Query 032665
Match_columns 136
No_of_seqs 164 out of 653
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 04:23:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032665.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032665hhsearch_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 4.6E-56 1E-60 329.9 11.6 135 1-135 1-135 (136)
2 PLN00121 histone H3; Provision 100.0 6.8E-56 1.5E-60 329.0 11.5 136 1-136 1-136 (136)
3 PLN00161 histone H3; Provision 100.0 2.2E-54 4.7E-59 319.9 11.0 128 1-135 1-129 (135)
4 KOG1745 Histones H3 and H4 [Ch 100.0 9.6E-52 2.1E-56 306.0 8.6 136 1-136 1-137 (137)
5 smart00428 H3 Histone H3. 100.0 4.3E-47 9.4E-52 271.6 9.8 101 35-135 2-104 (105)
6 PLN00160 histone H3; Provision 100.0 1.3E-46 2.8E-51 265.6 8.8 94 42-135 1-95 (97)
7 COG2036 HHT1 Histones H3 and H 99.9 2.9E-27 6.2E-32 165.5 8.0 87 44-135 1-87 (91)
8 PF00125 Histone: Core histone 99.8 4.3E-21 9.4E-26 127.8 7.3 75 58-132 1-75 (75)
9 cd07981 TAF12 TATA Binding Pro 99.4 6.2E-13 1.3E-17 89.1 7.9 58 73-130 8-65 (72)
10 cd00076 H4 Histone H4, one of 99.3 5.4E-12 1.2E-16 87.4 7.4 69 61-134 12-80 (85)
11 PLN00035 histone H4; Provision 99.3 8.7E-12 1.9E-16 89.1 7.5 67 63-134 30-96 (103)
12 PTZ00015 histone H4; Provision 99.3 1.3E-11 2.9E-16 88.1 7.2 69 61-134 29-97 (102)
13 smart00803 TAF TATA box bindin 99.2 3.1E-11 6.8E-16 79.6 6.0 64 62-130 2-65 (65)
14 smart00417 H4 Histone H4. 99.1 7.4E-11 1.6E-15 79.9 5.1 62 61-127 12-73 (74)
15 PTZ00463 histone H2B; Provisio 99.0 1.1E-09 2.4E-14 79.6 7.0 65 64-132 26-94 (117)
16 PLN00158 histone H2B; Provisio 99.0 1.4E-09 3E-14 79.1 7.1 65 64-132 25-93 (116)
17 smart00427 H2B Histone H2B. 99.0 2E-09 4.3E-14 75.2 7.2 62 67-132 2-67 (89)
18 cd07979 TAF9 TATA Binding Prot 98.8 2E-08 4.3E-13 73.1 8.0 65 69-134 4-68 (117)
19 PF00808 CBFD_NFYB_HMF: Histon 98.8 3.4E-08 7.5E-13 64.2 6.8 63 63-129 3-65 (65)
20 KOG1744 Histone H2B [Chromatin 98.6 7.7E-08 1.7E-12 71.0 5.4 66 63-132 34-103 (127)
21 cd00074 H2A Histone 2A; H2A is 98.4 5.5E-07 1.2E-11 65.6 5.1 67 60-130 18-84 (115)
22 smart00576 BTP Bromodomain tra 98.4 2.6E-06 5.6E-11 57.4 7.5 54 81-134 20-73 (77)
23 PF15630 CENP-S: Kinetochore c 98.3 2.4E-06 5.3E-11 58.0 6.1 66 65-130 4-71 (76)
24 KOG0870 DNA polymerase epsilon 98.3 2.8E-06 6.1E-11 65.3 6.9 69 60-130 8-76 (172)
25 PF03847 TFIID_20kDa: Transcri 98.2 5.4E-06 1.2E-10 55.2 6.7 59 72-130 5-63 (68)
26 cd08050 TAF6 TATA Binding Prot 98.2 7E-06 1.5E-10 69.1 7.8 62 72-134 5-66 (343)
27 PF02969 TAF: TATA box binding 98.1 2.4E-05 5.2E-10 51.9 7.1 58 72-130 9-66 (66)
28 PF02291 TFIID-31kDa: Transcri 97.9 4.7E-05 1E-09 56.5 7.4 65 69-134 15-79 (129)
29 PF15511 CENP-T: Centromere ki 97.9 2.5E-05 5.5E-10 67.5 6.0 62 63-124 352-414 (414)
30 KOG1142 Transcription initiati 97.7 4.6E-05 9.9E-10 62.3 4.4 73 54-130 146-218 (258)
31 KOG0869 CCAAT-binding factor, 97.4 0.00064 1.4E-08 52.1 6.3 72 59-133 29-100 (168)
32 KOG3334 Transcription initiati 97.1 0.0028 6.1E-08 47.9 7.6 65 70-135 17-81 (148)
33 KOG3467 Histone H4 [Chromatin 97.0 0.0032 7E-08 44.1 6.1 66 64-134 31-96 (103)
34 PF07524 Bromo_TP: Bromodomain 96.8 0.013 2.7E-07 39.1 8.1 52 83-134 22-73 (77)
35 KOG0871 Class 2 transcription 96.4 0.013 2.9E-07 44.5 6.4 72 59-133 9-80 (156)
36 PLN00154 histone H2A; Provisio 95.7 0.026 5.7E-07 42.3 5.1 68 60-130 36-103 (136)
37 smart00414 H2A Histone 2A. 95.7 0.019 4E-07 41.3 4.1 67 60-130 7-73 (106)
38 PTZ00017 histone H2A; Provisio 95.4 0.02 4.4E-07 42.8 3.7 67 60-130 25-91 (134)
39 COG5262 HTA1 Histone H2A [Chro 94.8 0.053 1.2E-06 39.9 4.4 66 61-130 25-90 (132)
40 KOG2549 Transcription initiati 94.5 0.12 2.7E-06 46.5 6.7 53 81-133 25-77 (576)
41 PF02269 TFIID-18kDa: Transcri 94.4 0.034 7.3E-07 38.8 2.4 59 72-130 7-65 (93)
42 PLN00156 histone H2AX; Provisi 94.3 0.064 1.4E-06 40.4 3.8 67 60-130 27-93 (139)
43 PLN00157 histone H2A; Provisio 94.2 0.051 1.1E-06 40.6 3.2 67 60-130 24-90 (132)
44 PLN00153 histone H2A; Provisio 93.9 0.078 1.7E-06 39.5 3.5 67 60-130 22-88 (129)
45 COG5094 TAF9 Transcription ini 93.2 0.31 6.7E-06 36.4 5.8 61 70-131 18-81 (145)
46 PTZ00252 histone H2A; Provisio 93.0 0.16 3.4E-06 38.1 4.0 67 60-130 23-91 (134)
47 COG5150 Class 2 transcription 93.0 0.42 9.2E-06 35.7 6.2 70 59-131 8-77 (148)
48 KOG1756 Histone 2A [Chromatin 91.4 0.34 7.4E-06 36.0 4.1 66 61-130 26-91 (131)
49 COG5208 HAP5 CCAAT-binding fac 91.2 0.62 1.3E-05 37.9 5.7 85 45-130 80-173 (286)
50 cd08045 TAF4 TATA Binding Prot 91.2 0.71 1.5E-05 36.3 6.0 56 60-116 42-97 (212)
51 cd07978 TAF13 The TATA Binding 90.2 2.7 5.9E-05 29.3 7.6 58 72-130 8-65 (92)
52 KOG4336 TBP-associated transcr 89.6 1.5 3.3E-05 37.1 6.9 51 84-134 22-72 (323)
53 PF05236 TAF4: Transcription i 89.5 0.43 9.3E-06 38.7 3.5 58 60-118 41-98 (264)
54 KOG1657 CCAAT-binding factor, 86.7 1.2 2.7E-05 36.1 4.6 72 57-129 66-137 (236)
55 PF09415 CENP-X: CENP-S associ 84.8 1.6 3.6E-05 29.1 3.7 57 71-127 4-63 (72)
56 PF09123 DUF1931: Domain of un 80.4 3.6 7.8E-05 31.0 4.4 59 68-131 1-59 (138)
57 COG5248 TAF19 Transcription in 80.0 13 0.00028 27.2 7.1 61 68-130 11-71 (126)
58 COG5095 TAF6 Transcription ini 79.8 6.7 0.00015 33.8 6.4 53 81-133 19-71 (450)
59 KOG3901 Transcription initiati 77.5 17 0.00038 26.2 7.0 63 65-130 8-70 (109)
60 KOG2389 Predicted bromodomain 74.9 10 0.00022 32.6 6.2 53 81-133 43-95 (353)
61 cd08048 TAF11 TATA Binding Pro 68.5 35 0.00076 23.3 8.0 64 63-131 17-83 (85)
62 PF13654 AAA_32: AAA domain; P 66.2 38 0.00083 30.3 8.1 67 66-133 430-507 (509)
63 COG1224 TIP49 DNA helicase TIP 65.1 14 0.00031 32.5 5.0 72 61-132 354-432 (450)
64 KOG1757 Histone 2A [Chromatin 64.8 10 0.00022 27.8 3.5 66 67-134 32-97 (131)
65 PF07278 DUF1441: Protein of u 63.7 38 0.00082 25.9 6.6 65 48-112 75-150 (152)
66 KOG1658 DNA polymerase epsilon 63.4 5.6 0.00012 30.6 2.1 64 64-129 58-122 (162)
67 TIGR00764 lon_rel lon-related 62.1 46 0.00099 30.4 8.0 64 69-132 315-391 (608)
68 TIGR02902 spore_lonB ATP-depen 58.9 40 0.00087 30.1 6.9 50 81-130 279-330 (531)
69 PRK07452 DNA polymerase III su 58.0 38 0.00083 27.5 6.3 59 69-129 136-196 (326)
70 TIGR03015 pepcterm_ATPase puta 53.3 59 0.0013 25.2 6.4 49 82-130 213-264 (269)
71 COG5624 TAF61 Transcription in 53.1 3.7 7.9E-05 36.3 -0.5 58 72-129 389-447 (505)
72 PF04719 TAFII28: hTAFII28-lik 49.8 85 0.0019 21.8 7.1 64 63-130 24-88 (90)
73 KOG2680 DNA helicase TIP49, TB 48.9 69 0.0015 27.9 6.5 72 61-132 351-429 (454)
74 PRK05907 hypothetical protein; 46.8 58 0.0013 27.2 5.7 67 63-129 131-200 (311)
75 KOG3219 Transcription initiati 44.9 45 0.00098 26.5 4.5 77 52-133 102-179 (195)
76 TIGR01128 holA DNA polymerase 44.3 1.3E+02 0.0028 23.7 7.2 62 68-131 116-177 (302)
77 TIGR02030 BchI-ChlI magnesium 43.0 88 0.0019 26.4 6.3 51 81-131 251-308 (337)
78 PRK08487 DNA polymerase III su 43.0 94 0.002 25.6 6.4 56 70-129 142-197 (328)
79 KOG1659 Class 2 transcription 41.7 92 0.002 25.3 5.8 65 63-129 11-76 (224)
80 PF08369 PCP_red: Proto-chloro 37.3 56 0.0012 19.6 3.1 43 85-128 1-44 (45)
81 PF10911 DUF2717: Protein of u 35.7 65 0.0014 22.0 3.5 60 49-111 2-64 (77)
82 PF08157 NUC129: NUC129 domain 34.7 59 0.0013 21.3 3.1 43 87-129 9-59 (63)
83 PRK05629 hypothetical protein; 34.5 1.5E+02 0.0033 24.2 6.3 48 81-129 142-189 (318)
84 PRK10840 transcriptional regul 34.3 43 0.00094 25.1 2.9 28 97-124 182-214 (216)
85 KOG1942 DNA helicase, TBP-inte 33.8 1.3E+02 0.0028 26.3 5.8 51 81-131 383-437 (456)
86 PRK06585 holA DNA polymerase I 32.0 1.5E+02 0.0032 24.3 5.8 50 81-130 158-208 (343)
87 PF13581 HATPase_c_2: Histidin 31.2 1.2E+02 0.0027 20.5 4.6 42 70-111 9-50 (125)
88 TIGR01924 rsbW_low_gc serine-p 30.8 1.1E+02 0.0023 22.6 4.4 45 65-109 15-59 (159)
89 COG1466 HolA DNA polymerase II 29.9 1.8E+02 0.004 24.0 6.1 49 81-129 156-204 (334)
90 smart00350 MCM minichromosome 29.8 1.7E+02 0.0038 25.8 6.3 39 83-132 466-504 (509)
91 PF13060 DUF3921: Protein of u 27.6 1.4E+02 0.0031 18.8 3.9 29 80-108 21-49 (58)
92 PRK00411 cdc6 cell division co 27.1 3.6E+02 0.0078 22.2 7.9 47 84-130 228-280 (394)
93 PF12767 SAGA-Tad1: Transcript 26.8 1E+02 0.0023 24.6 4.0 31 81-111 219-250 (252)
94 TIGR02442 Cob-chelat-sub cobal 26.7 1.8E+02 0.0039 26.6 5.9 51 81-131 246-303 (633)
95 PF07962 Swi3: Replication For 26.4 96 0.0021 20.9 3.2 29 47-75 34-62 (83)
96 CHL00081 chlI Mg-protoporyphyr 26.1 2.4E+02 0.0052 24.1 6.2 51 81-131 264-321 (350)
97 PRK07914 hypothetical protein; 25.3 2.2E+02 0.0048 23.3 5.8 60 69-129 131-191 (320)
98 PRK04069 serine-protein kinase 23.5 1.7E+02 0.0038 21.4 4.4 44 65-108 15-58 (161)
99 PRK13407 bchI magnesium chelat 23.3 2.4E+02 0.0052 23.8 5.7 51 81-131 248-305 (334)
100 cd00913 PCD_DCoH_subfamily_a P 23.2 53 0.0012 21.5 1.4 13 119-131 61-73 (76)
101 KOG1969 DNA replication checkp 22.9 1.7E+02 0.0037 28.2 5.1 80 45-126 449-531 (877)
102 PRK13531 regulatory ATPase Rav 22.8 3.1E+02 0.0066 24.9 6.5 74 47-131 207-283 (498)
103 PF04604 L_biotic_typeA: Type- 22.5 77 0.0017 20.0 1.9 20 88-107 7-26 (51)
104 cd00488 PCD_DCoH PCD_DCoH: The 21.7 60 0.0013 21.1 1.4 13 120-132 61-73 (75)
105 PF10788 DUF2603: Protein of u 21.3 68 0.0015 24.1 1.8 32 46-78 97-128 (137)
106 COG5304 Uncharacterized protei 21.1 67 0.0015 22.6 1.6 17 63-79 72-88 (92)
107 PF08681 DUF1778: Protein of u 20.6 1.9E+02 0.0042 19.0 3.8 50 82-131 3-60 (80)
108 TIGR02031 BchD-ChlD magnesium 20.2 2.6E+02 0.0057 25.4 5.6 52 81-132 200-258 (589)
109 COG1598 Predicted nuclease of 20.0 1.5E+02 0.0032 19.3 3.0 24 87-110 34-57 (73)
No 1
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=4.6e-56 Score=329.89 Aligned_cols=135 Identities=96% Similarity=1.337 Sum_probs=129.8
Q ss_pred CCcccccccccCCCCCCCcchhhhhcccCCCCCCCCCCCcccCCCchhhHHHhhhhhhhhhhhhhchhHHHHHHHHhhhh
Q 032665 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 Martk~~a~ks~g~kap~k~~~~k~~~~~~p~~~~~~k~~r~~~g~~~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 99999999999999999999988877777777778889999999999999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhccc
Q 032665 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~~ 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=6.8e-56 Score=329.01 Aligned_cols=136 Identities=99% Similarity=1.339 Sum_probs=130.6
Q ss_pred CCcccccccccCCCCCCCcchhhhhcccCCCCCCCCCCCcccCCCchhhHHHhhhhhhhhhhhhhchhHHHHHHHHhhhh
Q 032665 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 Martk~~a~ks~g~kap~k~~~~k~~~~~~p~~~~~~k~~r~~~g~~~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 032665 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~~~ 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 99999999999999999999999999999999999999999999999999999863
No 3
>PLN00161 histone H3; Provisional
Probab=100.00 E-value=2.2e-54 Score=319.90 Aligned_cols=128 Identities=66% Similarity=0.963 Sum_probs=119.0
Q ss_pred CCcccccccccCCCCCCCcchhhhhcccCCCCCCCCCCCcccCCCchhhHHHhhhhhhhhhhhhhchhHHHHHHHHhhhh
Q 032665 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK 80 (136)
Q Consensus 1 Martk~~a~ks~g~kap~k~~~~k~~~~~~p~~~~~~k~~r~~~g~~~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 23456689999999999999999999999999999999999999999996
Q ss_pred -ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhccc
Q 032665 81 -TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 81 -~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~~ 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 5799999999999999999999999999999999999999999999999999974
No 4
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=100.00 E-value=9.6e-52 Score=306.01 Aligned_cols=136 Identities=95% Similarity=1.294 Sum_probs=128.9
Q ss_pred CCcccccccccCCCCCCCcchhhhhcccC-CCCCCCCCCCcccCCCchhhHHHhhhhhhhhhhhhhchhHHHHHHHHhhh
Q 032665 1 MARTKQTARKSTGGKAPRKQLATKAARKS-APTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDF 79 (136)
Q Consensus 1 Martk~~a~ks~g~kap~k~~~~k~~~~~-~p~~~~~~k~~r~~~g~~~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 89999999999999999999998887765 34456668899999999999999999999999999999999999999999
Q ss_pred hccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcccC
Q 032665 80 KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 136 (136)
Q Consensus 80 ~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~~~ 136 (136)
..|+|||+.|+.+||||+|+|||+||||+|+||+|||||||||+|||||++|||++.
T Consensus 81 ~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrirg~~~ 137 (137)
T KOG1745|consen 81 KTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 137 (137)
T ss_pred cccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcccCCC
Confidence 999999999999999999999999999999999999999999999999999999863
No 5
>smart00428 H3 Histone H3.
Probab=100.00 E-value=4.3e-47 Score=271.58 Aligned_cols=101 Identities=87% Similarity=1.223 Sum_probs=97.8
Q ss_pred CCCCCcccCCCchhhHHHhhhhhhhhhhhhhchhHHHHHHHHhhhhc--cccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032665 35 GVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSHAVLALQEAAEAYLVGLFEDTNLCA 112 (136)
Q Consensus 35 ~~~k~~r~~~g~~~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 35788999999999999999999999999999999999999999986 9999999999999999999999999999999
Q ss_pred hhcCccccChhhHHHHHHHhccc
Q 032665 113 IHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 113 ~HakRvTi~~kDiqla~rir~~~ 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=1.3e-46 Score=265.57 Aligned_cols=94 Identities=71% Similarity=1.082 Sum_probs=91.0
Q ss_pred cCCCchhhHHHhhhhhhhhhhhhhchhHHHHHHHHhhhh-ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcccc
Q 032665 42 YRPGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTI 120 (136)
Q Consensus 42 ~~~g~~~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 032665 121 MPKDIQLARRIRGER 135 (136)
Q Consensus 121 ~~kDiqla~rir~~~ 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=2.9e-27 Score=165.46 Aligned_cols=87 Identities=47% Similarity=0.670 Sum_probs=83.0
Q ss_pred CCchhhHHHhhhhhhhhhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChh
Q 032665 44 PGTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPK 123 (136)
Q Consensus 44 ~g~~~l~EIr~~q~st~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~k 123 (136)
||+..++|||+||++++++||++||.|++|+.. ..|||.+|.++||+++|.|+.+|+|+|+.||.|+||+||+++
T Consensus 1 ~~~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~-----~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~ 75 (91)
T COG2036 1 PGAVGLKEIRRYQRSTDLLLPKAPVRRILRKAG-----AERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAE 75 (91)
T ss_pred CCcchHHHHHhhhhhhhhhcCchHHHHHHHHHh-----HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHH
Confidence 588999999999999999999999999999994 459999999999999999999999999999999999999999
Q ss_pred hHHHHHHHhccc
Q 032665 124 DIQLARRIRGER 135 (136)
Q Consensus 124 Diqla~rir~~~ 135 (136)
||+|+.+.+|..
T Consensus 76 DI~la~~~~~~~ 87 (91)
T COG2036 76 DIKLALKRLGRR 87 (91)
T ss_pred HHHHHHHHhccc
Confidence 999999999853
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=4.3e-21 Score=127.84 Aligned_cols=75 Identities=48% Similarity=0.665 Sum_probs=71.2
Q ss_pred hhhhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032665 58 STELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 58 st~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir 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 467899999999999999988877799999999999999999999999999999999999999999999999985
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=99.43 E-value=6.2e-13 Score=89.09 Aligned_cols=58 Identities=24% Similarity=0.292 Sum_probs=52.3
Q ss_pred HHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 73 REIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 73 rei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 3444444677999999999999999999999999999999999999999999999975
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=99.33 E-value=5.4e-12 Score=87.42 Aligned_cols=69 Identities=25% Similarity=0.271 Sum_probs=65.8
Q ss_pred hhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 61 llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 134 (136)
.-||+.|..||++.- +..|+|.++.+++.++.|.|+.++..|+..++.||+|.||+..||.+|.+..|.
T Consensus 12 ~gi~k~~I~RLarr~-----GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~ 80 (85)
T cd00076 12 KGITKPAIRRLARRG-----GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred ccCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 349999999999988 899999999999999999999999999999999999999999999999998885
No 11
>PLN00035 histone H4; Provisional
Probab=99.30 E-value=8.7e-12 Score=89.14 Aligned_cols=67 Identities=22% Similarity=0.263 Sum_probs=64.9
Q ss_pred hhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 63 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 63 ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 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 899999999999999999999999999999999999999999999999998875
No 12
>PTZ00015 histone H4; Provisional
Probab=99.28 E-value=1.3e-11 Score=88.06 Aligned_cols=69 Identities=22% Similarity=0.229 Sum_probs=65.6
Q ss_pred hhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 61 llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 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 899999999999999999999999999999999999999999999999988875
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=99.22 E-value=3.1e-11 Score=79.62 Aligned_cols=64 Identities=20% Similarity=0.214 Sum_probs=60.4
Q ss_pred hhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 62 LIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 62 lipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 47999999999888 88899999999999999999999999999999999999999999999863
No 14
>smart00417 H4 Histone H4.
Probab=99.14 E-value=7.4e-11 Score=79.85 Aligned_cols=62 Identities=21% Similarity=0.211 Sum_probs=58.8
Q ss_pred hhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHH
Q 032665 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 127 (136)
Q Consensus 61 llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiql 127 (136)
.-||+.|..||++.- |..|+|.++.+.|.++.|.|+.++..||..++.|++|.||+..||..
T Consensus 12 ~gI~k~~IrRLaRr~-----GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARRG-----GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 349999999999988 89999999999999999999999999999999999999999999864
No 15
>PTZ00463 histone H2B; Provisional
Probab=99.01 E-value=1.1e-09 Score=79.59 Aligned_cols=65 Identities=18% Similarity=0.287 Sum_probs=59.7
Q ss_pred hhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHH----HHHHhhcCccccChhhHHHHHHHh
Q 032665 64 RKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDT----NLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 64 pk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a----~~~a~HakRvTi~~kDiqla~rir 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 88888888875 888999999999999999999985
No 16
>PLN00158 histone H2B; Provisional
Probab=99.00 E-value=1.4e-09 Score=79.10 Aligned_cols=65 Identities=18% Similarity=0.327 Sum_probs=60.0
Q ss_pred hhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHH----HHHHhhcCccccChhhHHHHHHHh
Q 032665 64 RKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDT----NLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 64 pk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a----~~~a~HakRvTi~~kDiqla~rir 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 88888888875 888999999999999999999985
No 17
>smart00427 H2B Histone H2B.
Probab=98.99 E-value=2e-09 Score=75.17 Aligned_cols=62 Identities=19% Similarity=0.325 Sum_probs=57.5
Q ss_pred hhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHH----HHHHhhcCccccChhhHHHHHHHh
Q 032665 67 PFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDT----NLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 67 pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a----~~~a~HakRvTi~~kDiqla~rir 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 688999999999999999999999999 88888888875 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=98.83 E-value=2e-08 Score=73.14 Aligned_cols=65 Identities=22% Similarity=0.352 Sum_probs=59.9
Q ss_pred HHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 69 QRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 69 ~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 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 57788887765 667999999999999999999999999999999999999999999999999875
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=98.76 E-value=3.4e-08 Score=64.19 Aligned_cols=63 Identities=27% Similarity=0.294 Sum_probs=51.8
Q ss_pred hhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032665 63 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 63 ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ 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 LPLARVKRIMKSD----PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp S-HHHHHHHHHHT----STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CChHHHHHHhccC----CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 5666666666554 45678999999999999999999999999999999999999999998764
No 20
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=98.61 E-value=7.7e-08 Score=71.01 Aligned_cols=66 Identities=27% Similarity=0.372 Sum_probs=60.9
Q ss_pred hhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHH----HHHHhhcCccccChhhHHHHHHHh
Q 032665 63 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDT----NLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 63 ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a----~~~a~HakRvTi~~kDiqla~rir 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 88888888875 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=98.39 E-value=5.5e-07 Score=65.58 Aligned_cols=67 Identities=22% Similarity=0.206 Sum_probs=61.5
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 4889999999999762 146899999999999999999999999999999999999999999999975
No 22
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.36 E-value=2.6e-06 Score=57.41 Aligned_cols=54 Identities=24% Similarity=0.134 Sum_probs=50.8
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 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 667999999999999999999999999999999999999999999999877664
No 23
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.29 E-value=2.4e-06 Score=58.03 Aligned_cols=66 Identities=27% Similarity=0.272 Sum_probs=53.7
Q ss_pred hchhHHHHHHHHhhh--hccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 65 KLPFQRLVREIAQDF--KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 65 k~pF~Rlvrei~~~~--~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~r 130 (136)
|+.+.--|-+|+++. ..+..++++.+.+|-|.+=.++..+-+|--..|.||||.||+++|+.|..|
T Consensus 4 Kaal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 4 KAALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 344555566777665 367899999999999999999999999999999999999999999999764
No 24
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=98.28 E-value=2.8e-06 Score=65.31 Aligned_cols=69 Identities=28% Similarity=0.318 Sum_probs=64.5
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 68999999999999998866 6899999999999999999999999999999999999999999976654
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=5.4e-06 Score=55.19 Aligned_cols=59 Identities=20% Similarity=0.253 Sum_probs=46.7
Q ss_pred HHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 72 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 72 vrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~r 130 (136)
+.+++.++.+...+.+++.+.|.+.++.|+.++.+.+..+|.|.+--||.++||++...
T Consensus 5 l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 5 LQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 34555556789999999999999999999999999999999999999999999999864
No 26
>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=98.17 E-value=7e-06 Score=69.15 Aligned_cols=62 Identities=21% Similarity=0.262 Sum_probs=55.6
Q ss_pred HHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 72 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 72 vrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 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 55555544 566999999999999999999999999999999999999999999999999865
No 27
>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=98.06 E-value=2.4e-05 Score=51.87 Aligned_cols=58 Identities=28% Similarity=0.326 Sum_probs=45.4
Q ss_pred HHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 72 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 72 vrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 3468999999999999999999999999999999999999999999875
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=97.94 E-value=4.7e-05 Score=56.52 Aligned_cols=65 Identities=29% Similarity=0.359 Sum_probs=52.9
Q ss_pred HHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 69 QRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 69 ~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 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 34689999999999999999999999999999999999999999999987753
No 29
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.89 E-value=2.5e-05 Score=67.46 Aligned_cols=62 Identities=24% Similarity=0.293 Sum_probs=44.8
Q ss_pred hhhchhHHHHHHHHhh-hhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhh
Q 032665 63 IRKLPFQRLVREIAQD-FKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKD 124 (136)
Q Consensus 63 ipk~pF~Rlvrei~~~-~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kD 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 5555666666555553 3367899999999999999999999999999999999999999887
No 30
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.70 E-value=4.6e-05 Score=62.27 Aligned_cols=73 Identities=21% Similarity=0.272 Sum_probs=64.7
Q ss_pred hhhhhhhhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 54 KYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 54 ~~q~st~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 5667777888777777777776 578899999999999999999999999999999999999999999999864
No 31
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=97.35 E-value=0.00064 Score=52.12 Aligned_cols=72 Identities=15% Similarity=0.196 Sum_probs=64.6
Q ss_pred hhhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032665 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 59 t~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~ 133 (136)
.+.++|.+-..|+.+.++- .+-.|+.+|-+.+||.+-.|+-=+--.|+.-+.--+|+||+.+||-.|+--.|
T Consensus 29 qDr~LPIANV~RIMK~~lP---~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 29 QDRFLPIANVSRIMKKALP---ANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhhhccHHHHHHHHHhcCC---cccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 3456999999999999854 77899999999999999999999999999999999999999999999886655
No 32
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=97.13 E-value=0.0028 Score=47.89 Aligned_cols=65 Identities=25% Similarity=0.414 Sum_probs=55.4
Q ss_pred HHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhccc
Q 032665 70 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 135 (136)
Q Consensus 70 Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~~ 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 345677888888899999999999999999999999999999999999988753
No 33
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=96.96 E-value=0.0032 Score=44.12 Aligned_cols=66 Identities=23% Similarity=0.254 Sum_probs=55.8
Q ss_pred hhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 64 RKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 64 pk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 134 (136)
-|-...||.|.- +--|+..-..+....++..||.+..-+|...+-||||.||+.-|+--+.+-.|.
T Consensus 31 tKpaIRRlARr~-----GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 31 TKPAIRRLARRG-----GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred chHHHHHHHHhc-----CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 355566776655 667888888889999999999999999999999999999999999888876654
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=96.83 E-value=0.013 Score=39.07 Aligned_cols=52 Identities=23% Similarity=0.142 Sum_probs=48.5
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 83 LRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 83 ~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 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 4789999999999999999999999999999999999999999999876664
No 35
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.39 E-value=0.013 Score=44.53 Aligned_cols=72 Identities=18% Similarity=0.255 Sum_probs=66.0
Q ss_pred hhhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032665 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 59 t~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~ 133 (136)
.++-+||+....+|+|++ ..+.||..+|-+.|++..=.|+.-|--.||..+---.+.||.++-+.-|..-.|
T Consensus 9 de~sLPkAtv~KmIke~l---P~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~Lg 80 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEML---PKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLG 80 (156)
T ss_pred ccccCcHHHHHHHHHHhC---CcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcc
Confidence 457799999999999995 369999999999999999999999999999999999999999999998887665
No 36
>PLN00154 histone H2A; Provisional
Probab=95.67 E-value=0.026 Score=42.31 Aligned_cols=68 Identities=19% Similarity=0.154 Sum_probs=59.6
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 35699999999999999999999999999999999999999999999974
No 37
>smart00414 H2A Histone 2A.
Probab=95.67 E-value=0.019 Score=41.29 Aligned_cols=67 Identities=25% Similarity=0.223 Sum_probs=57.2
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 4667777777877654 235699999999999999999999999999999999999999999999874
No 38
>PTZ00017 histone H2A; Provisional
Probab=95.41 E-value=0.02 Score=42.80 Aligned_cols=67 Identities=24% Similarity=0.210 Sum_probs=58.7
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 4778888888888764 134699999999999999999999999999999999999999999999975
No 39
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=94.84 E-value=0.053 Score=39.93 Aligned_cols=66 Identities=24% Similarity=0.281 Sum_probs=53.6
Q ss_pred hhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 61 llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~r 130 (136)
+.+|---..||. ..-....|++++|...|--..|-....++|-|...|.-.+-..|+|+-+|||.+
T Consensus 25 l~fpvgrvkr~l----k~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 25 LIFPVGRVKRLL----KKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred ccccHHHHHHHH----HcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 344444444444 323467899999999999999999999999999999999999999999999864
No 40
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=94.47 E-value=0.12 Score=46.51 Aligned_cols=53 Identities=23% Similarity=0.286 Sum_probs=49.7
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032665 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~ 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 66679999999999999999999999999999999999999999999998764
No 41
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=94.38 E-value=0.034 Score=38.83 Aligned_cols=59 Identities=15% Similarity=0.201 Sum_probs=29.5
Q ss_pred HHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 72 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 72 vrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 34444445555678899999999999999999999999999999999999999988765
No 42
>PLN00156 histone H2AX; Provisional
Probab=94.25 E-value=0.064 Score=40.40 Aligned_cols=67 Identities=25% Similarity=0.222 Sum_probs=57.2
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 3677777777777653 234699999999998889999999999999999999999999999999975
No 43
>PLN00157 histone H2A; Provisional
Probab=94.23 E-value=0.051 Score=40.60 Aligned_cols=67 Identities=25% Similarity=0.224 Sum_probs=57.6
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 4778888888887663 234699999999998889999999999999999999999999999999974
No 44
>PLN00153 histone H2A; Provisional
Probab=93.85 E-value=0.078 Score=39.46 Aligned_cols=67 Identities=25% Similarity=0.218 Sum_probs=57.6
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 4778877788887653 235699999999999999999999999999999999999999999999975
No 45
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=93.25 E-value=0.31 Score=36.35 Aligned_cols=61 Identities=28% Similarity=0.355 Sum_probs=43.5
Q ss_pred HHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccCh---hhHHHHHHH
Q 032665 70 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMP---KDIQLARRI 131 (136)
Q Consensus 70 Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~---kDiqla~ri 131 (136)
||+.=|+... +-.........-|-+-|-.|-.+++|||...|.|++|-.+.. +|+.||.--
T Consensus 18 rlihliL~Sl-gi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 18 RLIHLILRSL-GIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred hHHHHHHHhc-CchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 4444444333 223344555556668889999999999999999999865555 999999754
No 46
>PTZ00252 histone H2A; Provisional
Probab=93.05 E-value=0.16 Score=38.10 Aligned_cols=67 Identities=19% Similarity=0.196 Sum_probs=55.1
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhh--cCccccChhhHHHHHH
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLARR 130 (136)
Q Consensus 60 ~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~H--akRvTi~~kDiqla~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 3677887788887654 23569999999999888899999999999888864 6778999999999975
No 47
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=92.99 E-value=0.42 Score=35.73 Aligned_cols=70 Identities=21% Similarity=0.180 Sum_probs=62.5
Q ss_pred hhhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032665 59 TELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 59 t~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 3567999999999999954 889999999999999999999999999999999999999999887666543
No 48
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=91.39 E-value=0.34 Score=36.04 Aligned_cols=66 Identities=26% Similarity=0.257 Sum_probs=54.8
Q ss_pred hhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 61 LLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 61 llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 55666656666655 2356899999999998888888899999999999999999999999999975
No 49
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=91.25 E-value=0.62 Score=37.90 Aligned_cols=85 Identities=20% Similarity=0.246 Sum_probs=64.9
Q ss_pred CchhhHHHhhhhhhhhh---------hhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 032665 45 GTVALREIRKYQKSTEL---------LIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHA 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 44455667889876432 2234899886 5565432233357888888889999999999999999999999
Q ss_pred CccccChhhHHHHHH
Q 032665 116 KRVTIMPKDIQLARR 130 (136)
Q Consensus 116 kRvTi~~kDiqla~r 130 (136)
+|-||...||--|+.
T Consensus 159 kRRtLQksDia~Av~ 173 (286)
T COG5208 159 KRRTLQKSDIAAAVK 173 (286)
T ss_pred hhhHHHHHHHHHHHH
Confidence 999999999988775
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=91.16 E-value=0.71 Score=36.34 Aligned_cols=56 Identities=18% Similarity=0.209 Sum_probs=50.0
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAK 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 36788999999999998876544 899999999999999999999999999999973
No 51
>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=90.16 E-value=2.7 Score=29.26 Aligned_cols=58 Identities=17% Similarity=0.232 Sum_probs=45.0
Q ss_pred HHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 72 VREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 72 vrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 334443344445667899999999999999999999999998 5566669999998864
No 52
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=89.57 E-value=1.5 Score=37.06 Aligned_cols=51 Identities=16% Similarity=0.081 Sum_probs=47.7
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 84 RFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 84 r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 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 478889999999999999999999999999999999999999999988775
No 53
>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=89.45 E-value=0.43 Score=38.69 Aligned_cols=58 Identities=21% Similarity=0.255 Sum_probs=38.6
Q ss_pred hhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcc
Q 032665 60 ELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRV 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 367888889999999986554 5689999999999999999999999999999986543
No 54
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=86.70 E-value=1.2 Score=36.08 Aligned_cols=72 Identities=19% Similarity=0.223 Sum_probs=61.1
Q ss_pred hhhhhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032665 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 57 ~st~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ 129 (136)
...++.+..+|..|+ |.|++.-..---|+.+|...+-.++|.|+..|-..+..-+--.+|.|+.-.|+.-++
T Consensus 66 ~~~d~~~~~lPlaRi-KkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av 137 (236)
T KOG1657|consen 66 GQLDFKNHILPLARI-KKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAV 137 (236)
T ss_pred cccchhhccCcHhhc-cccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHh
Confidence 355788999999986 566554333348999999999999999999999999999999999999999998765
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=84.82 E-value=1.6 Score=29.11 Aligned_cols=57 Identities=7% Similarity=0.061 Sum_probs=43.1
Q ss_pred HHHHHHhhh--hccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccc-cChhhHHH
Q 032665 71 LVREIAQDF--KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVT-IMPKDIQL 127 (136)
Q Consensus 71 lvrei~~~~--~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvT-i~~kDiql 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 455555543 3678999999999999999999999999988887777777 99999874
No 56
>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=80.38 E-value=3.6 Score=31.00 Aligned_cols=59 Identities=22% Similarity=0.316 Sum_probs=43.9
Q ss_pred hHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032665 68 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 68 F~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 66777777 456777888888999999999999999999999999999999998776655
No 57
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=80.04 E-value=13 Score=27.20 Aligned_cols=61 Identities=18% Similarity=0.200 Sum_probs=47.8
Q ss_pred hHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 68 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 68 F~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 4444555555555566667889999999999999999988888877 677788999999875
No 58
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=79.80 E-value=6.7 Score=33.84 Aligned_cols=53 Identities=21% Similarity=0.206 Sum_probs=47.7
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032665 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~ 133 (136)
+-.-+..+++.+|-.-.|--+.++-+.+...+.|.||--++..||.-|.+-+.
T Consensus 19 Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lN 71 (450)
T COG5095 19 GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLN 71 (450)
T ss_pred CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcC
Confidence 34567889999998899999999999999999999999999999999988764
No 59
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=77.53 E-value=17 Score=26.23 Aligned_cols=63 Identities=21% Similarity=0.248 Sum_probs=47.5
Q ss_pred hchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 65 KLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 65 k~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 344666666666666666666678899998889999999966665555 888899999998765
No 60
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=74.95 E-value=10 Score=32.61 Aligned_cols=53 Identities=21% Similarity=0.083 Sum_probs=47.6
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032665 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~ 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 34467788999999999999999999999999999999999999999987654
No 61
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=68.47 E-value=35 Score=23.35 Aligned_cols=64 Identities=17% Similarity=0.273 Sum_probs=52.4
Q ss_pred hhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCc---cccChhhHHHHHHH
Q 032665 63 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKR---VTIMPKDIQLARRI 131 (136)
Q Consensus 63 ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR---vTi~~kDiqla~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 6666666666555 4478899999999999999999999999877776554 78999999988775
No 62
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=66.21 E-value=38 Score=30.33 Aligned_cols=67 Identities=22% Similarity=0.263 Sum_probs=49.8
Q ss_pred chhHHHHHHHHhhhhccccccHHHHHHHHHHHH-----------HHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhc
Q 032665 66 LPFQRLVREIAQDFKTDLRFQSHAVLALQEAAE-----------AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 133 (136)
Q Consensus 66 ~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E-----------~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~ 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 45777887777655 335789999998766553 57899999999999999999999999999987653
No 63
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=65.14 E-value=14 Score=32.49 Aligned_cols=72 Identities=24% Similarity=0.374 Sum_probs=58.9
Q ss_pred hhhhhchhHH-HHHHHHhhh--hccccccHHHHHHHHHHHH----HHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032665 61 LLIRKLPFQR-LVREIAQDF--KTDLRFQSHAVLALQEAAE----AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 61 llipk~pF~R-lvrei~~~~--~~~~r~~~~Al~aLqea~E----~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir 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 6788888876 467775422 2678899999999976555 6999999999999999999999999999887763
No 64
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=64.78 E-value=10 Score=27.83 Aligned_cols=66 Identities=23% Similarity=0.272 Sum_probs=49.2
Q ss_pred hhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHhcc
Q 032665 67 PFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 134 (136)
Q Consensus 67 pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir~~ 134 (136)
|..|+=+-+-......-|+...|..-+-...|..-..++|-|...+.--|=..|+|+-+|||. ||+
T Consensus 32 pVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAi--RGD 97 (131)
T KOG1757|consen 32 PVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAI--RGD 97 (131)
T ss_pred chHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeee--cCc
Confidence 445554444444456678888887777667787788899999888888888889999999984 554
No 65
>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=63.73 E-value=38 Score=25.86 Aligned_cols=65 Identities=20% Similarity=0.191 Sum_probs=49.3
Q ss_pred hhHHHhhhhhhhhhhhhhchhHHH----HHHHHhhh-------hccccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032665 48 ALREIRKYQKSTELLIRKLPFQRL----VREIAQDF-------KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCA 112 (136)
Q Consensus 48 ~l~EIr~~q~st~llipk~pF~Rl----vrei~~~~-------~~~~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 345666789999999998765554 44444333 257899999999999999999999998876554
No 66
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=63.42 E-value=5.6 Score=30.61 Aligned_cols=64 Identities=25% Similarity=0.350 Sum_probs=49.2
Q ss_pred hhchhHHHHHHHHhhhhccccccHH-HHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032665 64 RKLPFQRLVREIAQDFKTDLRFQSH-AVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 64 pk~pF~Rlvrei~~~~~~~~r~~~~-Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ 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 34444443 34422 3478888765 56678899999999999999999999999999999987664
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=62.07 E-value=46 Score=30.39 Aligned_cols=64 Identities=16% Similarity=0.136 Sum_probs=45.6
Q ss_pred HHHHHHHHhhhhccccccHHHHHHHHHH-H------------HHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032665 69 QRLVREIAQDFKTDLRFQSHAVLALQEA-A------------EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 69 ~Rlvrei~~~~~~~~r~~~~Al~aLqea-~------------E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir 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 3444443333322348999999998642 2 36788888889888888899999999999876543
No 68
>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=58.89 E-value=40 Score=30.10 Aligned_cols=50 Identities=18% Similarity=0.226 Sum_probs=40.1
Q ss_pred ccccccHHHHHHHHHHHH--HHHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 81 TDLRFQSHAVLALQEAAE--AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E--~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 347889999988755544 56778888888888888999999999998864
No 69
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=58.03 E-value=38 Score=27.51 Aligned_cols=59 Identities=19% Similarity=0.231 Sum_probs=46.0
Q ss_pred HHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhh--cCccccChhhHHHHH
Q 032665 69 QRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLAR 129 (136)
Q Consensus 69 ~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~H--akRvTi~~kDiqla~ 129 (136)
..+|++.++. .+..++.+|+..|.+.++.=+..+-.....++.+ .+..+|+.+||+.+.
T Consensus 136 ~~~i~~~~~~--~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v 196 (326)
T PRK07452 136 KQLVERTAQE--LGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALV 196 (326)
T ss_pred HHHHHHHHHH--cCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHh
Confidence 4445554432 4678999999999999888777777778888888 568889999999765
No 70
>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=53.34 E-value=59 Score=25.23 Aligned_cols=49 Identities=14% Similarity=0.090 Sum_probs=41.4
Q ss_pred cccccHHHHHHHHHHHHH---HHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 82 DLRFQSHAVLALQEAAEA---YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 82 ~~r~~~~Al~aLqea~E~---~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 7888888888887777888999999988764
No 71
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=53.07 E-value=3.7 Score=36.28 Aligned_cols=58 Identities=19% Similarity=0.147 Sum_probs=48.1
Q ss_pred HHHHHhhh-hccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032665 72 VREIAQDF-KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 72 vrei~~~~-~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ 129 (136)
++|..+.+ .+...+..+.-+.|-+.|..|....-+-+..+|.|.|-.||-++|+||-.
T Consensus 389 L~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhl 447 (505)
T COG5624 389 LEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHL 447 (505)
T ss_pred HHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeee
Confidence 34444333 57788888888889999999999998889999999999999999999854
No 72
>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=49.80 E-value=85 Score=21.78 Aligned_cols=64 Identities=14% Similarity=0.253 Sum_probs=40.9
Q ss_pred hhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCc-cccChhhHHHHHH
Q 032665 63 IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKR-VTIMPKDIQLARR 130 (136)
Q Consensus 63 ipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakR-vTi~~kDiqla~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 6666666665554 45688999999999999999999999999766553222 2677777776654
No 73
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=48.88 E-value=69 Score=27.93 Aligned_cols=72 Identities=21% Similarity=0.352 Sum_probs=57.8
Q ss_pred hhhhhchhHH-HHHHHHhh-h-hccccccHHHHHHHHHHHH----HHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032665 61 LLIRKLPFQR-LVREIAQD-F-KTDLRFQSHAVLALQEAAE----AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 61 llipk~pF~R-lvrei~~~-~-~~~~r~~~~Al~aLqea~E----~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir 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 5899999999999999999999999999998874
No 74
>PRK05907 hypothetical protein; Provisional
Probab=46.82 E-value=58 Score=27.15 Aligned_cols=67 Identities=12% Similarity=0.025 Sum_probs=50.5
Q ss_pred hhhchhHHHHHHHHhhhh-ccccccHHHHHHHHHHH-HHHHHHHHHHHHHHHhh-cCccccChhhHHHHH
Q 032665 63 IRKLPFQRLVREIAQDFK-TDLRFQSHAVLALQEAA-EAYLVGLFEDTNLCAIH-AKRVTIMPKDIQLAR 129 (136)
Q Consensus 63 ipk~pF~Rlvrei~~~~~-~~~r~~~~Al~aLqea~-E~~lv~lfe~a~~~a~H-akRvTi~~kDiqla~ 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 344444666766766664 67899999999997777 56666777777788888 569999999998764
No 75
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=44.88 E-value=45 Score=26.51 Aligned_cols=77 Identities=16% Similarity=0.237 Sum_probs=56.6
Q ss_pred HhhhhhhhhhhhhhchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHH-HHHhhcCccccChhhHHHHHH
Q 032665 52 IRKYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTN-LCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 52 Ir~~q~st~llipk~pF~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~-~~a~HakRvTi~~kDiqla~r 130 (136)
+-+|-.-....+||+-..+|+.+|+. . -++..+..+++-.+..|+-.|-|.|. .|-.-..-=-|.|..|.-|.+
T Consensus 102 l~RYEvfRrs~f~Ka~iKkL~~~itg----~-~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~r 176 (195)
T KOG3219|consen 102 LSRYEVFRRSAFPKAQIKKLMSSITG----Q-SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYR 176 (195)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHhC----C-ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHH
Confidence 34444444456888888888888843 2 37788888999999999999999994 445555666788999988877
Q ss_pred Hhc
Q 032665 131 IRG 133 (136)
Q Consensus 131 ir~ 133 (136)
..+
T Consensus 177 rL~ 179 (195)
T KOG3219|consen 177 RLK 179 (195)
T ss_pred HHH
Confidence 654
No 76
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=44.26 E-value=1.3e+02 Score=23.75 Aligned_cols=62 Identities=23% Similarity=0.243 Sum_probs=41.4
Q ss_pred hHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032665 68 FQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 68 F~Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ri 131 (136)
+..+|++.+.+ .+..++.+|+..|-+.++.=+-.+-.....++.+++-.+|+.+||+-....
T Consensus 116 ~~~~i~~~~~~--~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~~ 177 (302)
T TIGR01128 116 LPRWIQARLKK--LGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVSD 177 (302)
T ss_pred HHHHHHHHHHH--cCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHhh
Confidence 34455555443 467899999999987777555555555556666654447999999876543
No 77
>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=43.03 E-value=88 Score=26.45 Aligned_cols=51 Identities=14% Similarity=0.147 Sum_probs=40.3
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032665 81 TDLRFQSHAVLALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~kDiqla~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 5667888888777776666544 26777888999999999999999987765
No 78
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=43.01 E-value=94 Score=25.58 Aligned_cols=56 Identities=25% Similarity=0.166 Sum_probs=43.8
Q ss_pred HHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032665 70 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 70 Rlvrei~~~~~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ 129 (136)
++|++.+++ .+..++.+|+..|-+..+.=+..+-...-.++.+++ +|+.+||+.+.
T Consensus 142 ~~i~~~~~~--~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 142 ELLQERAKE--LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred HHHHHHHHH--hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 344444332 467899999999998888888888888888888877 79999999765
No 79
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=41.66 E-value=92 Score=25.26 Aligned_cols=65 Identities=18% Similarity=0.253 Sum_probs=44.5
Q ss_pred hhhchhHHHHHHHHhhhhccc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032665 63 IRKLPFQRLVREIAQDFKTDL-RFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 63 ipk~pF~Rlvrei~~~~~~~~-r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ 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 34445555 47787632 122 2333333446677799999999999999999999999988776554
No 80
>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=37.25 E-value=56 Score=19.64 Aligned_cols=43 Identities=14% Similarity=0.092 Sum_probs=20.6
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHHH-HHHHhhcCccccChhhHHHH
Q 032665 85 FQSHAVLALQEAAEAYLVGLFEDT-NLCAIHAKRVTIMPKDIQLA 128 (136)
Q Consensus 85 ~~~~Al~aLqea~E~~lv~lfe~a-~~~a~HakRvTi~~kDiqla 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 344444444332 22333333322 45677788888888877654
No 81
>PF10911 DUF2717: Protein of unknown function (DUF2717); InterPro: IPR020121 The proteins in this entry are uncharacterised.
Probab=35.67 E-value=65 Score=21.98 Aligned_cols=60 Identities=23% Similarity=0.401 Sum_probs=41.7
Q ss_pred hHHHhhhhhhhhhhhhhchhHHHHHHHHhh-hhccccccHHHHHHHHH--HHHHHHHHHHHHHHHH
Q 032665 49 LREIRKYQKSTELLIRKLPFQRLVREIAQD-FKTDLRFQSHAVLALQE--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 577888887653 245443 566666552 45667777778888874 5899999999888776
No 82
>PF08157 NUC129: NUC129 domain; InterPro: IPR012579 This C-terminal domain is found in a novel family of hypothetical nucleolar proteins [].; GO: 0005634 nucleus
Probab=34.71 E-value=59 Score=21.30 Aligned_cols=43 Identities=14% Similarity=0.230 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHH--------HHHHHhhcCccccChhhHHHHH
Q 032665 87 SHAVLALQEAAEAYLVGLFED--------TNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 87 ~~Al~aLqea~E~~lv~lfe~--------a~~~a~HakRvTi~~kDiqla~ 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 456678899999999765522 1456777777777776666654
No 83
>PRK05629 hypothetical protein; Validated
Probab=34.48 E-value=1.5e+02 Score=24.18 Aligned_cols=48 Identities=15% Similarity=0.074 Sum_probs=35.7
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032665 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ 129 (136)
.+..++.+|++.|-+.++.=+..+-...-.++.+.+ -+|+.+||+-+.
T Consensus 142 ~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 189 (318)
T PRK05629 142 HGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYY 189 (318)
T ss_pred cCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHh
Confidence 568899999999988877655555555555666654 379999998664
No 84
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=34.29 E-value=43 Score=25.06 Aligned_cols=28 Identities=14% Similarity=-0.007 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHH-----HHHHhhcCccccChhh
Q 032665 97 AEAYLVGLFEDT-----NLCAIHAKRVTIMPKD 124 (136)
Q Consensus 97 ~E~~lv~lfe~a-----~~~a~HakRvTi~~kD 124 (136)
.+.|+..+|... ..+...+.|||+.|-|
T Consensus 182 V~~h~~~i~~Kl~v~~~~~l~~~~~~~~~~~~~ 214 (216)
T PRK10840 182 ISSQKKSAMMKLGVENDIALLNYLSSVTLSPAD 214 (216)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhcCCccc
Confidence 488999999877 5667789999999877
No 85
>KOG1942 consensus DNA helicase, TBP-interacting protein [Replication, recombination and repair]
Probab=33.78 E-value=1.3e+02 Score=26.27 Aligned_cols=51 Identities=22% Similarity=0.282 Sum_probs=44.8
Q ss_pred ccccccHHHHHHHHH----HHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032665 81 TDLRFQSHAVLALQE----AAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqe----a~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 86
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=32.01 E-value=1.5e+02 Score=24.28 Aligned_cols=50 Identities=16% Similarity=0.092 Sum_probs=39.7
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC-ccccChhhHHHHHH
Q 032665 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAK-RVTIMPKDIQLARR 130 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~Hak-RvTi~~kDiqla~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 568899999999999888877777777777777754 46799999976653
No 87
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=31.18 E-value=1.2e+02 Score=20.54 Aligned_cols=42 Identities=19% Similarity=0.144 Sum_probs=31.9
Q ss_pred HHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032665 70 RLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLC 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 445555555555688999999999889999999988887653
No 88
>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=30.79 E-value=1.1e+02 Score=22.61 Aligned_cols=45 Identities=11% Similarity=0.115 Sum_probs=35.1
Q ss_pred hchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHHH
Q 032665 65 KLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTN 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 345666777777777777889999999998888888888888764
No 89
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=29.89 E-value=1.8e+02 Score=24.00 Aligned_cols=49 Identities=20% Similarity=0.229 Sum_probs=37.9
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032665 81 TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ 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 5689999999999888886666666666666665555599999999875
No 90
>smart00350 MCM minichromosome maintenance proteins.
Probab=29.84 E-value=1.7e+02 Score=25.82 Aligned_cols=39 Identities=15% Similarity=0.119 Sum_probs=27.8
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032665 83 LRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 83 ~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~rir 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 4666789999999999999875
No 91
>PF13060 DUF3921: Protein of unknown function (DUF3921)
Probab=27.64 E-value=1.4e+02 Score=18.79 Aligned_cols=29 Identities=28% Similarity=0.383 Sum_probs=22.4
Q ss_pred hccccccHHHHHHHHHHHHHHHHHHHHHH
Q 032665 80 KTDLRFQSHAVLALQEAAEAYLVGLFEDT 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 34556778889999999999998875443
No 92
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=27.09 E-value=3.6e+02 Score=22.23 Aligned_cols=47 Identities=11% Similarity=0.145 Sum_probs=36.5
Q ss_pred cccHHHHHHHHHHHHH------HHHHHHHHHHHHHhhcCccccChhhHHHHHH
Q 032665 84 RFQSHAVLALQEAAEA------YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 130 (136)
Q Consensus 84 r~~~~Al~aLqea~E~------~lv~lfe~a~~~a~HakRvTi~~kDiqla~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 93
>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=26.77 E-value=1e+02 Score=24.61 Aligned_cols=31 Identities=19% Similarity=0.060 Sum_probs=27.3
Q ss_pred ccc-cccHHHHHHHHHHHHHHHHHHHHHHHHH
Q 032665 81 TDL-RFQSHAVLALQEAAEAYLVGLFEDTNLC 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 455 8999999999999999999999987654
No 94
>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=26.68 E-value=1.8e+02 Score=26.59 Aligned_cols=51 Identities=14% Similarity=0.166 Sum_probs=41.4
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032665 81 TDLRFQSHAVLALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~kDiqla~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 35566778888899999999999988876
No 95
>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=26.38 E-value=96 Score=20.92 Aligned_cols=29 Identities=21% Similarity=0.282 Sum_probs=24.5
Q ss_pred hhhHHHhhhhhhhhhhhhhchhHHHHHHH
Q 032665 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 34455788999889999999999999888
No 96
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=26.06 E-value=2.4e+02 Score=24.10 Aligned_cols=51 Identities=14% Similarity=0.127 Sum_probs=37.1
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032665 81 TDLRFQSHAVLALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~kDiqla~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 4456666666666666655443 35566788899999999999999988765
No 97
>PRK07914 hypothetical protein; Reviewed
Probab=25.28 E-value=2.2e+02 Score=23.26 Aligned_cols=60 Identities=12% Similarity=0.112 Sum_probs=40.3
Q ss_pred HHHHHHHHhhh-hccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChhhHHHHH
Q 032665 69 QRLVREIAQDF-KTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
Q Consensus 69 ~Rlvrei~~~~-~~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~kDiqla~ 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 34444444434 2567899999999988887666555555555665654 468899988664
No 98
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=23.47 E-value=1.7e+02 Score=21.37 Aligned_cols=44 Identities=9% Similarity=0.160 Sum_probs=32.5
Q ss_pred hchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHHH
Q 032665 65 KLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDT 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 34466778888877777888999998888777666666666555
No 99
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=23.28 E-value=2.4e+02 Score=23.81 Aligned_cols=51 Identities=8% Similarity=0.018 Sum_probs=37.1
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032665 81 TDLRFQSHAVLALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~kDiqla~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 4456667666666666655432 16677889999999999999999876654
No 100
>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=23.25 E-value=53 Score=21.49 Aligned_cols=13 Identities=23% Similarity=0.404 Sum_probs=11.1
Q ss_pred ccChhhHHHHHHH
Q 032665 119 TIMPKDIQLARRI 131 (136)
Q Consensus 119 Ti~~kDiqla~ri 131 (136)
.|+.+|+.||.+|
T Consensus 61 glT~~D~~lA~~i 73 (76)
T cd00913 61 GLSENDFIMAAKI 73 (76)
T ss_pred CCCHHHHHHHHHH
Confidence 3788999999987
No 101
>KOG1969 consensus DNA replication checkpoint protein CHL12/CTF18 [Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=22.92 E-value=1.7e+02 Score=28.16 Aligned_cols=80 Identities=23% Similarity=0.222 Sum_probs=49.4
Q ss_pred CchhhHHHhhhhhhhhhhhhhchhHHHHHHHHhhhh-ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCcc--ccC
Q 032665 45 GTVALREIRKYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRV--TIM 121 (136)
Q Consensus 45 g~~~l~EIr~~q~st~llipk~pF~Rlvrei~~~~~-~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRv--Ti~ 121 (136)
.+.+|+..|.|-.= ..++..+-.+||...-.-|+ .+++....||.+|-|.++.=+-.-.---..++.-++|. -+.
T Consensus 449 YaPaLR~Lr~~A~i--i~f~~p~~s~Lv~RL~~IC~rE~mr~d~~aL~~L~el~~~DIRsCINtLQfLa~~~~r~ds~i~ 526 (877)
T KOG1969|consen 449 YAPALRPLRPFAEI--IAFVPPSQSRLVERLNEICHRENMRADSKALNALCELTQNDIRSCINTLQFLASNVDRRDSSIS 526 (877)
T ss_pred cchhhhhcccceEE--EEecCCChhHHHHHHHHHHhhhcCCCCHHHHHHHHHHhcchHHHHHHHHHHHHHhcccccccch
Confidence 77889988887543 45566667788855433343 78999999999996665544333333334455555553 244
Q ss_pred hhhHH
Q 032665 122 PKDIQ 126 (136)
Q Consensus 122 ~kDiq 126 (136)
.+||.
T Consensus 527 ~~~i~ 531 (877)
T KOG1969|consen 527 VKLIC 531 (877)
T ss_pred hhhhh
Confidence 44544
No 102
>PRK13531 regulatory ATPase RavA; Provisional
Probab=22.81 E-value=3.1e+02 Score=24.86 Aligned_cols=74 Identities=15% Similarity=0.134 Sum_probs=46.2
Q ss_pred hhhHHHhhhhhhhhhhhhhchhHHHHHHHHhhhh---ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCccccChh
Q 032665 47 VALREIRKYQKSTELLIRKLPFQRLVREIAQDFK---TDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPK 123 (136)
Q Consensus 47 ~~l~EIr~~q~st~llipk~pF~Rlvrei~~~~~---~~~r~~~~Al~aLqea~E~~lv~lfe~a~~~a~HakRvTi~~k 123 (136)
....||..+|+....+---.+...|+.+|..... .+..+|+.+..+| ...+..+|.-.+|-.|.+.
T Consensus 207 is~eel~~lq~~v~~V~v~d~v~eyI~~L~~~lr~~r~~~~~SpR~~~~l-----------~~~akA~A~l~GR~~V~p~ 275 (498)
T PRK13531 207 ITDEEYQQWQKEIGKITLPDHVFELIFQLRQQLDALPNAPYVSDRRWKKA-----------IRLLQASAFFSGRDAIAPI 275 (498)
T ss_pred CCHHHHHHHHHHhcceeCCHHHHHHHHHHHHHHhcCCCCCCcCcHHHHHH-----------HHHHHHHHHHCCCCCCCHH
Confidence 4456777777665433333344555556654321 1234666666555 4445667899999999999
Q ss_pred hHHHHHHH
Q 032665 124 DIQLARRI 131 (136)
Q Consensus 124 Diqla~ri 131 (136)
|++++.-.
T Consensus 276 Dv~ll~~v 283 (498)
T PRK13531 276 DLILLKDC 283 (498)
T ss_pred HHHHhHHH
Confidence 99976654
No 103
>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=22.49 E-value=77 Score=19.96 Aligned_cols=20 Identities=25% Similarity=0.308 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 032665 88 HAVLALQEAAEAYLVGLFED 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 89999999999999888754
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=21.71 E-value=60 Score=21.10 Aligned_cols=13 Identities=31% Similarity=0.475 Sum_probs=11.3
Q ss_pred cChhhHHHHHHHh
Q 032665 120 IMPKDIQLARRIR 132 (136)
Q Consensus 120 i~~kDiqla~rir 132 (136)
|+.+|+.||.+|=
T Consensus 61 lt~~D~~lA~~id 73 (75)
T cd00488 61 LTENDFILAAKID 73 (75)
T ss_pred CCHHHHHHHHHHh
Confidence 8899999999873
No 105
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=21.33 E-value=68 Score=24.13 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=25.9
Q ss_pred chhhHHHhhhhhhhhhhhhhchhHHHHHHHHhh
Q 032665 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 58899999987666555 899999999999553
No 106
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.07 E-value=67 Score=22.56 Aligned_cols=17 Identities=35% Similarity=0.759 Sum_probs=13.9
Q ss_pred hhhchhHHHHHHHHhhh
Q 032665 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 35689999999998754
No 107
>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=20.64 E-value=1.9e+02 Score=19.04 Aligned_cols=50 Identities=14% Similarity=0.155 Sum_probs=27.1
Q ss_pred cccccHHHHHHHHHHHHHHHH--------HHHHHHHHHHhhcCccccChhhHHHHHHH
Q 032665 82 DLRFQSHAVLALQEAAEAYLV--------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 131 (136)
Q Consensus 82 ~~r~~~~Al~aLqea~E~~lv--------~lfe~a~~~a~HakRvTi~~kDiqla~ri 131 (136)
++|++++..+.|+.||+..-+ ..++.|-..-.-...+++..+|.+.....
T Consensus 3 ~iR~~~e~k~li~~AA~~~G~sls~Fi~~aa~~~A~~~i~~~~~~~Ls~~~~~~f~~a 60 (80)
T PF08681_consen 3 EIRVTPEEKELIERAAALSGVSLSDFILSAALEAAEEVIEEHERIRLSAEDFEAFMAA 60 (80)
T ss_dssp EEE--HHHHHHHHHHHHHTTS-HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_pred eEecCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcceeEcCHHHHHHHHHH
Confidence 467778888888887764332 33333433222234567777777665544
No 108
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=20.21 E-value=2.6e+02 Score=25.39 Aligned_cols=52 Identities=15% Similarity=0.142 Sum_probs=38.6
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHHHHHHHhhcCccccChhhHHHHHHHh
Q 032665 81 TDLRFQSHAVLALQEAAEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRIR 132 (136)
Q Consensus 81 ~~~r~~~~Al~aLqea~E~~lv-------~lfe~a~~~a~HakRvTi~~kDiqla~rir 132 (136)
....++.+.++.|-+.+-.+-+ .+...|.-+|.-.+|-+|.++|++.|..+-
T Consensus 200 ~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~lv 258 (589)
T TIGR02031 200 PQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVELV 258 (589)
T ss_pred CCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHH
Confidence 4567888887766555544433 245666788889999999999999998763
No 109
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=20.04 E-value=1.5e+02 Score=19.28 Aligned_cols=24 Identities=29% Similarity=0.293 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 032665 87 SHAVLALQEAAEAYLVGLFEDTNL 110 (136)
Q Consensus 87 ~~Al~aLqea~E~~lv~lfe~a~~ 110 (136)
.+|+.-++||.|-++..+.++...
T Consensus 34 eea~~n~~eai~l~~e~~~~~~~~ 57 (73)
T COG1598 34 EEALQNAKEAIELHLEALLEEGEP 57 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCc
Confidence 578889999999999998887643
Done!