)
T PRK06585 146 DLARLIDDELAEAGLR-ITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGD 209 (343)
T ss_pred HHHHHHHHHHHHCCCC-CCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Confidence 3455789999999999 68899999999998766666666665555543 456889998777654
No 64
>PLN00156 histone H2AX; Provisional
Probab=28.91 E-value=1.3e+02 Score=26.88 Aligned_cols=57 Identities=9% Similarity=-0.027 Sum_probs=44.0
Q ss_pred HHHHHcCCC-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 39 QICESVGFQ-GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 39 qIL~~~GF~-s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
..|+...|. .+...|.-.|+.+++-...+|...+-..|.-.+++.+++.++.+|.+.
T Consensus 37 R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 37 RFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred HHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 445554343 577788888888887777788888888888889999999999888754
No 65
>PRK09087 hypothetical protein; Validated
Probab=27.42 E-value=4.5e+02 Score=24.62 Aligned_cols=63 Identities=5% Similarity=-0.119 Sum_probs=46.7
Q ss_pred HHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHH---HHHHHHHhhCCCCCCHHHHHHHHHhcc
Q 017508 33 SKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGK---TSSFQANLACRTECNLFDIIRGIEDLE 97 (370)
Q Consensus 33 Lr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~---~a~~yAe~agRT~p~~~DV~~AL~~mG 97 (370)
+..++-+.++..|+. +++.+++.|..-+.+=+..+-. .+..++...+|. ++...+..+|.+++
T Consensus 158 ~~~iL~~~~~~~~~~-l~~ev~~~La~~~~r~~~~l~~~l~~L~~~~~~~~~~-it~~~~~~~l~~~~ 223 (226)
T PRK09087 158 LSQVIFKLFADRQLY-VDPHVVYYLVSRMERSLFAAQTIVDRLDRLALERKSR-ITRALAAEVLNEMG 223 (226)
T ss_pred HHHHHHHHHHHcCCC-CCHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHhhc
Confidence 344555666777887 6789999999888776666664 555677776766 89999999998764
No 66
>PLN00153 histone H2A; Provisional
Probab=24.96 E-value=2.7e+02 Score=24.61 Aligned_cols=57 Identities=9% Similarity=-0.026 Sum_probs=43.9
Q ss_pred HHHHHcCC-CcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 39 QICESVGF-QGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 39 qIL~~~GF-~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
..|+.-.| ..+...|.-.|+-+++-...+|...+-..|.-.+++.+++..+.+|...
T Consensus 32 R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 32 RYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred HHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 34544333 3577788888888888877888888888888889999999999887753
No 67
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=24.63 E-value=3.1e+02 Score=26.50 Aligned_cols=63 Identities=19% Similarity=0.124 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhc
Q 017508 33 SKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDL 96 (370)
Q Consensus 33 Lr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~m 96 (370)
+...|.+.|+..|.. +++.|++.|.+.+..=+..+-..+...+..++=...+..||...+-..
T Consensus 151 ~~~~i~~~~~~~g~~-i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~ 213 (340)
T PRK05574 151 LPQWIQQRLKQQGLQ-IDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPDS 213 (340)
T ss_pred HHHHHHHHHHHcCCC-CCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhh
Confidence 455788999999998 678999999999876666666666666655532228999988776553
No 68
>PTZ00017 histone H2A; Provisional
Probab=23.91 E-value=1.8e+02 Score=25.83 Aligned_cols=48 Identities=10% Similarity=-0.039 Sum_probs=42.6
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 48 GFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 48 s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
.+...|.-.|+-+++-...+|...+-.+|.-.+++.+++.++.+|+..
T Consensus 45 RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 45 RVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred cccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 577888889999998888899999999999999999999999888754
No 69
>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=23.76 E-value=4.6e+02 Score=25.67 Aligned_cols=52 Identities=15% Similarity=0.075 Sum_probs=41.9
Q ss_pred cccHHHHHHHHHHHH------HHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 48 GFKDSALDALSDIAI------RYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 48 s~~~sALe~Ltdl~~------~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
.+...+++.+.+++. ++..+++..+..+|...++..++..||..|+..+..+
T Consensus 220 ~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~ 277 (365)
T TIGR02928 220 VLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKD 277 (365)
T ss_pred CCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Confidence 367788888877764 5777788888888888888899999999999887544
No 70
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=23.36 E-value=2.9e+02 Score=26.87 Aligned_cols=62 Identities=13% Similarity=0.055 Sum_probs=49.9
Q ss_pred HHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhh--CCCCCCHHHHHHHHHh
Q 017508 33 SKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLA--CRTECNLFDIIRGIED 95 (370)
Q Consensus 33 Lr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~a--gRT~p~~~DV~~AL~~ 95 (370)
+..-|.+.++..|.. +++.|++.|.+.+..=+..+...+...+..+ .+..++..||......
T Consensus 135 l~~~i~~~~~~~g~~-i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~~ 198 (326)
T PRK07452 135 LKQLVERTAQELGVK-LTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVSN 198 (326)
T ss_pred HHHHHHHHHHHcCCC-CCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhcc
Confidence 566788999999999 7889999999999887777777777777663 3667889998877654
No 71
>PRK05907 hypothetical protein; Provisional
Probab=22.87 E-value=2.3e+02 Score=28.22 Aligned_cols=64 Identities=6% Similarity=-0.105 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHHcCCCcccHHHHHHHHHHH-HHHHHHHHHHHHHHHHhhC-CCCCCHHHHHHHHHh
Q 017508 31 AVSKMAVAQICESVGFQGFKDSALDALSDIA-IRYICDLGKTSSFQANLAC-RTECNLFDIIRGIED 95 (370)
Q Consensus 31 ~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~-~~YL~~L~~~a~~yAe~ag-RT~p~~~DV~~AL~~ 95 (370)
.-|..-|.+.++..|.. +++.|++.|.+.+ ..-|..+.......+..+| +..++..||.....+
T Consensus 137 ~~L~~Wi~~~~~~~g~~-i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv~~ 202 (311)
T PRK05907 137 KRIAQLLIQRAKELGIS-CSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFVVK 202 (311)
T ss_pred HHHHHHHHHHHHHcCCC-cCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHhcC
Confidence 34567889999999998 6789999999988 4777788888888777755 777889998876544
No 72
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=22.75 E-value=2.8e+02 Score=26.70 Aligned_cols=63 Identities=16% Similarity=0.097 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcc
Q 017508 32 VSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIEDLE 97 (370)
Q Consensus 32 lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mG 97 (370)
-+...+..+|+..|.. +++.|++.|......-+..+...+..++. +...++..||..++.+..
T Consensus 188 ~~~~~l~~~~~~~~~~-~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~~ 250 (337)
T PRK12402 188 ELVDVLESIAEAEGVD-YDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDVG 250 (337)
T ss_pred HHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCCC
Confidence 3466677788889987 67899999998887777777777776662 334688999988776533
No 73
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=22.18 E-value=2e+02 Score=30.18 Aligned_cols=70 Identities=23% Similarity=0.300 Sum_probs=56.9
Q ss_pred hHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHH----HHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhc
Q 017508 26 EDFSRAVSKMAVAQICESVGFQGFKDSALDALSDIA----IRYICDLGKTSSFQANLACRTECNLFDIIRGIEDL 96 (370)
Q Consensus 26 ddf~r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~----~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~m 96 (370)
--|.+.-++-+|..-++..+.. .+.+|||.|+++- .+|-.+|..-+...|...|+..+...||..|.+.+
T Consensus 359 ~py~~~EireIi~iRa~ee~i~-l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~lF 432 (450)
T COG1224 359 RPYSREEIREIIRIRAKEEDIE-LSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKELF 432 (450)
T ss_pred CCCCHHHHHHHHHHhhhhhccc-cCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHHH
Confidence 3444555566666778888888 4679999999875 47999999999999999999999999999998764
No 74
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=21.08 E-value=4.4e+02 Score=24.92 Aligned_cols=65 Identities=12% Similarity=0.125 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 30 RAVSKMAVAQICESVGFQGFKDSALDALSDIAIRYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 30 r~lLr~aVaqIL~~~GF~s~~~sALe~Ltdl~~~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
..-+...|..+++..|.+ +++.|++.|.+.+..=+..+...+...+..++-...+..||...+..
T Consensus 113 ~~~~~~~i~~~~~~~g~~-i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 113 EQELPRWIQARLKKLGLR-IDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred HHHHHHHHHHHHHHcCCC-CCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 334556788999999998 67899999988886544444444444444333335888888877654
No 75
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=20.96 E-value=2.7e+02 Score=28.42 Aligned_cols=48 Identities=19% Similarity=0.068 Sum_probs=36.9
Q ss_pred cccHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 48 GFKDSALDALSDIAIRY-------ICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 48 s~~~sALe~Ltdl~~~Y-------L~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
.++...++.+++++... -.-+.+.|+.+|-+.||..++..||..+...
T Consensus 267 ~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~ 321 (350)
T CHL00081 267 EIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITL 321 (350)
T ss_pred ccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 35666777777776642 2356788999999999999999999877765
No 76
>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=20.86 E-value=5.3e+02 Score=28.21 Aligned_cols=49 Identities=18% Similarity=0.228 Sum_probs=39.6
Q ss_pred cccHHHHHHHHHHHHHH-------HHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhc
Q 017508 48 GFKDSALDALSDIAIRY-------ICDLGKTSSFQANLACRTECNLFDIIRGIEDL 96 (370)
Q Consensus 48 s~~~sALe~Ltdl~~~Y-------L~~L~~~a~~yAe~agRT~p~~~DV~~AL~~m 96 (370)
.+...+++.|.+++..+ ...+.+.|+.+|-+.||+.++..||..|++..
T Consensus 249 ~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~lv 304 (633)
T TIGR02442 249 RISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAELV 304 (633)
T ss_pred CCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHH
Confidence 45677888888877653 23577888999999999999999999988764
No 77
>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=20.59 E-value=3.4e+02 Score=29.09 Aligned_cols=61 Identities=20% Similarity=0.125 Sum_probs=42.8
Q ss_pred HHHHHHHHHHcCCCcccHHHHHHHHHHHH--HHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHh
Q 017508 34 KMAVAQICESVGFQGFKDSALDALSDIAI--RYICDLGKTSSFQANLACRTECNLFDIIRGIED 95 (370)
Q Consensus 34 r~aVaqIL~~~GF~s~~~sALe~Ltdl~~--~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~ 95 (370)
...+-..|+..|+. ++..|++.|..-.. +.+.++.+.+..+|...+|...+..||..++..
T Consensus 269 ~~Il~~~a~k~~i~-is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~ 331 (531)
T TIGR02902 269 KEIAKNAAEKIGIN-LEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAEN 331 (531)
T ss_pred HHHHHHHHHHcCCC-cCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCC
Confidence 33445667778876 57788887755432 566677777777777778888889998888753
No 78
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=20.28 E-value=5e+02 Score=25.43 Aligned_cols=65 Identities=11% Similarity=-0.008 Sum_probs=48.5
Q ss_pred HHHHHHHHHHcCCCcccHHHHHHHHHHHH---HHHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHhcccc
Q 017508 34 KMAVAQICESVGFQGFKDSALDALSDIAI---RYICDLGKTSSFQANLACRTECNLFDIIRGIEDLEVL 99 (370)
Q Consensus 34 r~aVaqIL~~~GF~s~~~sALe~Ltdl~~---~YL~~L~~~a~~yAe~agRT~p~~~DV~~AL~~mGi~ 99 (370)
..++...+...|.. +++.+++.|..... +.+..+...+..|+...+...++..++..++..+++.
T Consensus 186 ~~il~~~~~~~~~~-~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~ 253 (328)
T PRK00080 186 EKIVKRSARILGVE-IDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVD 253 (328)
T ss_pred HHHHHHHHHHcCCC-cCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 34445556666777 57788988887764 4566777777778877666789999999999988776
No 79
>COG0299 PurN Folate-dependent phosphoribosylglycinamide formyltransferase PurN [Nucleotide transport and metabolism]
Probab=20.10 E-value=34 Score=32.35 Aligned_cols=15 Identities=53% Similarity=0.789 Sum_probs=13.3
Q ss_pred CCCCCCCCCCCcccc
Q 017508 165 PSWLPAFPDPHTYIY 179 (370)
Q Consensus 165 P~~LP~FP~~HTY~~ 179 (370)
|+.||.||..||+.+
T Consensus 109 PSLLP~f~G~h~~~~ 123 (200)
T COG0299 109 PSLLPAFPGLHAHEQ 123 (200)
T ss_pred cccccCCCCchHHHH
Confidence 788999999999765
Done!