Query 032664
Match_columns 136
No_of_seqs 159 out of 652
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 04:22:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032664.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032664hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00018 histone H3; Provision 100.0 4.3E-56 9.2E-61 330.2 11.7 135 1-135 1-135 (136)
2 PLN00121 histone H3; Provision 100.0 5.5E-56 1.2E-60 329.6 11.6 136 1-136 1-136 (136)
3 PLN00161 histone H3; Provision 100.0 1.7E-54 3.7E-59 320.6 11.2 128 1-135 1-129 (135)
4 KOG1745 Histones H3 and H4 [Ch 100.0 7E-52 1.5E-56 306.8 8.4 136 1-136 1-137 (137)
5 smart00428 H3 Histone H3. 100.0 3E-47 6.6E-52 272.4 10.0 101 35-135 2-104 (105)
6 PLN00160 histone H3; Provision 100.0 7.9E-47 1.7E-51 266.7 8.9 94 42-135 1-95 (97)
7 COG2036 HHT1 Histones H3 and H 99.9 6.2E-27 1.3E-31 163.8 7.8 87 44-135 1-87 (91)
8 PF00125 Histone: Core histone 99.8 4.1E-21 8.9E-26 128.0 6.9 75 58-132 1-75 (75)
9 cd07981 TAF12 TATA Binding Pro 99.4 9.5E-13 2E-17 88.2 7.9 58 73-130 8-65 (72)
10 cd00076 H4 Histone H4, one of 99.3 2.2E-11 4.8E-16 84.4 7.1 68 62-134 13-80 (85)
11 PLN00035 histone H4; Provision 99.2 3.5E-11 7.7E-16 86.0 7.2 67 63-134 30-96 (103)
12 PTZ00015 histone H4; Provision 99.2 5.1E-11 1.1E-15 85.1 7.0 69 61-134 29-97 (102)
13 smart00803 TAF TATA box bindin 99.1 9.5E-11 2.1E-15 77.3 5.7 64 62-130 2-65 (65)
14 PTZ00463 histone H2B; Provisio 99.1 5.2E-10 1.1E-14 81.4 7.1 65 64-132 26-94 (117)
15 PLN00158 histone H2B; Provisio 99.1 6.6E-10 1.4E-14 80.8 7.2 65 64-132 25-93 (116)
16 smart00417 H4 Histone H4. 99.0 3.1E-10 6.7E-15 76.9 4.8 61 62-127 13-73 (74)
17 smart00427 H2B Histone H2B. 99.0 9.4E-10 2E-14 76.8 7.4 62 67-132 2-67 (89)
18 cd07979 TAF9 TATA Binding Prot 98.8 3.9E-08 8.4E-13 71.6 8.0 65 69-134 4-68 (117)
19 PF00808 CBFD_NFYB_HMF: Histon 98.7 5.6E-08 1.2E-12 63.2 6.8 63 63-129 3-65 (65)
20 KOG1744 Histone H2B [Chromatin 98.7 3E-08 6.6E-13 73.2 5.6 66 63-132 34-103 (127)
21 cd00074 H2A Histone 2A; H2A is 98.3 9.3E-07 2E-11 64.4 4.9 67 60-130 18-84 (115)
22 KOG0870 DNA polymerase epsilon 98.3 2.6E-06 5.7E-11 65.5 6.5 69 60-130 8-76 (172)
23 smart00576 BTP Bromodomain tra 98.3 5.2E-06 1.1E-10 55.9 7.1 54 81-134 20-73 (77)
24 PF15630 CENP-S: Kinetochore c 98.2 2.9E-06 6.2E-11 57.7 5.7 64 67-130 6-71 (76)
25 PF03847 TFIID_20kDa: Transcri 98.2 5.5E-06 1.2E-10 55.2 6.8 58 73-130 6-63 (68)
26 PF02969 TAF: TATA box binding 98.0 3.1E-05 6.6E-10 51.4 7.1 58 72-130 9-66 (66)
27 cd08050 TAF6 TATA Binding Prot 98.0 2.7E-05 5.8E-10 65.7 7.5 62 72-134 5-66 (343)
28 PF02291 TFIID-31kDa: Transcri 97.9 7.5E-05 1.6E-09 55.4 7.4 65 69-134 15-79 (129)
29 PF15511 CENP-T: Centromere ki 97.7 5.7E-05 1.2E-09 65.3 5.6 62 63-124 352-414 (414)
30 KOG1142 Transcription initiati 97.7 4.4E-05 9.5E-10 62.4 4.5 73 54-130 146-218 (258)
31 KOG0869 CCAAT-binding factor, 97.3 0.0006 1.3E-08 52.3 6.0 71 60-133 30-100 (168)
32 KOG3334 Transcription initiati 96.8 0.0084 1.8E-07 45.4 7.6 65 70-135 17-81 (148)
33 KOG3467 Histone H4 [Chromatin 96.7 0.0064 1.4E-07 42.7 5.9 65 65-134 32-96 (103)
34 PF07524 Bromo_TP: Bromodomain 96.6 0.011 2.5E-07 39.3 6.5 52 83-134 22-73 (77)
35 KOG0871 Class 2 transcription 96.4 0.012 2.6E-07 44.8 6.2 72 59-133 9-80 (156)
36 PLN00154 histone H2A; Provisio 95.7 0.025 5.4E-07 42.4 4.9 68 60-130 36-103 (136)
37 smart00414 H2A Histone 2A. 95.6 0.02 4.3E-07 41.2 3.9 67 60-130 7-73 (106)
38 PTZ00017 histone H2A; Provisio 95.4 0.02 4.3E-07 42.9 3.5 67 60-130 25-91 (134)
39 COG5262 HTA1 Histone H2A [Chro 95.0 0.049 1.1E-06 40.2 4.5 58 73-130 33-90 (132)
40 PLN00156 histone H2AX; Provisi 94.3 0.058 1.3E-06 40.6 3.7 67 60-130 27-93 (139)
41 PLN00157 histone H2A; Provisio 94.3 0.047 1E-06 40.8 3.1 67 60-130 24-90 (132)
42 KOG2549 Transcription initiati 94.1 0.18 3.8E-06 45.6 6.8 53 81-133 25-77 (576)
43 PLN00153 histone H2A; Provisio 94.0 0.07 1.5E-06 39.7 3.4 67 60-130 22-88 (129)
44 PF02269 TFIID-18kDa: Transcri 93.8 0.053 1.2E-06 37.8 2.5 59 72-130 7-65 (93)
45 COG5150 Class 2 transcription 93.6 0.26 5.7E-06 36.8 6.0 70 59-131 8-77 (148)
46 PTZ00252 histone H2A; Provisio 93.3 0.13 2.7E-06 38.6 3.8 67 60-130 23-91 (134)
47 COG5094 TAF9 Transcription ini 92.3 0.58 1.3E-05 34.9 6.1 47 85-131 32-81 (145)
48 KOG1756 Histone 2A [Chromatin 91.1 0.34 7.3E-06 36.1 3.8 66 61-130 26-91 (131)
49 KOG4336 TBP-associated transcr 90.7 1.1 2.4E-05 37.8 7.0 51 84-134 22-72 (323)
50 cd08045 TAF4 TATA Binding Prot 90.7 0.74 1.6E-05 36.2 5.7 56 60-116 42-97 (212)
51 COG5208 HAP5 CCAAT-binding fac 90.4 0.83 1.8E-05 37.2 5.8 85 45-130 80-173 (286)
52 PF05236 TAF4: Transcription i 89.2 0.38 8.3E-06 39.0 3.1 58 60-118 41-98 (264)
53 cd07978 TAF13 The TATA Binding 89.2 3.7 8E-05 28.6 7.7 58 72-130 8-65 (92)
54 KOG1657 CCAAT-binding factor, 86.3 1.5 3.2E-05 35.7 4.8 73 57-130 66-138 (236)
55 PF09415 CENP-X: CENP-S associ 84.1 1.9 4.2E-05 28.8 3.8 57 71-127 4-63 (72)
56 COG5248 TAF19 Transcription in 80.5 13 0.00027 27.3 7.1 61 68-130 11-71 (126)
57 KOG3901 Transcription initiati 76.9 19 0.00041 26.0 7.1 63 65-130 8-70 (109)
58 PF09123 DUF1931: Domain of un 74.0 5.9 0.00013 29.8 4.0 59 68-131 1-59 (138)
59 COG5095 TAF6 Transcription ini 73.1 8.3 0.00018 33.3 5.2 52 82-133 20-71 (450)
60 KOG2389 Predicted bromodomain 72.1 11 0.00024 32.4 5.7 53 81-133 43-95 (353)
61 PF13654 AAA_32: AAA domain; P 65.2 41 0.0009 30.1 8.2 67 66-133 430-507 (509)
62 KOG1757 Histone 2A [Chromatin 64.2 11 0.00024 27.7 3.6 67 66-134 31-97 (131)
63 cd08048 TAF11 TATA Binding Pro 63.4 45 0.00098 22.8 7.5 64 63-131 17-83 (85)
64 PF07278 DUF1441: Protein of u 60.7 38 0.00082 25.8 6.2 65 48-112 75-150 (152)
65 KOG1658 DNA polymerase epsilon 60.6 6.4 0.00014 30.3 1.9 64 64-129 58-122 (162)
66 COG1224 TIP49 DNA helicase TIP 59.8 21 0.00046 31.4 5.2 72 61-132 354-432 (450)
67 TIGR00764 lon_rel lon-related 59.7 53 0.0012 30.0 8.0 64 69-132 315-391 (608)
68 PRK07452 DNA polymerase III su 58.3 37 0.00079 27.6 6.2 59 69-129 136-196 (326)
69 TIGR02902 spore_lonB ATP-depen 56.3 48 0.001 29.6 7.0 50 81-130 279-330 (531)
70 COG5624 TAF61 Transcription in 54.7 3.3 7E-05 36.6 -0.6 57 73-129 390-447 (505)
71 TIGR03015 pepcterm_ATPase puta 53.1 61 0.0013 25.1 6.5 49 82-130 213-264 (269)
72 PRK05907 hypothetical protein; 49.2 51 0.0011 27.5 5.7 67 63-129 131-200 (311)
73 PF04719 TAFII28: hTAFII28-lik 45.8 1E+02 0.0022 21.4 7.0 64 63-130 24-88 (90)
74 TIGR01128 holA DNA polymerase 44.8 1.3E+02 0.0027 23.8 7.2 61 69-131 117-177 (302)
75 KOG2680 DNA helicase TIP49, TB 43.7 93 0.002 27.2 6.4 72 61-132 351-429 (454)
76 KOG3219 Transcription initiati 43.0 42 0.00091 26.7 4.0 78 51-133 101-179 (195)
77 PRK08487 DNA polymerase III su 43.0 1E+02 0.0022 25.4 6.6 47 81-129 151-197 (328)
78 TIGR02030 BchI-ChlI magnesium 42.5 91 0.002 26.3 6.3 51 81-131 251-308 (337)
79 PF08369 PCP_red: Proto-chloro 36.9 58 0.0013 19.6 3.1 43 85-128 1-44 (45)
80 PF08157 NUC129: NUC129 domain 34.3 59 0.0013 21.3 3.0 43 87-129 9-59 (63)
81 PRK05629 hypothetical protein; 33.8 1.5E+02 0.0033 24.1 6.2 59 70-129 130-189 (318)
82 PRK10840 transcriptional regul 33.8 46 0.001 24.9 2.9 28 97-124 182-214 (216)
83 KOG1659 Class 2 transcription 33.8 1.4E+02 0.0031 24.2 5.8 65 63-129 11-76 (224)
84 PRK06585 holA DNA polymerase I 32.5 1.4E+02 0.003 24.4 5.8 50 81-130 158-208 (343)
85 COG1466 HolA DNA polymerase II 32.4 1.5E+02 0.0032 24.6 6.0 49 81-129 156-204 (334)
86 TIGR01924 rsbW_low_gc serine-p 29.5 1.1E+02 0.0025 22.5 4.4 45 65-109 15-59 (159)
87 PF13581 HATPase_c_2: Histidin 29.5 1.3E+02 0.0027 20.5 4.4 42 70-111 9-50 (125)
88 KOG1942 DNA helicase, TBP-inte 29.2 1.6E+02 0.0034 25.7 5.6 51 81-131 383-437 (456)
89 PF10911 DUF2717: Protein of u 28.1 96 0.0021 21.1 3.4 60 49-111 2-64 (77)
90 PF07962 Swi3: Replication For 27.1 92 0.002 21.0 3.2 29 47-75 34-62 (83)
91 TIGR02442 Cob-chelat-sub cobal 26.4 1.9E+02 0.004 26.5 6.0 51 81-131 246-303 (633)
92 smart00350 MCM minichromosome 26.3 2.2E+02 0.0047 25.2 6.2 39 83-132 466-504 (509)
93 CHL00081 chlI Mg-protoporyphyr 25.7 2.5E+02 0.0055 24.0 6.3 51 81-131 264-321 (350)
94 PF04604 L_biotic_typeA: Type- 25.3 63 0.0014 20.4 1.9 20 88-107 7-26 (51)
95 PF10788 DUF2603: Protein of u 24.9 59 0.0013 24.4 2.1 32 46-78 97-128 (137)
96 PRK07914 hypothetical protein; 24.4 2.3E+02 0.005 23.1 5.7 60 69-129 131-191 (320)
97 PF13060 DUF3921: Protein of u 24.3 1.7E+02 0.0037 18.5 3.8 29 80-108 21-49 (58)
98 PRK00411 cdc6 cell division co 24.2 4.1E+02 0.0089 21.9 7.9 47 84-130 228-280 (394)
99 cd00913 PCD_DCoH_subfamily_a P 22.8 55 0.0012 21.4 1.4 13 119-131 61-73 (76)
100 PF12767 SAGA-Tad1: Transcript 22.7 1.4E+02 0.0031 23.8 4.1 31 81-111 219-250 (252)
101 PRK05574 holA DNA polymerase I 22.5 4.1E+02 0.0089 21.3 7.3 50 81-131 162-212 (340)
102 PRK04069 serine-protein kinase 22.4 1.8E+02 0.0038 21.4 4.3 44 65-108 15-58 (161)
103 PRK13407 bchI magnesium chelat 22.3 2.6E+02 0.0057 23.6 5.8 51 81-131 248-305 (334)
104 cd00488 PCD_DCoH PCD_DCoH: The 21.1 63 0.0014 21.0 1.4 13 120-132 61-73 (75)
105 COG5304 Uncharacterized protei 20.9 69 0.0015 22.5 1.6 17 63-79 72-88 (92)
106 PF08681 DUF1778: Protein of u 20.1 1.9E+02 0.004 19.1 3.6 51 82-132 3-61 (80)
No 1
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=4.3e-56 Score=330.19 Aligned_cols=135 Identities=96% Similarity=1.324 Sum_probs=129.7
Q ss_pred CCcccccccccCCCCCCCchhhhhhhccCCCCCCCCCCccccCCCchhhHHHhhhhhhhhhhhhcCchhHHHHHHHhhhc
Q 032664 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 MartK~~a~ks~g~kaprk~~~~k~~~~~~p~~~~~~k~~r~~pg~~~l~EIr~~q~st~llipk~pF~RlVreI~~~~~ 80 (136)
|||||+++++++|+++|+++.++++..++.+..++.++++||+||+++|+|||+||+||+|||||+||+||||||++++.
T Consensus 1 MaRtk~~~~k~~~~~~prk~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PTZ00018 1 MARTKQTARKSTGGKAPRKQLASKAARKSAPVTGGIKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCCchhHHHHHHHHcccchhccccccHHHHHHHHHHHcC
Confidence 99999999999999999999988877777777778899999999999999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhccc
Q 032664 81 TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~~ 135 (136)
.++||+++||++||||+|+|||+||||+|+||+||||||||++||+|+.+|||++
T Consensus 81 ~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~ 135 (136)
T PTZ00018 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
T ss_pred CcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHHHhcccC
Confidence 9999999999999999999999999999999999999999999999999999986
No 2
>PLN00121 histone H3; Provisional
Probab=100.00 E-value=5.5e-56 Score=329.60 Aligned_cols=136 Identities=99% Similarity=1.330 Sum_probs=130.6
Q ss_pred CCcccccccccCCCCCCCchhhhhhhccCCCCCCCCCCccccCCCchhhHHHhhhhhhhhhhhhcCchhHHHHHHHhhhc
Q 032664 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 MartK~~a~ks~g~kaprk~~~~k~~~~~~p~~~~~~k~~r~~pg~~~l~EIr~~q~st~llipk~pF~RlVreI~~~~~ 80 (136)
|||||+++++++|+++|+++.++++..++.+..++.++++||+||+++|+|||+||+||+|||||+||+||||||++++.
T Consensus 1 MaRtk~~~~k~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~r~rpGt~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~ 80 (136)
T PLN00121 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
T ss_pred CCCCCcCccCCCCCCCCcccccccccccCCCCCCCCCCCcccCchhHHHHHHHHhccccccccccccHHHHHHHHHHHhC
Confidence 99999999999999999999988877777777788899999999999999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcccC
Q 032664 81 TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~~~ 136 (136)
+++||+++||++||||+|+|||+||||+|+||+|+||||||++||+|+.+|||+++
T Consensus 81 ~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~rirg~~~ 136 (136)
T PLN00121 81 TDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
T ss_pred ccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHHHhccccC
Confidence 99999999999999999999999999999999999999999999999999999864
No 3
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=1.7e-54 Score=320.56 Aligned_cols=128 Identities=65% Similarity=0.941 Sum_probs=118.9
Q ss_pred CCcccccccccCCCCCCCchhhhhhhccCCCCCCCCCCccccCCCchhhHHHhhhhhhhhhhhhcCchhHHHHHHHhhhc
Q 032664 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 MartK~~a~ks~g~kaprk~~~~k~~~~~~p~~~~~~k~~r~~pg~~~l~EIr~~q~st~llipk~pF~RlVreI~~~~~ 80 (136)
||||||+ +++++|+.|++++..+ ...+++++++||+||+++|+|||+||+||++|||++||+||||||++++.
T Consensus 1 mar~k~~-~~~~~~~~~~~~~~~~------~~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RLVREI~~~~~ 73 (135)
T PLN00161 1 MARRLQG-KRFRKGKKPQKEASGV------TRQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEML 73 (135)
T ss_pred CCccccc-ccccCCCCCcccCCCC------CCCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHHHHHHHHhcC
Confidence 9999999 7788999998887653 13456689999999999999999999999999999999999999999996
Q ss_pred -ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhccc
Q 032664 81 -TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 81 -~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~~ 135 (136)
.++||+++||+|||||+|+|||++|||+|+||+||||||||++||+||.+|||+.
T Consensus 74 ~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~ 129 (135)
T PLN00161 74 REPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPI 129 (135)
T ss_pred CCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhcccc
Confidence 5899999999999999999999999999999999999999999999999999975
No 4
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=100.00 E-value=7e-52 Score=306.84 Aligned_cols=136 Identities=96% Similarity=1.301 Sum_probs=128.9
Q ss_pred CCcccccccccCCCCCCCchhhhhhhccC-CCCCCCCCCccccCCCchhhHHHhhhhhhhhhhhhcCchhHHHHHHHhhh
Q 032664 1 MARTKQTARKSTGGKAPRKQLATKAARKS-APATGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDF 79 (136)
Q Consensus 1 MartK~~a~ks~g~kaprk~~~~k~~~~~-~p~~~~~~k~~r~~pg~~~l~EIr~~q~st~llipk~pF~RlVreI~~~~ 79 (136)
|+|++++++++.++++|++..+.+..+++ .|..+...++++|+||+++++|||+||+||+|||+|+||+|||+||.++|
T Consensus 1 m~r~~~t~~k~~~~~~~r~~~a~~~~~~~~~~~~~~~~k~~r~rpg~~al~eirkyQkstdLlI~K~PFqRlvrei~q~f 80 (137)
T KOG1745|consen 1 MARTKQTARKSTGGKAPRKQLAGKAARKSAAPRTGRVKKPHRYRPGTVALREIRKYQKSTDLLIRKLPFQRLVREIAQDF 80 (137)
T ss_pred CCCCCcccccccCCCCCccccccccccccccccccccCccccccCchHHHHHHHHHHhhhHHHhhcCcHHHHhHHHHhcc
Confidence 89999999999999999999998877765 34456678899999999999999999999999999999999999999999
Q ss_pred cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcccC
Q 032664 80 KTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
Q Consensus 80 ~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~~~ 136 (136)
..|+|||+.|+.+||||+|+|||+||||+|+||+||||||||++|||||++|||++.
T Consensus 81 ~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg~~~ 137 (137)
T KOG1745|consen 81 KTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 137 (137)
T ss_pred cccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcccCCC
Confidence 999999999999999999999999999999999999999999999999999999864
No 5
>smart00428 H3 Histone H3.
Probab=100.00 E-value=3e-47 Score=272.45 Aligned_cols=101 Identities=87% Similarity=1.211 Sum_probs=97.9
Q ss_pred CCCCccccCCCchhhHHHhhhhhhhhhhhhcCchhHHHHHHHhhhcc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032664 35 GVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSSAVAALQEAAEAYLVGLFEDTNLCA 112 (136)
Q Consensus 35 ~~~k~~r~~pg~~~l~EIr~~q~st~llipk~pF~RlVreI~~~~~~--~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a 112 (136)
++++++||+||+++|+|||+||+||++||||+||+||||||++++.+ ++|||++|+++|||++|+||+++|||+++||
T Consensus 2 ~~~~~~r~rpg~~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a 81 (105)
T smart00428 2 GKTKHRRYRPGQVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLA 81 (105)
T ss_pred CCCCCcCCCCcchHHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35788999999999999999999999999999999999999999987 9999999999999999999999999999999
Q ss_pred hhcCccccChhhHHHHHHHhccc
Q 032664 113 IHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 113 ~HakRvTi~~~Diqla~ri~~~~ 135 (136)
+||||||||++||+||.+|||++
T Consensus 82 ~HAkRvTl~~kDi~La~rir~~~ 104 (105)
T smart00428 82 IHAKRVTIMPKDIQLARRIRGER 104 (105)
T ss_pred HHhCCccCcHhhHHHHHHHhccC
Confidence 99999999999999999999985
No 6
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=7.9e-47 Score=266.70 Aligned_cols=94 Identities=71% Similarity=1.078 Sum_probs=91.1
Q ss_pred cCCCchhhHHHhhhhhhhhhhhhcCchhHHHHHHHhhhc-ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcccc
Q 032664 42 FRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTI 120 (136)
Q Consensus 42 ~~pg~~~l~EIr~~q~st~llipk~pF~RlVreI~~~~~-~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi 120 (136)
++||+++|+|||+||+||++||||+||+||||||++++. +++||+++|++|||||+|+|||++|||+|+||+|||||||
T Consensus 1 ~rpGt~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl 80 (97)
T PLN00160 1 MRPGEKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTI 80 (97)
T ss_pred CCCccHHHHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhccccc
Confidence 689999999999999999999999999999999999986 5699999999999999999999999999999999999999
Q ss_pred ChhhHHHHHHHhccc
Q 032664 121 MPKDIQLARRIRGER 135 (136)
Q Consensus 121 ~~~Diqla~ri~~~~ 135 (136)
|++|||||.+|||+.
T Consensus 81 ~~kD~~L~~rirg~~ 95 (97)
T PLN00160 81 MPKDMQLARRIRGQT 95 (97)
T ss_pred chhhHHHHHHhhccc
Confidence 999999999999974
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.94 E-value=6.2e-27 Score=163.83 Aligned_cols=87 Identities=48% Similarity=0.691 Sum_probs=82.9
Q ss_pred CCchhhHHHhhhhhhhhhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChh
Q 032664 44 PGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPK 123 (136)
Q Consensus 44 pg~~~l~EIr~~q~st~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~ 123 (136)
||+..++|||+||++++++||++||.|++|+... .|||.+|.++||+++|.|+.+|+|+|+.||.|+||+||+++
T Consensus 1 ~~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~-----~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~ 75 (91)
T COG2036 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAGA-----ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAE 75 (91)
T ss_pred CCcchHHHHHhhhhhhhhhcCchHHHHHHHHHhH-----HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHH
Confidence 5889999999999999999999999999999944 49999999999999999999999999999999999999999
Q ss_pred hHHHHHHHhccc
Q 032664 124 DIQLARRIRGER 135 (136)
Q Consensus 124 Diqla~ri~~~~ 135 (136)
||+|+.+.+|..
T Consensus 76 DI~la~~~~~~~ 87 (91)
T COG2036 76 DIKLALKRLGRR 87 (91)
T ss_pred HHHHHHHHhccc
Confidence 999999998853
No 8
>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=99.84 E-value=4.1e-21 Score=127.97 Aligned_cols=75 Identities=48% Similarity=0.656 Sum_probs=71.3
Q ss_pred hhhhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032664 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 58 st~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
+|.++||+.||.|++++|..++...++|+.+|+++||.++|.|++++||+|+.||.|+||+||+++||++|.+++
T Consensus 1 ~~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~~ 75 (75)
T PF00125_consen 1 RTRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRID 75 (75)
T ss_dssp HHSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHHT
T ss_pred CcccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhcC
Confidence 467899999999999999998877799999999999999999999999999999999999999999999999975
No 9
>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=99.42 E-value=9.5e-13 Score=88.22 Aligned_cols=58 Identities=24% Similarity=0.309 Sum_probs=52.4
Q ss_pred HHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 73 REIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.+.+.++.+..+++++|.++||+.+|+|+.+++++++.||.|++|.||+++||+|+..
T Consensus 8 ~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~ 65 (72)
T cd07981 8 QELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLE 65 (72)
T ss_pred HHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 3444445667999999999999999999999999999999999999999999999975
No 10
>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=99.25 E-value=2.2e-11 Score=84.41 Aligned_cols=68 Identities=25% Similarity=0.312 Sum_probs=65.2
Q ss_pred hhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 62 lipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
-||+.|..||++.- +..|+|.++.+++.++.|.|+.++..|+..++.|++|.||+..||.+|.+..|.
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 GITKPAIRRLARRG-----GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred cCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 39999999999987 889999999999999999999999999999999999999999999999998885
No 11
>PLN00035 histone H4; Provisional
Probab=99.23 E-value=3.5e-11 Score=86.03 Aligned_cols=67 Identities=22% Similarity=0.276 Sum_probs=64.6
Q ss_pred hhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 63 IRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 63 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
||+.|..||++.- +..|+|.+|.++|.++.|.|+.++..|+..+|.||+|.||+..||.+|.+..|.
T Consensus 30 ipk~~IrRLARr~-----GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~ 96 (103)
T PLN00035 30 ITKPAIRRLARRG-----GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred CCHHHHHHHHHHc-----CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC
Confidence 9999999999988 889999999999999999999999999999999999999999999999988775
No 12
>PTZ00015 histone H4; Provisional
Probab=99.20 E-value=5.1e-11 Score=85.10 Aligned_cols=69 Identities=22% Similarity=0.243 Sum_probs=65.3
Q ss_pred hhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 61 llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
.-||+.|..||++.- +..|+|.++.+.+.++.|.|+.++..||..+|.||+|.||+..||.+|.+..|.
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 RGITKGAIRRLARRG-----GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred cCCCHHHHHHHHHHc-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 349999999999988 899999999999999999999999999999999999999999999999988775
No 13
>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=99.14 E-value=9.5e-11 Score=77.34 Aligned_cols=64 Identities=20% Similarity=0.222 Sum_probs=60.0
Q ss_pred hhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 62 lipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.+|+.|..|+.+.+ |-.+++.++..+|.+..|.++-++.++|..++.|++|.||+..||.+|.+
T Consensus 2 ~~p~~~i~ria~~~-----Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL-----GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC-----CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 47899999998887 88899999999999999999999999999999999999999999999863
No 14
>PTZ00463 histone H2B; Provisional
Probab=99.06 E-value=5.2e-10 Score=81.36 Aligned_cols=65 Identities=18% Similarity=0.298 Sum_probs=60.0
Q ss_pred hcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHH----HHHHhhcCccccChhhHHHHHHHh
Q 032664 64 RKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDT----NLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 64 pk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a----~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
++.+|..||+.++.++++|..++..||..| ++|++|+||.. ..++.+.+|.||+++|||.|++|.
T Consensus 26 r~esy~~YI~KVLKqVhPd~gIS~kaM~Im----nSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 26 RYDSYGLYIFKVLKQVHPDTGISRKSMNIM----NSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred ccchHHHHHHHHHHhhCCCCCccHHHHHHH----HHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 356799999999999999999999999999 89999988876 889999999999999999999985
No 15
>PLN00158 histone H2B; Provisional
Probab=99.05 E-value=6.6e-10 Score=80.82 Aligned_cols=65 Identities=18% Similarity=0.340 Sum_probs=60.3
Q ss_pred hcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHH----HHHHhhcCccccChhhHHHHHHHh
Q 032664 64 RKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDT----NLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 64 pk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a----~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
++..|..||+.++.++++|..|+..|+..| ++|++|+||.. ..++.+.+|.||+++|||.|++|.
T Consensus 25 r~esy~~YI~kVLKQVhPd~gIS~kaM~Im----nSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 25 KTETYKIYIYKVLKQVHPDTGISSKAMSIM----NSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccccHHHHHHHHHHHhCCCCCccHHHHHHH----HHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 467899999999999999999999999999 88888888876 889999999999999999999985
No 16
>smart00417 H4 Histone H4.
Probab=99.04 E-value=3.1e-10 Score=76.85 Aligned_cols=61 Identities=21% Similarity=0.243 Sum_probs=58.2
Q ss_pred hhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHH
Q 032664 62 LIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 127 (136)
Q Consensus 62 lipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diql 127 (136)
-||+.|..||++.- +..|+|.++.+.|.++.|.|+.++..||..+|.|++|.||+..||..
T Consensus 13 gI~k~~IrRLaRr~-----GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 13 GITKPAIRRLARRG-----GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred CCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 49999999999987 89999999999999999999999999999999999999999999864
No 17
>smart00427 H2B Histone H2B.
Probab=99.04 E-value=9.4e-10 Score=76.81 Aligned_cols=62 Identities=19% Similarity=0.339 Sum_probs=57.8
Q ss_pred chhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHH----HHHHhhcCccccChhhHHHHHHHh
Q 032664 67 PFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDT----NLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 67 pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a----~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
.|..||+.++.++++|..++..|+..| ++|++++||.. ..++.+.+|.||+++|||.|++|.
T Consensus 2 sy~~Yi~kvLKqVhpd~giS~kam~im----nSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 2 TYAIYIYKVLKQVHPDTGISSKAMSIM----NSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred cHHHHHHHHHHHhCCCccccHHHHHHH----HHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 689999999999999999999999999 88888888876 888999999999999999999985
No 18
>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=98.77 E-value=3.9e-08 Score=71.64 Aligned_cols=65 Identities=22% Similarity=0.362 Sum_probs=59.7
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 69 QRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 69 ~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
.++|..|+.+. +..++++++...|-|.++.|..++..||..+|.||+|.||+.+||+||...++.
T Consensus 4 ~~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 4 ARVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 57788887755 567999999999999999999999999999999999999999999999998875
No 19
>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=98.72 E-value=5.6e-08 Score=63.22 Aligned_cols=63 Identities=27% Similarity=0.304 Sum_probs=50.5
Q ss_pred hhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032664 63 IRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 63 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 129 (136)
+|.....++++. ..+..+++.+|.++|+.++|.|+..|-.+|+..|.+.+|.||+.+||..|+
T Consensus 3 lP~a~vkri~k~----~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 3 LPLARVKRIMKS----DPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp S-HHHHHHHHHH----TSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CChHHHHHHhcc----CCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 344444454444 445678999999999999999999999999999999999999999998764
No 20
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=98.70 E-value=3e-08 Score=73.18 Aligned_cols=66 Identities=27% Similarity=0.395 Sum_probs=61.4
Q ss_pred hhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHH----HHHHhhcCccccChhhHHHHHHHh
Q 032664 63 IRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDT----NLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 63 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a----~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
..+..|..+|+.++.++++++.+++.|+.+| ++|++++||+. +.+|.+.||-||..+|||+|.+|.
T Consensus 34 ~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vm----nsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 34 RRKESYSEYVYKVLKQVHPDLGISSKAMGVM----NSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred cccCceeeehhhhhhcccCCCCcCHHHHHHH----HHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 4678899999999999999999999999999 88888888876 999999999999999999999985
No 21
>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=98.32 E-value=9.3e-07 Score=64.42 Aligned_cols=67 Identities=22% Similarity=0.206 Sum_probs=61.3
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.|.+|-.++.|++++- ....|++++|...|....|.+..+++|.|...|.|.++.+|+++||++|.+
T Consensus 18 gL~fPV~ri~R~Lk~~----~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 18 GLQFPVGRIHRYLKKG----RYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred CccCcHHHHHHHHHcC----ccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 4889999999998762 145899999999999999999999999999999999999999999999985
No 22
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.26 E-value=2.6e-06 Score=65.49 Aligned_cols=69 Identities=26% Similarity=0.292 Sum_probs=64.7
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
++.+|.+-..|||++++.+. +.-++.+|..||+.+|--|+..|--.++.+|.-.+|.||++.|+--++.
T Consensus 8 dl~lP~AiI~rlvke~l~E~--~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~ 76 (172)
T KOG0870|consen 8 DLNLPNAIITRLVKEVLPES--NVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALD 76 (172)
T ss_pred HhhccHHHHHHHHHHhCccc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHH
Confidence 58899999999999998876 6899999999999999999999999999999999999999999976654
No 23
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.25 E-value=5.2e-06 Score=55.93 Aligned_cols=54 Identities=26% Similarity=0.166 Sum_probs=50.4
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 81 TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
+-.+++++|++.|.+..|.|+..|-+.+..+|.|++|.+..+.||.+|..-.|.
T Consensus 20 Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi 73 (77)
T smart00576 20 GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGI 73 (77)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCc
Confidence 557999999999999999999999999999999999999999999999876664
No 24
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.25 E-value=2.9e-06 Score=57.71 Aligned_cols=64 Identities=28% Similarity=0.283 Sum_probs=52.7
Q ss_pred chhHHHHHHHhhh--cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 67 PFQRLVREIAQDF--KTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 67 pF~RlVreI~~~~--~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.+.--|-+|.++. ..+..++++.+.+|-|.+=.++..+-.|--..|.||||.||+++|+.|..|
T Consensus 6 al~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 6 ALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 3445566676665 367899999999999999999999999999999999999999999999875
No 25
>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=98.24 E-value=5.5e-06 Score=55.16 Aligned_cols=58 Identities=21% Similarity=0.264 Sum_probs=46.5
Q ss_pred HHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 73 REIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.+++.++.+...+.+++.+.|.+.++.|+.++.+.+..+|.|.+--||.++|||+...
T Consensus 6 ~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 6 QELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 4555556789999999999999999999999999999999999999999999999875
No 26
>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=98.03 E-value=3.1e-05 Score=51.37 Aligned_cols=58 Identities=28% Similarity=0.335 Sum_probs=45.4
Q ss_pred HHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 72 VREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
|+-|++.++ -..++.++...|.+-+|.-|-.+.++|..++.|+||.+|+..||..|.|
T Consensus 9 vk~iAes~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 9 VKDIAESLG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp HHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred HHHHHHHcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 455555443 2358999999999999999999999999999999999999999999875
No 27
>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=97.97 E-value=2.7e-05 Score=65.66 Aligned_cols=62 Identities=21% Similarity=0.269 Sum_probs=55.2
Q ss_pred HHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 72 VREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
|+.|++.+ +..+++.+|..+|.+-.|.++-.+.++|..+|.|+||.||+.+||.+|.+.++.
T Consensus 5 i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~ 66 (343)
T cd08050 5 IKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNV 66 (343)
T ss_pred HHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCC
Confidence 45555533 456999999999999999999999999999999999999999999999998865
No 28
>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=97.86 E-value=7.5e-05 Score=55.43 Aligned_cols=65 Identities=29% Similarity=0.369 Sum_probs=52.6
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 69 QRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 69 ~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
.++|..|+.+.+ -..++...+.-|-|.+-.|..++++||...|-||+|.+|...|++||...+..
T Consensus 15 a~~i~~iL~~~G-v~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~ 79 (129)
T PF02291_consen 15 ARVIHLILKSMG-VTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLD 79 (129)
T ss_dssp HHHHHHHHHHTT----B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT--
T ss_pred HHHHHHHHHHcC-CcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHh
Confidence 478888888774 34579999999999999999999999999999999999999999999987643
No 29
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.72 E-value=5.7e-05 Score=65.27 Aligned_cols=62 Identities=24% Similarity=0.308 Sum_probs=43.8
Q ss_pred hhcCchhHHHHHHHhh-hcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhh
Q 032664 63 IRKLPFQRLVREIAQD-FKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKD 124 (136)
Q Consensus 63 ipk~pF~RlVreI~~~-~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~D 124 (136)
+|..+..+|+.-.++. +....+++.+||.+|..|+|-|..+|-+|---.|.||+|+||...|
T Consensus 352 lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 352 LPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4444555555555442 3367899999999999999999999999999999999999999887
No 30
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.72 E-value=4.4e-05 Score=62.38 Aligned_cols=73 Identities=21% Similarity=0.290 Sum_probs=65.4
Q ss_pred hhhhhhhhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 54 KYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 54 ~~q~st~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.++-+++.++-|--...||++| .++.-+..++-+.|.|.|++|+.++-..++.+|.|.|--||-++||+|++.
T Consensus 146 ~~~~~~~~il~k~kl~dLvqqI----d~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLE 218 (258)
T KOG1142|consen 146 QDEPGNNPILSKRKLDDLVQQI----DGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLE 218 (258)
T ss_pred cccCCCCccccccchhHHHHhh----cCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeee
Confidence 5667788888887777777777 578899999999999999999999999999999999999999999999864
No 31
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=97.34 E-value=0.0006 Score=52.29 Aligned_cols=71 Identities=15% Similarity=0.212 Sum_probs=64.3
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 133 (136)
+.++|.+...|+.+.++. .+-.|+.+|-+.+||.+-.|+-=+-..|+.-+.--||+||+.+||-.|+--.|
T Consensus 30 Dr~LPIANV~RIMK~~lP---~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 30 DRFLPIANVSRIMKKALP---ANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhhccHHHHHHHHHhcCC---cccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 456999999999998854 77899999999999999999999999999999999999999999999886655
No 32
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.79 E-value=0.0084 Score=45.38 Aligned_cols=65 Identities=25% Similarity=0.424 Sum_probs=54.7
Q ss_pred HHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhccc
Q 032664 70 RLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 70 RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~~ 135 (136)
++|..|+.+++ -.-+....+.-|-|.+=.|.+++++||...+-||++-||..+|++||...++.+
T Consensus 17 ~~i~~iL~s~G-I~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~ 81 (148)
T KOG3334|consen 17 RVIASILKSLG-IQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDH 81 (148)
T ss_pred HHHHHHHHHcC-ccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhcc
Confidence 56666666553 335667788888899999999999999999999999999999999999887753
No 33
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=96.68 E-value=0.0064 Score=42.68 Aligned_cols=65 Identities=23% Similarity=0.272 Sum_probs=54.5
Q ss_pred cCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 65 KLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 65 k~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
|-...||.|.- +--|+..-..+....++..||.+..-+|...+-||||.||+.-|+--+.+-.|.
T Consensus 32 KpaIRRlARr~-----GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 32 KPAIRRLARRG-----GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred hHHHHHHHHhc-----CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 55556666654 566888888888889999999999999999999999999999999888876554
No 34
>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=96.59 E-value=0.011 Score=39.27 Aligned_cols=52 Identities=25% Similarity=0.181 Sum_probs=48.4
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 83 LRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 83 ~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
..+++.|++.|-+.+..||..|...+...|-|++|-...+.|+.++..-.|.
T Consensus 22 ~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi 73 (77)
T PF07524_consen 22 DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI 73 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 3789999999999999999999999999999999999999999999876664
No 35
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.40 E-value=0.012 Score=44.79 Aligned_cols=72 Identities=18% Similarity=0.269 Sum_probs=66.2
Q ss_pred hhhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032664 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 59 t~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 133 (136)
.++-+||+....+|+|++. .+.||..+|-+.|++.+=.|+.-|--.||.++---.+.||.++-+.-|..-.|
T Consensus 9 de~sLPkAtv~KmIke~lP---~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~Lg 80 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLP---KDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLG 80 (156)
T ss_pred ccccCcHHHHHHHHHHhCC---cccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcc
Confidence 4577999999999999953 79999999999999999999999999999999999999999999998887665
No 36
>PLN00154 histone H2A; Provisional
Probab=95.66 E-value=0.025 Score=42.45 Aligned_cols=68 Identities=19% Similarity=0.154 Sum_probs=59.4
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.|.+|-.-+.|++++-.. ...|+++.|..-|--+.|....+++|-+...|...++..|+|++|+||.+
T Consensus 36 gL~FPVgRi~r~Lk~g~~---~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVS---AHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhh---hccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 477888888888887621 35699999999999999999999999999999999999999999999975
No 37
>smart00414 H2A Histone 2A.
Probab=95.56 E-value=0.02 Score=41.18 Aligned_cols=67 Identities=25% Similarity=0.223 Sum_probs=56.7
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
+|.+|-.-|.|++++- .-..|+++.|..-|--..|.+..+++|-+...+...++..|+++||++|.+
T Consensus 7 gL~fPVgRi~r~Lk~~----~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 7 GLQFPVGRIHRLLRKG----TYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred CccCchHHHHHHHHcC----ccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 4667777777777654 235699999999999999999999999999999999999999999999974
No 38
>PTZ00017 histone H2A; Provisional
Probab=95.37 E-value=0.02 Score=42.87 Aligned_cols=67 Identities=24% Similarity=0.211 Sum_probs=58.4
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.|.+|-.-+.|+.++- ....|++..|..-|--..|.+..+++|.+...+...+...|+|++|+||.+
T Consensus 25 gL~FPVgRi~R~Lk~g----~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKG----RYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhcc----chhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 4778888888887654 234699999999999999999999999999999999999999999999975
No 39
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=94.96 E-value=0.049 Score=40.16 Aligned_cols=58 Identities=22% Similarity=0.279 Sum_probs=50.3
Q ss_pred HHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 73 REIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 73 reI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
+.++..-....|+.++|...|....|.....++|-|...|.-.|-..|+|+-+|||.+
T Consensus 33 kr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 33 KRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred HHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 3444433467899999999999999999999999999999999999999999999964
No 40
>PLN00156 histone H2AX; Provisional
Probab=94.31 E-value=0.058 Score=40.63 Aligned_cols=67 Identities=25% Similarity=0.223 Sum_probs=56.9
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.|.+|-.-+.|++++- ....|++..|..-|--..|....+++|.+...+...++..|+|+.|+||.+
T Consensus 27 gL~FPVgRi~R~Lk~g----~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAG----KYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcC----ChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 3667777777776553 234699999999999999999999999999999999999999999999975
No 41
>PLN00157 histone H2A; Provisional
Probab=94.27 E-value=0.047 Score=40.78 Aligned_cols=67 Identities=25% Similarity=0.224 Sum_probs=57.3
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.|.+|-.-+.|++++- ....|+++.|..-|--..|....+++|.+...|...+...|++++|+||.+
T Consensus 24 gL~FPVgRi~R~Lk~g----~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAG----KYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcC----chhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 4777777777777653 234699999999999999999999999999999999999999999999974
No 42
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.07 E-value=0.18 Score=45.59 Aligned_cols=53 Identities=21% Similarity=0.252 Sum_probs=49.5
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032664 81 TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 133 (136)
+-..++.+|..+|-+-.|.-+-++.+++..++.|+||-+++..||.-|.+.+.
T Consensus 25 Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~n 77 (576)
T KOG2549|consen 25 GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLN 77 (576)
T ss_pred CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcc
Confidence 56679999999999999999999999999999999999999999999998764
No 43
>PLN00153 histone H2A; Provisional
Probab=93.95 E-value=0.07 Score=39.73 Aligned_cols=67 Identities=25% Similarity=0.219 Sum_probs=57.3
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.|.+|-.-+.|++++= ....|+++.|..-|--..|...-+++|.+...|...+...|+|+.|+||.+
T Consensus 22 gL~FpVgRi~R~Lr~g----~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKG----KYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcC----chhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 4677777777777553 235699999999999999999999999999999999999999999999975
No 44
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=93.81 E-value=0.053 Score=37.83 Aligned_cols=59 Identities=15% Similarity=0.221 Sum_probs=29.5
Q ss_pred HHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 72 VREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
|+.++--++....-..+.+..|.+..-.|++++...|..+|...++.+|..+|+-.+.|
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR 65 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLR 65 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC--------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHh
Confidence 34444445555678899999999999999999999999999999999999999998875
No 45
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=93.65 E-value=0.26 Score=36.85 Aligned_cols=70 Identities=21% Similarity=0.193 Sum_probs=62.7
Q ss_pred hhhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032664 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 59 t~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 131 (136)
.++-+||+-.+..|.+|+. .|+-|+.+|-+.+++++=.|+.-|--.||..+-.-...||.++-+--|..-
T Consensus 8 De~sLPKATVqKMvS~iLp---~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALen 77 (148)
T COG5150 8 DENSLPKATVQKMVSSILP---KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALEN 77 (148)
T ss_pred ccccCcHHHHHHHHHHhcc---ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHh
Confidence 3567999999999999965 899999999999999999999999999999999999999999887666543
No 46
>PTZ00252 histone H2A; Provisional
Probab=93.29 E-value=0.13 Score=38.60 Aligned_cols=67 Identities=21% Similarity=0.199 Sum_probs=55.0
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhh--cCccccChhhHHHHHH
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~H--akRvTi~~~Diqla~r 130 (136)
.|.+|-.-+.|++++- .-..|+++.|..-|--..|....+++|.+...|.. .++..|+|++|+||.+
T Consensus 23 GL~FPVgRi~R~Lr~g----~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRG----QYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcC----CcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 3667777777777554 23569999999999888999999999999888864 6778999999999975
No 47
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.27 E-value=0.58 Score=34.91 Aligned_cols=47 Identities=28% Similarity=0.343 Sum_probs=37.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccC---hhhHHHHHHH
Q 032664 85 FQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIM---PKDIQLARRI 131 (136)
Q Consensus 85 ~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~---~~Diqla~ri 131 (136)
.......-|-+.|-.|-.+++|||...|.|++|-.+. ++|+.||.--
T Consensus 32 ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 32 YEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred hCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 3444555566888999999999999999999886555 4999999753
No 48
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=91.14 E-value=0.34 Score=36.10 Aligned_cols=66 Identities=26% Similarity=0.258 Sum_probs=53.8
Q ss_pred hhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 61 LLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 61 llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
+.+|---..|++|+ -....|++.+|...|--..|.....++|.+...|.-.++..|+|+-++||.+
T Consensus 26 l~fPvgri~r~Lr~----~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 26 LQFPVGRIHRLLRK----GRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred cccCHHHHHHHHHc----cchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 44555545555554 2356789999999998888888899999999999999999999999999975
No 49
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=90.68 E-value=1.1 Score=37.82 Aligned_cols=51 Identities=16% Similarity=0.112 Sum_probs=47.3
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 84 RFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 84 r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
.++..|++.|-++.-.|+-.+|+.+-..+.|++|.-.+..|+.|.....|.
T Consensus 22 ~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI 72 (323)
T KOG4336|consen 22 SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNI 72 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCC
Confidence 478889999999999999999999999999999999999999999987775
No 50
>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=90.67 E-value=0.74 Score=36.23 Aligned_cols=56 Identities=18% Similarity=0.231 Sum_probs=49.8
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAK 116 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Hak 116 (136)
..++...|+...+..|+.+.... .++.+.+..|..|+|.+|-+|.+.+..++.|-.
T Consensus 42 ~~fl~~~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~ 97 (212)
T cd08045 42 PSFLNPSPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEERLRNLLEKLIEVSEHRV 97 (212)
T ss_pred hhccCHHHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 36788899999999998876544 899999999999999999999999999999973
No 51
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=90.41 E-value=0.83 Score=37.18 Aligned_cols=85 Identities=20% Similarity=0.239 Sum_probs=64.9
Q ss_pred CchhhHHHhhhhhhhhh---------hhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 032664 45 GTVALREIRKYQKSTEL---------LIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHA 115 (136)
Q Consensus 45 g~~~l~EIr~~q~st~l---------lipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Ha 115 (136)
|...-+-+|+||+..+- -...+||.|+ +++++.-.+--=|+++|=...-.++|-|+..|-=.|-+.|-..
T Consensus 80 g~~~e~i~ryWq~ti~~~e~~~q~~~k~h~LPlARI-kkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~N 158 (286)
T COG5208 80 GLLDERISRYWQQTIKAAEEERQILLKDHNLPLARI-KKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEEN 158 (286)
T ss_pred hhHHHHHHHHHHHHHHHHHHhHHHHHHhccCcHHHH-HHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHh
Confidence 44455567888876432 2334899886 5565432233357888888889999999999999999999999
Q ss_pred CccccChhhHHHHHH
Q 032664 116 KRVTIMPKDIQLARR 130 (136)
Q Consensus 116 kRvTi~~~Diqla~r 130 (136)
||-||.-.||--|+.
T Consensus 159 kRRtLQksDia~Av~ 173 (286)
T COG5208 159 KRRTLQKSDIAAAVK 173 (286)
T ss_pred hhhHHHHHHHHHHHH
Confidence 999999999988875
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=89.24 E-value=0.38 Score=38.99 Aligned_cols=58 Identities=21% Similarity=0.271 Sum_probs=38.4
Q ss_pred hhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcc
Q 032664 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRV 118 (136)
Q Consensus 60 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRv 118 (136)
.+++...|+...+.+|+..+. ...+..+.+..|-.|+|.+|-+|.|++..++.|-...
T Consensus 41 ~~fL~~~~L~~~i~~i~~~~g-~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~ 98 (264)
T PF05236_consen 41 EPFLNPSPLQKRIQKIAKKHG-LKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDS 98 (264)
T ss_dssp ---S-HHHHHHHHHHHHHCTT---EE-TCHHHHHHHHHHHHHHHHHHHHH---------
T ss_pred ccccCHHHHHHHHHHHHHHcC-CcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 367788889999999986554 6689999999999999999999999999999986543
No 53
>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=89.24 E-value=3.7 Score=28.60 Aligned_cols=58 Identities=17% Similarity=0.252 Sum_probs=45.3
Q ss_pred HHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 72 VREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 72 VreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
++.++--++..-.-..+.+..|.+..=.|+++|.-.|..+|. .++--+.++|+-.+.|
T Consensus 8 i~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 8 IRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 344444344445667899999999999999999999999998 5666669999998875
No 54
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=86.26 E-value=1.5 Score=35.69 Aligned_cols=73 Identities=19% Similarity=0.210 Sum_probs=61.6
Q ss_pred hhhhhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 57 ~st~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
...++.+..+|..|+ |.|++.-..---|+.+|...+-.|+|.|+..|-..+..-+--.+|.|+.-.||.-++.
T Consensus 66 ~~~d~~~~~lPlaRi-KkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~ 138 (236)
T KOG1657|consen 66 GQLDFKNHILPLARI-KKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVT 138 (236)
T ss_pred cccchhhccCcHhhc-cccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhc
Confidence 456789999999997 5665533333489999999999999999999999999999999999999999987653
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=84.12 E-value=1.9 Score=28.79 Aligned_cols=57 Identities=7% Similarity=0.072 Sum_probs=43.3
Q ss_pred HHHHHHhhh--cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccc-cChhhHHH
Q 032664 71 LVREIAQDF--KTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVT-IMPKDIQL 127 (136)
Q Consensus 71 lVreI~~~~--~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvT-i~~~Diql 127 (136)
+|.+|++.. +..++++.+|+..+++..+-|+..-...|+..+.--+--+ |.++|++=
T Consensus 4 li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEk 63 (72)
T PF09415_consen 4 LIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEK 63 (72)
T ss_dssp HHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHH
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHH
Confidence 455666543 3678999999999999999999999999988887777777 99999874
No 56
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=80.48 E-value=13 Score=27.29 Aligned_cols=61 Identities=18% Similarity=0.216 Sum_probs=48.6
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 68 FQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 68 F~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
|..=|+..+--++....--.+.+++|.|..-.|++.+.-.|..+|- .|-.+..+|...|.|
T Consensus 11 F~KDikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq--~rnK~k~eDfkfaLr 71 (126)
T COG5248 11 FMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQ--VRNKTKTEDFKFALR 71 (126)
T ss_pred HHHHHHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHH--hcccchHHHHHHHHh
Confidence 4444555555566666777889999999999999999998888887 677888999999876
No 57
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=76.86 E-value=19 Score=26.04 Aligned_cols=63 Identities=21% Similarity=0.266 Sum_probs=47.7
Q ss_pred cCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 65 KLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 65 k~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
+--|+.=++-.+--|+.+.---.+.+++|.+..=.|++++.+.|..+. +|-.+.++|+..+.|
T Consensus 8 k~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 8 KHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred HHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 344666666666666666666788899998888899999966555554 888899999998875
No 58
>PF09123 DUF1931: Domain of unknown function (DUF1931); InterPro: IPR015207 This entry represents a set of hypothetical bacterial proteins containing a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined []. ; PDB: 1WWS_A 1WWI_A 1R4V_A.
Probab=73.97 E-value=5.9 Score=29.84 Aligned_cols=59 Identities=22% Similarity=0.323 Sum_probs=43.5
Q ss_pred hhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032664 68 FQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 68 F~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 131 (136)
|.++.|+. .++-+..+-+.-+-+..|.-+-+||+-+..-|...+|-.|.+.|+-+...+
T Consensus 1 fe~lFR~a-----a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPITkGl 59 (138)
T PF09123_consen 1 FERLFRKA-----AGLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPITKGL 59 (138)
T ss_dssp HHHHHHHH-----HS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS---HHH
T ss_pred ChHHHHHH-----hccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCccHHH
Confidence 56777777 456777888888889999999999999999999999999999998776654
No 59
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=73.14 E-value=8.3 Score=33.32 Aligned_cols=52 Identities=21% Similarity=0.227 Sum_probs=46.9
Q ss_pred cccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032664 82 DLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 82 ~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 133 (136)
---+..+++.+|.--.|.-+-++-+.+...+.|.||--++..||.-|.|-+.
T Consensus 20 i~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lN 71 (450)
T COG5095 20 ISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLN 71 (450)
T ss_pred CcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcC
Confidence 3457789999998889999999999999999999999999999999988664
No 60
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=72.12 E-value=11 Score=32.41 Aligned_cols=53 Identities=23% Similarity=0.115 Sum_probs=47.5
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032664 81 TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 133 (136)
+--.++..|++.|+..+-.|+-+|-+.|...+-|++|+-....||-+|..-.|
T Consensus 43 g~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls 95 (353)
T KOG2389|consen 43 GYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLS 95 (353)
T ss_pred CCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhh
Confidence 33467778999999999999999999999999999999999999999987654
No 61
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=65.16 E-value=41 Score=30.13 Aligned_cols=67 Identities=25% Similarity=0.293 Sum_probs=48.9
Q ss_pred CchhHHHHHHHhhhcccccccHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032664 66 LPFQRLVREIAQDFKTDLRFQSSAVAALQEAAE-----------AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 66 ~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E-----------~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~ 133 (136)
..|.++|..++++. +-..|+.+|+..|=+.+- ..|.+|+..|+.+|.-.+...|...||+.|..-+-
T Consensus 430 ~~~~~~i~~~~~~~-~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r~ 507 (509)
T PF13654_consen 430 RQYARFIASICQKE-GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEERR 507 (509)
T ss_dssp HHHHHHHHHHHHHH-SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH--
T ss_pred HHHHHHHHHHHHhC-CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHccc
Confidence 34677777776644 335789999988766543 57899999999999999999999999999987553
No 62
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=64.25 E-value=11 Score=27.71 Aligned_cols=67 Identities=22% Similarity=0.279 Sum_probs=50.6
Q ss_pred CchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032664 66 LPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 66 ~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~~~ 134 (136)
.|..|+=+-+-......-|+-..|..-+-...|..-..++|-|...+.--|=..|+|+-+|||. ||+
T Consensus 31 FpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAi--RGD 97 (131)
T KOG1757|consen 31 FPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAI--RGD 97 (131)
T ss_pred cchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeee--cCc
Confidence 3555555555444556678888887777667788888899999888888888899999999985 554
No 63
>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=63.37 E-value=45 Score=22.80 Aligned_cols=64 Identities=17% Similarity=0.253 Sum_probs=51.4
Q ss_pred hhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCc---cccChhhHHHHHHH
Q 032664 63 IRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKR---VTIMPKDIQLARRI 131 (136)
Q Consensus 63 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR---vTi~~~Diqla~ri 131 (136)
+++....+++..+ .+..++.+.+.+|.-.+..|+-+|-|.|..+.-.-+. --|.|..|+-|.+.
T Consensus 17 f~k~~iKr~~~~~-----~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rr 83 (85)
T cd08048 17 FPKAAIKRLIQSV-----TGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRR 83 (85)
T ss_pred ccHHHHHHHHHHH-----cCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHH
Confidence 6666666665555 3478899999999999999999999999777766544 78999999988875
No 64
>PF07278 DUF1441: Protein of unknown function (DUF1441); InterPro: IPR009901 This entry is represented by Bacteriophage VT1-Sakai, H0025. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=60.66 E-value=38 Score=25.84 Aligned_cols=65 Identities=22% Similarity=0.216 Sum_probs=49.2
Q ss_pred hhHHHhhhhhhhhhhhhcCchhHHH----HHHHhhh-------cccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032664 48 ALREIRKYQKSTELLIRKLPFQRLV----REIAQDF-------KTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCA 112 (136)
Q Consensus 48 ~l~EIr~~q~st~llipk~pF~RlV----reI~~~~-------~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a 112 (136)
+-+|--+|++.+.-|||-.-+.+.. +-|.+.+ .-+..++++++..+|.+......+|.+....++
T Consensus 75 sE~eRlk~e~e~g~Lipa~eV~~~~s~~~Kav~q~LetlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~~ 150 (152)
T PF07278_consen 75 SENERLKFEKETGQLIPAEEVRREMSEMAKAVVQVLETLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEAC 150 (152)
T ss_pred HHHHHHHHHHHHcccCcHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455667889999999987655544 4443332 257899999999999999999999998886554
No 65
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=60.60 E-value=6.4 Score=30.33 Aligned_cols=64 Identities=25% Similarity=0.358 Sum_probs=49.5
Q ss_pred hcCchhHHHHHHHhhhcccccccHH-HHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032664 64 RKLPFQRLVREIAQDFKTDLRFQSS-AVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 64 pk~pF~RlVreI~~~~~~~~r~~~~-Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 129 (136)
-++|.+|+ ++|.. ..+++++..+ |+.++-.++|-|+-.|-..++.|+.-.+|+|+.-+|+..+.
T Consensus 58 ~rLpL~ri-k~vvk-l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai 122 (162)
T KOG1658|consen 58 SRLPLARI-KQVVK-LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAI 122 (162)
T ss_pred hhccHHHH-Hhhcc-CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccc
Confidence 34455443 34422 3578888765 56678899999999999999999999999999999987664
No 66
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=59.79 E-value=21 Score=31.45 Aligned_cols=72 Identities=24% Similarity=0.387 Sum_probs=59.0
Q ss_pred hhhhcCchhH-HHHHHHhhh--cccccccHHHHHHHHHHHH----HHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032664 61 LLIRKLPFQR-LVREIAQDF--KTDLRFQSSAVAALQEAAE----AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 61 llipk~pF~R-lVreI~~~~--~~~~r~~~~Al~aLqea~E----~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
++|+-.||.+ =++||..-= ..+.-++++|++-|-...+ -|.++|++-|+.+|.-.+..+|..+|+.-|..+-
T Consensus 354 lII~t~py~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~lF 432 (450)
T COG1224 354 LIISTRPYSREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKELF 432 (450)
T ss_pred eEEecCCCCHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHHHH
Confidence 6778888876 467775532 2678999999999976655 6999999999999999999999999999887763
No 67
>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=59.75 E-value=53 Score=29.97 Aligned_cols=64 Identities=16% Similarity=0.151 Sum_probs=45.3
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHH-H------------HHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032664 69 QRLVREIAQDFKTDLRFQSSAVAALQEA-A------------EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 69 ~RlVreI~~~~~~~~r~~~~Al~aLqea-~------------E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
.++|.........-..|+.+|+..|.+. + ..-|.+|+..|+.+|...+..+|+.+|++-|...+
T Consensus 315 ~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 315 VQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 3344433333322348999999998642 2 36788888889888888899999999999876543
No 68
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=58.35 E-value=37 Score=27.61 Aligned_cols=59 Identities=19% Similarity=0.237 Sum_probs=45.5
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhh--cCccccChhhHHHHH
Q 032664 69 QRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLAR 129 (136)
Q Consensus 69 ~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~H--akRvTi~~~Diqla~ 129 (136)
..+|++.++ ..+..++.+|+..|.+.++.=+..+-.....++.+ ++..+|+.+||+.+.
T Consensus 136 ~~~i~~~~~--~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v 196 (326)
T PRK07452 136 KQLVERTAQ--ELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALV 196 (326)
T ss_pred HHHHHHHHH--HcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHh
Confidence 344444433 24678999999999988888777777778888888 568889999999765
No 69
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=56.26 E-value=48 Score=29.63 Aligned_cols=50 Identities=16% Similarity=0.203 Sum_probs=40.1
Q ss_pred ccccccHHHHHHHHHHHH--HHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 81 TDLRFQSSAVAALQEAAE--AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E--~~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
.++.++.+|++.|...+. ..+.++++.+...|...+|.+|+.+|+.-+..
T Consensus 279 ~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~ 330 (531)
T TIGR02902 279 IGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAE 330 (531)
T ss_pred cCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhC
Confidence 347889999988755443 56778888888888888999999999998864
No 70
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=54.66 E-value=3.3 Score=36.60 Aligned_cols=57 Identities=19% Similarity=0.155 Sum_probs=47.8
Q ss_pred HHHHhhh-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032664 73 REIAQDF-KTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 73 reI~~~~-~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 129 (136)
+|..+.. .++..|..+.-+.|-+.|..|....-+-+..+|.|-|-.||-++|+||-.
T Consensus 390 ~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhl 447 (505)
T COG5624 390 EELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHL 447 (505)
T ss_pred HHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeee
Confidence 4443333 57788888988889999999999998888999999999999999999854
No 71
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=53.14 E-value=61 Score=25.15 Aligned_cols=49 Identities=14% Similarity=0.127 Sum_probs=41.6
Q ss_pred cccccHHHHHHHHHHHHH---HHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 82 DLRFQSSAVAALQEAAEA---YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 82 ~~r~~~~Al~aLqea~E~---~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
+..|++++++.|.+.+.- +++.+...+...|.-.+--+|+..||..+..
T Consensus 213 ~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~ 264 (269)
T TIGR03015 213 APVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIA 264 (269)
T ss_pred CCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 356999999999999986 7888888888888777888999999998764
No 72
>PRK05907 hypothetical protein; Provisional
Probab=49.20 E-value=51 Score=27.46 Aligned_cols=67 Identities=12% Similarity=0.050 Sum_probs=50.8
Q ss_pred hhcCchhHHHHHHHhhhc-ccccccHHHHHHHHHHH-HHHHHHHHHHHHHHHhh-cCccccChhhHHHHH
Q 032664 63 IRKLPFQRLVREIAQDFK-TDLRFQSSAVAALQEAA-EAYLVGLFEDTNLCAIH-AKRVTIMPKDIQLAR 129 (136)
Q Consensus 63 ipk~pF~RlVreI~~~~~-~~~r~~~~Al~aLqea~-E~~lv~lfe~a~~~a~H-akRvTi~~~Diqla~ 129 (136)
.+...-..|.+-|.+.+. .+..++.+|++.|-+.+ +.=|..+......++.+ +.+.+|+.+||+.++
T Consensus 131 ~~~l~e~~L~~Wi~~~~~~~g~~i~~~a~~~L~~~~~~~nL~~l~~EleKL~ly~g~~~~It~e~V~~lv 200 (311)
T PRK05907 131 WFADRDKRIAQLLIQRAKELGISCSLGLASLFVSKFPQTGLFEILSEFQKLLCQMGKKESLEASDIQSFV 200 (311)
T ss_pred cCCCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHccCCCHHHHHHHHHHHHHhcCCCCeECHHHHHHHh
Confidence 344444677777766664 67899999999997777 56666777777888888 669999999998764
No 73
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=45.79 E-value=1e+02 Score=21.44 Aligned_cols=64 Identities=14% Similarity=0.230 Sum_probs=40.5
Q ss_pred hhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-ccccChhhHHHHHH
Q 032664 63 IRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAK-RVTIMPKDIQLARR 130 (136)
Q Consensus 63 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Hak-RvTi~~~Diqla~r 130 (136)
++|....+|+..+ .++..++.....++.-.+-.|+-+|-|.|..+..--+ ---|.|..+.-|.+
T Consensus 24 ~~k~~ikkli~~~----~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~r 88 (90)
T PF04719_consen 24 FNKAAIKKLINQV----LGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYR 88 (90)
T ss_dssp --HHHHHHHHHHH----HS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHH
T ss_pred CCHHHHHHHHHHH----cCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHH
Confidence 5665555555554 4568899999999999999999999999966655322 22677777776654
No 74
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=44.81 E-value=1.3e+02 Score=23.80 Aligned_cols=61 Identities=23% Similarity=0.244 Sum_probs=40.5
Q ss_pred hHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032664 69 QRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 69 ~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 131 (136)
..+|++.+.+ .+..++.+|+..|-+.++.=+-.+-.....++.+++-.+|+.+||+-....
T Consensus 117 ~~~i~~~~~~--~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 117 PRWIQARLKK--LGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred HHHHHHHHHH--cCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 3444444442 467899999999977777545555555566666654447999999866543
No 75
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=43.74 E-value=93 Score=27.19 Aligned_cols=72 Identities=21% Similarity=0.369 Sum_probs=57.9
Q ss_pred hhhhcCchhH-HHHHHHhh-h-cccccccHHHHHHHHHHHH----HHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032664 61 LLIRKLPFQR-LVREIAQD-F-KTDLRFQSSAVAALQEAAE----AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 61 llipk~pF~R-lVreI~~~-~-~~~~r~~~~Al~aLqea~E----~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
++|.-.||.. =+++|+.- | ..+.-++++|++.|-...| .|..+|...+++.+...|-.++...||+-|.+|-
T Consensus 351 lII~t~py~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~LF 429 (454)
T KOG2680|consen 351 LIISTQPYTEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRLF 429 (454)
T ss_pred heeecccCcHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHHH
Confidence 6677777754 45666542 2 3678899999999876665 6899999999999999999999999999998874
No 76
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=43.03 E-value=42 Score=26.71 Aligned_cols=78 Identities=15% Similarity=0.247 Sum_probs=57.5
Q ss_pred HHhhhhhhhhhhhhcCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHH-HHHHhhcCccccChhhHHHHH
Q 032664 51 EIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDT-NLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 51 EIr~~q~st~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a-~~~a~HakRvTi~~~Diqla~ 129 (136)
.+-+|..-....+||+-..+|+.+|+. . -++..+..+++-.+..|+-.|-|.| ..|-.-..-=-|.|..|.-|.
T Consensus 101 Ql~RYEvfRrs~f~Ka~iKkL~~~itg----~-~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~ 175 (195)
T KOG3219|consen 101 QLSRYEVFRRSAFPKAQIKKLMSSITG----Q-SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAY 175 (195)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHhC----C-ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHH
Confidence 344554444456788888888888843 2 2777778889999999999999999 445555666679999999888
Q ss_pred HHhc
Q 032664 130 RIRG 133 (136)
Q Consensus 130 ri~~ 133 (136)
+..+
T Consensus 176 rrL~ 179 (195)
T KOG3219|consen 176 RRLK 179 (195)
T ss_pred HHHH
Confidence 7654
No 77
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=42.99 E-value=1e+02 Score=25.37 Aligned_cols=47 Identities=23% Similarity=0.105 Sum_probs=40.1
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032664 81 TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 129 (136)
.+..++.+|++.|-+..+.=+..+--..-.++.+++ +|+.+||+.++
T Consensus 151 ~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 151 LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 567899999999988888888888888888888877 79999999765
No 78
>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=42.51 E-value=91 Score=26.35 Aligned_cols=51 Identities=14% Similarity=0.137 Sum_probs=40.6
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032664 81 TDLRFQSSAVAALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~~Diqla~ri 131 (136)
.+..++.+.++.+.+.+.+.=+ .++..|.-+|.-.+|-.|+++|++.+..+
T Consensus 251 ~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~~ 308 (337)
T TIGR02030 251 PQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAVL 308 (337)
T ss_pred ccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 5677888888877777666544 26777888999999999999999987765
No 79
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=36.87 E-value=58 Score=19.58 Aligned_cols=43 Identities=16% Similarity=0.118 Sum_probs=20.9
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHH-HHHHhhcCccccChhhHHHH
Q 032664 85 FQSSAVAALQEAAEAYLVGLFEDT-NLCAIHAKRVTIMPKDIQLA 128 (136)
Q Consensus 85 ~~~~Al~aLqea~E~~lv~lfe~a-~~~a~HakRvTi~~~Diqla 128 (136)
|+.+|...|... =.|+-....+. -.+|...+...|++.+|.-|
T Consensus 1 W~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 1 WTDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp E-HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred CCHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 444454444333 22333333332 45677788888888777654
No 80
>PF08157 NUC129: NUC129 domain; InterPro: IPR012579 This C-terminal domain is found in a novel family of hypothetical nucleolar proteins [].; GO: 0005634 nucleus
Probab=34.27 E-value=59 Score=21.29 Aligned_cols=43 Identities=16% Similarity=0.278 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHH--------HHHHHhhcCccccChhhHHHHH
Q 032664 87 SSAVAALQEAAEAYLVGLFED--------TNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 87 ~~Al~aLqea~E~~lv~lfe~--------a~~~a~HakRvTi~~~Diqla~ 129 (136)
.+..+..|++|++||.+-+=- -..+.++.||.-++.--+|++-
T Consensus 9 ~~l~~~~QqaAk~Fi~~~LYGpgsnRTT~N~flSL~NKr~~vKkAAvQFv~ 59 (63)
T PF08157_consen 9 QSLRDSQQQAAKDFIQSRLYGPGSNRTTVNEFLSLANKRLPVKKAAVQFVN 59 (63)
T ss_pred chhhhHHHHHHHHHHHHhccCCCCCcccHHHHhhhhhcccccHHHHHHHHh
Confidence 456678899999999875532 1456778888777776666654
No 81
>PRK05629 hypothetical protein; Validated
Probab=33.78 E-value=1.5e+02 Score=24.12 Aligned_cols=59 Identities=15% Similarity=0.112 Sum_probs=39.8
Q ss_pred HHHHHHHhhh-cccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032664 70 RLVREIAQDF-KTDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 70 RlVreI~~~~-~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 129 (136)
.+++=|.+.+ .....++.+|++.|-+.++.=+..+-...-.++.+.+ -+|+.+||+-+.
T Consensus 130 ~l~~wi~~~~~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 189 (318)
T PRK05629 130 ERPGWVTQEFKNHGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYY 189 (318)
T ss_pred HHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHh
Confidence 3333344434 2568899999999988777655555555556666654 479999998664
No 82
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=33.77 E-value=46 Score=24.92 Aligned_cols=28 Identities=14% Similarity=-0.007 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHH-----HHHHhhcCccccChhh
Q 032664 97 AEAYLVGLFEDT-----NLCAIHAKRVTIMPKD 124 (136)
Q Consensus 97 ~E~~lv~lfe~a-----~~~a~HakRvTi~~~D 124 (136)
.+.|+..+|... ..+...+.|||+.|-|
T Consensus 182 V~~h~~~i~~Kl~v~~~~~l~~~~~~~~~~~~~ 214 (216)
T PRK10840 182 ISSQKKSAMMKLGVENDIALLNYLSSVTLSPAD 214 (216)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhcCCccc
Confidence 388999999887 5667789999999877
No 83
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=33.77 E-value=1.4e+02 Score=24.15 Aligned_cols=65 Identities=18% Similarity=0.254 Sum_probs=44.7
Q ss_pred hhcCchhHHHHHHHhhhcccc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032664 63 IRKLPFQRLVREIAQDFKTDL-RFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 63 ipk~pF~RlVreI~~~~~~~~-r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 129 (136)
+-+.|-.| |++|++.- .|. ++....=..+-.|.|-||..|...+...+.-.+-.||++.-|+-++
T Consensus 11 ~trfp~aR-iKKIMQ~d-EdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v 76 (224)
T KOG1659|consen 11 KTRFPPAR-IKKIMQSD-EDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAV 76 (224)
T ss_pred hccCCHHH-HHHHHhhh-hhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHH
Confidence 34555555 47787622 122 2333333446677799999999999999999999999988776554
No 84
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=32.52 E-value=1.4e+02 Score=24.41 Aligned_cols=50 Identities=18% Similarity=0.116 Sum_probs=39.7
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-ccccChhhHHHHHH
Q 032664 81 TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAK-RVTIMPKDIQLARR 130 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Hak-RvTi~~~Diqla~r 130 (136)
.+..++.+|++.|-+.++.=+..+..+...++.+++ .-+|+.+||+.+.-
T Consensus 158 ~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~ 208 (343)
T PRK06585 158 AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVG 208 (343)
T ss_pred CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhC
Confidence 568899999999988888877777777777777754 45799999976643
No 85
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=32.44 E-value=1.5e+02 Score=24.57 Aligned_cols=49 Identities=20% Similarity=0.237 Sum_probs=38.3
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032664 81 TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 129 (136)
...+++.+|++.|-+..|.=+-.+....+.++.++.=.+|+..||+.++
T Consensus 156 ~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v 204 (334)
T COG1466 156 LGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVV 204 (334)
T ss_pred cCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHH
Confidence 5789999999999888886666666666666666655599999999876
No 86
>TIGR01924 rsbW_low_gc serine-protein kinase RsbW. This model describes the anti-sigma B factor also known as serine-protein kinase RsbW. Sigma B controls the general stress regulon in B subtilis and is activated by cell stresses such as stationary phase and heat shock. RsbW binds to sigma B and prevents formation of the transcription complex at the promoter. RsbV (anti-anti-sigma factor) binds to RsbW to inhibit association with sigma B, however RsbW can phosphorylate RsbV, causing disassociation of the RsbV/RsbW complex. Low ATP level or environmental stress causes the dephosphorylation of RsbV.
Probab=29.51 E-value=1.1e+02 Score=22.48 Aligned_cols=45 Identities=11% Similarity=0.137 Sum_probs=35.3
Q ss_pred cCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHH
Q 032664 65 KLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTN 109 (136)
Q Consensus 65 k~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~ 109 (136)
..-+-+.|+..+..+-....|+.+.+..++-+++..+++.++.++
T Consensus 15 ~~~~~~~vr~~~~~~a~~~g~~~~~~~~l~lav~Ea~~Nai~ha~ 59 (159)
T TIGR01924 15 KPEYVGLIRLTLSGIASRAGYTYDDIEDLKIAVSEACTNAVKHAY 59 (159)
T ss_pred cHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhcc
Confidence 344667777777777777889999999998888888888887764
No 87
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=29.47 E-value=1.3e+02 Score=20.49 Aligned_cols=42 Identities=19% Similarity=0.172 Sum_probs=32.0
Q ss_pred HHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032664 70 RLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDTNLC 111 (136)
Q Consensus 70 RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~ 111 (136)
..++..+..+-....|+.+.+..+.-+.+..+++.++.++..
T Consensus 9 ~~~r~~~~~~~~~~~~~~~~~~~~~lav~E~~~Nav~H~~~~ 50 (125)
T PF13581_consen 9 REARAFLREFLERLGLPEEDRDDLELAVSEALTNAVEHGYPG 50 (125)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 445555555555688999999999889999999888887653
No 88
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=29.18 E-value=1.6e+02 Score=25.73 Aligned_cols=51 Identities=22% Similarity=0.305 Sum_probs=44.9
Q ss_pred ccccccHHHHHHHHH----HHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032664 81 TDLRFQSSAVAALQE----AAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqe----a~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri 131 (136)
.++.+..+|++-|-+ .+=.|.++|+--++.||.-.+|.-|..+|+.-+..|
T Consensus 383 E~l~~~e~a~~~l~~~gt~tsLRy~vqLl~p~~~~ak~~g~~~i~v~dvee~~~L 437 (456)
T KOG1942|consen 383 EGLQVEEEALDLLAEIGTSTSLRYAVQLLTPASILAKTNGRKEISVEDVEEVTEL 437 (456)
T ss_pred hcceecHHHHHHHHhhccchhHHHHHHhcCHHHHHHHHcCCceeecccHHHHHHH
Confidence 578899999999866 455899999999999999999999999999987665
No 89
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=28.12 E-value=96 Score=21.15 Aligned_cols=60 Identities=23% Similarity=0.429 Sum_probs=43.7
Q ss_pred hHHHhhhhhhhhhhhhcCchhHHHHHHHhh-hcccccccHHHHHHHHH--HHHHHHHHHHHHHHHH
Q 032664 49 LREIRKYQKSTELLIRKLPFQRLVREIAQD-FKTDLRFQSSAVAALQE--AAEAYLVGLFEDTNLC 111 (136)
Q Consensus 49 l~EIr~~q~st~llipk~pF~RlVreI~~~-~~~~~r~~~~Al~aLqe--a~E~~lv~lfe~a~~~ 111 (136)
|++|.+|+...+ =||-.| |.+.|-++. |+.++-+.+..+..|+. -+|+|+-+..+-.+.+
T Consensus 2 L~~I~h~l~np~-DiP~ip--ra~aeyLqvrfN~~yl~~sG~i~~lr~~G~SE~~I~Gfl~Gl~~A 64 (77)
T PF10911_consen 2 LKPIQHLLDNPD-DIPDIP--RAAAEYLQVRFNAAYLMASGIISALRKQGWSESYILGFLAGLQYA 64 (77)
T ss_pred cchHHHHhcCCc-ccCCcc--HHHHHHHHHHhcHHHHHHhhhHHHHHHccccHHHHHHHHHHHHHH
Confidence 578888887653 245544 666666653 46777788888888874 5899999999888776
No 90
>PF07962 Swi3: Replication Fork Protection Component Swi3; InterPro: IPR012923 Replication fork pausing is required to initiate recombination events. More specifically, Swi1 is required for recombination near the mat1 locus. Swi3 has been found to co-purify with Swi1. Together they define a fork protection complex that coordinates leading- and lagging-strand synthesis and stabilises stalled replication forks []. This complex is required for accurate replication, fork protection and replication checkpoint signalling [, ].; GO: 0006974 response to DNA damage stimulus, 0007049 cell cycle, 0048478 replication fork protection, 0005634 nucleus
Probab=27.13 E-value=92 Score=21.02 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=24.3
Q ss_pred hhhHHHhhhhhhhhhhhhcCchhHHHHHH
Q 032664 47 VALREIRKYQKSTELLIRKLPFQRLVREI 75 (136)
Q Consensus 47 ~~l~EIr~~q~st~llipk~pF~RlVreI 75 (136)
..-+=+..||.=..-|.|+++|...|..|
T Consensus 34 dL~~ll~~Yq~W~h~LfPk~~F~d~i~~v 62 (83)
T PF07962_consen 34 DLRRLLQFYQLWAHRLFPKASFEDFIERV 62 (83)
T ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHH
Confidence 34455788999889999999999999887
No 91
>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=26.44 E-value=1.9e+02 Score=26.47 Aligned_cols=51 Identities=16% Similarity=0.192 Sum_probs=41.4
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032664 81 TDLRFQSSAVAALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~~Diqla~ri 131 (136)
....++.++++.|.+.+..+-+ .+..-|--+|.-.+|-+|..+|++.|..+
T Consensus 246 ~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~l 303 (633)
T TIGR02442 246 PSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAEL 303 (633)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence 4578899999988888877644 35566777888899999999999998876
No 92
>smart00350 MCM minichromosome maintenance proteins.
Probab=26.29 E-value=2.2e+02 Score=25.24 Aligned_cols=39 Identities=15% Similarity=0.136 Sum_probs=27.8
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032664 83 LRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 83 ~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
++++.-++++|-.+||+ .|.-..|-+|+++|++.|.+|-
T Consensus 466 ~~~t~R~l~sliRla~A-----------~A~l~~r~~V~~~Dv~~ai~l~ 504 (509)
T smart00350 466 IPITVRQLESIIRLSEA-----------HAKMRLSDVVEEADVEEAIRLL 504 (509)
T ss_pred cCcCHHHHHHHHHHHHH-----------HHHHcCCCccCHHHHHHHHHHH
Confidence 34555555555555554 4667789999999999999875
No 93
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=25.68 E-value=2.5e+02 Score=23.96 Aligned_cols=51 Identities=14% Similarity=0.117 Sum_probs=37.3
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032664 81 TDLRFQSSAVAALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~~Diqla~ri 131 (136)
....++.+.++.+.+.+.+.-+ .+...|.-+|.-.+|-.|.++||+.+..+
T Consensus 264 ~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~ 321 (350)
T CHL00081 264 PKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITL 321 (350)
T ss_pred CCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 4456666666666666665443 35566688899999999999999988765
No 94
>PF04604 L_biotic_typeA: Type-A lantibiotic; InterPro: IPR007682 Lantibiotics are antibiotic peptides distinguished by the presence of the rare thioether amino acids lanthionine and/or methyllanthionine. They are produced by Gram-positive bacteria as gene-encoded precursor peptides and undergo post-translational modification to generate the mature peptide. Based on their structural and functional features lantibiotics are currently divided into two major groups: the flexible amphiphilic type-A and the rather rigid and globular type-B. Type-A lantibiotics act primarily by pore formation in the bacterial membrane by a mechanism involving the interaction with specific docking molecules such as the membrane precursor lipid II [].; GO: 0019748 secondary metabolic process, 0005576 extracellular region
Probab=25.32 E-value=63 Score=20.36 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 032664 88 SAVAALQEAAEAYLVGLFED 107 (136)
Q Consensus 88 ~Al~aLqea~E~~lv~lfe~ 107 (136)
+|+.+|||.+++-|.+|..-
T Consensus 7 ea~~~lqevs~eELd~ilGg 26 (51)
T PF04604_consen 7 EALNSLQEVSDEELDQILGG 26 (51)
T ss_pred HHHHHHHhcCHHHHHHHhCC
Confidence 89999999999999988764
No 95
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=24.89 E-value=59 Score=24.44 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=26.2
Q ss_pred chhhHHHhhhhhhhhhhhhcCchhHHHHHHHhh
Q 032664 46 TVALREIRKYQKSTELLIRKLPFQRLVREIAQD 78 (136)
Q Consensus 46 ~~~l~EIr~~q~st~llipk~pF~RlVreI~~~ 78 (136)
.+|+.||.++..+...+ |...+.+||++|=.+
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~ 128 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKE 128 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHh
Confidence 58999999997666555 999999999999543
No 96
>PRK07914 hypothetical protein; Reviewed
Probab=24.40 E-value=2.3e+02 Score=23.15 Aligned_cols=60 Identities=12% Similarity=0.138 Sum_probs=40.5
Q ss_pred hHHHHHHHhhhc-ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032664 69 QRLVREIAQDFK-TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 69 ~RlVreI~~~~~-~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~~Diqla~ 129 (136)
..+.+=|.+.+. .+..++.+|++.|.+..+.=+..+-.....++.+.+ -+|+..||+-++
T Consensus 131 ~~l~~wi~~~a~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 191 (320)
T PRK07914 131 AERADFVRKEFRSLRVKVDDDTVTALLDAVGSDLRELASACSQLVADTG-GAVDAAAVRRYH 191 (320)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHhcCCC-CCcCHHHHHHHc
Confidence 444444444443 567899999999988887655555555555665554 468899988664
No 97
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=24.34 E-value=1.7e+02 Score=18.46 Aligned_cols=29 Identities=28% Similarity=0.437 Sum_probs=22.3
Q ss_pred cccccccHHHHHHHHHHHHHHHHHHHHHH
Q 032664 80 KTDLRFQSSAVAALQEAAEAYLVGLFEDT 108 (136)
Q Consensus 80 ~~~~r~~~~Al~aLqea~E~~lv~lfe~a 108 (136)
..++-.+.-+.+.+|.|-|.||..|--+.
T Consensus 21 gkei~~~g~~~d~i~kaqeeylsals~et 49 (58)
T PF13060_consen 21 GKEIDLQGVIADEIQKAQEEYLSALSHET 49 (58)
T ss_pred hHHhhhcchHHHHHHHHHHHHHHHhhHHH
Confidence 34556777889999999999998875443
No 98
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=24.18 E-value=4.1e+02 Score=21.89 Aligned_cols=47 Identities=11% Similarity=0.169 Sum_probs=36.5
Q ss_pred cccHHHHHHHHHHHHH------HHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032664 84 RFQSSAVAALQEAAEA------YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 84 r~~~~Al~aLqea~E~------~lv~lfe~a~~~a~HakRvTi~~~Diqla~r 130 (136)
-|+.++++.+.+.+.. ++.+++..|...|...+..+|+.+|+.-|..
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~ 280 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYE 280 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHH
Confidence 5888999888777744 4456677777778777888999999987764
No 99
>cd00913 PCD_DCoH_subfamily_a PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein).
Probab=22.81 E-value=55 Score=21.43 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=11.0
Q ss_pred ccChhhHHHHHHH
Q 032664 119 TIMPKDIQLARRI 131 (136)
Q Consensus 119 Ti~~~Diqla~ri 131 (136)
.|+.+|+.||.+|
T Consensus 61 glT~~D~~lA~~i 73 (76)
T cd00913 61 GLSENDFIMAAKI 73 (76)
T ss_pred CCCHHHHHHHHHH
Confidence 3778999999987
No 100
>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=22.66 E-value=1.4e+02 Score=23.83 Aligned_cols=31 Identities=19% Similarity=0.090 Sum_probs=27.2
Q ss_pred ccc-cccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032664 81 TDL-RFQSSAVAALQEAAEAYLVGLFEDTNLC 111 (136)
Q Consensus 81 ~~~-r~~~~Al~aLqea~E~~lv~lfe~a~~~ 111 (136)
.++ .++.+|.+.|.-|.|.||-+|++.+...
T Consensus 219 ~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~ 250 (252)
T PF12767_consen 219 HGLGGVSDDCANLLNLALEVHLKNLIKSCLDL 250 (252)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 456 8999999999999999999999987654
No 101
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=22.47 E-value=4.1e+02 Score=21.28 Aligned_cols=50 Identities=22% Similarity=0.229 Sum_probs=36.6
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-CccccChhhHHHHHHH
Q 032664 81 TDLRFQSSAVAALQEAAEAYLVGLFEDTNLCAIHA-KRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Ha-kRvTi~~~Diqla~ri 131 (136)
.+..++.+|++.|-+.++.=+..+-.....++.++ +.. |+.+||+-....
T Consensus 162 ~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~ 212 (340)
T PRK05574 162 QGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPD 212 (340)
T ss_pred cCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhh
Confidence 45689999999998888766666666666777765 333 999999866543
No 102
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=22.37 E-value=1.8e+02 Score=21.35 Aligned_cols=44 Identities=9% Similarity=0.182 Sum_probs=32.5
Q ss_pred cCchhHHHHHHHhhhcccccccHHHHHHHHHHHHHHHHHHHHHH
Q 032664 65 KLPFQRLVREIAQDFKTDLRFQSSAVAALQEAAEAYLVGLFEDT 108 (136)
Q Consensus 65 k~pF~RlVreI~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a 108 (136)
..-+.++|+..+..+.....|+.+.++.|+-+.+..+.+..+.+
T Consensus 15 ~~~~~~~vr~~v~~~~~~~g~~~~~~~~l~lav~Ea~~Nai~Hg 58 (161)
T PRK04069 15 KAEYVSIIRLTLSGVANRMGFSYDDIEDMKIAVSEACTNAVQHA 58 (161)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 34466778888887777889999998888777666666665554
No 103
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=22.32 E-value=2.6e+02 Score=23.57 Aligned_cols=51 Identities=8% Similarity=0.037 Sum_probs=37.2
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032664 81 TDLRFQSSAVAALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~~Diqla~ri 131 (136)
....++.+.+..+.+.+.+.=+ .|...|..+|+..+|-.|+++||+-+..+
T Consensus 248 ~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~~~ 305 (334)
T PRK13407 248 PQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVATM 305 (334)
T ss_pred CCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHHHH
Confidence 4556667766666666655432 16677789999999999999999876654
No 104
>cd00488 PCD_DCoH PCD_DCoH: The bifunctional protein pterin-4alpha-carbinolamine dehydratase (PCD), also known as DCoH (dimerization cofactor of hepatocyte nuclear factor-1), is both a transcription activator and a metabolic enzyme. DCoH stimulates gene expression by associating with specific DNA binding proteins such as HNF-1alpha (hepatocyte nuclear factor-1) and Xenopus enhancer of rudimentary homologue (XERH). DCoH also catalyzes the dehydration of 4alpha- hydroxy- tetrahydrobiopterin (4alpha-OH-BH4) to quinoiddihydrobiopterin, a percursor of the phenylalanine hydroxylase cofactor BH4 (tetrahydrobiopterin). The DCoH homodimer has a saddle-shaped structure similar to that of TBP (TATA binding protein). Two DCoH proteins have been identifed in humans: DCoH1 and DCoH2. Mutations in human DCoH1 cause hyperphenylalaninemia. Loss of enzymic activity of DCoH in humans is associated with the depigmentation disorder vitiligo. DCoH1 has been reported to be overexpessed in colon cancer carc
Probab=21.12 E-value=63 Score=21.01 Aligned_cols=13 Identities=31% Similarity=0.475 Sum_probs=11.2
Q ss_pred cChhhHHHHHHHh
Q 032664 120 IMPKDIQLARRIR 132 (136)
Q Consensus 120 i~~~Diqla~ri~ 132 (136)
|+.+|+.||.+|-
T Consensus 61 lt~~D~~lA~~id 73 (75)
T cd00488 61 LTENDFILAAKID 73 (75)
T ss_pred CCHHHHHHHHHHh
Confidence 8889999999873
No 105
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.86 E-value=69 Score=22.49 Aligned_cols=17 Identities=35% Similarity=0.759 Sum_probs=14.0
Q ss_pred hhcCchhHHHHHHHhhh
Q 032664 63 IRKLPFQRLVREIAQDF 79 (136)
Q Consensus 63 ipk~pF~RlVreI~~~~ 79 (136)
-.-+||++|+++|+...
T Consensus 72 a~GlpYQtyIreiLh~~ 88 (92)
T COG5304 72 AEGLPYQTYIREILHKY 88 (92)
T ss_pred hcCCcHHHHHHHHHHhh
Confidence 36689999999998754
No 106
>PF08681 DUF1778: Protein of unknown function (DUF1778); InterPro: IPR014795 This entry is represented by Vibrio phage ICP1, Orf50. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a family of uncharacterised proteins. The structure of one of the hypothetical proteins in this family has been solved and it forms a helix structure which may form interactions with DNA. ; PDB: 1Y9B_A.
Probab=20.14 E-value=1.9e+02 Score=19.15 Aligned_cols=51 Identities=12% Similarity=0.126 Sum_probs=28.6
Q ss_pred cccccHHHHHHHHHHHHHHH--------HHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032664 82 DLRFQSSAVAALQEAAEAYL--------VGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 82 ~~r~~~~Al~aLqea~E~~l--------v~lfe~a~~~a~HakRvTi~~~Diqla~ri~ 132 (136)
++|++++..+.|+.||+..- ...++.|-..-.-...+++..+|.+......
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~aL 61 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAAL 61 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHHH
Confidence 46788888888888877432 3334444333333345677777776655443
Done!