Query psy10959
Match_columns 132
No_of_seqs 140 out of 571
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 22:49:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10959.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10959hhsearch_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 5.7E-54 1.2E-58 318.5 11.0 131 1-131 1-135 (136)
2 PLN00121 histone H3; Provision 100.0 7.6E-54 1.6E-58 317.8 11.0 132 1-132 1-136 (136)
3 PLN00161 histone H3; Provision 100.0 3E-52 6.4E-57 308.4 10.4 124 1-131 1-129 (135)
4 KOG1745|consensus 100.0 6.1E-50 1.3E-54 296.4 8.0 132 1-132 1-137 (137)
5 PLN00160 histone H3; Provision 100.0 2.7E-45 5.8E-50 258.7 8.2 90 42-131 5-95 (97)
6 smart00428 H3 Histone H3. 100.0 1.2E-44 2.5E-49 258.9 9.0 90 42-131 13-104 (105)
7 COG2036 HHT1 Histones H3 and H 99.9 2.3E-26 4.9E-31 160.9 7.3 85 42-131 3-87 (91)
8 PF00125 Histone: Core histone 99.9 1.7E-21 3.6E-26 129.5 6.6 75 54-128 1-75 (75)
9 cd07981 TAF12 TATA Binding Pro 99.4 1E-12 2.2E-17 87.9 7.2 62 61-126 4-65 (72)
10 cd00076 H4 Histone H4, one of 99.3 1E-11 2.2E-16 86.0 6.6 68 58-130 13-80 (85)
11 PLN00035 histone H4; Provision 99.2 2.4E-11 5.1E-16 86.9 6.7 67 59-130 30-96 (103)
12 PTZ00015 histone H4; Provision 99.2 3E-11 6.5E-16 86.2 6.5 67 59-130 31-97 (102)
13 smart00803 TAF TATA box bindin 99.2 5.1E-11 1.1E-15 78.5 5.4 64 58-126 2-65 (65)
14 smart00417 H4 Histone H4. 99.1 1.7E-10 3.7E-15 78.1 4.5 61 58-123 13-73 (74)
15 PLN00158 histone H2B; Provisio 98.9 1.4E-08 3E-13 73.9 8.0 69 60-128 25-93 (116)
16 cd07979 TAF9 TATA Binding Prot 98.8 2E-08 4.3E-13 73.0 7.4 66 64-130 3-68 (117)
17 PTZ00463 histone H2B; Provisio 98.8 3E-08 6.5E-13 72.2 7.2 69 60-128 26-94 (117)
18 PF00808 CBFD_NFYB_HMF: Histon 98.8 1.8E-08 3.9E-13 65.4 5.4 63 59-125 3-65 (65)
19 smart00427 H2B Histone H2B. 98.7 4.8E-08 1E-12 68.2 7.4 66 63-128 2-67 (89)
20 PF15630 CENP-S: Kinetochore c 98.3 1.3E-06 2.7E-11 59.4 5.5 65 62-126 5-71 (76)
21 smart00576 BTP Bromodomain tra 98.3 2.3E-06 5.1E-11 57.5 6.6 54 77-130 20-73 (77)
22 KOG1744|consensus 98.3 1.5E-06 3.2E-11 64.2 5.4 70 59-128 34-103 (127)
23 cd00074 H2A Histone 2A; H2A is 98.2 1.8E-06 3.8E-11 62.9 4.8 67 56-126 18-84 (115)
24 KOG0870|consensus 98.1 6.1E-06 1.3E-10 63.5 6.1 69 56-126 8-76 (172)
25 PF03847 TFIID_20kDa: Transcri 98.1 1.5E-05 3.3E-10 53.0 6.2 58 69-126 6-63 (68)
26 PF02969 TAF: TATA box binding 98.0 2.8E-05 6.1E-10 51.5 6.4 58 68-126 9-66 (66)
27 cd08050 TAF6 TATA Binding Prot 98.0 2.1E-05 4.6E-10 66.1 7.1 63 67-130 4-66 (343)
28 PF02291 TFIID-31kDa: Transcri 97.9 5.5E-05 1.2E-09 56.1 7.0 65 65-130 15-79 (129)
29 PF15511 CENP-T: Centromere ki 97.8 3.1E-05 6.8E-10 66.7 5.4 62 59-120 352-414 (414)
30 KOG1142|consensus 97.6 7.2E-05 1.6E-09 61.1 4.5 73 50-126 146-218 (258)
31 KOG0869|consensus 97.0 0.0016 3.5E-08 49.9 5.6 71 56-129 30-100 (168)
32 KOG3334|consensus 96.7 0.0073 1.6E-07 45.7 7.0 64 66-130 17-80 (148)
33 KOG3467|consensus 96.6 0.0064 1.4E-07 42.7 5.6 67 59-130 30-96 (103)
34 PF07524 Bromo_TP: Bromodomain 96.6 0.0077 1.7E-07 40.0 5.8 52 79-130 22-73 (77)
35 KOG0871|consensus 95.8 0.028 6E-07 42.8 5.8 72 55-129 9-80 (156)
36 PLN00154 histone H2A; Provisio 94.9 0.06 1.3E-06 40.4 4.9 68 56-126 36-103 (136)
37 smart00414 H2A Histone 2A. 94.6 0.052 1.1E-06 39.0 3.9 67 56-126 7-73 (106)
38 PF02269 TFIID-18kDa: Transcri 94.5 0.051 1.1E-06 37.9 3.6 59 68-126 7-65 (93)
39 PTZ00017 histone H2A; Provisio 94.3 0.054 1.2E-06 40.5 3.4 67 56-126 25-91 (134)
40 COG5262 HTA1 Histone H2A [Chro 93.5 0.13 2.8E-06 38.0 4.1 52 75-126 39-90 (132)
41 KOG2549|consensus 93.0 0.26 5.7E-06 44.4 6.1 53 77-129 25-77 (576)
42 PLN00156 histone H2AX; Provisi 92.9 0.13 2.9E-06 38.7 3.5 67 56-126 27-93 (139)
43 PLN00157 histone H2A; Provisio 92.7 0.12 2.6E-06 38.6 3.0 67 56-126 24-90 (132)
44 PLN00153 histone H2A; Provisio 92.1 0.18 3.9E-06 37.5 3.3 67 56-126 22-88 (129)
45 PTZ00252 histone H2A; Provisio 91.1 0.31 6.8E-06 36.5 3.7 67 56-126 23-91 (134)
46 COG5150 Class 2 transcription 90.9 0.81 1.7E-05 34.3 5.7 69 55-126 8-76 (148)
47 COG5094 TAF9 Transcription ini 90.6 0.48 1E-05 35.4 4.2 48 80-127 31-81 (145)
48 KOG1756|consensus 90.4 0.41 8.9E-06 35.6 3.7 67 56-126 25-91 (131)
49 cd08045 TAF4 TATA Binding Prot 90.3 0.93 2E-05 35.6 5.9 56 56-112 42-97 (212)
50 cd07978 TAF13 The TATA Binding 90.3 2 4.3E-05 29.9 6.9 61 65-126 5-65 (92)
51 PF05236 TAF4: Transcription i 89.3 0.48 1E-05 38.3 3.7 58 56-114 41-98 (264)
52 KOG4336|consensus 87.6 2.1 4.6E-05 36.2 6.4 50 81-130 23-72 (323)
53 COG5248 TAF19 Transcription in 84.3 6 0.00013 29.0 6.6 61 64-126 11-71 (126)
54 KOG1657|consensus 84.2 1.7 3.7E-05 35.2 4.2 72 53-125 66-137 (236)
55 PF09123 DUF1931: Domain of un 82.7 2.4 5.3E-05 31.9 4.2 59 64-127 1-59 (138)
56 KOG3901|consensus 80.9 9.9 0.00021 27.5 6.6 64 60-126 7-70 (109)
57 COG5208 HAP5 CCAAT-binding fac 80.8 2.7 5.9E-05 34.3 4.2 78 47-126 86-173 (286)
58 KOG2389|consensus 78.5 5.6 0.00012 34.2 5.5 54 77-130 43-96 (353)
59 COG5095 TAF6 Transcription ini 75.0 6 0.00013 34.1 4.8 61 68-129 11-71 (450)
60 PF09415 CENP-X: CENP-S associ 74.6 4.9 0.00011 26.8 3.4 56 67-122 4-62 (72)
61 COG1224 TIP49 DNA helicase TIP 66.2 12 0.00025 33.0 4.7 72 57-128 354-432 (450)
62 KOG1658|consensus 63.4 5.9 0.00013 30.5 2.1 64 60-125 58-122 (162)
63 KOG1757|consensus 58.7 16 0.00035 26.9 3.7 67 62-130 31-97 (131)
64 TIGR02902 spore_lonB ATP-depen 58.0 34 0.00074 30.4 6.3 50 77-126 279-330 (531)
65 PF13654 AAA_32: AAA domain; P 56.9 58 0.0013 29.1 7.6 66 62-128 430-506 (509)
66 PRK07452 DNA polymerase III su 56.2 34 0.00074 27.7 5.7 60 64-125 135-196 (326)
67 TIGR00764 lon_rel lon-related 54.2 63 0.0014 29.4 7.5 64 65-128 315-391 (608)
68 KOG2680|consensus 54.0 44 0.00096 29.1 6.1 72 57-128 351-429 (454)
69 cd08048 TAF11 TATA Binding Pro 49.1 84 0.0018 21.5 6.6 64 59-127 17-83 (85)
70 COG5624 TAF61 Transcription in 48.3 5.1 0.00011 35.4 -0.4 58 68-125 389-447 (505)
71 PF07278 DUF1441: Protein of u 46.6 91 0.002 23.8 6.2 67 42-108 73-150 (152)
72 TIGR03015 pepcterm_ATPase puta 40.4 1E+02 0.0022 23.8 5.9 49 78-126 213-264 (269)
73 PRK08487 DNA polymerase III su 39.8 92 0.002 25.6 5.8 47 77-125 151-197 (328)
74 PRK05907 hypothetical protein; 38.7 79 0.0017 26.3 5.2 67 59-125 131-200 (311)
75 TIGR01128 holA DNA polymerase 35.7 1.7E+02 0.0036 23.0 6.6 61 64-126 116-176 (302)
76 PF08369 PCP_red: Proto-chloro 35.6 51 0.0011 19.8 2.8 19 106-124 26-44 (45)
77 TIGR02030 BchI-ChlI magnesium 34.6 1.1E+02 0.0024 25.8 5.5 51 77-127 251-308 (337)
78 PF13581 HATPase_c_2: Histidin 34.0 73 0.0016 21.6 3.8 45 64-108 7-51 (125)
79 PRK06585 holA DNA polymerase I 33.8 1.1E+02 0.0023 25.0 5.3 49 77-125 158-207 (343)
80 PF04719 TAFII28: hTAFII28-lik 33.4 1.7E+02 0.0036 20.3 5.4 62 59-124 24-86 (90)
81 TIGR01924 rsbW_low_gc serine-p 32.6 1E+02 0.0022 22.7 4.6 45 61-105 15-59 (159)
82 KOG1942|consensus 32.0 1.5E+02 0.0032 25.9 5.9 51 77-127 383-437 (456)
83 PRK05629 hypothetical protein; 30.0 1.6E+02 0.0034 24.0 5.7 60 65-125 129-189 (318)
84 PF10788 DUF2603: Protein of u 28.2 41 0.00089 25.3 1.7 32 42-74 97-128 (137)
85 COG2118 DNA-binding protein [G 25.5 1.3E+02 0.0028 22.1 3.8 33 88-128 67-99 (116)
86 PF07962 Swi3: Replication For 25.1 99 0.0021 20.8 3.1 24 48-71 39-62 (83)
87 COG1466 HolA DNA polymerase II 25.1 2E+02 0.0044 23.7 5.5 49 77-125 156-204 (334)
88 PF04604 L_biotic_typeA: Type- 24.9 65 0.0014 20.3 1.9 20 84-103 7-26 (51)
89 PF07105 DUF1367: Protein of u 23.1 1.5E+02 0.0033 23.6 4.1 17 87-103 91-107 (196)
90 PRK04069 serine-protein kinase 22.8 2E+02 0.0043 21.0 4.6 45 61-105 15-59 (161)
91 PRK07914 hypothetical protein; 22.5 2.1E+02 0.0047 23.2 5.2 60 65-125 131-191 (320)
92 PRK14562 haloacid dehalogenase 21.5 1.2E+02 0.0027 23.6 3.4 25 77-101 71-95 (204)
93 TIGR02442 Cob-chelat-sub cobal 21.4 2E+02 0.0044 26.2 5.2 51 77-127 246-303 (633)
94 COG1067 LonB Predicted ATP-dep 21.1 4E+02 0.0086 24.8 7.0 63 66-128 321-399 (647)
95 PF03172 Sp100: Sp100 domain; 20.9 2.3E+02 0.0049 20.3 4.3 48 49-109 40-87 (103)
96 COG1598 Predicted nuclease of 20.8 1.4E+02 0.003 19.4 3.1 25 83-107 34-58 (73)
No 1
>PTZ00018 histone H3; Provisional
Probab=100.00 E-value=5.7e-54 Score=318.53 Aligned_cols=131 Identities=95% Similarity=1.291 Sum_probs=124.3
Q ss_pred CCCccccccccCCCCCCcchhhhhhhccCCCCCCCCCCccc----cchhhhHHhhhcchhhhhhcchhHHHHHHHHhhhh
Q psy10959 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHR----TVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 76 (132)
Q Consensus 1 Martk~~a~k~~~~kap~k~~~~~~~~~~~p~~~~~~~~~r----~~alrEIr~~Qkst~llipk~pF~RlVreI~~~~~ 76 (132)
|||||+++++++|+++|+++.++++..++.+.+++.++++| +++|+|||+||+||+|||||+||+||||||++++.
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 99999999999999999999988877777766777777766 99999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhccc
Q psy10959 77 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 131 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~~ 131 (132)
.++|||++||++|||++|+|||+||||+|+||+||||||||++||+|+.+|||++
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=7.6e-54 Score=317.84 Aligned_cols=132 Identities=95% Similarity=1.291 Sum_probs=125.2
Q ss_pred CCCccccccccCCCCCCcchhhhhhhccCCCCCCCCCCccc----cchhhhHHhhhcchhhhhhcchhHHHHHHHHhhhh
Q psy10959 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHR----TVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 76 (132)
Q Consensus 1 Martk~~a~k~~~~kap~k~~~~~~~~~~~p~~~~~~~~~r----~~alrEIr~~Qkst~llipk~pF~RlVreI~~~~~ 76 (132)
|||||+++++++++++|+++.++++..++.+..++.++++| +++|+|||+||+||+|||||+||+||||||++++.
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 99999999999999999999988877777777777787777 89999999999999999999999999999999999
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcccC
Q psy10959 77 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 132 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~~~ 132 (132)
+++||+++||++|||++|+|||+||||+|+||+||||||||++||+|+++|||+++
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=3e-52 Score=308.40 Aligned_cols=124 Identities=64% Similarity=0.904 Sum_probs=113.2
Q ss_pred CCCccccccccCCCCCCcchhhhhhhccCCCCCCCCCCccc----cchhhhHHhhhcchhhhhhcchhHHHHHHHHhhhh
Q psy10959 1 MARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHR----TVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK 76 (132)
Q Consensus 1 Martk~~a~k~~~~kap~k~~~~~~~~~~~p~~~~~~~~~r----~~alrEIr~~Qkst~llipk~pF~RlVreI~~~~~ 76 (132)
||||||+ +++++|+.|++.+..+ . ..++.++++| ++||+|||+||+||+||||++||+||||||++++.
T Consensus 1 mar~k~~-~~~~~~~~~~~~~~~~-~-----~~~~~kk~~r~rpGtvaLrEIR~yQkst~lLIpklPF~RLVREI~~~~~ 73 (135)
T PLN00161 1 MARRLQG-KRFRKGKKPQKEASGV-T-----RQELDKKPHRYRPGTVALREIRKYQKSTELLIRKLPFARLVREISNEML 73 (135)
T ss_pred CCccccc-ccccCCCCCcccCCCC-C-----CCCCCCCCccCCCcchHHHHHHHHccccccccccccHHHHHHHHHHhcC
Confidence 9999999 7788999998887764 1 2445566666 99999999999999999999999999999999996
Q ss_pred -ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhccc
Q psy10959 77 -TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGER 131 (132)
Q Consensus 77 -~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~~ 131 (132)
+++|||++||+|||||+|+|||++|||+|+||+||||||||++||+||.+|||++
T Consensus 74 ~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~rirg~~ 129 (135)
T PLN00161 74 REPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLARRIRGPI 129 (135)
T ss_pred CCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHHHhcccc
Confidence 5899999999999999999999999999999999999999999999999999975
No 4
>KOG1745|consensus
Probab=100.00 E-value=6.1e-50 Score=296.35 Aligned_cols=132 Identities=94% Similarity=1.271 Sum_probs=121.4
Q ss_pred CCCccccccccCCCCCCcchhhhhhhccC-CCCCCCCCCccc----cchhhhHHhhhcchhhhhhcchhHHHHHHHHhhh
Q psy10959 1 MARTKQTARKSTGGKAPRKQLATKAARKS-APSTGGVKKPHR----TVALREIRRYQKSTELLIRKLPFQRLVREIAQDF 75 (132)
Q Consensus 1 Martk~~a~k~~~~kap~k~~~~~~~~~~-~p~~~~~~~~~r----~~alrEIr~~Qkst~llipk~pF~RlVreI~~~~ 75 (132)
|+|++++++++.++++|++..+.++.+.+ .|..+...++++ +++++|||+||+||+|||+|+||+||||||.++|
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 89999999999999999999998877655 333444455554 8999999999999999999999999999999999
Q ss_pred hccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcccC
Q psy10959 76 KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA 132 (132)
Q Consensus 76 ~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~~~ 132 (132)
..|+|||+.|+.+|||++|+|||+||||+|+||+||||||||++|||||++|+|++.
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
>PLN00160 histone H3; Provisional
Probab=100.00 E-value=2.7e-45 Score=258.74 Aligned_cols=90 Identities=70% Similarity=1.032 Sum_probs=87.4
Q ss_pred cchhhhHHhhhcchhhhhhcchhHHHHHHHHhhhh-ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCccc
Q psy10959 42 TVALREIRRYQKSTELLIRKLPFQRLVREIAQDFK-TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKD 120 (132)
Q Consensus 42 ~~alrEIr~~Qkst~llipk~pF~RlVreI~~~~~-~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kD 120 (132)
++||+|||+||+||++||||+||+||||||++++. +++|||++|++|||||+|+|||++|||+|+||+||||||||++|
T Consensus 5 t~aLrEIR~yQkst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD 84 (97)
T PLN00160 5 EKALKEIKMYQKSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKD 84 (97)
T ss_pred cHHHHHHHHHccchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhh
Confidence 89999999999999999999999999999999986 56999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhccc
Q psy10959 121 IQLARRIRGER 131 (132)
Q Consensus 121 i~La~rirg~~ 131 (132)
|+||.+|||+.
T Consensus 85 ~~L~~rirg~~ 95 (97)
T PLN00160 85 MQLARRIRGQT 95 (97)
T ss_pred HHHHHHhhccc
Confidence 99999999974
No 6
>smart00428 H3 Histone H3.
Probab=100.00 E-value=1.2e-44 Score=258.90 Aligned_cols=90 Identities=89% Similarity=1.206 Sum_probs=88.4
Q ss_pred cchhhhHHhhhcchhhhhhcchhHHHHHHHHhhhhc--cccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcc
Q psy10959 42 TVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKT--DLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPK 119 (132)
Q Consensus 42 ~~alrEIr~~Qkst~llipk~pF~RlVreI~~~~~~--~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~k 119 (132)
++||+|||+||+||++||||+||+||||||++++.+ ++|||++|+++|||++|+||+++|||||+||+||||||||++
T Consensus 13 ~~aLrEIr~yQkst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~k 92 (105)
T smart00428 13 QVALREIRKYQKSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPK 92 (105)
T ss_pred chHHHHHHHHccCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHh
Confidence 999999999999999999999999999999999987 999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHhccc
Q psy10959 120 DIQLARRIRGER 131 (132)
Q Consensus 120 Di~La~rirg~~ 131 (132)
||+||.+|||++
T Consensus 93 Di~La~rir~~~ 104 (105)
T smart00428 93 DIQLARRIRGER 104 (105)
T ss_pred hHHHHHHHhccC
Confidence 999999999975
No 7
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.93 E-value=2.3e-26 Score=160.86 Aligned_cols=85 Identities=48% Similarity=0.652 Sum_probs=80.5
Q ss_pred cchhhhHHhhhcchhhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccH
Q psy10959 42 TVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDI 121 (132)
Q Consensus 42 ~~alrEIr~~Qkst~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi 121 (132)
.++++|||+||++++++||++||.||+|+... .|||.+|.++||+++|.|++.++++|+.||.|+||+||+++||
T Consensus 3 ~~~~~~~r~~~~~~~~~Lp~apv~Ri~r~~~~-----~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI 77 (91)
T COG2036 3 AVGLKEIRRYQRSTDLLLPKAPVRRILRKAGA-----ERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDI 77 (91)
T ss_pred cchHHHHHhhhhhhhhhcCchHHHHHHHHHhH-----HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHH
Confidence 46789999999999999999999999999954 4999999999999999999999999999999999999999999
Q ss_pred HHHHHHhccc
Q psy10959 122 QLARRIRGER 131 (132)
Q Consensus 122 ~La~rirg~~ 131 (132)
+|+.+.+|..
T Consensus 78 ~la~~~~~~~ 87 (91)
T COG2036 78 KLALKRLGRR 87 (91)
T ss_pred HHHHHHhccc
Confidence 9999998853
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=99.85 E-value=1.7e-21 Score=129.46 Aligned_cols=75 Identities=48% Similarity=0.641 Sum_probs=71.3
Q ss_pred chhhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 54 STELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 54 st~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
+|..+||+.||.|++++|..++...+||+.+|+..||+++|+|++.+|++|+.||.|+||+||+++||++|.+++
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 367889999999999999998877799999999999999999999999999999999999999999999999985
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=99.40 E-value=1e-12 Score=87.90 Aligned_cols=62 Identities=27% Similarity=0.321 Sum_probs=54.0
Q ss_pred cchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 61 KLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 61 k~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
+.-..-||++| .+..|++++|.++||+.+|+|+..++++|+.+|.|++|.||+++||+|+..
T Consensus 4 k~~l~~lv~~i----d~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~ 65 (72)
T cd07981 4 KRKLQELLKEI----DPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLE 65 (72)
T ss_pred HHHHHHHHHhh----CCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHH
Confidence 33344455555 567999999999999999999999999999999999999999999999964
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=99.28 E-value=1e-11 Score=85.99 Aligned_cols=68 Identities=25% Similarity=0.312 Sum_probs=65.2
Q ss_pred hhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 58 LIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 58 lipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
-||+.|..||+|.- +..|++.++.+++.++.|.|+..+..||..++-||+|.||+..||.+|.+-.|.
T Consensus 13 gi~k~~I~RLarr~-----GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~ 80 (85)
T cd00076 13 GITKPAIRRLARRG-----GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 80 (85)
T ss_pred cCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCC
Confidence 39999999999987 889999999999999999999999999999999999999999999999998885
No 11
>PLN00035 histone H4; Provisional
Probab=99.24 E-value=2.4e-11 Score=86.88 Aligned_cols=67 Identities=22% Similarity=0.274 Sum_probs=64.7
Q ss_pred hhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 59 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 59 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
||+.|..||+|.- +..|++.+|.++|.++.|.|+..+..||...|.||+|.||+.+||.+|.+-.|.
T Consensus 30 ipk~~IrRLARr~-----GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~ 96 (103)
T PLN00035 30 ITKPAIRRLARRG-----GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred CCHHHHHHHHHHc-----CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC
Confidence 9999999999988 889999999999999999999999999999999999999999999999988775
No 12
>PTZ00015 histone H4; Provisional
Probab=99.22 E-value=3e-11 Score=86.22 Aligned_cols=67 Identities=22% Similarity=0.272 Sum_probs=64.6
Q ss_pred hhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 59 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 59 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
||+.|..||+|.- +..|++.++.+++.++.|.|+..+..||..+|-||+|.||+..||.+|.+..|.
T Consensus 31 I~k~~IrRLarr~-----GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~ 97 (102)
T PTZ00015 31 ITKGAIRRLARRG-----GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR 97 (102)
T ss_pred CCHHHHHHHHHHc-----CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC
Confidence 9999999999987 899999999999999999999999999999999999999999999999988775
No 13
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=99.17 E-value=5.1e-11 Score=78.53 Aligned_cols=64 Identities=20% Similarity=0.207 Sum_probs=60.3
Q ss_pred hhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 58 LIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 58 lipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.+|+.|..|+.+.+ |..|++.++..+|.+..|.++-.+.++|..++.|+||.||+..||.+|.+
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=99.07 E-value=1.7e-10 Score=78.07 Aligned_cols=61 Identities=21% Similarity=0.247 Sum_probs=58.1
Q ss_pred hhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHH
Q psy10959 58 LIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQL 123 (132)
Q Consensus 58 lipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~L 123 (132)
-||+.|..||+|.- +..|++.++.+.|.++.|.|+..+..||..+|-|++|.||+..||..
T Consensus 13 gI~k~~IrRLaRr~-----GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 13 GITKPAIRRLARRG-----GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred CCCHHHHHHHHHHc-----CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 39999999999987 88999999999999999999999999999999999999999999864
No 15
>PLN00158 histone H2B; Provisional
Probab=98.86 E-value=1.4e-08 Score=73.95 Aligned_cols=69 Identities=14% Similarity=0.215 Sum_probs=66.6
Q ss_pred hcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 60 RKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 60 pk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
++..|..+|..++.++++|..++..|+..|.....|++..+..+|..++.+.+|.||+++|||.|++|.
T Consensus 25 r~esy~~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLv 93 (116)
T PLN00158 25 KTETYKIYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLI 93 (116)
T ss_pred ccccHHHHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHh
Confidence 567899999999999999999999999999999999999999999999999999999999999999985
No 16
>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=98.81 E-value=2e-08 Score=72.99 Aligned_cols=66 Identities=21% Similarity=0.333 Sum_probs=59.8
Q ss_pred hHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 64 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 64 F~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
..++|..|+.+. +..++++++...|-|.++.|...++.||...|.||+|.||+.+||+||...++.
T Consensus 3 d~~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~ 68 (117)
T cd07979 3 DARVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVD 68 (117)
T ss_pred HHHHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhc
Confidence 356777787654 567999999999999999999999999999999999999999999999999875
No 17
>PTZ00463 histone H2B; Provisional
Probab=98.77 E-value=3e-08 Score=72.18 Aligned_cols=69 Identities=12% Similarity=0.148 Sum_probs=66.2
Q ss_pred hcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 60 RKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 60 pk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
++..|..+|..++.++++|..++..|+..|...+.|++..+..+|..++.+.+|.||+++|||.|+||.
T Consensus 26 r~esy~~YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLl 94 (117)
T PTZ00463 26 RYDSYGLYIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLV 94 (117)
T ss_pred ccchHHHHHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhc
Confidence 456799999999999999999999999999999999999999999999999999999999999999985
No 18
>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=1.8e-08 Score=65.42 Aligned_cols=63 Identities=24% Similarity=0.294 Sum_probs=52.0
Q ss_pred hhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHH
Q psy10959 59 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 59 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ 125 (132)
+|.....|++++. .+..+++.+|..+|+.++|.|+..|..+|+..+.+.+|.||+.+||..|+
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 4666666666554 46678999999999999999999999999999999999999999998764
No 19
>smart00427 H2B Histone H2B.
Probab=98.74 E-value=4.8e-08 Score=68.24 Aligned_cols=66 Identities=15% Similarity=0.222 Sum_probs=63.8
Q ss_pred hhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 63 PFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 63 pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
.|..++..++.++++|..++..|+..|...+.|++..+..+|..++.+.+|.||+++|||.|.++.
T Consensus 2 sy~~Yi~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~ 67 (89)
T smart00427 2 TYAIYIYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLI 67 (89)
T ss_pred cHHHHHHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHH
Confidence 588899999999999999999999999999999999999999999999999999999999999985
No 20
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=98.33 E-value=1.3e-06 Score=59.41 Aligned_cols=65 Identities=28% Similarity=0.260 Sum_probs=53.2
Q ss_pred chhHHHHHHHHhhh--hccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 62 LPFQRLVREIAQDF--KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 62 ~pF~RlVreI~~~~--~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
+.+.--|-+|+++. ..+..++++.+.+|-|.+=.++..+..|--..|.||||.||+++|+.|..|
T Consensus 5 aal~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 5 AALWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 34455566666665 367899999999999999999999999999999999999999999999764
No 21
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.32 E-value=2.3e-06 Score=57.52 Aligned_cols=54 Identities=24% Similarity=0.155 Sum_probs=50.6
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 77 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
+-.+++++|++.|.+..|.|+..|.+.+...+.|++|.++.+.||.+|..-.|.
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 557999999999999999999999999999999999999999999999877664
No 22
>KOG1744|consensus
Probab=98.29 E-value=1.5e-06 Score=64.25 Aligned_cols=70 Identities=24% Similarity=0.314 Sum_probs=65.2
Q ss_pred hhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 59 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 59 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
..+..|..+|+.++.++++++.++..|+.+|.....+++.++..+|+.+|.+.||-||..++||+|.+|.
T Consensus 34 ~~~e~~s~yv~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 34 RRKESYSEYVYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred cccCceeeehhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 3566777888889999999999999999999999999999999999999999999999999999999985
No 23
>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=98.24 E-value=1.8e-06 Score=62.89 Aligned_cols=67 Identities=22% Similarity=0.182 Sum_probs=61.5
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.|.+|-.++.|++++- ....|++.+|...|-.+.|.+...++|.|...|.|+++.+|+++||+||.+
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 6789999999999862 145899999999999999999999999999999999999999999999975
No 24
>KOG0870|consensus
Probab=98.13 E-value=6.1e-06 Score=63.47 Aligned_cols=69 Identities=25% Similarity=0.268 Sum_probs=64.5
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
+|.+|.+-..|||++++.+. +.-++.+|..||+.+|--|+..|.-.|+..|.-.+|.||++.|+-=++.
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 68899999999999998865 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=98.07 E-value=1.5e-05 Score=52.99 Aligned_cols=58 Identities=19% Similarity=0.243 Sum_probs=45.6
Q ss_pred HHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 69 REIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 69 reI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.|++.++.+...+.+++-+.|.+.|++|+..+.+.|..+|.|-+--||.++||++...
T Consensus 6 ~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Le 63 (68)
T PF03847_consen 6 QELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLE 63 (68)
T ss_dssp HHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHH
T ss_pred HHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHH
Confidence 3444445788999999999999999999999999999999999999999999999864
No 26
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=98.00 E-value=2.8e-05 Score=51.53 Aligned_cols=58 Identities=28% Similarity=0.318 Sum_probs=45.8
Q ss_pred HHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 68 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 68 VreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
|+-|++.++ -..++.++...|.+-+|.-|-.+.++|..++.|+||.+|+..||..|.|
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 555555443 2358999999999999999999999999999999999999999999875
No 27
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=97.98 E-value=2.1e-05 Score=66.06 Aligned_cols=63 Identities=21% Similarity=0.238 Sum_probs=55.8
Q ss_pred HHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 67 LVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 67 lVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
-|+.|++.. +..+++.+|..+|.+-+|.++-.+.++|..++.|+||.||+.+||++|.+.++.
T Consensus 4 ~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~ 66 (343)
T cd08050 4 SIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNV 66 (343)
T ss_pred HHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCC
Confidence 355565533 456999999999999999999999999999999999999999999999999865
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=97.88 E-value=5.5e-05 Score=56.06 Aligned_cols=65 Identities=26% Similarity=0.362 Sum_probs=52.7
Q ss_pred HHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 65 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 65 ~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
.++|..|+.+.+ -..+++.++.-|-|.+=.|...+++||...|-||+|.+|...|++||...+..
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 478888887663 44689999999999999999999999999999999999999999999987743
No 29
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.82 E-value=3.1e-05 Score=66.70 Aligned_cols=62 Identities=26% Similarity=0.311 Sum_probs=42.8
Q ss_pred hhcchhHHHHHHHHhh-hhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCccc
Q psy10959 59 IRKLPFQRLVREIAQD-FKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKD 120 (132)
Q Consensus 59 ipk~pF~RlVreI~~~-~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kD 120 (132)
+|..+..+|+.-.++. +....+++.+||.+|..++|-|+.+|-+|--..|.||||+||...|
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 3444444444444432 2367999999999999999999999999999999999999998876
No 30
>KOG1142|consensus
Probab=97.62 E-value=7.2e-05 Score=61.08 Aligned_cols=73 Identities=19% Similarity=0.278 Sum_probs=65.2
Q ss_pred hhhcchhhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 50 RYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 50 ~~Qkst~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.++-+++.++-|--..-||++| .++.-+.+++-+.|.|.|++|+.++-.-+..+|.|-|--||.++||+|++.
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 4667788888887777777777 578899999999999999999999999999999999999999999999763
No 31
>KOG0869|consensus
Probab=97.03 E-value=0.0016 Score=49.92 Aligned_cols=71 Identities=15% Similarity=0.198 Sum_probs=63.6
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhc
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg 129 (132)
+-++|.+-..|+.+.++. .+-.++.+|-+.+||.+-.|+-=+--+|..-+.--||+||+.+||-.|+--.|
T Consensus 30 Dr~LPIANV~RIMK~~lP---~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLG 100 (168)
T KOG0869|consen 30 DRFLPIANVSRIMKKALP---ANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLG 100 (168)
T ss_pred hhhccHHHHHHHHHhcCC---cccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcC
Confidence 334899999999988854 78899999999999999999999999999999999999999999999986655
No 32
>KOG3334|consensus
Probab=96.75 E-value=0.0073 Score=45.69 Aligned_cols=64 Identities=25% Similarity=0.427 Sum_probs=54.3
Q ss_pred HHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 66 RLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 66 RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
+++..|+.++ +-.-+.+..+.-|=|++=.|...+++||...+-||++-||..+|++||...++.
T Consensus 17 ~~i~~iL~s~-GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~ 80 (148)
T KOG3334|consen 17 RVIASILKSL-GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVD 80 (148)
T ss_pred HHHHHHHHHc-CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhc
Confidence 4555555544 334577888999999999999999999999999999999999999999998875
No 33
>KOG3467|consensus
Probab=96.64 E-value=0.0064 Score=42.70 Aligned_cols=67 Identities=24% Similarity=0.281 Sum_probs=56.8
Q ss_pred hhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 59 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 59 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
|-|....||.|.- +--|+..-..+....++..||....-+|...+-||||.||+.-|+--+.+-.|.
T Consensus 30 itKpaIRRlARr~-----GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~ 96 (103)
T KOG3467|consen 30 ITKPAIRRLARRG-----GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGR 96 (103)
T ss_pred cchHHHHHHHHhc-----CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCc
Confidence 3466667777665 667888888999999999999999999999999999999999999888765553
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=96.62 E-value=0.0077 Score=40.02 Aligned_cols=52 Identities=23% Similarity=0.178 Sum_probs=48.6
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 79 LRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 79 ~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
..++++|++.|-+.+..|+..|...+...|-|++|-...+.|+.++..-.|.
T Consensus 22 ~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi 73 (77)
T PF07524_consen 22 DSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI 73 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 3789999999999999999999999999999999999999999999876664
No 35
>KOG0871|consensus
Probab=95.83 E-value=0.028 Score=42.83 Aligned_cols=72 Identities=18% Similarity=0.261 Sum_probs=65.6
Q ss_pred hhhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhc
Q psy10959 55 TELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 55 t~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg 129 (132)
.++-+||+....+|+|++. .++||..+|-+.|++..=.|+--+--+||.++---.+.||.++-+.=|..-.|
T Consensus 9 de~sLPkAtv~KmIke~lP---~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~Lg 80 (156)
T KOG0871|consen 9 DELSLPKATVNKMIKEMLP---KDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLG 80 (156)
T ss_pred ccccCcHHHHHHHHHHhCC---cccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcc
Confidence 3567999999999999954 79999999999999999999999999999999999999999999988876655
No 36
>PLN00154 histone H2A; Provisional
Probab=94.87 E-value=0.06 Score=40.38 Aligned_cols=68 Identities=19% Similarity=0.125 Sum_probs=60.1
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.|.+|-.-+.|+.|+-.. ...|+...|..-|--+.|.....++|-|...|...++..|++++|+||.+
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 567888888888888631 35799999999999999999999999999999999999999999999974
No 37
>smart00414 H2A Histone 2A.
Probab=94.63 E-value=0.052 Score=38.96 Aligned_cols=67 Identities=25% Similarity=0.201 Sum_probs=58.1
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
+|.+|-.-|.|+.++-. -..|+...|..-|--+.|.....++|-|...+...++..|+++|+++|.+
T Consensus 7 gL~fPVgRi~r~Lk~~~----~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 7 GLQFPVGRIHRLLRKGT----YAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred CccCchHHHHHHHHcCc----cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 56678888888877642 34699999999999999999999999999999999999999999999864
No 38
>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=94.54 E-value=0.051 Score=37.88 Aligned_cols=59 Identities=14% Similarity=0.214 Sum_probs=30.3
Q ss_pred HHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 68 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 68 VreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
|++++--|+....-..+.+..|.+.+=.|++.+...|..+|...++.+|..+|+-.+.|
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 34455555666788899999999999999999999999999999999999999988765
No 39
>PTZ00017 histone H2A; Provisional
Probab=94.29 E-value=0.054 Score=40.53 Aligned_cols=67 Identities=24% Similarity=0.170 Sum_probs=59.2
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.|.+|-.-+.|+.++-. ...|+...|..-|--+.|.....++|-|...+...++..|++++|+||.+
T Consensus 25 gL~FPVgRi~R~Lk~g~----~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGR----YAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhccc----hhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 56788888888887642 34599999999999999999999999999999999999999999999975
No 40
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=93.48 E-value=0.13 Score=37.97 Aligned_cols=52 Identities=25% Similarity=0.236 Sum_probs=48.1
Q ss_pred hhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 75 FKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 75 ~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
-...+|+.++|...|--..|.....++|-|...|.-.|-..|+|+-+|||.+
T Consensus 39 ~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 39 GNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred CccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 3467999999999999999999999999999999999999999999999853
No 41
>KOG2549|consensus
Probab=93.04 E-value=0.26 Score=44.42 Aligned_cols=53 Identities=21% Similarity=0.218 Sum_probs=49.3
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhc
Q psy10959 77 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg 129 (132)
+-.-++.+|..+|-+-+|.-+-.+.+||..++.|+||-++++.||.-|.+.+.
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 55678999999999999999999999999999999999999999999988764
No 42
>PLN00156 histone H2AX; Provisional
Probab=92.88 E-value=0.13 Score=38.68 Aligned_cols=67 Identities=25% Similarity=0.198 Sum_probs=57.9
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.|.+|-.-+.|+.++- ....|+...|..-|--+.|.....++|-|...+...++..|+++.|+|+.+
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 4667777777887664 234699999999999999999999999999999999999999999999974
No 43
>PLN00157 histone H2A; Provisional
Probab=92.69 E-value=0.12 Score=38.60 Aligned_cols=67 Identities=25% Similarity=0.199 Sum_probs=58.1
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.|.+|---+.|++++- ....|+...|..-|--..|.....++|-|...+...++..|++++|+||.+
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 5667877788887663 234699999999999999999999999999999999999999999999864
No 44
>PLN00153 histone H2A; Provisional
Probab=92.15 E-value=0.18 Score=37.53 Aligned_cols=67 Identities=25% Similarity=0.194 Sum_probs=58.0
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.|.+|---+.|++++= ....|+...|..-|--..|.....++|-|...+...+...|+++.|+||.+
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 4667777788887663 235699999999999999999999999999999999999999999999974
No 45
>PTZ00252 histone H2A; Provisional
Probab=91.08 E-value=0.31 Score=36.47 Aligned_cols=67 Identities=19% Similarity=0.168 Sum_probs=56.0
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhh--cCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~H--akRvTi~~kDi~La~r 126 (132)
.|.+|-.-+.|++++- .-..|+.+.|..-|--..|.....++|-|...|.. .++..|++++|+||.+
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 4667877788887654 23569999999999999999999999999998865 6788999999999974
No 46
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=90.90 E-value=0.81 Score=34.29 Aligned_cols=69 Identities=22% Similarity=0.200 Sum_probs=61.6
Q ss_pred hhhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 55 TELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 55 t~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.++-+||+..+..|.+|+. .|+-|+.+|-+.++++.=.|+--|--+||.++-.-...||-.+-+--|..
T Consensus 8 De~sLPKATVqKMvS~iLp---~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALe 76 (148)
T COG5150 8 DENSLPKATVQKMVSSILP---KDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALE 76 (148)
T ss_pred ccccCcHHHHHHHHHHhcc---ccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHH
Confidence 4566999999999999965 89999999999999999999999999999999999999999887765544
No 47
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=90.60 E-value=0.48 Score=35.36 Aligned_cols=48 Identities=25% Similarity=0.311 Sum_probs=39.1
Q ss_pred cccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCc---ccHHHHHHH
Q psy10959 80 RFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMP---KDIQLARRI 127 (132)
Q Consensus 80 r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~---kDi~La~ri 127 (132)
.+......-|-++|--|...+++||...|-|++|-.+.. +|+.||.--
T Consensus 31 ~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at 81 (145)
T COG5094 31 EYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALAT 81 (145)
T ss_pred hhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHH
Confidence 344555666778999999999999999999999876555 999998753
No 48
>KOG1756|consensus
Probab=90.37 E-value=0.41 Score=35.63 Aligned_cols=67 Identities=25% Similarity=0.225 Sum_probs=56.1
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.+.+|---..|+.|+ -....|++.+|...|--..|.....++|.|-..|.-.++..|+|+-++||.+
T Consensus 25 gl~fPvgri~r~Lr~----~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRK----GRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred ccccCHHHHHHHHHc----cchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 455666666666666 2367899999999999888888889999999999999999999999999975
No 49
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=90.29 E-value=0.93 Score=35.56 Aligned_cols=56 Identities=18% Similarity=0.230 Sum_probs=50.2
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcC
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAK 112 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~Hak 112 (132)
..++...|+...+..|+.+.+.. -++.+.+..|..|+|.||-.|.++...++.|-.
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 46788999999999998876544 889999999999999999999999999999973
No 50
>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=90.27 E-value=2 Score=29.93 Aligned_cols=61 Identities=15% Similarity=0.232 Sum_probs=47.9
Q ss_pred HHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 65 QRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 65 ~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
..=++.++--++..-.-..+.+..|.+.+=+|++.+.-.|..+|. .++--+.++|+..+.|
T Consensus 5 ~~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR 65 (92)
T cd07978 5 TKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLR 65 (92)
T ss_pred HHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHh
Confidence 333444444455555678899999999999999999999999998 6666679999988764
No 51
>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=89.32 E-value=0.48 Score=38.31 Aligned_cols=58 Identities=21% Similarity=0.273 Sum_probs=38.8
Q ss_pred hhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCcc
Q psy10959 56 ELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRV 114 (132)
Q Consensus 56 ~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRv 114 (132)
.+++...|+...+.+|+..+. ...+.++.+..|--|+|.+|-.|++++..++.|-...
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 567888899999999986555 6789999999999999999999999999999996544
No 52
>KOG4336|consensus
Probab=87.55 E-value=2.1 Score=36.21 Aligned_cols=50 Identities=18% Similarity=0.119 Sum_probs=46.0
Q ss_pred ccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 81 FQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 81 ~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
++..|++.|-++.-.|+-.+|+.+-..+.|++|.-.+..|+.|.....|.
T Consensus 23 is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI 72 (323)
T KOG4336|consen 23 ISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNI 72 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCC
Confidence 67788888888888999999999999999999999999999999987775
No 53
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=84.25 E-value=6 Score=28.99 Aligned_cols=61 Identities=18% Similarity=0.196 Sum_probs=51.2
Q ss_pred hHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 64 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 64 F~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
|..=|+..+--|+...--..+.+++|.|.+-+|++.+.-+|-.+|- .|-.+..+|.+.+.|
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 5555666666677777778899999999999999999999988887 677788999999875
No 54
>KOG1657|consensus
Probab=84.19 E-value=1.7 Score=35.24 Aligned_cols=72 Identities=19% Similarity=0.192 Sum_probs=60.7
Q ss_pred cchhhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHH
Q psy10959 53 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 53 kst~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ 125 (132)
...++.+..+|..|+ |.|...-..---|+.+|....-.++|.|+..|-..+..-+--++|.|+.-.|+.-++
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 456889999999997 556543333347999999999999999999999999999999999999999987665
No 55
>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=82.70 E-value=2.4 Score=31.88 Aligned_cols=59 Identities=22% Similarity=0.302 Sum_probs=44.4
Q ss_pred hHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHH
Q psy10959 64 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 64 F~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ri 127 (132)
|.++.|+. .++-+..+-+.-+-+.+|.-+-.||.-|...|...+|-.|.+.|+-+-..+
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 456677888899999999999999999999999999999999999876654
No 56
>KOG3901|consensus
Probab=80.87 E-value=9.9 Score=27.50 Aligned_cols=64 Identities=20% Similarity=0.280 Sum_probs=51.9
Q ss_pred hcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 60 RKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 60 pk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
++--|.+=++..+--|+.+.---.+.+++|.+.+=+|++.+...|..+. +|=.+.++|+..+.|
T Consensus 7 rk~lF~Kdl~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lR 70 (109)
T KOG3901|consen 7 RKHLFSKDLRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLR 70 (109)
T ss_pred HHHHHHHHHHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHH
Confidence 3445777777787778777777789999999999999999977666665 888899999998764
No 57
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=80.77 E-value=2.7 Score=34.26 Aligned_cols=78 Identities=21% Similarity=0.274 Sum_probs=59.5
Q ss_pred hHHhhhcchhh---------hhhcchhHHHHHHHHhhhhccc-cccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCcccc
Q psy10959 47 EIRRYQKSTEL---------LIRKLPFQRLVREIAQDFKTDL-RFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTI 116 (132)
Q Consensus 47 EIr~~Qkst~l---------lipk~pF~RlVreI~~~~~~~~-r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi 116 (132)
-+|.||+..+. -..-+||.|+ +.++.. .++. =++++|=...-.++|-|+..|---|-..|-..||-||
T Consensus 86 i~ryWq~ti~~~e~~~q~~~k~h~LPlARI-kkvMKt-dedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtL 163 (286)
T COG5208 86 ISRYWQQTIKAAEEERQILLKDHNLPLARI-KKVMKT-DEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTL 163 (286)
T ss_pred HHHHHHHHHHHHHHhHHHHHHhccCcHHHH-HHHHhc-ccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHH
Confidence 37778764322 2234899987 444332 2233 4788888889999999999999999999999999999
Q ss_pred CcccHHHHHH
Q psy10959 117 MPKDIQLARR 126 (132)
Q Consensus 117 ~~kDi~La~r 126 (132)
.-.||--|+.
T Consensus 164 QksDia~Av~ 173 (286)
T COG5208 164 QKSDIAAAVK 173 (286)
T ss_pred HHHHHHHHHH
Confidence 9999988764
No 58
>KOG2389|consensus
Probab=78.49 E-value=5.6 Score=34.17 Aligned_cols=54 Identities=20% Similarity=0.102 Sum_probs=48.6
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 77 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
+---++..|++.|+..+-.|+-+|-+.|-..+-|++|+-....||-+|..-.|.
T Consensus 43 g~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~ 96 (353)
T KOG2389|consen 43 GYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSA 96 (353)
T ss_pred CCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhh
Confidence 444678889999999999999999999999999999999999999999876553
No 59
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=74.97 E-value=6 Score=34.14 Aligned_cols=61 Identities=20% Similarity=0.274 Sum_probs=51.1
Q ss_pred HHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhc
Q psy10959 68 VREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRG 129 (132)
Q Consensus 68 VreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg 129 (132)
++.+++.. +-.-+..+++.+|-.-.|.-+-.+-++|...+.|.||--++..||.-|.|-+.
T Consensus 11 ~KdvAesl-Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lN 71 (450)
T COG5095 11 LKDVAESL-GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLN 71 (450)
T ss_pred HHHHHHHc-CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcC
Confidence 34444422 34467899999999999999999999999999999999999999999988654
No 60
>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=74.58 E-value=4.9 Score=26.82 Aligned_cols=56 Identities=9% Similarity=0.119 Sum_probs=40.4
Q ss_pred HHHHHHhh-h-hccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccc-cCcccHH
Q psy10959 67 LVREIAQD-F-KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVT-IMPKDIQ 122 (132)
Q Consensus 67 lVreI~~~-~-~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvT-i~~kDi~ 122 (132)
+|..|++. | +..++++.+|+..+.+..+-|...-+.-|+.-+.--+-.. |.++|++
T Consensus 4 li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LE 62 (72)
T PF09415_consen 4 LIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLE 62 (72)
T ss_dssp HHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHH
T ss_pred HHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHH
Confidence 44455553 2 3779999999999999999999888888888777677666 8888876
No 61
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=66.21 E-value=12 Score=33.03 Aligned_cols=72 Identities=24% Similarity=0.387 Sum_probs=59.3
Q ss_pred hhhhcchhHH-HHHHHHhhh--hccccccHHHHHHHHHHHHH----HHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 57 LLIRKLPFQR-LVREIAQDF--KTDLRFQSAAIGALQEASEA----YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 57 llipk~pF~R-lVreI~~~~--~~~~r~~~~Al~aLQeaaE~----~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
|+|+-.||.+ =++||..-= ..+.-.+++|++-|-...|. |.++|++-|+..|.-.+..+|..+|++-|..+-
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 5677788865 467775532 26788999999999887775 999999999999999999999999999887663
No 62
>KOG1658|consensus
Probab=63.40 E-value=5.9 Score=30.52 Aligned_cols=64 Identities=23% Similarity=0.339 Sum_probs=50.2
Q ss_pred hcchhHHHHHHHHhhhhccccccHH-HHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHH
Q psy10959 60 RKLPFQRLVREIAQDFKTDLRFQSA-AIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 60 pk~pF~RlVreI~~~~~~~~r~~~~-Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ 125 (132)
.++|.+|+ ++|.. ..+++++..+ |+.++-.++|.|+-.|-..++-|+--.+|+|+.-+|+..+.
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 45555553 44422 3578888765 56778899999999999999999999999999999987654
No 63
>KOG1757|consensus
Probab=58.66 E-value=16 Score=26.85 Aligned_cols=67 Identities=22% Similarity=0.248 Sum_probs=51.8
Q ss_pred chhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHhcc
Q psy10959 62 LPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE 130 (132)
Q Consensus 62 ~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rirg~ 130 (132)
.|..|+=|-+-.......|+...|..-+-...|..-...+|-|...+.--|=..|+++-+|||. ||+
T Consensus 31 FpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAi--RGD 97 (131)
T KOG1757|consen 31 FPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAI--RGD 97 (131)
T ss_pred cchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHcccccccceeeeccchhheeee--cCc
Confidence 4556665555444557788888888877777888888888988888888888889999999984 565
No 64
>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=57.96 E-value=34 Score=30.44 Aligned_cols=50 Identities=14% Similarity=0.192 Sum_probs=41.2
Q ss_pred ccccccHHHHHHHHHHHH--HHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 77 TDLRFQSAAIGALQEASE--AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE--~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
.++.++.+|++.|-..+. ..+..+++.|...|...+|.+|+.+|++-+..
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 457899999998766655 37888899998888888999999999998753
No 65
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=56.91 E-value=58 Score=29.13 Aligned_cols=66 Identities=23% Similarity=0.291 Sum_probs=49.9
Q ss_pred chhHHHHHHHHhhhhccccccHHHHHHHHHHHH-----------HHHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 62 LPFQRLVREIAQDFKTDLRFQSAAIGALQEASE-----------AYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 62 ~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE-----------~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
..|.++|..++++. +-..|+.+|+..|=+.+- ..|..|+.+|+..|.-.+...|...||+-|..-|
T Consensus 430 ~~~~~~i~~~~~~~-~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~r 506 (509)
T PF13654_consen 430 RQYARFIASICQKE-GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEER 506 (509)
T ss_dssp HHHHHHHHHHHHHH-SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH-
T ss_pred HHHHHHHHHHHHhC-CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHcc
Confidence 35778888887654 335789999988766553 5889999999999999999999999999998655
No 66
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=56.21 E-value=34 Score=27.68 Aligned_cols=60 Identities=18% Similarity=0.228 Sum_probs=48.1
Q ss_pred hHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhh--cCccccCcccHHHHH
Q psy10959 64 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIH--AKRVTIMPKDIQLAR 125 (132)
Q Consensus 64 F~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~H--akRvTi~~kDi~La~ 125 (132)
..++|++.++ ..+..++.+|+..|.+.++.=+..+-.+-..++.+ .+..+|+.+||+.+.
T Consensus 135 l~~~i~~~~~--~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v 196 (326)
T PRK07452 135 LKQLVERTAQ--ELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALV 196 (326)
T ss_pred HHHHHHHHHH--HcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHh
Confidence 3445555543 25678999999999999999888888888899998 568889999999765
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=54.22 E-value=63 Score=29.43 Aligned_cols=64 Identities=14% Similarity=0.143 Sum_probs=45.4
Q ss_pred HHHHHHHHhhhhccccccHHHHHHHHHH-H------------HHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 65 QRLVREIAQDFKTDLRFQSAAIGALQEA-S------------EAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 65 ~RlVreI~~~~~~~~r~~~~Al~aLQea-a------------E~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
.+++.........-..|+.+|+..|-+. + +..|..+...|+..|...+..+|..+|++-|...+
T Consensus 315 ~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 315 VQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred HHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 3344433333322348999999998642 2 36788899999888888899999999998775543
No 68
>KOG2680|consensus
Probab=54.00 E-value=44 Score=29.09 Aligned_cols=72 Identities=22% Similarity=0.385 Sum_probs=58.0
Q ss_pred hhhhcchhHH-HHHHHHhh-h-hccccccHHHHHHHHHHHHH----HHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 57 LLIRKLPFQR-LVREIAQD-F-KTDLRFQSAAIGALQEASEA----YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 57 llipk~pF~R-lVreI~~~-~-~~~~r~~~~Al~aLQeaaE~----~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
++|.-.|+.+ =+++|+.- + ..+.-.+++|++.|-...|+ |-..|...|++.+...|-.++..+||+-|.+|-
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 5566666653 45566442 2 37888999999999888776 999999999999999999999999999988874
No 69
>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=49.07 E-value=84 Score=21.46 Aligned_cols=64 Identities=14% Similarity=0.220 Sum_probs=51.1
Q ss_pred hhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCc---cccCcccHHHHHHH
Q psy10959 59 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKR---VTIMPKDIQLARRI 127 (132)
Q Consensus 59 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakR---vTi~~kDi~La~ri 127 (132)
+++....|++..+ .+..++.+.+.+|.-.+..|+..|-|.|..+.-.-+. -=|.|+.|.-|.|.
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 3478889999999999999999999999999887555 56788888777664
No 70
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=48.28 E-value=5.1 Score=35.39 Aligned_cols=58 Identities=17% Similarity=0.145 Sum_probs=48.9
Q ss_pred HHHHHhhh-hccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHH
Q psy10959 68 VREIAQDF-KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 68 VreI~~~~-~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ 125 (132)
++|..+.. ++...+..+.-+.|-+.|.+|....-+-+..+|.|-|-.||.++|+||-.
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 44444443 57788999999999999999999999989999999999999999999854
No 71
>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=46.58 E-value=91 Score=23.76 Aligned_cols=67 Identities=15% Similarity=0.158 Sum_probs=50.3
Q ss_pred cchhhhHHhhhcchhhhhhcchh----HHHHHHHHhhh-------hccccccHHHHHHHHHHHHHHHHHHHHhHHHHh
Q psy10959 42 TVALREIRRYQKSTELLIRKLPF----QRLVREIAQDF-------KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCA 108 (132)
Q Consensus 42 ~~alrEIr~~Qkst~llipk~pF----~RlVreI~~~~-------~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a 108 (132)
--+-+|--+|++.+.-|||-.-+ ..+++-|.+.+ ..+..++++++..+|.+.-+...+|.+..+.++
T Consensus 73 ~qsE~eRlk~e~e~g~Lipa~eV~~~~s~~~Kav~q~LetlPD~LERd~gL~p~~v~~vQ~~iD~lR~~l~~~i~~~~ 150 (152)
T PF07278_consen 73 WQSENERLKFEKETGQLIPAEEVRREMSEMAKAVVQVLETLPDILERDAGLPPEQVARVQSVIDDLRDQLAERIQEAC 150 (152)
T ss_pred HHHHHHHHHHHHHHcccCcHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 44556667788999999998654 44555554443 267899999999999999999999887766543
No 72
>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=40.37 E-value=1e+02 Score=23.82 Aligned_cols=49 Identities=16% Similarity=0.144 Sum_probs=41.1
Q ss_pred cccccHHHHHHHHHHHHH---HHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 78 DLRFQSAAIGALQEASEA---YLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 78 ~~r~~~~Al~aLQeaaE~---~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
+..|+++++..|.+.+.- ++..+...+...|.-.+--+|..+||+.+.+
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 7788888888888777888999999987764
No 73
>PRK08487 DNA polymerase III subunit delta; Validated
Probab=39.77 E-value=92 Score=25.57 Aligned_cols=47 Identities=23% Similarity=0.113 Sum_probs=41.6
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHH
Q psy10959 77 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ 125 (132)
.+..++.+|+..|-+.++.=+..+-.+-..++.+++ +|+.+||+.+.
T Consensus 151 ~g~~i~~~a~~~L~~~~g~dl~~l~~ELeKL~ly~~--~It~edV~~~v 197 (328)
T PRK08487 151 LGLDIDQNALNHLYFIHNEDLALAANELEKLAILNE--PITLKDIQELV 197 (328)
T ss_pred hCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHHhcC--CCCHHHHHHHh
Confidence 567899999999999999988888888888999977 69999998765
No 74
>PRK05907 hypothetical protein; Provisional
Probab=38.66 E-value=79 Score=26.30 Aligned_cols=67 Identities=12% Similarity=0.040 Sum_probs=53.1
Q ss_pred hhcchhHHHHHHHHhhhh-ccccccHHHHHHHHHHH-HHHHHHHHHhHHHHhhh-cCccccCcccHHHHH
Q psy10959 59 IRKLPFQRLVREIAQDFK-TDLRFQSAAIGALQEAS-EAYLVGLFEDTNLCAIH-AKRVTIMPKDIQLAR 125 (132)
Q Consensus 59 ipk~pF~RlVreI~~~~~-~~~r~~~~Al~aLQeaa-E~~lv~lfe~a~~~a~H-akRvTi~~kDi~La~ 125 (132)
.+...-..|.+-|.+.+. .+..++.+|+..|=+.+ +.-|-.+..+-..++.+ +.+-+|+.+||+.+.
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 444445677777777774 67899999999999988 67777888888888888 568999999998764
No 75
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=35.73 E-value=1.7e+02 Score=22.97 Aligned_cols=61 Identities=21% Similarity=0.260 Sum_probs=42.2
Q ss_pred hHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHH
Q psy10959 64 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 126 (132)
Q Consensus 64 F~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~r 126 (132)
+..+|++.+.. .+..++++|+..|-+.++.=+-.+-.+-..++.+++-.+|+.+||+-...
T Consensus 116 ~~~~i~~~~~~--~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~~It~e~I~~~~~ 176 (302)
T TIGR01128 116 LPRWIQARLKK--LGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDGKITLEDVEEAVS 176 (302)
T ss_pred HHHHHHHHHHH--cCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCCCCCHHHHHHHHh
Confidence 33445554442 56789999999999888865666666666666665444799999976654
No 76
>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=35.64 E-value=51 Score=19.82 Aligned_cols=19 Identities=16% Similarity=-0.060 Sum_probs=11.3
Q ss_pred HHhhhcCccccCcccHHHH
Q psy10959 106 LCAIHAKRVTIMPKDIQLA 124 (132)
Q Consensus 106 ~~a~HakRvTi~~kDi~La 124 (132)
.+|...+...|++.+|.-|
T Consensus 26 ~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 26 KYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHcCCCeECHHHHHhh
Confidence 4567777777777776644
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=34.63 E-value=1.1e+02 Score=25.82 Aligned_cols=51 Identities=14% Similarity=0.113 Sum_probs=41.2
Q ss_pred ccccccHHHHHHHHHHHHHHHH-------HHHHhHHHHhhhcCccccCcccHHHHHHH
Q psy10959 77 TDLRFQSAAIGALQEASEAYLV-------GLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv-------~lfe~a~~~a~HakRvTi~~kDi~La~ri 127 (132)
.+..++++.+..+.+.+.+.=+ .+...|...|.-.+|-.|+++|++.+..+
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 5667888888877777776443 37888999999999999999999977654
No 78
>PF13581 HATPase_c_2: Histidine kinase-like ATPase domain
Probab=34.05 E-value=73 Score=21.65 Aligned_cols=45 Identities=18% Similarity=0.102 Sum_probs=34.5
Q ss_pred hHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHh
Q psy10959 64 FQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCA 108 (132)
Q Consensus 64 F~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a 108 (132)
+-+.++..+..+-....|..+.+..+.-+++..++..++.++...
T Consensus 7 ~i~~~r~~~~~~~~~~~~~~~~~~~~~lav~E~~~Nav~H~~~~~ 51 (125)
T PF13581_consen 7 DIREARAFLREFLERLGLPEEDRDDLELAVSEALTNAVEHGYPGD 51 (125)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 334556666666566889999999999999999999888877643
No 79
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=33.82 E-value=1.1e+02 Score=25.02 Aligned_cols=49 Identities=16% Similarity=0.098 Sum_probs=40.9
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcC-ccccCcccHHHHH
Q psy10959 77 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAK-RVTIMPKDIQLAR 125 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~Hak-RvTi~~kDi~La~ 125 (132)
.+..++++|+..|-+.++.=+..+-.+-..++.+++ .-+|+.+||+-+.
T Consensus 158 ~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv 207 (343)
T PRK06585 158 AGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVV 207 (343)
T ss_pred CCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHh
Confidence 568899999999999999988888888888888854 4579999997654
No 80
>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=33.37 E-value=1.7e+02 Score=20.33 Aligned_cols=62 Identities=10% Similarity=0.192 Sum_probs=37.2
Q ss_pred hhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCcc-ccCcccHHHH
Q psy10959 59 IRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRV-TIMPKDIQLA 124 (132)
Q Consensus 59 ipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRv-Ti~~kDi~La 124 (132)
++|....+|+.. +.++.-++.....++.-.+-.|+-.|-|.|..+.---+-. -|.|..+.-|
T Consensus 24 ~~k~~ikkli~~----~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA 86 (90)
T PF04719_consen 24 FNKAAIKKLINQ----VLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREA 86 (90)
T ss_dssp --HHHHHHHHHH----HHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHH
T ss_pred CCHHHHHHHHHH----HcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHH
Confidence 555555555554 4456789999999999999999999999998876633221 3444444433
No 81
>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=32.62 E-value=1e+02 Score=22.67 Aligned_cols=45 Identities=13% Similarity=0.124 Sum_probs=37.0
Q ss_pred cchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHH
Q psy10959 61 KLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTN 105 (132)
Q Consensus 61 k~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~ 105 (132)
..-+-+.|+..+..+-....|+.+.+..|+-+++..++..++.++
T Consensus 15 ~~~~~~~vr~~~~~~a~~~g~~~~~~~~l~lav~Ea~~Nai~ha~ 59 (159)
T TIGR01924 15 KPEYVGLIRLTLSGIASRAGYTYDDIEDLKIAVSEACTNAVKHAY 59 (159)
T ss_pred cHHHHHHHHHHHHHHHHhcCCChHHHHHHHHHHHHHHHHHHHhcc
Confidence 445667788888888778889999999999999988888888775
No 82
>KOG1942|consensus
Probab=31.98 E-value=1.5e+02 Score=25.87 Aligned_cols=51 Identities=24% Similarity=0.311 Sum_probs=44.4
Q ss_pred ccccccHHHHHHHHHH----HHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHH
Q psy10959 77 TDLRFQSAAIGALQEA----SEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 77 ~~~r~~~~Al~aLQea----aE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ri 127 (132)
.++.+..+|++-|-+. +=-|.++|+.-|++||.-++|..|.++|++=+..+
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 6788999999988773 44699999999999999999999999999877655
No 83
>PRK05629 hypothetical protein; Validated
Probab=29.96 E-value=1.6e+02 Score=23.96 Aligned_cols=60 Identities=13% Similarity=0.103 Sum_probs=42.1
Q ss_pred HHHHHHHHhhh-hccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHH
Q psy10959 65 QRLVREIAQDF-KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 65 ~RlVreI~~~~-~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ 125 (132)
..+++=|.+.+ ..+..++.+|++.|-+.++.=+..+-.+--.++.+.+ -+|+.+||+-+.
T Consensus 129 ~~l~~wi~~~~~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v 189 (318)
T PRK05629 129 RERPGWVTQEFKNHGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYY 189 (318)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHh
Confidence 33444444444 3678899999999999998766666666666666654 369999998653
No 84
>PF10788 DUF2603: Protein of unknown function (DUF2603); InterPro: IPR019724 This entry represents a conserved protein in epsilon-Proteobacteria. The function is not known.
Probab=28.21 E-value=41 Score=25.29 Aligned_cols=32 Identities=25% Similarity=0.536 Sum_probs=26.0
Q ss_pred cchhhhHHhhhcchhhhhhcchhHHHHHHHHhh
Q psy10959 42 TVALREIRRYQKSTELLIRKLPFQRLVREIAQD 74 (132)
Q Consensus 42 ~~alrEIr~~Qkst~llipk~pF~RlVreI~~~ 74 (132)
+||+.||+++-.+...+ |..-+.+||++|=.+
T Consensus 97 ~VAm~ei~~~~~~~~~~-~~id~~~lvk~IKk~ 128 (137)
T PF10788_consen 97 AVAMDEIKKMRQKDGNL-PNIDLDKLVKNIKKE 128 (137)
T ss_pred HHHHHHHHHHHhcCCCc-CCCCHHHHHHHHHHh
Confidence 89999999996555444 899999999999553
No 85
>COG2118 DNA-binding protein [General function prediction only]
Probab=25.53 E-value=1.3e+02 Score=22.10 Aligned_cols=33 Identities=27% Similarity=0.310 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 88 ALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 88 aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
.+-+++|.+|+.|.. .||+|....|=+|..-|.
T Consensus 67 e~AeavE~qLi~Laq--------tGri~~~I~e~~lk~IL~ 99 (116)
T COG2118 67 ELAEAVENQLIQLAQ--------TGRITHKIDEEELKEILE 99 (116)
T ss_pred HHHHHHHHHHHHHHH--------cCCCCCCCCHHHHHHHHH
Confidence 367899999999864 799999999988876554
No 86
>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=25.11 E-value=99 Score=20.84 Aligned_cols=24 Identities=21% Similarity=0.402 Sum_probs=21.7
Q ss_pred HHhhhcchhhhhhcchhHHHHHHH
Q psy10959 48 IRRYQKSTELLIRKLPFQRLVREI 71 (132)
Q Consensus 48 Ir~~Qkst~llipk~pF~RlVreI 71 (132)
+..||.=..-|.|+++|...|..|
T Consensus 39 l~~Yq~W~h~LfPk~~F~d~i~~v 62 (83)
T PF07962_consen 39 LQFYQLWAHRLFPKASFEDFIERV 62 (83)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHH
Confidence 788998889999999999999877
No 87
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=25.06 E-value=2e+02 Score=23.68 Aligned_cols=49 Identities=22% Similarity=0.230 Sum_probs=38.5
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHH
Q psy10959 77 TDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ 125 (132)
..++++.+|+..|-+..|.=+-.+..+-+.++.++.=.+|+.+||+.+.
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 5789999999999999997666666666666555555599999999775
No 88
>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=24.90 E-value=65 Score=20.31 Aligned_cols=20 Identities=30% Similarity=0.393 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q psy10959 84 AAIGALQEASEAYLVGLFED 103 (132)
Q Consensus 84 ~Al~aLQeaaE~~lv~lfe~ 103 (132)
+|+.+|||+.++-|..+...
T Consensus 7 ea~~~lqevs~eELd~ilGg 26 (51)
T PF04604_consen 7 EALNSLQEVSDEELDQILGG 26 (51)
T ss_pred HHHHHHHhcCHHHHHHHhCC
Confidence 89999999999999988764
No 89
>PF07105 DUF1367: Protein of unknown function (DUF1367); InterPro: IPR009797 This entry is represented by Bacteriophage VT2phi_272, P37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Probab=23.06 E-value=1.5e+02 Score=23.58 Aligned_cols=17 Identities=41% Similarity=0.604 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHh
Q psy10959 87 GALQEASEAYLVGLFED 103 (132)
Q Consensus 87 ~aLQeaaE~~lv~lfe~ 103 (132)
++||++++.||..+.+.
T Consensus 91 ~~l~~~A~~yL~~va~~ 107 (196)
T PF07105_consen 91 DALQEAADQYLAKVAKK 107 (196)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 88999999999988763
No 90
>PRK04069 serine-protein kinase RsbW; Provisional
Probab=22.81 E-value=2e+02 Score=21.04 Aligned_cols=45 Identities=11% Similarity=0.155 Sum_probs=34.1
Q ss_pred cchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHH
Q psy10959 61 KLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTN 105 (132)
Q Consensus 61 k~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~ 105 (132)
..-+-++||..+..+.....|+.+.+..|.-+++..+....+.++
T Consensus 15 ~~~~~~~vr~~v~~~~~~~g~~~~~~~~l~lav~Ea~~Nai~Hg~ 59 (161)
T PRK04069 15 KAEYVSIIRLTLSGVANRMGFSYDDIEDMKIAVSEACTNAVQHAY 59 (161)
T ss_pred cHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 445668888888888888889999888888877766666666554
No 91
>PRK07914 hypothetical protein; Reviewed
Probab=22.54 E-value=2.1e+02 Score=23.25 Aligned_cols=60 Identities=10% Similarity=0.102 Sum_probs=42.1
Q ss_pred HHHHHHHHhhh-hccccccHHHHHHHHHHHHHHHHHHHHhHHHHhhhcCccccCcccHHHHH
Q psy10959 65 QRLVREIAQDF-KTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 125 (132)
Q Consensus 65 ~RlVreI~~~~-~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~HakRvTi~~kDi~La~ 125 (132)
..+.+=|.+.+ ..+..++.+|+..|-+.++.-+..+-.+-..++.+.+ -+|+.+||+-+.
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 44444454444 3567899999999999998766666666666666654 468888887654
No 92
>PRK14562 haloacid dehalogenase superfamily protein; Provisional
Probab=21.55 E-value=1.2e+02 Score=23.63 Aligned_cols=25 Identities=36% Similarity=0.287 Sum_probs=18.4
Q ss_pred ccccccHHHHHHHHHHHHHHHHHHH
Q psy10959 77 TDLRFQSAAIGALQEASEAYLVGLF 101 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~lv~lf 101 (132)
++++|+...-.++||.+|++....|
T Consensus 71 ~~~~y~~~~~~~lQEyvEA~~f~~~ 95 (204)
T PRK14562 71 PELYYAGYVGTALQEYVEALLVYSL 95 (204)
T ss_pred chhhhhhhcchHHHHHHHHHHHHHH
Confidence 5678888888899999987544333
No 93
>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=21.38 E-value=2e+02 Score=26.17 Aligned_cols=51 Identities=14% Similarity=0.184 Sum_probs=42.4
Q ss_pred ccccccHHHHHHHHHHHHHHH-------HHHHHhHHHHhhhcCccccCcccHHHHHHH
Q psy10959 77 TDLRFQSAAIGALQEASEAYL-------VGLFEDTNLCAIHAKRVTIMPKDIQLARRI 127 (132)
Q Consensus 77 ~~~r~~~~Al~aLQeaaE~~l-------v~lfe~a~~~a~HakRvTi~~kDi~La~ri 127 (132)
....++.+++..|.+++..+- ..+..-|--+|.-.+|-+|..+|++.|..+
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 557889999999888887754 346677888899999999999999988775
No 94
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=21.08 E-value=4e+02 Score=24.84 Aligned_cols=63 Identities=21% Similarity=0.228 Sum_probs=47.7
Q ss_pred HHHHHHHhhhh---ccccccHHHHHHHHHHHHH-------------HHHHHHHhHHHHhhhcCccccCcccHHHHHHHh
Q psy10959 66 RLVREIAQDFK---TDLRFQSAAIGALQEASEA-------------YLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 128 (132)
Q Consensus 66 RlVreI~~~~~---~~~r~~~~Al~aLQeaaE~-------------~lv~lfe~a~~~a~HakRvTi~~kDi~La~rir 128 (132)
+++.-+++++. .-..|+.+|+..|-..++. .|..|...|+.+|.-.++.-|+.+|++-|.+.+
T Consensus 321 k~~~~~~q~v~~d~~ip~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~Ve~a~~~~ 399 (647)
T COG1067 321 KLVQFYVQELARDGNIPHLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAEDVEEALQKR 399 (647)
T ss_pred HHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHHHHHHHHhh
Confidence 44444444442 3368999999887666553 688899999999999999999999999988763
No 95
>PF03172 Sp100: Sp100 domain; InterPro: IPR004865 The Sp100 and promyelocytic leukemia proteins (PML) are constituents of nuclear domains, known as nuclear dots (NDs or NBs - nuclear bodies or PML bodies), and are both covalently modified by the small ubiquitin-related protein SUMO-1. NBs play a role in autoimmunity, virus infections, and in the etiology of acute promyelocytic leukemia []. A functional nuclear localization signal and an NB-targeting region that coincides with an Sp100 homodimerization domain have been mapped. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins, which include the autoimmune regulator proteins (AIRE) and other numerous other transiently or permanently localised proteins. PML is expressed as a family of isoforms (PML I-VII) as a result of alternative splicing, most of which are found in the nucleus. Although there are many other functions of PML NBs in a wide range of cellular pathways, there is accumulating evidence that they represent preferential targets for viral infections and that PML plays a role in the mechanism of the antiviral action of interferon []. The Sp100 domain is usually found at the amino terminus of proteins that contain a SAND domain IPR000770 from INTERPRO. ; GO: 0005634 nucleus
Probab=20.93 E-value=2.3e+02 Score=20.35 Aligned_cols=48 Identities=27% Similarity=0.376 Sum_probs=36.3
Q ss_pred HhhhcchhhhhhcchhHHHHHHHHhhhhccccccHHHHHHHHHHHHHHHHHHHHhHHHHhh
Q psy10959 49 RRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAI 109 (132)
Q Consensus 49 r~~Qkst~llipk~pF~RlVreI~~~~~~~~r~~~~Al~aLQeaaE~~lv~lfe~a~~~a~ 109 (132)
+.|+.+-+.+--+.|-+|.|.+|+..... ...-.++..||.+.|+..+
T Consensus 40 ~~y~e~~e~crnlvpv~rvvY~vLs~Lek-------------~f~~~fl~~LFs~~nL~~Y 87 (103)
T PF03172_consen 40 QMYKESQEACRNLVPVQRVVYNVLSWLEK-------------TFIRSFLEALFSDYNLKEY 87 (103)
T ss_pred HHHHHHHHHHhccccHHHHHHHHHHHHHH-------------HhhHHHHHHHhhHHHHHHC
Confidence 46777777778889999999999775522 2345688889999888764
No 96
>COG1598 Predicted nuclease of the RNAse H fold, HicB family [General function prediction only]
Probab=20.79 E-value=1.4e+02 Score=19.36 Aligned_cols=25 Identities=28% Similarity=0.270 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhHHHH
Q psy10959 83 SAAIGALQEASEAYLVGLFEDTNLC 107 (132)
Q Consensus 83 ~~Al~aLQeaaE~~lv~lfe~a~~~ 107 (132)
.+|+..+++|.|-|+..+.++....
T Consensus 34 eea~~n~~eai~l~~e~~~~~~~~i 58 (73)
T COG1598 34 EEALQNAKEAIELHLEALLEEGEPI 58 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHhcCCcC
Confidence 5788899999999999988876654
Done!