Query 023473
Match_columns 281
No_of_seqs 154 out of 296
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 04:18:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023473.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023473hhsearch_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 1.7E-35 3.7E-40 279.2 14.7 208 22-236 18-226 (353)
2 KOG4336 TBP-associated transcr 99.9 2.4E-26 5.3E-31 214.1 13.5 142 33-193 5-150 (323)
3 smart00576 BTP Bromodomain tra 99.9 1.6E-22 3.4E-27 155.2 10.4 74 28-101 1-74 (77)
4 PF07524 Bromo_TP: Bromodomain 99.9 6.1E-22 1.3E-26 151.2 10.3 74 28-101 1-74 (77)
5 PF10406 TAF8_C: Transcription 98.9 1.1E-09 2.5E-14 78.4 2.7 28 166-193 1-28 (51)
6 cd08049 TAF8 TATA Binding Prot 98.8 1.4E-09 3.1E-14 78.6 2.5 27 166-192 1-27 (54)
7 cd07979 TAF9 TATA Binding Prot 98.8 4.3E-08 9.4E-13 81.2 11.3 94 37-142 5-98 (117)
8 PF02291 TFIID-31kDa: Transcri 98.6 2.1E-07 4.6E-12 78.6 8.0 90 37-139 16-106 (129)
9 cd00076 H4 Histone H4, one of 98.5 8E-07 1.7E-11 70.2 8.3 68 33-100 13-80 (85)
10 PLN00035 histone H4; Provision 98.5 1E-06 2.2E-11 71.9 8.9 71 34-104 30-101 (103)
11 PTZ00015 histone H4; Provision 98.4 1E-06 2.2E-11 71.8 7.9 69 32-100 29-97 (102)
12 smart00803 TAF TATA box bindin 98.4 1.8E-06 3.9E-11 64.8 7.8 60 37-96 6-65 (65)
13 COG2036 HHT1 Histones H3 and H 98.3 2.2E-06 4.8E-11 68.5 7.0 65 36-100 22-86 (91)
14 PF15630 CENP-S: Kinetochore c 98.1 1.3E-05 2.9E-10 62.0 7.5 66 32-97 4-72 (76)
15 KOG3334 Transcription initiati 98.1 6.3E-05 1.4E-09 64.6 11.3 95 37-143 17-111 (148)
16 smart00417 H4 Histone H4. 97.9 2.3E-05 5.1E-10 60.4 5.3 63 32-94 12-74 (74)
17 PF02969 TAF: TATA box binding 97.8 0.00017 3.6E-09 54.6 8.1 61 36-96 6-66 (66)
18 cd07981 TAF12 TATA Binding Pro 97.4 0.0014 2.9E-08 49.9 8.7 52 47-98 16-67 (72)
19 cd08050 TAF6 TATA Binding Prot 97.4 0.0011 2.3E-08 64.0 9.7 69 37-105 3-73 (343)
20 PF00125 Histone: Core histone 97.3 0.00099 2.1E-08 49.9 7.3 60 37-96 13-73 (75)
21 COG5094 TAF9 Transcription ini 97.2 0.0028 6.1E-08 53.6 9.5 62 37-98 18-82 (145)
22 KOG3467 Histone H4 [Chromatin 96.9 0.0053 1.2E-07 49.1 7.5 69 33-101 29-97 (103)
23 PF00808 CBFD_NFYB_HMF: Histon 96.8 0.006 1.3E-07 44.8 7.0 57 39-95 8-65 (65)
24 cd07978 TAF13 The TATA Binding 96.3 0.024 5.1E-07 45.4 8.0 62 36-98 5-67 (92)
25 smart00428 H3 Histone H3. 96.1 0.03 6.4E-07 46.0 7.5 51 47-98 51-101 (105)
26 PF02269 TFIID-18kDa: Transcri 95.7 0.013 2.9E-07 46.7 3.7 60 39-98 7-67 (93)
27 PF03540 TFIID_30kDa: Transcri 95.2 0.088 1.9E-06 38.1 6.4 44 37-80 6-49 (51)
28 KOG3423 Transcription initiati 95.2 0.093 2E-06 46.5 7.8 87 15-101 61-168 (176)
29 PLN00161 histone H3; Provision 94.8 0.18 3.8E-06 43.3 8.1 62 38-100 67-128 (135)
30 KOG2549 Transcription initiati 94.7 0.15 3.2E-06 52.5 8.7 68 37-104 15-84 (576)
31 PF15511 CENP-T: Centromere ki 94.5 0.099 2.1E-06 51.9 6.9 57 34-90 356-414 (414)
32 cd00074 H2A Histone 2A; H2A is 94.4 0.15 3.2E-06 42.5 6.6 57 41-97 28-85 (115)
33 PLN00160 histone H3; Provision 94.1 0.23 5E-06 40.4 7.0 48 50-97 44-91 (97)
34 PTZ00018 histone H3; Provision 93.3 0.33 7.1E-06 41.7 6.9 51 47-98 82-132 (136)
35 PLN00121 histone H3; Provision 93.1 0.41 8.9E-06 41.1 7.2 50 47-97 82-131 (136)
36 KOG0870 DNA polymerase epsilon 92.1 0.73 1.6E-05 40.9 7.6 72 28-100 9-80 (172)
37 COG5095 TAF6 Transcription ini 89.7 1.6 3.6E-05 42.6 8.2 70 37-106 9-80 (450)
38 PF03847 TFIID_20kDa: Transcri 89.5 1.2 2.6E-05 33.8 5.7 50 48-97 15-64 (68)
39 KOG0869 CCAAT-binding factor, 87.3 2.5 5.5E-05 37.3 7.1 62 39-100 38-101 (168)
40 KOG3901 Transcription initiati 84.3 3 6.5E-05 34.5 5.7 64 32-98 8-72 (109)
41 KOG1744 Histone H2B [Chromatin 82.1 4.6 0.0001 34.4 6.2 69 23-98 35-103 (127)
42 KOG0871 Class 2 transcription 81.0 5.6 0.00012 34.8 6.4 67 31-100 14-81 (156)
43 smart00427 H2B Histone H2B. 80.7 9 0.0002 30.7 7.1 64 28-98 4-67 (89)
44 COG5162 Transcription initiati 79.7 9.4 0.0002 34.1 7.5 44 37-80 92-135 (197)
45 cd08045 TAF4 TATA Binding Prot 78.9 7 0.00015 35.2 6.7 73 27-99 42-120 (212)
46 PLN00158 histone H2B; Provisio 74.3 30 0.00064 29.1 8.7 68 24-98 26-93 (116)
47 COG5248 TAF19 Transcription in 73.2 11 0.00023 31.6 5.8 62 36-99 12-74 (126)
48 KOG1745 Histones H3 and H4 [Ch 70.8 2.5 5.5E-05 36.4 1.6 49 51-99 86-134 (137)
49 KOG1142 Transcription initiati 69.1 9.6 0.00021 36.0 5.2 63 33-98 158-220 (258)
50 cd08048 TAF11 TATA Binding Pro 68.6 34 0.00073 27.0 7.4 65 30-98 17-84 (85)
51 TIGR03015 pepcterm_ATPase puta 68.1 24 0.00053 31.5 7.5 64 35-98 197-266 (269)
52 PF05236 TAF4: Transcription i 65.5 11 0.00023 35.0 4.8 67 32-98 46-118 (264)
53 PTZ00463 histone H2B; Provisio 64.5 40 0.00087 28.4 7.4 68 24-98 27-94 (117)
54 COG5150 Class 2 transcription 62.5 42 0.00091 28.9 7.3 68 31-100 13-80 (148)
55 PF09415 CENP-X: CENP-S associ 61.8 17 0.00036 27.9 4.4 60 38-98 4-68 (72)
56 PF13654 AAA_32: AAA domain; P 61.7 59 0.0013 33.5 9.6 66 33-98 430-506 (509)
57 PRK00411 cdc6 cell division co 61.0 57 0.0012 31.0 9.0 50 50-99 228-283 (394)
58 TIGR00764 lon_rel lon-related 50.6 89 0.0019 32.8 9.0 64 35-98 314-391 (608)
59 smart00414 H2A Histone 2A. 48.8 58 0.0013 26.7 5.9 50 48-97 25-74 (106)
60 PF12767 SAGA-Tad1: Transcript 46.4 60 0.0013 29.9 6.3 44 33-76 206-249 (252)
61 CHL00081 chlI Mg-protoporyphyr 38.1 94 0.002 30.5 6.5 48 51-98 268-322 (350)
62 TIGR02928 orc1/cdc6 family rep 37.1 2E+02 0.0044 26.9 8.5 50 50-99 220-275 (365)
63 TIGR02442 Cob-chelat-sub cobal 36.0 2.2E+02 0.0047 29.9 9.2 51 48-98 247-304 (633)
64 TIGR01501 MthylAspMutase methy 35.7 1.2E+02 0.0027 25.7 6.1 20 36-55 18-37 (134)
65 PF13335 Mg_chelatase_2: Magne 33.8 2E+02 0.0044 22.7 6.8 47 50-96 42-94 (96)
66 PF14920 MTBP_C: MDM2-binding 33.3 1.4E+02 0.003 28.2 6.4 67 11-77 166-236 (251)
67 PLN00154 histone H2A; Provisio 32.5 1.5E+02 0.0032 25.7 6.0 57 41-97 46-104 (136)
68 PF12014 DUF3506: Domain of un 31.4 77 0.0017 27.3 4.2 32 218-252 70-101 (134)
69 PRK06585 holA DNA polymerase I 31.4 1.7E+02 0.0036 27.6 6.9 66 32-98 144-210 (343)
70 COG5126 FRQ1 Ca2+-binding prot 30.1 2.6E+02 0.0057 24.6 7.4 76 36-133 39-123 (160)
71 PRK05574 holA DNA polymerase I 29.8 2.6E+02 0.0057 25.8 7.8 64 34-98 150-213 (340)
72 PRK07452 DNA polymerase III su 27.9 2.3E+02 0.0051 26.3 7.2 62 35-97 135-198 (326)
73 PTZ00017 histone H2A; Provisio 27.4 1.5E+02 0.0033 25.5 5.3 50 48-97 43-92 (134)
74 COG3079 Uncharacterized protei 27.0 58 0.0013 29.3 2.7 90 33-131 67-165 (186)
75 PRK12402 replication factor C 24.7 2.3E+02 0.005 26.1 6.4 62 34-98 188-249 (337)
76 TIGR02030 BchI-ChlI magnesium 24.0 2.5E+02 0.0054 27.3 6.7 31 68-98 279-309 (337)
77 TIGR02031 BchD-ChlD magnesium 22.9 2.8E+02 0.006 29.0 7.3 49 50-98 203-258 (589)
78 TIGR01128 holA DNA polymerase 21.5 4.8E+02 0.01 23.6 7.8 65 33-98 114-178 (302)
79 PF02130 UPF0054: Uncharacteri 21.3 2.3E+02 0.005 24.0 5.3 44 28-71 102-145 (145)
80 TIGR00635 ruvB Holliday juncti 21.2 4.9E+02 0.011 23.7 7.9 65 35-100 164-231 (305)
81 cd02071 MM_CoA_mut_B12_BD meth 21.0 4.4E+02 0.0096 21.1 7.4 82 37-129 17-121 (122)
82 PLN00157 histone H2A; Provisio 20.3 2.4E+02 0.0053 24.2 5.2 50 48-97 42-91 (132)
83 PF03444 HrcA_DNA-bdg: Winged 20.2 2.1E+02 0.0045 22.5 4.3 49 53-101 4-53 (78)
84 PF01388 ARID: ARID/BRIGHT DNA 20.2 1.6E+02 0.0034 22.4 3.8 31 39-69 60-90 (92)
No 1
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=100.00 E-value=1.7e-35 Score=279.15 Aligned_cols=208 Identities=34% Similarity=0.482 Sum_probs=175.2
Q ss_pred CCCCCchHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473 22 QGEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG 101 (281)
Q Consensus 22 ~~~~s~defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~ 101 (281)
+.....++|++++++++|||||+++||++.+.+||++||+++++||++||++||.|++++||++||++|+++||.+|+++
T Consensus 18 ~~~~~~~~ya~sla~~avaQIcqslg~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 18 RSESEEAEYAFSLARVAVAQICQSLGYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred ccchhHHHHHHHHHHHHHHHHHHhcCCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 46778999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCcccccccccchhhHHHHhhhhhcCCCCCCCCCCCCCCCCCCccccccccccCCCCCCCCCCCCCC-CCCCccc
Q 023473 102 QGFPGASALNRNCMLDSGVLKEIAGFVRHGCEIPFAKPIPRSKNAHANSVCCKKENDRGSRSLHLHIPKWLP-AFPDERS 180 (281)
Q Consensus 102 ~gF~g~s~~~~~~ll~S~~l~eL~~yv~~~~~iPf~~plP~fPv~~~~~l~~~~~l~~~~r~~~~HIP~~LP-~FPd~HT 180 (281)
.||.|++... +||++|+++++|+.|...+++|||.+++|+||+.+....++++.-+.+.-++..|||.||| +||+.|+
T Consensus 98 ~~~~~~~~~s-~~L~ds~v~rdii~~~g~~eevpF~~~lP~Fp~s~s~~k~~l~~~~~g~~pp~~~Ip~wLP~~fp~~~~ 176 (353)
T KOG2389|consen 98 LGASGSSGES-HCLLDSKVLRDIIIFNGKAEEVPFKDDLPRFPVSKSVNKPFLKFGSVGAEPPGESIPIWLPPAFPDLEG 176 (353)
T ss_pred cccccccchh-HHHhhhhhHHHHHhhccccccCCCCCCCCccccccccccCCCCccccCCCCCCccccccCCCCCCCccc
Confidence 9999999866 9999999999999999999999999999999999754556643334555555699999999 8999999
Q ss_pred ccccCCCCCCCCccccccCCCCCCCCccccCCCcccccCCCccccccceeeecccc
Q 023473 181 YNKECQGPVCNRSEKLWENSEFPEGERFTFGGYKWEVLGGDLAKEREKVRFKIGVK 236 (281)
Q Consensus 181 Y~~T~~~~~~~r~~~l~e~~~~~~~~~~~~~~~~~~~~~g~~~~~r~~v~f~~~~~ 236 (281)
|..+| .+..+...|+......++......++ ...+|.+++.+.. +.+++-
T Consensus 177 ~~~s~---e~~~~~~~~~~~~~~~~s~~~~~~ls-~~~~~r~~v~k~~--~~~~~~ 226 (353)
T KOG2389|consen 177 CSKSP---EGNVTVPKPEGRPPEKASLELRASLS-EDSGGRLQVKKDS--EEKEKP 226 (353)
T ss_pred CCCCc---cccccccCcccCchhhhhhhhhhhhh-hhccccchhhhhh--hhhcCc
Confidence 99997 44444557777766555444433334 3457788888777 444443
No 2
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=99.94 E-value=2.4e-26 Score=214.14 Aligned_cols=142 Identities=22% Similarity=0.260 Sum_probs=110.3
Q ss_pred HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCCCCCCCCcccc
Q 023473 33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNR 112 (281)
Q Consensus 33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~~gF~g~s~~~~ 112 (281)
.+|..+|+++|...||++++..|+++|+++++.||.+||+.++.||+|+|||+|+..||..+|++|||.
T Consensus 5 ~vl~~VV~~Ll~~~gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~----------- 73 (323)
T KOG4336|consen 5 RVLAPVVSNLLKTKGFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK----------- 73 (323)
T ss_pred hHHHHHHHHHHHHhCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC-----------
Confidence 399999999999999999999999999999999999999999999999999999999999999999973
Q ss_pred cccccchhhHHHHhhhhhcCCCC--CCCCCCCCCCCCCCccccc-ccc-ccCCCCCCCCCCCCCCCCCCcccccccCCCC
Q 023473 113 NCMLDSGVLKEIAGFVRHGCEIP--FAKPIPRSKNAHANSVCCK-KEN-DRGSRSLHLHIPKWLPAFPDERSYNKECQGP 188 (281)
Q Consensus 113 ~~ll~S~~l~eL~~yv~~~~~iP--f~~plP~fPv~~~~~l~~~-~~l-~~~~r~~~~HIP~~LP~FPd~HTY~~T~~~~ 188 (281)
+.+|..|.+.....- ....+|.-..+...+.+-. ..+ -..+++++.|||+|||||||+|||++|+...
T Consensus 74 --------v~sL~~~~q~~~~sl~~~~~~aP~~~~q~~ds~~~~~~~l~~gv~~php~yIpshLPpfPdpHTYi~Tpi~~ 145 (323)
T KOG4336|consen 74 --------VSSLYAYFQKQEFSLWSVLIAAPENQEQEEDSEQQPELLLTLGVSRPHPKYIPSHLPPFPDPHTYIKTPIYK 145 (323)
T ss_pred --------hhhhHHHHHhccchhhhccccCCCcCCccccccccchHhhhcCCCCCCCccccccCCCCCCCcccccCCccC
Confidence 677778876654310 1122222111100111110 111 3345666799999999999999999999887
Q ss_pred CCCCc
Q 023473 189 VCNRS 193 (281)
Q Consensus 189 ~~~r~ 193 (281)
+...+
T Consensus 146 ~p~ts 150 (323)
T KOG4336|consen 146 VPDTS 150 (323)
T ss_pred CCCCC
Confidence 77776
No 3
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=99.88 E-value=1.6e-22 Score=155.15 Aligned_cols=74 Identities=42% Similarity=0.608 Sum_probs=72.3
Q ss_pred hHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473 28 SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG 101 (281)
Q Consensus 28 defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~ 101 (281)
++|+|++|+++|+|||+++||++++++|+|+|||++++||.+|++.++.||+|+||++|++.||.+||++||+.
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 58999999999999999999999999999999999999999999999999999999999999999999999974
No 4
>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=99.87 E-value=6.1e-22 Score=151.20 Aligned_cols=74 Identities=39% Similarity=0.586 Sum_probs=72.4
Q ss_pred hHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473 28 SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG 101 (281)
Q Consensus 28 defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~ 101 (281)
++|++++|+++|+|||+++||++++++|||+|+|++.+||++||+.++.|||++|||+|++.||.+||++||++
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 68999999999999999999999999999999999999999999999999999999999999999999999973
No 5
>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=98.87 E-value=1.1e-09 Score=78.44 Aligned_cols=28 Identities=32% Similarity=0.667 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCcccccccCCCCCCCCc
Q 023473 166 LHIPKWLPAFPDERSYNKECQGPVCNRS 193 (281)
Q Consensus 166 ~HIP~~LP~FPd~HTY~~T~~~~~~~r~ 193 (281)
+|||+|||+||++|||++|+.....+.+
T Consensus 1 ~~IP~~lP~fP~~HTY~~Tp~~~~~~~d 28 (51)
T PF10406_consen 1 SHIPDWLPPFPPPHTYKRTPIYNERETD 28 (51)
T ss_pred CCCcccCCCCCCCcccccCCCCCCCCCC
Confidence 5999999999999999999985544443
No 6
>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=98.85 E-value=1.4e-09 Score=78.63 Aligned_cols=27 Identities=37% Similarity=0.797 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCCcccccccCCCCCCCC
Q 023473 166 LHIPKWLPAFPDERSYNKECQGPVCNR 192 (281)
Q Consensus 166 ~HIP~~LP~FPd~HTY~~T~~~~~~~r 192 (281)
.|||+|||+||++|||++|+.....+.
T Consensus 1 ~hIP~~LP~FP~~HTY~~Tp~~~~~~~ 27 (54)
T cd08049 1 AHIPSWLPPFPDPHTYKRTPTYSERET 27 (54)
T ss_pred CCCCcCCCCCCCchhhccCCCCCCCcc
Confidence 499999999999999999997544333
No 7
>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=98.83 E-value=4.3e-08 Score=81.22 Aligned_cols=94 Identities=19% Similarity=0.259 Sum_probs=79.6
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCCCCCCCCcccccccc
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCML 116 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~~gF~g~s~~~~~~ll 116 (281)
.+|.+||++.|-+..++.|...|.|++.+|..+|+..|..||+||||...+..||.+|+...+- ..|...
T Consensus 5 ~~v~~iLk~~Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~-~~f~~~--------- 74 (117)
T cd07979 5 RVIAAILKSMGITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD-YSFTSP--------- 74 (117)
T ss_pred HHHHHHHHHCCCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc-cCCCCC---------
Confidence 5789999999999999999999999999999999999999999999999999999999998753 234321
Q ss_pred cchhhHHHHhhhhhcCCCCCCCCCCC
Q 023473 117 DSGVLKEIAGFVRHGCEIPFAKPIPR 142 (281)
Q Consensus 117 ~S~~l~eL~~yv~~~~~iPf~~plP~ 142 (281)
-..+.|.+.+...+.+|+|.+.+.
T Consensus 75 --p~~~~l~~~a~~~N~~pLP~~~~~ 98 (117)
T cd07979 75 --PPRDFLLELAREKNSIPLPPIPPS 98 (117)
T ss_pred --CcHHHHHHHHHHhccCCCCCCCCC
Confidence 136678888888888887755444
No 8
>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=98.57 E-value=2.1e-07 Score=78.57 Aligned_cols=90 Identities=20% Similarity=0.245 Sum_probs=53.6
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc-CCCCCCCCCCccccccc
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV-SSGQGFPGASALNRNCM 115 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm-Gi~~gF~g~s~~~~~~l 115 (281)
++|.+||++.|.+..++.+...|.|.+.+|..+|...|+.||+||||+.++..||.+|..-. +- -|...
T Consensus 16 ~~i~~iL~~~Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~--~f~~p-------- 85 (129)
T PF02291_consen 16 RVIHLILKSMGVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDH--SFTQP-------- 85 (129)
T ss_dssp HHHHHHHHHTT---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT------------------
T ss_pred HHHHHHHHHcCCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhh--hccCC--------
Confidence 67899999999999999999999999999999999999999999999999999999999843 21 23221
Q ss_pred ccchhhHHHHhhhhhcCCCCCCCC
Q 023473 116 LDSGVLKEIAGFVRHGCEIPFAKP 139 (281)
Q Consensus 116 l~S~~l~eL~~yv~~~~~iPf~~p 139 (281)
-..+-|.+.++..+.+|+|..
T Consensus 86 ---ppre~llelA~e~N~~PLP~i 106 (129)
T PF02291_consen 86 ---PPREFLLELAREKNSIPLPPI 106 (129)
T ss_dssp ------------------------
T ss_pred ---CChHHHHHHHHHhcCCCCCCC
Confidence 124566677777788776643
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=98.48 E-value=8e-07 Score=70.16 Aligned_cols=68 Identities=24% Similarity=0.368 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473 33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS 100 (281)
Q Consensus 33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi 100 (281)
.+-..+|-.+++..|-..++..|.+.+.+++..|+.+|++.+..||+||+|...+..||.+||+.+|-
T Consensus 13 gi~k~~I~RLarr~GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~ 80 (85)
T cd00076 13 GITKPAIRRLARRGGVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred cCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 35577888999999999999999999999999999999999999999999999999999999999973
No 10
>PLN00035 histone H4; Provisional
Probab=98.46 E-value=1e-06 Score=71.91 Aligned_cols=71 Identities=25% Similarity=0.352 Sum_probs=65.4
Q ss_pred HHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC-CCC
Q 023473 34 VTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG-QGF 104 (281)
Q Consensus 34 lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~-~gF 104 (281)
+-..+|-.|++..|-..++..|.+.|.+++..|+.+|++.+..||+||+|...+..||.+||+.+|-. .||
T Consensus 30 ipk~~IrRLARr~GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~lyGf 101 (103)
T PLN00035 30 ITKPAIRRLARRGGVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRTLYGF 101 (103)
T ss_pred CCHHHHHHHHHHcCcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCcCCCC
Confidence 55677888999999999999999999999999999999999999999999999999999999999843 444
No 11
>PTZ00015 histone H4; Provisional
Probab=98.42 E-value=1e-06 Score=71.78 Aligned_cols=69 Identities=22% Similarity=0.320 Sum_probs=65.0
Q ss_pred HHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473 32 FTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS 100 (281)
Q Consensus 32 r~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi 100 (281)
..+...+|-.|++..|-..++..|-+.+.+++..|+.+|++.|..||+||+|...+..||.+||...|-
T Consensus 29 ~gI~k~~IrRLarr~GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~ 97 (102)
T PTZ00015 29 RGITKGAIRRLARRGGVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred cCCCHHHHHHHHHHcCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 445678899999999999999999999999999999999999999999999999999999999999873
No 12
>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=98.38 E-value=1.8e-06 Score=64.77 Aligned_cols=60 Identities=15% Similarity=0.252 Sum_probs=57.1
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN 96 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~ 96 (281)
.+|-.|.++.|.+.++..|.+.|.+.++.|+.+|++.|..||+|++|...+..||.+||+
T Consensus 6 ~~i~ria~~~Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 6 ETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred HHHHHHHHHCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 467788999999999999999999999999999999999999999999999999999984
No 13
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.30 E-value=2.2e-06 Score=68.51 Aligned_cols=65 Identities=29% Similarity=0.389 Sum_probs=60.3
Q ss_pred HHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473 36 KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS 100 (281)
Q Consensus 36 r~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi 100 (281)
...|..|++.+|=+.++.+|.+.|.++++.|+.+|+..|..+|.|+||-.....||.+|+..+|.
T Consensus 22 ~apv~Ri~r~~~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~ 86 (91)
T COG2036 22 KAPVRRILRKAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGR 86 (91)
T ss_pred chHHHHHHHHHhHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcc
Confidence 34577788888888999999999999999999999999999999999999999999999999974
No 14
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.10 E-value=1.3e-05 Score=61.98 Aligned_cols=66 Identities=20% Similarity=0.170 Sum_probs=57.0
Q ss_pred HHHHHHHHHHHHHHcCcCc---cChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473 32 FTVTKVAVSQICRSVGFKA---AESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND 97 (281)
Q Consensus 32 r~lLr~sVaqIL~~~GFds---a~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d 97 (281)
.+-|.-+|++||++.+=+. +++.++..|++++-+|+..+|.....||.||||+.++..||.+..+.
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 4678889999999986443 89999999999999999999999999999999999999999987765
No 15
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=98.05 E-value=6.3e-05 Score=64.64 Aligned_cols=95 Identities=16% Similarity=0.198 Sum_probs=76.5
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCCCCCCCCcccccccc
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQGFPGASALNRNCML 116 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~~gF~g~s~~~~~~ll 116 (281)
.+|++||++.|.+..++-...-|-|...+|.+.|...|.-|++||+++.....||.+|..-.. +.-|.+. ..
T Consensus 17 ~~i~~iL~s~GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~-~~sf~~p--Pp----- 88 (148)
T KOG3334|consen 17 RVIASILKSLGIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRV-DHSFTPP--PP----- 88 (148)
T ss_pred HHHHHHHHHcCccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHh-ccccCCC--Cc-----
Confidence 579999999999999999999999999999999999999999999999999999999998764 3344331 11
Q ss_pred cchhhHHHHhhhhhcCCCCCCCCCCCC
Q 023473 117 DSGVLKEIAGFVRHGCEIPFAKPIPRS 143 (281)
Q Consensus 117 ~S~~l~eL~~yv~~~~~iPf~~plP~f 143 (281)
-+-|.+.+...+..|++++.+.+
T Consensus 89 ----Re~lL~lA~~rN~~pLp~i~~~~ 111 (148)
T KOG3334|consen 89 ----REFLLELAAERNSKPLPQIRAGP 111 (148)
T ss_pred ----hHHHHHHHHhhccCCCCcccCCC
Confidence 23344556666777777665543
No 16
>smart00417 H4 Histone H4.
Probab=97.89 E-value=2.3e-05 Score=60.42 Aligned_cols=63 Identities=22% Similarity=0.322 Sum_probs=58.2
Q ss_pred HHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHH
Q 023473 32 FTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNA 94 (281)
Q Consensus 32 r~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~A 94 (281)
..+...+|-.|++..|-..++..+-+.|.+++..|+.+|++.|-.||+|++|-..+..||..|
T Consensus 12 ~gI~k~~IrRLaRr~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 12 QGITKPAIRRLARRGGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred cCCCHHHHHHHHHHcCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 345577889999999999999999999999999999999999999999999999999999754
No 17
>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=97.77 E-value=0.00017 Score=54.56 Aligned_cols=61 Identities=20% Similarity=0.283 Sum_probs=51.2
Q ss_pred HHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473 36 KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN 96 (281)
Q Consensus 36 r~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~ 96 (281)
..+|-.+..+.|+...+..+...|++-++.-|.+|.+.|..|+.|+.|+..+..||..||+
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 3567788899999999999999999999999999999999999999999999999999985
No 18
>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=97.41 E-value=0.0014 Score=49.89 Aligned_cols=52 Identities=12% Similarity=0.136 Sum_probs=49.4
Q ss_pred CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
+-..+++.|.+.|.+++..|+..++..+..+|.|+||....+.||.++|+..
T Consensus 16 ~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~ 67 (72)
T cd07981 16 PREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERN 67 (72)
T ss_pred CCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 3478999999999999999999999999999999999999999999999875
No 19
>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=97.38 E-value=0.0011 Score=63.99 Aligned_cols=69 Identities=19% Similarity=0.262 Sum_probs=64.6
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC--CCCC
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG--QGFP 105 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~--~gF~ 105 (281)
.+|-.|.+++|.+..+..|...|++.++.++.+|++.|..||.|++|...+..||.+||+..++. .||.
T Consensus 3 ~~i~~ia~~~Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG~~ 73 (343)
T cd08050 3 ESIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYGFS 73 (343)
T ss_pred hHHHHHHHHcCCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccCCC
Confidence 46788999999999999999999999999999999999999999999999999999999999876 6664
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=97.35 E-value=0.00099 Score=49.90 Aligned_cols=60 Identities=22% Similarity=0.175 Sum_probs=52.7
Q ss_pred HHHHHHHHHcCcC-ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473 37 VAVSQICRSVGFK-AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALN 96 (281)
Q Consensus 37 ~sVaqIL~~~GFd-sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~ 96 (281)
+++-.+....+.+ .++..|++.|..+++.|+.+|...|..+|.+++|...++.|+..|+.
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 3444555555665 99999999999999999999999999999999999999999999976
No 21
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.24 E-value=0.0028 Score=53.60 Aligned_cols=62 Identities=24% Similarity=0.242 Sum_probs=57.5
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCH---HHHHHHHHhc
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNL---VDLTNALNDV 98 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl---~DV~~AL~dm 98 (281)
+.|..||.+.|.+.+++..-=.|.+...+|-+.+.+.|.-||+|+||++... .||.+|+.--
T Consensus 18 rlihliL~Slgi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~ 82 (145)
T COG5094 18 RLIHLILRSLGIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATK 82 (145)
T ss_pred hHHHHHHHhcCchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHH
Confidence 5688899999999999999999999999999999999999999999997776 9999999764
No 22
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=96.87 E-value=0.0053 Score=49.06 Aligned_cols=69 Identities=23% Similarity=0.301 Sum_probs=63.4
Q ss_pred HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473 33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG 101 (281)
Q Consensus 33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~ 101 (281)
-+.+.+|-.+.+..|...+.--..+....++..||+++...|.-|++||-|-..+..||..+|..||+-
T Consensus 29 gitKpaIRRlARr~GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 29 GITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccchHHHHHHHHhcCcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 344666778899999999999999999999999999999999999999999999999999999999964
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=96.81 E-value=0.006 Score=44.84 Aligned_cols=57 Identities=23% Similarity=0.317 Sum_probs=49.3
Q ss_pred HHHHHHHc-CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHH
Q 023473 39 VSQICRSV-GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNAL 95 (281)
Q Consensus 39 VaqIL~~~-GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL 95 (281)
|-.|++.. +-..++..|.+.|+..++.|+..|+..|...|+..+|-..+..||..|+
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 44556666 6777999999999999999999999999999999999999999999886
No 24
>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=96.34 E-value=0.024 Score=45.37 Aligned_cols=62 Identities=18% Similarity=0.249 Sum_probs=54.7
Q ss_pred HHHHHHHHHHcCcC-ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 36 KVAVSQICRSVGFK-AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 36 r~sVaqIL~~~GFd-sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
..-|.+|+-..|=. .-.+...+.|.+|+..||.+|+..|...|. ++|..+.+.|+..+|+.-
T Consensus 5 ~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D 67 (92)
T cd07978 5 TKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD 67 (92)
T ss_pred HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC
Confidence 45578899988875 457789999999999999999999999999 888888999999999874
No 25
>smart00428 H3 Histone H3.
Probab=96.08 E-value=0.03 Score=46.03 Aligned_cols=51 Identities=24% Similarity=0.108 Sum_probs=47.2
Q ss_pred CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
+| .++++|++.|.+..+.||..+...+...|.||+|....+.|+.+|..--
T Consensus 51 ~~-R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~rir 101 (105)
T smart00428 51 DL-RFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARRIR 101 (105)
T ss_pred Cc-eeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHHHh
Confidence 45 8899999999999999999999999999999999999999999887543
No 26
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=95.65 E-value=0.013 Score=46.68 Aligned_cols=60 Identities=13% Similarity=0.181 Sum_probs=31.6
Q ss_pred HHHHHHHcCc-CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 39 VSQICRSVGF-KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 39 VaqIL~~~GF-dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
|.+|+-..|= ....+.+...+.+|+..||.++...|...|...||..+.+.|+..+|+.-
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D 67 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKD 67 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcC
Confidence 6778887775 46678889999999999999999999999999999999999999999985
No 27
>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=95.23 E-value=0.088 Score=38.08 Aligned_cols=44 Identities=18% Similarity=0.394 Sum_probs=41.1
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHV 80 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAel 80 (281)
.++..+|+.+||++..+.....+.-..++||.+|+..|.+||-+
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 46788999999999999999999999999999999999999864
No 28
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.23 E-value=0.093 Score=46.49 Aligned_cols=87 Identities=17% Similarity=0.291 Sum_probs=68.2
Q ss_pred cCCCCCCCCCCCchHHHHHHH-------HHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-----
Q 023473 15 NQKPPTEQGEETPSEFAFTVT-------KVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAH----- 82 (281)
Q Consensus 15 ~~~p~~~~~~~s~defar~lL-------r~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaG----- 82 (281)
++.+..+.....-++|...+. ..++...|..+||.+..+.....+.-..+.||..|+..|-+||-..+
T Consensus 61 ~~~~~~~~~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~ 140 (176)
T KOG3423|consen 61 NGELNPTTKDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIG 140 (176)
T ss_pred cCCcCCCCcchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccc
Confidence 333344333344445555443 46788999999999999999999999999999999999999998876
Q ss_pred ---------CCCCCHHHHHHHHHhcCCC
Q 023473 83 ---------RSESNLVDLTNALNDVSSG 101 (281)
Q Consensus 83 ---------RT~pnl~DV~~AL~dmGi~ 101 (281)
+..-+..|+.-||.+.||.
T Consensus 141 ~~k~~~kdkK~tLtmeDL~~AL~EyGin 168 (176)
T KOG3423|consen 141 KDKKQAKDKKYTLTMEDLSPALAEYGIN 168 (176)
T ss_pred cccccccccceeeeHHHHHHHHHHhCcc
Confidence 2346789999999999974
No 29
>PLN00161 histone H3; Provisional
Probab=94.78 E-value=0.18 Score=43.29 Aligned_cols=62 Identities=18% Similarity=0.059 Sum_probs=51.4
Q ss_pred HHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473 38 AVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS 100 (281)
Q Consensus 38 sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi 100 (281)
-|++-+...+| ..+++||+.|-+..+.||..+-..+...|.||+|....+-|+.+|..--|.
T Consensus 67 EI~~~~~~~~~-Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~ 128 (135)
T PLN00161 67 EISNEMLREPF-RWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGP 128 (135)
T ss_pred HHHHhcCCCCc-EeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhccc
Confidence 34443332345 788999999999999999999999999999999999999999999765543
No 30
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.70 E-value=0.15 Score=52.48 Aligned_cols=68 Identities=19% Similarity=0.267 Sum_probs=61.0
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC--CCC
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG--QGF 104 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~--~gF 104 (281)
.+|--+.++.|.......|+..|++-+..-|.+|.+.+.+|+.|+-|+..++.||..||+-..+. .||
T Consensus 15 Es~k~vAEslGi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg~ 84 (576)
T KOG2549|consen 15 ESVKVVAESLGITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYGF 84 (576)
T ss_pred HHHHHHHHHhCccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccCc
Confidence 34555667889999999999999999999999999999999999999999999999999998755 455
No 31
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=94.51 E-value=0.099 Score=51.89 Aligned_cols=57 Identities=25% Similarity=0.300 Sum_probs=40.3
Q ss_pred HHHHHHHHHHHHcCc--CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHH
Q 023473 34 VTKVAVSQICRSVGF--KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVD 90 (281)
Q Consensus 34 lLr~sVaqIL~~~GF--dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~D 90 (281)
+.+..+...++..|| ..++..||++|...+..|+++||.....||.||||-.+...|
T Consensus 356 ~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 356 VVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp HHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred HHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 334444444554333 568999999999999999999999999999999998887766
No 32
>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=94.41 E-value=0.15 Score=42.55 Aligned_cols=57 Identities=11% Similarity=0.004 Sum_probs=52.3
Q ss_pred HHHHH-cCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473 41 QICRS-VGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND 97 (281)
Q Consensus 41 qIL~~-~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d 97 (281)
.+|+. .+...++.+|.-.|+.+++.+..+|...|-.+|..++|...++.||.+|...
T Consensus 28 R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 28 RYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred HHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 34554 6788999999999999999999999999999999999999999999999887
No 33
>PLN00160 histone H3; Provisional
Probab=94.10 E-value=0.23 Score=40.36 Aligned_cols=48 Identities=19% Similarity=0.005 Sum_probs=45.4
Q ss_pred ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473 50 AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND 97 (281)
Q Consensus 50 sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d 97 (281)
..+++||++|-+..+.||..+-..+...|.||+|....+-|+.+|..-
T Consensus 44 Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ri 91 (97)
T PLN00160 44 RWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLARRI 91 (97)
T ss_pred EeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHHHh
Confidence 789999999999999999999999999999999999999999888743
No 34
>PTZ00018 histone H3; Provisional
Probab=93.29 E-value=0.33 Score=41.68 Aligned_cols=51 Identities=24% Similarity=0.093 Sum_probs=47.2
Q ss_pred CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
+| ..+++||+.|-+..+.||..+-..+...|.||.|.....-|+.+|..--
T Consensus 82 ~~-rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rir 132 (136)
T PTZ00018 82 DL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
T ss_pred cc-eeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhc
Confidence 56 8999999999999999999999999999999999999999998887443
No 35
>PLN00121 histone H3; Provisional
Probab=93.08 E-value=0.41 Score=41.10 Aligned_cols=50 Identities=24% Similarity=0.108 Sum_probs=46.9
Q ss_pred CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473 47 GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND 97 (281)
Q Consensus 47 GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d 97 (281)
+| ..+.+||++|-+..+.||..+-..+...|.|+.|.....-|+.++..-
T Consensus 82 ~~-Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ri 131 (136)
T PLN00121 82 DL-RFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
T ss_pred cc-eeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHh
Confidence 56 899999999999999999999999999999999999999999888743
No 36
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=92.11 E-value=0.73 Score=40.85 Aligned_cols=72 Identities=13% Similarity=0.113 Sum_probs=63.1
Q ss_pred hHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473 28 SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS 100 (281)
Q Consensus 28 defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi 100 (281)
..|..++..++|--.|.+. =-+++..|+..|..-..=|+..|...+..+|.-..|-..+..||..||.+|+.
T Consensus 9 l~lP~AiI~rlvke~l~E~-~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eief 80 (172)
T KOG0870|consen 9 LNLPNAIITRLVKEVLPES-NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEF 80 (172)
T ss_pred hhccHHHHHHHHHHhCccc-cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhch
Confidence 3456677888888888765 56799999999999999999999999999999999999999999999999963
No 37
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=89.69 E-value=1.6 Score=42.64 Aligned_cols=70 Identities=16% Similarity=0.318 Sum_probs=62.8
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC--CCCCC
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG--QGFPG 106 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~--~gF~g 106 (281)
..|-...++.|...+...|+..|+-=++--|.++++.+..|+-|+-||.-+..||..||+-+++. -||.+
T Consensus 9 et~KdvAeslGi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVePLyGyd~ 80 (450)
T COG5095 9 ETLKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVEPLYGYDP 80 (450)
T ss_pred HHHHHHHHHcCCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCCcccCCCC
Confidence 34555677889999999999999999999999999999999999999999999999999999876 66655
No 38
>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=89.54 E-value=1.2 Score=33.79 Aligned_cols=50 Identities=16% Similarity=0.163 Sum_probs=41.8
Q ss_pred cCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473 48 FKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND 97 (281)
Q Consensus 48 Fdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d 97 (281)
=....+.+-+.|.+++..|+..+...+...|-|-+-....+.||.+.|+.
T Consensus 15 ~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 15 NEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp S----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 45678899999999999999999999999999999889999999999986
No 39
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=87.32 E-value=2.5 Score=37.30 Aligned_cols=62 Identities=19% Similarity=0.198 Sum_probs=52.6
Q ss_pred HHHHHHHc--CcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473 39 VSQICRSV--GFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS 100 (281)
Q Consensus 39 VaqIL~~~--GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi 100 (281)
|+.|++.+ .=-.+...|-|++-+.+-+||.=|...|..-|+.--|-..|-.||..||..+|.
T Consensus 38 V~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGF 101 (168)
T KOG0869|consen 38 VSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGF 101 (168)
T ss_pred HHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCc
Confidence 44454432 123577889999999999999999999999999999999999999999999974
No 40
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=84.33 E-value=3 Score=34.51 Aligned_cols=64 Identities=13% Similarity=0.190 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHHHHcCcCc-cChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 32 FTVTKVAVSQICRSVGFKA-AESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 32 r~lLr~sVaqIL~~~GFds-a~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
..+...=+-.|+-..|=+- --+.+++.|.+++..||.++...| .+...|-..-+.|+..+|+.=
T Consensus 8 k~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a---~~~g~rgk~~veD~~f~lRkD 72 (109)
T KOG3901|consen 8 KHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAA---MEIGKRGKVKVEDFKFLLRKD 72 (109)
T ss_pred HHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHH---HHhcccCceeHHHHHHHHHhC
Confidence 3555566666666444222 235678999999999999994444 455567778899999999884
No 41
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=82.11 E-value=4.6 Score=34.39 Aligned_cols=69 Identities=22% Similarity=0.327 Sum_probs=56.3
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 23 GEETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 23 ~~~s~defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
.-.+-..|+.++|+.+. -..| +...|+..+-..+-..++.|+..+.++|...+|+..+..++..|++-+
T Consensus 35 ~~e~~s~yv~kvlk~Vh----pd~g---is~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 35 RKESYSEYVYKVLKQVH----PDLG---ISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred ccCceeeehhhhhhccc----CCCC---cCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 34555566666665544 4445 888888888888888899999999999999999999999999999987
No 42
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=80.99 E-value=5.6 Score=34.81 Aligned_cols=67 Identities=10% Similarity=0.150 Sum_probs=57.1
Q ss_pred HHHHHHHHHHHHHH-HcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473 31 AFTVTKVAVSQICR-SVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS 100 (281)
Q Consensus 31 ar~lLr~sVaqIL~-~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi 100 (281)
.++.+...|.-||- .. .+...|-|.|-+....||..|++.|...|+--.+-...+..|..||+.+|.
T Consensus 14 PkAtv~KmIke~lP~d~---rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF 81 (156)
T KOG0871|consen 14 PKATVNKMIKEMLPKDV---RVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGF 81 (156)
T ss_pred cHHHHHHHHHHhCCccc---ccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcch
Confidence 34666667777765 33 456789999999999999999999999999999999999999999999963
No 43
>smart00427 H2B Histone H2B.
Probab=80.66 E-value=9 Score=30.75 Aligned_cols=64 Identities=14% Similarity=0.266 Sum_probs=53.5
Q ss_pred hHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 28 SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 28 defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
.-|..++|+ |+.... +++..|+..+..++...++.|+..|...+....|...+..+|..|.+.+
T Consensus 4 ~~Yi~kvLK----qVhpd~---giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 4 AIYIYKVLK----QVHPDT---GISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred HHHHHHHHH----HhCCCc---cccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 345555555 444444 5788999999999999999999999999999999999999999998887
No 44
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=79.74 E-value=9.4 Score=34.10 Aligned_cols=44 Identities=23% Similarity=0.404 Sum_probs=39.1
Q ss_pred HHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023473 37 VAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHV 80 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAel 80 (281)
.++--.|..+||..+.+..-..|.-+.+.|+..|+..|-+|+..
T Consensus 92 ~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrI 135 (197)
T COG5162 92 SVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRI 135 (197)
T ss_pred HHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666789999999999999999999999999999999888755
No 45
>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=78.88 E-value=7 Score=35.20 Aligned_cols=73 Identities=18% Similarity=0.215 Sum_probs=61.5
Q ss_pred chHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC------CCCHHHHHHHHHhcC
Q 023473 27 PSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRS------ESNLVDLTNALNDVS 99 (281)
Q Consensus 27 ~defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT------~pnl~DV~~AL~dmG 99 (281)
+.=|....|..-|.+|+...|+..+++.+++.|...++.||..|...+...|+|-... .....|+...|..|.
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~ 120 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLE 120 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHH
Confidence 3445558999999999999999999999999999999999999999999999986332 345678888887774
No 46
>PLN00158 histone H2B; Provisional
Probab=74.29 E-value=30 Score=29.14 Aligned_cols=68 Identities=16% Similarity=0.279 Sum_probs=57.9
Q ss_pred CCCchHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 24 EETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 24 ~~s~defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
.++-.-|+.++|+ |+....| ++..|+..+..++...++.|+..|...|....|...+..+|..|.+-+
T Consensus 26 ~esy~~YI~kVLK----QVhPd~g---IS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 26 TETYKIYIYKVLK----QVHPDTG---ISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred cccHHHHHHHHHH----HhCCCCC---ccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 4666777777776 5566666 478899999999999999999999999999999999999999998876
No 47
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=73.21 E-value=11 Score=31.64 Aligned_cols=62 Identities=18% Similarity=0.196 Sum_probs=48.6
Q ss_pred HHHHHHHHHHcCcCcc-ChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473 36 KVAVSQICRSVGFKAA-ESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS 99 (281)
Q Consensus 36 r~sVaqIL~~~GFdsa-~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG 99 (281)
..=|..++-+.|=... .+...+.|-+++..||..++..|+..|. .|...-+.|+..||++--
T Consensus 12 ~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr~Dp 74 (126)
T COG5248 12 MKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALRRDP 74 (126)
T ss_pred HHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHhhCh
Confidence 3445666666663332 3567889999999999999999999998 566778999999999853
No 48
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=70.76 E-value=2.5 Score=36.39 Aligned_cols=49 Identities=24% Similarity=0.115 Sum_probs=44.5
Q ss_pred cChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473 51 AESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS 99 (281)
Q Consensus 51 a~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG 99 (281)
.+..|+.+|-+..+.||..|-..+...|-||.|....+-|+-+|..--|
T Consensus 86 fqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg 134 (137)
T KOG1745|consen 86 FQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 134 (137)
T ss_pred ehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhccc
Confidence 5778999999999999999999999999999999999999998876543
No 49
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=69.09 E-value=9.6 Score=36.04 Aligned_cols=63 Identities=14% Similarity=0.175 Sum_probs=55.2
Q ss_pred HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
..|...|-+| .|=...++.+-|.|.+|+..|+..|...+.++|-|-.-....+.||.+.|+.-
T Consensus 158 ~kl~dLvqqI---d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~ 220 (258)
T KOG1142|consen 158 RKLDDLVQQI---DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERN 220 (258)
T ss_pred cchhHHHHhh---cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeecc
Confidence 5566667777 56678889999999999999999999999999999888889999999999863
No 50
>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=68.57 E-value=34 Score=26.99 Aligned_cols=65 Identities=9% Similarity=0.132 Sum_probs=52.5
Q ss_pred HHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC--C-CCCHHHHHHHHHhc
Q 023473 30 FAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHR--S-ESNLVDLTNALNDV 98 (281)
Q Consensus 30 far~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGR--T-~pnl~DV~~AL~dm 98 (281)
|.+..+++.|.+++. .++.......|.-+..-|+.+|-..|....+.-+. + -.-+.+|..|++.+
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 555666666666654 79999999999999999999999999999999777 3 34677888888765
No 51
>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=68.06 E-value=24 Score=31.46 Aligned_cols=64 Identities=9% Similarity=0.164 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHcCc---CccChHHHHHHHHHHHH---HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 35 TKVAVSQICRSVGF---KAAESSALETLTLVAAK---YLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 35 Lr~sVaqIL~~~GF---dsa~~sALetLTdil~~---YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
++..+...+..+|+ ...++.+++.|.+...- +|..++..+-..|-..+-...+..||..++.++
T Consensus 197 ~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~ 266 (269)
T TIGR03015 197 TREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEI 266 (269)
T ss_pred HHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHh
Confidence 44556666677786 35788999999888764 899999999888888888899999999999886
No 52
>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=65.50 E-value=11 Score=35.02 Aligned_cols=67 Identities=21% Similarity=0.292 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCC------HHHHHHHHHhc
Q 023473 32 FTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESN------LVDLTNALNDV 98 (281)
Q Consensus 32 r~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pn------l~DV~~AL~dm 98 (281)
...|..-|..|+...|-..+.+..++.|...++.||..|...+...|.|-..+... ..||...|..+
T Consensus 46 ~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~~~~~~~~~~sdv~~qlr~l 118 (264)
T PF05236_consen 46 PSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSSKSDPRYEIRSDVRKQLRFL 118 (264)
T ss_dssp HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH-----------------------------
T ss_pred HHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCCCcccccchHHHHHHHHH
Confidence 37888999999999999999999999999999999999999999999886665442 55665555555
No 53
>PTZ00463 histone H2B; Provisional
Probab=64.51 E-value=40 Score=28.41 Aligned_cols=68 Identities=13% Similarity=0.225 Sum_probs=57.1
Q ss_pred CCCchHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 24 EETPSEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 24 ~~s~defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
.++-.-|+.++|+++ -...| ++..|+..+..++...++.|+..|...|....|...+..||..|.+-+
T Consensus 27 ~esy~~YI~KVLKqV----hPd~g---IS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 27 YDSYGLYIFKVLKQV----HPDTG---ISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred cchHHHHHHHHHHhh----CCCCC---ccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 456677777777744 44444 588899999999999999999999999999999999999999998776
No 54
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=62.45 E-value=42 Score=28.91 Aligned_cols=68 Identities=15% Similarity=0.114 Sum_probs=58.1
Q ss_pred HHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473 31 AFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS 100 (281)
Q Consensus 31 ar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi 100 (281)
..+..+..|+.||-.- -.....|-|.|-+..+.||.-|...|...|+---.-......|+.||++++.
T Consensus 13 PKATVqKMvS~iLp~d--l~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef 80 (148)
T COG5150 13 PKATVQKMVSSILPKD--LVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEF 80 (148)
T ss_pred cHHHHHHHHHHhcccc--ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccH
Confidence 3467788888888532 3456789999999999999999999999999988888999999999999963
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=61.84 E-value=17 Score=27.86 Aligned_cols=60 Identities=15% Similarity=0.202 Sum_probs=48.3
Q ss_pred HHHHHHHHcCcC----ccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC-CCHHHHHHHHHhc
Q 023473 38 AVSQICRSVGFK----AAESSALETLTLVAAKYLQQLASRAASYSHVAHRSE-SNLVDLTNALNDV 98 (281)
Q Consensus 38 sVaqIL~~~GFd----sa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~-pnl~DV~~AL~dm 98 (281)
.|+.||+ ..|. .++..|+..+++.+.-|+.+-...|..-++.-|.+. ..+.|++..+-++
T Consensus 4 li~rll~-~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pqL 68 (72)
T PF09415_consen 4 LIARLLH-EHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQL 68 (72)
T ss_dssp HHHHHHC-TTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHCH
T ss_pred HHHHHHH-HHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHH
Confidence 5778888 6775 577889999999999999999999999999999888 8999988765544
No 56
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=61.72 E-value=59 Score=33.46 Aligned_cols=66 Identities=17% Similarity=0.250 Sum_probs=54.0
Q ss_pred HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAK-----------YLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~-----------YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
..+-..|+++|+..|.-..+.+|+..|-+-..| .|.+|...|..+|...|....+..||..|+..-
T Consensus 430 ~~~~~~i~~~~~~~~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 430 RQYARFIASICQKEGLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHHSS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 445568899999999999999999999887654 688999999999999999999999999999864
No 57
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=60.96 E-value=57 Score=31.04 Aligned_cols=50 Identities=14% Similarity=0.161 Sum_probs=44.1
Q ss_pred ccChHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473 50 AAESSALETLTLVA------AKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS 99 (281)
Q Consensus 50 sa~~sALetLTdil------~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG 99 (281)
.....|++.+.++. .+++..+...|..+|+..|+...+..||..|+..+.
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~ 283 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSE 283 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHH
Confidence 67899999999988 667778888888899988999999999999999873
No 58
>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=50.57 E-value=89 Score=32.75 Aligned_cols=64 Identities=16% Similarity=0.070 Sum_probs=52.3
Q ss_pred HHHHHHHHHHHcC-cCccChHHHHHHHHHHH-------------HHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 35 TKVAVSQICRSVG-FKAAESSALETLTLVAA-------------KYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 35 Lr~sVaqIL~~~G-Fdsa~~sALetLTdil~-------------~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
+-..|++.++..| +...+.+|++.|.+-+. +-|..|.+.|..+|...+....+..||..|++..
T Consensus 314 ~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 314 LVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 3557778787774 88899999999976544 6777888888888988899999999999998754
No 59
>smart00414 H2A Histone 2A.
Probab=48.79 E-value=58 Score=26.73 Aligned_cols=50 Identities=14% Similarity=0.048 Sum_probs=45.2
Q ss_pred cCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473 48 FKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND 97 (281)
Q Consensus 48 Fdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d 97 (281)
...+..+|.-.|+.+++-...+|...+-..|.-.++...++.|+.+|..+
T Consensus 25 ~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 25 AKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred ccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 44888999999999999999999999999999999999999999988776
No 60
>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=46.35 E-value=60 Score=29.89 Aligned_cols=44 Identities=16% Similarity=0.188 Sum_probs=40.0
Q ss_pred HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHH
Q 023473 33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAAS 76 (281)
Q Consensus 33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~ 76 (281)
..|+.=+-+||.+.|.++++..|.+.|...++.||.+|...+-.
T Consensus 206 ~~L~~Rm~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~ 249 (252)
T PF12767_consen 206 QSLRKRMEQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLD 249 (252)
T ss_pred HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56777888999999999999999999999999999999988754
No 61
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=38.11 E-value=94 Score=30.48 Aligned_cols=48 Identities=8% Similarity=0.023 Sum_probs=34.6
Q ss_pred cChHHHHHHHHHHHH-------HHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 51 AESSALETLTLVAAK-------YLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 51 a~~sALetLTdil~~-------YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
++...++.+++++.. =-.-+.+.|+.+|-+.||..+++.||..+..-.
T Consensus 268 v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~v 322 (350)
T CHL00081 268 IDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITLC 322 (350)
T ss_pred cCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 344455555555433 223567899999999999999999998877654
No 62
>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=37.11 E-value=2e+02 Score=26.93 Aligned_cols=50 Identities=10% Similarity=0.068 Sum_probs=42.1
Q ss_pred ccChHHHHHHHHHH------HHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcC
Q 023473 50 AAESSALETLTLVA------AKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVS 99 (281)
Q Consensus 50 sa~~sALetLTdil------~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmG 99 (281)
.+...+++.++++. .++...+.+.|..+|+..++...+..||..|+..+.
T Consensus 220 ~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~ 275 (365)
T TIGR02928 220 VLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIE 275 (365)
T ss_pred CCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 46788888888776 467788888888889888888999999999998874
No 63
>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=36.02 E-value=2.2e+02 Score=29.90 Aligned_cols=51 Identities=14% Similarity=0.109 Sum_probs=41.1
Q ss_pred cCccChHHHHHHHHHHHHH-------HHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 48 FKAAESSALETLTLVAAKY-------LQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 48 Fdsa~~sALetLTdil~~Y-------L~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
.-.+...+++.|.+++..+ ...+.+.|+.+|-+.||+.++..||..|++-.
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~lv 304 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAELV 304 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHH
Confidence 3355777788887777554 24577899999999999999999999998886
No 64
>TIGR01501 MthylAspMutase methylaspartate mutase, S subunit. This model represents the S (sigma) subunit of methylaspartate mutase (glutamate mutase), a cobalamin-dependent enzyme that catalyzes the first step in a pathway of glutamate fermentation.
Probab=35.68 E-value=1.2e+02 Score=25.71 Aligned_cols=20 Identities=10% Similarity=0.250 Sum_probs=14.9
Q ss_pred HHHHHHHHHHcCcCccChHH
Q 023473 36 KVAVSQICRSVGFKAAESSA 55 (281)
Q Consensus 36 r~sVaqIL~~~GFdsa~~sA 55 (281)
...|+.+|++.||+-+.-..
T Consensus 18 k~iv~~~l~~~GfeVi~LG~ 37 (134)
T TIGR01501 18 NKILDHAFTNAGFNVVNLGV 37 (134)
T ss_pred HHHHHHHHHHCCCEEEECCC
Confidence 36788899999998765443
No 65
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=33.77 E-value=2e+02 Score=22.71 Aligned_cols=47 Identities=15% Similarity=0.137 Sum_probs=37.0
Q ss_pred ccChHHHHHHHHHHH------HHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q 023473 50 AAESSALETLTLVAA------KYLQQLASRAASYSHVAHRSESNLVDLTNALN 96 (281)
Q Consensus 50 sa~~sALetLTdil~------~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~ 96 (281)
..++.+...|..++. +=+..|.+-|+..|.+.|...+...||..||.
T Consensus 42 ~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 42 PLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred CCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 345566666666654 34678889999999999999999999999985
No 66
>PF14920 MTBP_C: MDM2-binding
Probab=33.28 E-value=1.4e+02 Score=28.23 Aligned_cols=67 Identities=21% Similarity=0.268 Sum_probs=46.6
Q ss_pred hhhhcCCCCCC-CCCCCchHHHHHHHHHHHHHHHHHcCcCccCh---HHHHHHHHHHHHHHHHHHHHHHHH
Q 023473 11 HQKQNQKPPTE-QGEETPSEFAFTVTKVAVSQICRSVGFKAAES---SALETLTLVAAKYLQQLASRAASY 77 (281)
Q Consensus 11 ~~~~~~~p~~~-~~~~s~defar~lLr~sVaqIL~~~GFdsa~~---sALetLTdil~~YL~~Lg~sa~~y 77 (281)
.|++.+..-+. +.-++...=+..+|+.+|+..|+..|....+. +.-..|=+|-.-||.+|-.+=..|
T Consensus 166 ~q~~~~~~~~~~~~keSrSqKHtR~LkeVVa~tLk~hgI~e~H~cF~aCSqRLFeISKfyLKDLKTSRGL~ 236 (251)
T PF14920_consen 166 GQKSAHESKTSRQTKESRSQKHTRMLKEVVAETLKKHGITEAHECFKACSQRLFEISKFYLKDLKTSRGLF 236 (251)
T ss_pred CCcccCcccccccchhhHHHHHHHHHHHHHHHHHHHcCCcccchhHHHHHHHHHHHHHHHHHHhhhcccHH
Confidence 34444443333 35566677788999999999999999876553 556678888888888886554333
No 67
>PLN00154 histone H2A; Provisional
Probab=32.47 E-value=1.5e+02 Score=25.69 Aligned_cols=57 Identities=9% Similarity=-0.064 Sum_probs=48.7
Q ss_pred HHHHHcC-c-CccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473 41 QICRSVG-F-KAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND 97 (281)
Q Consensus 41 qIL~~~G-F-dsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d 97 (281)
.+|++-. | ..+..+|.-.|+.+++-...+|..-+-..|.-.++...++.++.+|..+
T Consensus 46 r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 46 RQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred HHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 3466654 3 4899999999999998888899999999999999999999999988866
No 68
>PF12014 DUF3506: Domain of unknown function (DUF3506); InterPro: IPR021894 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 131 to 148 amino acids in length. This domain has a conserved KLTGD sequence motif.
Probab=31.41 E-value=77 Score=27.30 Aligned_cols=32 Identities=25% Similarity=0.261 Sum_probs=22.0
Q ss_pred cCCCccccccceeeeccccCCCCccceeecCCccc
Q 023473 218 LGGDLAKEREKVRFKIGVKGNNGVGFGVDLRNGVC 252 (281)
Q Consensus 218 ~~g~~~~~r~~v~f~~~~~~~~~~g~~v~~~n~~~ 252 (281)
.-||..+-||-|+|+-..- +.+.+|...+..|
T Consensus 70 LTGDpNVPrGevtF~A~Di---G~~~~i~~a~~~~ 101 (134)
T PF12014_consen 70 LTGDPNVPRGEVTFRADDI---GPGGRIRVAHEGP 101 (134)
T ss_pred ecCCCCCcCccEEEEeccc---CCCcccccccCCC
Confidence 3799999999999997744 3334444444444
No 69
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=31.41 E-value=1.7e+02 Score=27.59 Aligned_cols=66 Identities=14% Similarity=0.095 Sum_probs=51.3
Q ss_pred HHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCCHHHHHHHHHhc
Q 023473 32 FTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAH-RSESNLVDLTNALNDV 98 (281)
Q Consensus 32 r~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaG-RT~pnl~DV~~AL~dm 98 (281)
..-+...|.+.++..|.. +++.|++.|.+.+..=+..+.+.....+..++ ....+..||...+...
T Consensus 144 ~~~l~~~i~~~~~~~g~~-i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~~ 210 (343)
T PRK06585 144 ERDLARLIDDELAEAGLR-ITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGDA 210 (343)
T ss_pred HHHHHHHHHHHHHHCCCC-CCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCCc
Confidence 345666789999999998 79999999999998877777777777776654 4568888887665554
No 70
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=30.07 E-value=2.6e+02 Score=24.57 Aligned_cols=76 Identities=16% Similarity=0.329 Sum_probs=55.9
Q ss_pred HHHHHHHHHHcCcCccChHHHHHHHHHH--------HHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC-CCCCC
Q 023473 36 KVAVSQICRSVGFKAAESSALETLTLVA--------AKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSG-QGFPG 106 (281)
Q Consensus 36 r~sVaqIL~~~GFdsa~~sALetLTdil--------~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~-~gF~g 106 (281)
+--+..|+++.||...++.+.+.+.++= ..||.-++.... ....-.++..||+-+..+ .|.
T Consensus 39 ~~el~~ilr~lg~~~s~~ei~~l~~~~d~~~~~idf~~Fl~~ms~~~~--------~~~~~Eel~~aF~~fD~d~dG~-- 108 (160)
T COG5126 39 RNELGKILRSLGFNPSEAEINKLFEEIDAGNETVDFPEFLTVMSVKLK--------RGDKEEELREAFKLFDKDHDGY-- 108 (160)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHhccCCCCccCHHHHHHHHHHHhc--------cCCcHHHHHHHHHHhCCCCCce--
Confidence 3456788999999999999999998775 466666665543 346789999999999765 333
Q ss_pred CCcccccccccchhhHHHHhhhhhcCC
Q 023473 107 ASALNRNCMLDSGVLKEIAGFVRHGCE 133 (281)
Q Consensus 107 ~s~~~~~~ll~S~~l~eL~~yv~~~~~ 133 (281)
| .+.+|..+++...+
T Consensus 109 ---I---------s~~eL~~vl~~lge 123 (160)
T COG5126 109 ---I---------SIGELRRVLKSLGE 123 (160)
T ss_pred ---e---------cHHHHHHHHHhhcc
Confidence 2 27788888875443
No 71
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=29.79 E-value=2.6e+02 Score=25.82 Aligned_cols=64 Identities=19% Similarity=0.185 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 34 VTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 34 lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
-+...|.+.|+..|.. +++.|++.|.+.+..=+..+-......+..++=...+..||...+..-
T Consensus 150 ~~~~~i~~~~~~~g~~-i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~It~~~I~~~i~~~ 213 (340)
T PRK05574 150 ELPQWIQQRLKQQGLQ-IDAAALQLLAERVEGNLLALAQELEKLALLYPDGKITLEDVEEAVPDS 213 (340)
T ss_pred HHHHHHHHHHHHcCCC-CCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCCCCHHHHHHHHhhh
Confidence 3566788899999995 888999999999987777888888887777642238888887766554
No 72
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=27.88 E-value=2.3e+02 Score=26.31 Aligned_cols=62 Identities=15% Similarity=0.150 Sum_probs=50.2
Q ss_pred HHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhc--CCCCCCHHHHHHHHHh
Q 023473 35 TKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVA--HRSESNLVDLTNALND 97 (281)
Q Consensus 35 Lr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAela--GRT~pnl~DV~~AL~d 97 (281)
+..-|.+.++..|.. +++.|++.|.+.+..=+..+.+.....+..+ ++...+..||.....+
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 667788899999998 8999999999999888888888888888764 3556788888766544
No 73
>PTZ00017 histone H2A; Provisional
Probab=27.42 E-value=1.5e+02 Score=25.46 Aligned_cols=50 Identities=12% Similarity=0.042 Sum_probs=45.2
Q ss_pred cCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473 48 FKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND 97 (281)
Q Consensus 48 Fdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d 97 (281)
...+...|.-.|+.+++-...+|...+-..|.-.+++..++.++.+|..+
T Consensus 43 a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 43 AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 34788889999999999999999999999999999999999999999876
No 74
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.02 E-value=58 Score=29.34 Aligned_cols=90 Identities=19% Similarity=0.157 Sum_probs=60.3
Q ss_pred HHHHHHHHHHHHHcCcCcc---------ChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCCCCC
Q 023473 33 TVTKVAVSQICRSVGFKAA---------ESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSSGQG 103 (281)
Q Consensus 33 ~lLr~sVaqIL~~~GFdsa---------~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi~~g 103 (281)
.-|-.++++-|..-||.-. =-.=-|+|.+-+..||.-+|=+.+..+...|-..-.+.|+ ..+-++|.+
T Consensus 67 ~~l~~a~s~~L~d~~F~f~LlLpe~e~~vf~rADAL~eW~nhFL~GlGL~~~~l~~~~gE~~EaldDL-~~iaQlg~D-- 143 (186)
T COG3079 67 EQLLQATSQQLEDDGFAFQLLLPEGEDVVFDRADALAEWCNHFLLGLGLTQPKLSKLTGEAGEALDDL-ANIAQLGYD-- 143 (186)
T ss_pred HHHHHHHHHHhcCCCeEEEEecCCCCcHHHHHHHHHHHHHHHHHHhhcccccchhhhcccHHHHHHHH-HHHHHhcCC--
Confidence 4455677778888887521 1222466777778888888888888888888776667776 556666653
Q ss_pred CCCCCcccccccccchhhHHHHhhhhhc
Q 023473 104 FPGASALNRNCMLDSGVLKEIAGFVRHG 131 (281)
Q Consensus 104 F~g~s~~~~~~ll~S~~l~eL~~yv~~~ 131 (281)
.+.+.-....+++++++|++-.
T Consensus 144 ------eded~EE~~~~leEiiEyvRva 165 (186)
T COG3079 144 ------EDEDQEELEESLEEIIEYVRVA 165 (186)
T ss_pred ------ccccHHHHHHHHHHHHHHHHHH
Confidence 2212223366799999999764
No 75
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=24.65 E-value=2.3e+02 Score=26.05 Aligned_cols=62 Identities=18% Similarity=0.162 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 34 VTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 34 lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
-+...+.++|+..|.. +.+.|++.|......-+..+......++. +....+..||..++.+.
T Consensus 188 ~~~~~l~~~~~~~~~~-~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~~ 249 (337)
T PRK12402 188 ELVDVLESIAEAEGVD-YDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGDV 249 (337)
T ss_pred HHHHHHHHHHHHcCCC-CCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCCC
Confidence 4566677788888987 88999999998887667777666666662 22357778887766653
No 76
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=23.97 E-value=2.5e+02 Score=27.28 Aligned_cols=31 Identities=16% Similarity=0.131 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 68 QQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 68 ~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
..+.+.|+.+|-+.||...+..||..+..-.
T Consensus 279 i~l~raArA~Aal~GR~~V~~dDv~~~a~~v 309 (337)
T TIGR02030 279 LTLNRAAKALAAFEGRTEVTVDDIRRVAVLA 309 (337)
T ss_pred HHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 3477899999999999999999998766553
No 77
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=22.91 E-value=2.8e+02 Score=28.95 Aligned_cols=49 Identities=22% Similarity=0.152 Sum_probs=37.4
Q ss_pred ccChHHHHHHHHHHHHHH-------HHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 50 AAESSALETLTLVAAKYL-------QQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 50 sa~~sALetLTdil~~YL-------~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
.+....++.|.+++.++- ..+.+.|+.+|-+.||+.++..||..|..-.
T Consensus 203 ~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~lv 258 (589)
T TIGR02031 203 TISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVELV 258 (589)
T ss_pred cCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence 345566666666664432 2467889999999999999999999998876
No 78
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=21.52 E-value=4.8e+02 Score=23.55 Aligned_cols=65 Identities=15% Similarity=0.201 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhc
Q 023473 33 TVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALNDV 98 (281)
Q Consensus 33 ~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dm 98 (281)
.-+...|.++++..|.+ +++.|++.|.+.+..=+..+-......+..++-...+..||...+..-
T Consensus 114 ~~~~~~i~~~~~~~g~~-i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~~ 178 (302)
T TIGR01128 114 QELPRWIQARLKKLGLR-IDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSDS 178 (302)
T ss_pred HHHHHHHHHHHHHcCCC-CCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhhh
Confidence 44556788888888886 788899999888866566666666665555543357778887666543
No 79
>PF02130 UPF0054: Uncharacterized protein family UPF0054; InterPro: IPR002036 These, as yet, uncharacterised proteins are of 17 to 21 kDa. They contain a conserved region with three histidines at the C terminus. The protein family is represented by a single member sequence only in nearly every bacterium. The crystal structure of the protein from the hyperthermophilic bacteria Aquifex aeolicus has been determined. The overall fold consists of one central alpha-helix surrounded by a four-stranded beta-sheet and four other alpha-helices. Structure-based homology analysis reveals a good resemblance to the metal-dependent proteinases such as collagenases and gelatinases. However, experimental tests for collagenase and gelatinase-type function show no detectable activity under standard assay conditions [].; GO: 0046872 metal ion binding; PDB: 1TVI_A 1OZ9_A 1XM5_A 1XAX_A.
Probab=21.31 E-value=2.3e+02 Score=24.02 Aligned_cols=44 Identities=14% Similarity=0.318 Sum_probs=35.5
Q ss_pred hHHHHHHHHHHHHHHHHHcCcCccChHHHHHHHHHHHHHHHHHH
Q 023473 28 SEFAFTVTKVAVSQICRSVGFKAAESSALETLTLVAAKYLQQLA 71 (281)
Q Consensus 28 defar~lLr~sVaqIL~~~GFdsa~~sALetLTdil~~YL~~Lg 71 (281)
..|.+.++..+|--+|.=.|||..++.--..+..+=.++|..+|
T Consensus 102 ~~~~~el~~l~vHG~LHLlGyDH~~~~~~~~M~~~E~~il~~lg 145 (145)
T PF02130_consen 102 HSFEEELARLLVHGLLHLLGYDHETEEEAEEMEALEEEILKKLG 145 (145)
T ss_dssp S-HHHHHHHHHHHHHHHHTT-SSTTTHHHHHHHHHHHHHHHHTT
T ss_pred CChHHHHhHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHhcC
Confidence 45888999999999999999999988877777777777777654
No 80
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=21.18 E-value=4.9e+02 Score=23.73 Aligned_cols=65 Identities=15% Similarity=0.076 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHcCcCccChHHHHHHHHHHH---HHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHhcCC
Q 023473 35 TKVAVSQICRSVGFKAAESSALETLTLVAA---KYLQQLASRAASYSHVAHRSESNLVDLTNALNDVSS 100 (281)
Q Consensus 35 Lr~sVaqIL~~~GFdsa~~sALetLTdil~---~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~dmGi 100 (281)
++..+..++...+. .+++.|++.|..... +.+..++..+..+|...+....+..++..++..++.
T Consensus 164 ~~~il~~~~~~~~~-~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~ 231 (305)
T TIGR00635 164 LAEIVSRSAGLLNV-EIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMI 231 (305)
T ss_pred HHHHHHHHHHHhCC-CcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCC
Confidence 33444455555566 478889999888764 345666777777777666666889999999998754
No 81
>cd02071 MM_CoA_mut_B12_BD methylmalonyl CoA mutase B12 binding domain. This domain binds to B12 (adenosylcobamide), which initiates the conversion of succinyl CoA and methylmalonyl CoA by forming an adenosyl radical, which then undergoes a rearrangement exchanging a hydrogen atom with a group attached to a neighboring carbon atom. This family is present in both mammals and bacteria. Bacterial members are heterodimers and involved in the fermentation of pyruvate to propionate. Mammalian members are homodimers and responsible for the conversion of odd-chain fatty acids and branched-chain amino acids via propionyl CoA to succinyl CoA for further degradation.
Probab=21.02 E-value=4.4e+02 Score=21.14 Aligned_cols=82 Identities=12% Similarity=0.129 Sum_probs=43.0
Q ss_pred HHHHHHHHHcCcCccChHH---HHHHHHHH--------------HHHHHHHHHHHHHHHHhcCCCCC------CHHHHHH
Q 023473 37 VAVSQICRSVGFKAAESSA---LETLTLVA--------------AKYLQQLASRAASYSHVAHRSES------NLVDLTN 93 (281)
Q Consensus 37 ~sVaqIL~~~GFdsa~~sA---LetLTdil--------------~~YL~~Lg~sa~~yAelaGRT~p------nl~DV~~ 93 (281)
..++.+++..||+.+...+ .+.+.+.+ ..|+..+-..+....+..-+.-+ .+.|...
T Consensus 17 ~~~~~~l~~~G~~vi~lG~~vp~e~~~~~a~~~~~d~V~iS~~~~~~~~~~~~~~~~L~~~~~~~i~i~~GG~~~~~~~~ 96 (122)
T cd02071 17 KVIARALRDAGFEVIYTGLRQTPEEIVEAAIQEDVDVIGLSSLSGGHMTLFPEVIELLRELGAGDILVVGGGIIPPEDYE 96 (122)
T ss_pred HHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHcCCCEEEEcccchhhHHHHHHHHHHHHhcCCCCCEEEEECCCCHHHHH
Confidence 5677889999998665444 33333322 33444444434443333111110 2456667
Q ss_pred HHHhcCCCCCCCCCCcccccccccchhhHHHHhhhh
Q 023473 94 ALNDVSSGQGFPGASALNRNCMLDSGVLKEIAGFVR 129 (281)
Q Consensus 94 AL~dmGi~~gF~g~s~~~~~~ll~S~~l~eL~~yv~ 129 (281)
.|..+|++..|...+ ..++...|++
T Consensus 97 ~~~~~G~d~~~~~~~-----------~~~~~~~~~~ 121 (122)
T cd02071 97 LLKEMGVAEIFGPGT-----------SIEEIIDKIR 121 (122)
T ss_pred HHHHCCCCEEECCCC-----------CHHHHHHHHh
Confidence 788888753333222 2667766664
No 82
>PLN00157 histone H2A; Provisional
Probab=20.28 E-value=2.4e+02 Score=24.20 Aligned_cols=50 Identities=12% Similarity=0.011 Sum_probs=44.2
Q ss_pred cCccChHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHh
Q 023473 48 FKAAESSALETLTLVAAKYLQQLASRAASYSHVAHRSESNLVDLTNALND 97 (281)
Q Consensus 48 Fdsa~~sALetLTdil~~YL~~Lg~sa~~yAelaGRT~pnl~DV~~AL~d 97 (281)
...+...|.-.|+.+++-...+|...+-..|.-.+++..++.++.+|..+
T Consensus 42 a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 42 ATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred hhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 45778888999999998888899999999999999999999999988765
No 83
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=20.19 E-value=2.1e+02 Score=22.50 Aligned_cols=49 Identities=12% Similarity=0.134 Sum_probs=35.7
Q ss_pred hHHHHHHHHHHHHHHHHH-HHHHHHHHHhcCCCCCCHHHHHHHHHhcCCC
Q 023473 53 SSALETLTLVAAKYLQQL-ASRAASYSHVAHRSESNLVDLTNALNDVSSG 101 (281)
Q Consensus 53 ~sALetLTdil~~YL~~L-g~sa~~yAelaGRT~pnl~DV~~AL~dmGi~ 101 (281)
+--.+.|..|+..|+..= .-.++..|+.-++...++-....+|++||..
T Consensus 4 ~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlv 53 (78)
T PF03444_consen 4 ERQREILKALVELYIETGEPVGSKTIAEELGRSPATIRNEMADLEELGLV 53 (78)
T ss_pred HHHHHHHHHHHHHHHhcCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCc
Confidence 344678888888888741 1223445566788889999999999999875
No 84
>PF01388 ARID: ARID/BRIGHT DNA binding domain; InterPro: IPR001606 Members of the recently discovered ARID (AT-rich interaction domain; also known as BRIGHT domain)) family of DNA-binding proteins are found in fungi and invertebrate and vertebrate metazoans. ARID-encoding genes are involved in a variety of biological processes including embryonic development, cell lineage gene regulation and cell cycle control. Although the specific roles of this domain and of ARID-containing proteins in transcriptional regulation are yet to be elucidated, they include both positive and negative transcriptional regulation and a likely involvement in the modification of chromatin structure []. The basic structure of the ARID domain domain appears to be a series of six alpha-helices separated by beta-strands, loops, or turns, but the structured region may extend to an additional helix at either or both ends of the basic six. Based on primary sequence homology, they can be partitioned into three structural classes: Minimal ARID proteins that consist of a core domain formed by six alpha helices; ARID proteins that supplement the core domain with an N-terminal alpha-helix; and Extended-ARID proteins, which contain the core domain and additional alpha-helices at their N- and C-termini. The human SWI-SNF complex protein p270 is an ARID family member with non-sequence-specific DNA binding activity. The ARID consensus and other structural features are common to both p270 and yeast SWI1, suggesting that p270 is a human counterpart of SWI1 []. The approximately 100-residue ARID sequence is present in a series of proteins strongly implicated in the regulation of cell growth, development, and tissue-specific gene expression. Although about a dozen ARID proteins can be identified from database searches, to date, only Bright (a regulator of B-cell-specific gene expression), dead ringer (a Drosophila melanogaster gene product required for normal development), and MRF-2 (which represses expression from the Cytomegalovirus enhancer) have been analyzed directly in regard to their DNA binding properties. Each binds preferentially to AT-rich sites. In contrast, p270 shows no sequence preference in its DNA binding activity, thereby demonstrating that AT-rich binding is not an intrinsic property of ARID domains and that ARID family proteins may be involved in a wider range of DNA interactions [].; GO: 0003677 DNA binding, 0005622 intracellular; PDB: 1C20_A 1KQQ_A 2JRZ_A 2LM1_A 2YQE_A 2JXJ_A 2EH9_A 2CXY_A 2LI6_A 1KN5_A ....
Probab=20.18 E-value=1.6e+02 Score=22.39 Aligned_cols=31 Identities=29% Similarity=0.447 Sum_probs=25.8
Q ss_pred HHHHHHHcCcCccChHHHHHHHHHHHHHHHH
Q 023473 39 VSQICRSVGFKAAESSALETLTLVAAKYLQQ 69 (281)
Q Consensus 39 VaqIL~~~GFdsa~~sALetLTdil~~YL~~ 69 (281)
-..|++..||.....++...|..++.+||..
T Consensus 60 W~~va~~lg~~~~~~~~~~~L~~~Y~~~L~~ 90 (92)
T PF01388_consen 60 WREVARKLGFPPSSTSAAQQLRQHYEKYLLP 90 (92)
T ss_dssp HHHHHHHTTS-TTSCHHHHHHHHHHHHHTHH
T ss_pred HHHHHHHhCCCCCCCcHHHHHHHHHHHHhHh
Confidence 4568999999998888889999999999864
Done!