Query 034732
Match_columns 85
No_of_seqs 103 out of 412
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:53:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034732.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034732hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00156 histone H2AX; Provisi 100.0 3.3E-32 7.2E-37 191.9 5.8 67 17-83 13-79 (139)
2 PLN00153 histone H2A; Provisio 100.0 6.2E-32 1.3E-36 188.6 6.0 65 19-83 10-74 (129)
3 PLN00157 histone H2A; Provisio 100.0 6.7E-32 1.4E-36 189.0 6.2 66 18-83 11-76 (132)
4 PLN00154 histone H2A; Provisio 100.0 1.5E-31 3.3E-36 188.0 6.0 67 17-83 22-89 (136)
5 PTZ00017 histone H2A; Provisio 100.0 1.7E-31 3.6E-36 187.4 6.0 64 20-83 14-77 (134)
6 PTZ00252 histone H2A; Provisio 100.0 2.9E-31 6.2E-36 186.3 5.2 60 22-81 13-73 (134)
7 smart00414 H2A Histone 2A. 100.0 8.3E-30 1.8E-34 172.3 4.7 59 25-83 1-59 (106)
8 KOG1756 Histone 2A [Chromatin 100.0 8.8E-30 1.9E-34 177.9 4.8 64 20-83 14-77 (131)
9 cd00074 H2A Histone 2A; H2A is 100.0 2.6E-29 5.7E-34 171.9 5.8 66 17-82 4-69 (115)
10 COG5262 HTA1 Histone H2A [Chro 99.9 2E-26 4.3E-31 160.3 4.7 64 20-83 13-76 (132)
11 PLN00155 histone H2A; Provisio 99.9 3.4E-26 7.4E-31 141.4 3.6 49 19-67 10-58 (58)
12 KOG1757 Histone 2A [Chromatin 99.9 4.9E-26 1.1E-30 157.7 3.1 62 20-81 17-79 (131)
13 PF00125 Histone: Core histone 99.0 2.7E-10 5.8E-15 70.3 2.1 56 27-82 2-58 (75)
14 COG5247 BUR6 Class 2 transcrip 97.2 0.00033 7.2E-09 48.2 3.1 50 33-82 23-72 (113)
15 PLN00035 histone H4; Provision 97.2 0.00034 7.4E-09 47.5 3.0 46 34-80 30-75 (103)
16 PF00808 CBFD_NFYB_HMF: Histon 96.5 0.0029 6.3E-08 38.2 3.0 50 33-82 2-51 (65)
17 PTZ00015 histone H4; Provision 95.4 0.022 4.9E-07 38.6 3.5 46 34-80 31-76 (102)
18 KOG1659 Class 2 transcription 94.0 0.052 1.1E-06 41.4 2.9 48 33-80 13-60 (224)
19 smart00803 TAF TATA box bindin 92.9 0.16 3.4E-06 31.4 3.3 48 33-81 2-49 (65)
20 COG2036 HHT1 Histones H3 and H 92.2 0.12 2.7E-06 34.3 2.3 50 30-80 16-65 (91)
21 smart00417 H4 Histone H4. 90.7 0.34 7.3E-06 31.0 3.1 46 34-80 14-59 (74)
22 cd00076 H4 Histone H4, one of 90.1 0.38 8.2E-06 31.5 3.0 46 34-80 14-59 (85)
23 KOG1657 CCAAT-binding factor, 88.0 0.69 1.5E-05 35.2 3.5 52 29-80 70-121 (236)
24 COG5208 HAP5 CCAAT-binding fac 80.3 2.3 5E-05 33.1 3.5 51 32-82 108-158 (286)
25 cd07981 TAF12 TATA Binding Pro 73.4 6.1 0.00013 24.4 3.4 45 36-80 4-48 (72)
26 PF12096 DUF3572: Protein of u 65.7 3.4 7.5E-05 27.3 1.1 32 38-69 23-57 (88)
27 PTZ00463 histone H2B; Provisio 63.3 28 0.0006 24.3 5.3 43 38-80 33-75 (117)
28 cd07979 TAF9 TATA Binding Prot 55.5 19 0.00042 24.3 3.4 42 38-80 6-47 (117)
29 KOG3219 Transcription initiati 46.5 9 0.00019 28.8 0.7 45 33-78 112-156 (195)
30 PLN00158 histone H2B; Provisio 46.2 36 0.00079 23.7 3.6 46 37-82 31-76 (116)
31 COG4905 Predicted membrane pro 45.9 22 0.00047 27.4 2.7 20 57-76 71-90 (243)
32 cd08048 TAF11 TATA Binding Pro 44.1 41 0.0009 21.7 3.5 46 34-80 17-62 (85)
33 PF04719 TAFII28: hTAFII28-lik 40.0 18 0.00039 23.8 1.3 46 34-80 24-70 (90)
34 cd08050 TAF6 TATA Binding Prot 38.9 40 0.00086 26.4 3.3 33 49-81 14-46 (343)
35 PF09415 CENP-X: CENP-S associ 38.7 86 0.0019 19.6 4.3 47 35-81 1-49 (72)
36 PF09377 SBDS_C: SBDS protein 34.4 41 0.00089 22.8 2.4 39 29-67 18-56 (125)
37 PF11208 DUF2992: Protein of u 28.0 27 0.00059 24.4 0.7 44 33-76 8-51 (132)
38 PF06541 DUF1113: Protein of u 27.6 61 0.0013 22.6 2.4 21 57-77 65-85 (157)
39 PF02969 TAF: TATA box binding 26.6 1E+02 0.0023 19.0 3.1 31 51-81 20-50 (66)
40 PF10093 DUF2331: Uncharacteri 24.8 31 0.00067 28.1 0.6 14 57-70 90-114 (374)
41 TIGR01764 excise DNA binding d 24.2 41 0.00089 17.6 0.8 36 32-67 11-47 (49)
42 PF11850 DUF3370: Protein of u 23.5 45 0.00098 27.9 1.3 38 30-67 180-217 (441)
43 PF11486 DUF3212: Protein of u 23.4 63 0.0014 22.6 1.8 32 49-80 66-97 (120)
44 COG1694 MazG Predicted pyropho 22.9 1E+02 0.0022 19.6 2.6 21 60-80 28-48 (102)
45 KOG1585 Protein required for f 20.9 74 0.0016 25.5 2.0 40 42-81 173-215 (308)
No 1
>PLN00156 histone H2AX; Provisional
Probab=99.97 E-value=3.3e-32 Score=191.94 Aligned_cols=67 Identities=64% Similarity=0.887 Sum_probs=63.2
Q ss_pred CCCCCCCCCccccccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhccc
Q 034732 17 GGPKKKPVSRSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACNF 83 (85)
Q Consensus 17 ~~~~~k~~s~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~~ 83 (85)
++.+++..|+|+||||||||+||||+|++++|+.||+++||||||||||||++||||||||.|+|+-
T Consensus 13 ~~~~~k~~srS~rAgL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~k 79 (139)
T PLN00156 13 KPKATKSVSRSSKAGLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNK 79 (139)
T ss_pred cccccCCcCcccccCcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 3346788999999999999999999999999999999999999999999999999999999999874
No 2
>PLN00153 histone H2A; Provisional
Probab=99.97 E-value=6.2e-32 Score=188.62 Aligned_cols=65 Identities=69% Similarity=0.979 Sum_probs=61.7
Q ss_pred CCCCCCCccccccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhccc
Q 034732 19 PKKKPVSRSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACNF 83 (85)
Q Consensus 19 ~~~k~~s~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~~ 83 (85)
.+++.+|+|+||||||||+||||+|++++|++||+++||||||||||||++||||||||.|+||-
T Consensus 10 ~~~k~~srS~ragL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~k 74 (129)
T PLN00153 10 SGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNK 74 (129)
T ss_pred cccCccCcccccCcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 34578999999999999999999999999999999999999999999999999999999999974
No 3
>PLN00157 histone H2A; Provisional
Probab=99.97 E-value=6.7e-32 Score=189.05 Aligned_cols=66 Identities=70% Similarity=0.954 Sum_probs=62.5
Q ss_pred CCCCCCCCccccccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhccc
Q 034732 18 GPKKKPVSRSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACNF 83 (85)
Q Consensus 18 ~~~~k~~s~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~~ 83 (85)
+.+++..|+|+||||||||+||||+|++++|++||+++||||||||||||++||||||||.|+|+-
T Consensus 11 ~~~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~k 76 (132)
T PLN00157 11 GGGKKATSRSAKAGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNK 76 (132)
T ss_pred ccCcCCcCcccccCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 445678999999999999999999999999999999999999999999999999999999999874
No 4
>PLN00154 histone H2A; Provisional
Probab=99.97 E-value=1.5e-31 Score=188.05 Aligned_cols=67 Identities=54% Similarity=0.637 Sum_probs=61.9
Q ss_pred CCCCCCCCCccccccccccccchhhhhccCC-ccccccCchhHHHHHHHHHHHHHHHHHhhHhhhccc
Q 034732 17 GGPKKKPVSRSVKAGLQFPVGRIGRYLKKGR-YSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACNF 83 (85)
Q Consensus 17 ~~~~~k~~s~SsragLqFpV~rv~r~Lr~~~-~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~~ 83 (85)
++.+++..|+|+||||||||+||||+||+++ |.+||+++|||||||||||||+||||||||+|+|+-
T Consensus 22 ~~~~~k~~srS~rAgL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~k 89 (136)
T PLN00154 22 DKDKKKPTSRSSRAGLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLK 89 (136)
T ss_pred ccCCcCCcCcccccCccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3345688999999999999999999999998 468999999999999999999999999999999974
No 5
>PTZ00017 histone H2A; Provisional
Probab=99.97 E-value=1.7e-31 Score=187.38 Aligned_cols=64 Identities=75% Similarity=1.049 Sum_probs=61.5
Q ss_pred CCCCCCccccccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhccc
Q 034732 20 KKKPVSRSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACNF 83 (85)
Q Consensus 20 ~~k~~s~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~~ 83 (85)
+++..|+|+||||||||+||||+|++++|+.||+++||||||||||||++||||||||+|+|+-
T Consensus 14 ~~k~~srS~ragL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~k 77 (134)
T PTZ00017 14 KKKPVSRSAKAGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNK 77 (134)
T ss_pred CcCcccccccCCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4678999999999999999999999999999999999999999999999999999999999874
No 6
>PTZ00252 histone H2A; Provisional
Probab=99.97 E-value=2.9e-31 Score=186.27 Aligned_cols=60 Identities=55% Similarity=0.874 Sum_probs=57.1
Q ss_pred CCCC-ccccccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhc
Q 034732 22 KPVS-RSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAAC 81 (85)
Q Consensus 22 k~~s-~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~ 81 (85)
+..+ +|+||||||||+||||+|++++|++||+++||||||||||||++||||||||.|+|
T Consensus 13 ~~~~~rS~rAGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d 73 (134)
T PTZ00252 13 KSGSGRSAKAGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQ 73 (134)
T ss_pred ccccccccccCccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4555 99999999999999999999999999999999999999999999999999999975
No 7
>smart00414 H2A Histone 2A.
Probab=99.96 E-value=8.3e-30 Score=172.25 Aligned_cols=59 Identities=68% Similarity=0.949 Sum_probs=57.2
Q ss_pred CccccccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhccc
Q 034732 25 SRSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACNF 83 (85)
Q Consensus 25 s~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~~ 83 (85)
|+|+||||||||+||||+|++++|++||+++||||||||||||++||||||||+|+++-
T Consensus 1 srS~ragL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k 59 (106)
T smart00414 1 SRSARAGLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNK 59 (106)
T ss_pred CccccCCccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 68999999999999999999999999999999999999999999999999999999873
No 8
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=99.96 E-value=8.8e-30 Score=177.90 Aligned_cols=64 Identities=66% Similarity=0.904 Sum_probs=61.1
Q ss_pred CCCCCCccccccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhccc
Q 034732 20 KKKPVSRSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACNF 83 (85)
Q Consensus 20 ~~k~~s~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~~ 83 (85)
+++..|+|.++|||||||||+|+||+++|++||+++|||||+||||||++||||+|||+|+||-
T Consensus 14 ~~~~~srs~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnk 77 (131)
T KOG1756|consen 14 AKAKSSRSSRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNK 77 (131)
T ss_pred hhhhcchhhhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcC
Confidence 4567899999999999999999999999999999999999999999999999999999999973
No 9
>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=99.96 E-value=2.6e-29 Score=171.94 Aligned_cols=66 Identities=70% Similarity=0.977 Sum_probs=62.6
Q ss_pred CCCCCCCCCccccccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhcc
Q 034732 17 GGPKKKPVSRSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACN 82 (85)
Q Consensus 17 ~~~~~k~~s~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~ 82 (85)
+|.+++.+|+|+|+||||||+||||+|++++|++||+++|+|||+||||||++||||||+|.|+++
T Consensus 4 ~k~~~~~~s~s~ragL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~ 69 (115)
T cd00074 4 GKKKSKKRSRSARAGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDN 69 (115)
T ss_pred CccCcCccccccccCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 356677889999999999999999999999999999999999999999999999999999999986
No 10
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=99.93 E-value=2e-26 Score=160.28 Aligned_cols=64 Identities=61% Similarity=0.840 Sum_probs=60.5
Q ss_pred CCCCCCccccccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhccc
Q 034732 20 KKKPVSRSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACNF 83 (85)
Q Consensus 20 ~~k~~s~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~~ 83 (85)
.+-..|+|.++||+|||+||+|+||+++|..||+++|+||++||||||++||||||||.|.|+-
T Consensus 13 ~r~~~s~sa~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~k 76 (132)
T COG5262 13 ARVSQSRSAKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNK 76 (132)
T ss_pred chhccchhhhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcC
Confidence 3456799999999999999999999999999999999999999999999999999999999873
No 11
>PLN00155 histone H2A; Provisional
Probab=99.92 E-value=3.4e-26 Score=141.40 Aligned_cols=49 Identities=80% Similarity=1.280 Sum_probs=46.3
Q ss_pred CCCCCCCccccccccccccchhhhhccCCccccccCchhHHHHHHHHHH
Q 034732 19 PKKKPVSRSVKAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYL 67 (85)
Q Consensus 19 ~~~k~~s~SsragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYL 67 (85)
.+++.+|+|+||||||||+||||+|++++|++||+++||||||||||||
T Consensus 10 ~~~k~~srS~rAgL~FPVgri~r~Lr~g~~a~Rvga~apVYlAAVLEYL 58 (58)
T PLN00155 10 SGKKAVSRSAKAGLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYL 58 (58)
T ss_pred cccCccCcccccccccchHHHHHHHhcCChhhcccCCcHHHHHHHHHhC
Confidence 3456789999999999999999999999999999999999999999997
No 12
>KOG1757 consensus Histone 2A [Chromatin structure and dynamics]
Probab=99.92 E-value=4.9e-26 Score=157.71 Aligned_cols=62 Identities=58% Similarity=0.706 Sum_probs=58.7
Q ss_pred CCCCCCccccccccccccchhhhhccCCcc-ccccCchhHHHHHHHHHHHHHHHHHhhHhhhc
Q 034732 20 KKKPVSRSVKAGLQFPVGRIGRYLKKGRYS-QRVGTGAPVYLAAVLEYLAAEVVLLVLFYAAC 81 (85)
Q Consensus 20 ~~k~~s~SsragLqFpV~rv~r~Lr~~~~~-~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~ 81 (85)
+.+..|+|+|+||||||+||||+|+....+ .||++++.||+||||||||+||||||||.++|
T Consensus 17 ~~k~vs~s~raGlqFpVgRihr~LK~r~t~h~rVGataavy~aaileYLTaEVLeLAgNasKd 79 (131)
T KOG1757|consen 17 KAKAVSRSARAGLQFPVGRIHRHLKTRTTSHGRVGATAAVYSAAILEYLTAEVLELAGNASKD 79 (131)
T ss_pred hhhhhhHHHhcccccchHHHHHHHHHhcccccccchHHHHHHHHHHHHHHHHHHHHccccccc
Confidence 478899999999999999999999997777 79999999999999999999999999999987
No 13
>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=98.97 E-value=2.7e-10 Score=70.27 Aligned_cols=56 Identities=29% Similarity=0.310 Sum_probs=51.0
Q ss_pred cccccccccccchhhhhccCCccc-cccCchhHHHHHHHHHHHHHHHHHhhHhhhcc
Q 034732 27 SVKAGLQFPVGRIGRYLKKGRYSQ-RVGTGAPVYLAAVLEYLAAEVVLLVLFYAACN 82 (85)
Q Consensus 27 SsragLqFpV~rv~r~Lr~~~~~~-Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~ 82 (85)
+.+..+.||+.|+.+.+....+.. ||++.|.+||.+++||++.+|+|+|++.|..+
T Consensus 2 ~~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~ 58 (75)
T PF00125_consen 2 TRRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHA 58 (75)
T ss_dssp HSHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred cccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhc
Confidence 456788999999999999988885 99999999999999999999999999998754
No 14
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=97.21 E-value=0.00033 Score=48.21 Aligned_cols=50 Identities=28% Similarity=0.428 Sum_probs=46.6
Q ss_pred cccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhcc
Q 034732 33 QFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACN 82 (85)
Q Consensus 33 qFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~ 82 (85)
.||+.|+.+.|+....-..|+..+||...-.||.+.++|+.+++.+|..-
T Consensus 23 rFP~ar~KkIMQ~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~ 72 (113)
T COG5247 23 RFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKK 72 (113)
T ss_pred cCCHHHHHHHHHhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 49999999999998888999999999999999999999999999998753
No 15
>PLN00035 histone H4; Provisional
Probab=97.20 E-value=0.00034 Score=47.54 Aligned_cols=46 Identities=17% Similarity=0.190 Sum_probs=41.5
Q ss_pred ccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 34 FPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 34 FpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
+|..-|.|+++.+. ..|||..+..-|..+||.+..+|+.-|..++.
T Consensus 30 ipk~~IrRLARr~G-vkRIS~~ay~elr~vle~~l~~I~~dav~ya~ 75 (103)
T PLN00035 30 ITKPAIRRLARRGG-VKRISGLIYEETRGVLKIFLENVIRDAVTYTE 75 (103)
T ss_pred CCHHHHHHHHHHcC-cccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 88889999999874 89999999999999999999999998887764
No 16
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=96.53 E-value=0.0029 Score=38.16 Aligned_cols=50 Identities=20% Similarity=0.150 Sum_probs=41.9
Q ss_pred cccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhcc
Q 034732 33 QFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACN 82 (85)
Q Consensus 33 qFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~ 82 (85)
.||+++|.+.+|...-..+|+..+...++-..|.+..++..-|...|..+
T Consensus 2 ~lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~ 51 (65)
T PF00808_consen 2 SLPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRD 51 (65)
T ss_dssp SS-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred CCChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 48999999999998666899999999999999988888888888777654
No 17
>PTZ00015 histone H4; Provisional
Probab=95.38 E-value=0.022 Score=38.56 Aligned_cols=46 Identities=22% Similarity=0.243 Sum_probs=39.6
Q ss_pred ccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 34 FPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 34 FpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
+|..-|.|+++.+ =..|||..+..-+..+||.+..+|+.-|..+|.
T Consensus 31 I~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~ae 76 (102)
T PTZ00015 31 ITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTE 76 (102)
T ss_pred CCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6667899999985 569999999999999999888999988877764
No 18
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=93.99 E-value=0.052 Score=41.36 Aligned_cols=48 Identities=21% Similarity=0.366 Sum_probs=44.9
Q ss_pred cccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 33 QFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 33 qFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
.||+.||.+.|+...--.+|....||...--||.+..+||..++.+++
T Consensus 13 rfp~aRiKKIMQ~dEdIGKvaqavPViisralElFl~~l~~~t~~~t~ 60 (224)
T KOG1659|consen 13 RFPPARIKKIMQSDEDIGKVAQAVPVIISRALELFLESLLQKTLEITR 60 (224)
T ss_pred cCCHHHHHHHHhhhhhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 499999999999988889999999999999999999999999988765
No 19
>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=92.94 E-value=0.16 Score=31.42 Aligned_cols=48 Identities=21% Similarity=0.159 Sum_probs=41.0
Q ss_pred cccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhc
Q 034732 33 QFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAAC 81 (85)
Q Consensus 33 qFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~ 81 (85)
.+|..-|.++.+... ..||+..+...|+-.+||...+|++-|-+.++.
T Consensus 2 ~~p~~~i~ria~~~G-i~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~h 49 (65)
T smart00803 2 WLPKETIKDVAESLG-IGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRH 49 (65)
T ss_pred CCCHHHHHHHHHHCC-CccccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478888888888753 359999999999999999999999999887753
No 20
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=92.21 E-value=0.12 Score=34.28 Aligned_cols=50 Identities=26% Similarity=0.265 Sum_probs=42.1
Q ss_pred ccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 30 AGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 30 agLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
..+.+|+-=|.|++|+. -.+||+++|...|.-++|-+..+|.|.|...|.
T Consensus 16 ~~~~Lp~apv~Ri~r~~-~~~Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ 65 (91)
T COG2036 16 TDLLLPKAPVRRILRKA-GAERVSSSAIEELQEALEEYLEEIAEDAVELAE 65 (91)
T ss_pred hhhhcCchHHHHHHHHH-hHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567888888999883 456999999999999999999999999987764
No 21
>smart00417 H4 Histone H4.
Probab=90.65 E-value=0.34 Score=31.04 Aligned_cols=46 Identities=20% Similarity=0.149 Sum_probs=40.3
Q ss_pred ccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 34 FPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 34 FpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
+|..-|.|+++.+ =..|||..+...+..+||.+..+|+..|..++.
T Consensus 14 I~k~~IrRLaRr~-GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ 59 (74)
T smart00417 14 ITKPAIRRLARRG-GVKRISGLIYDETRNVLKSFLENVVRDAVTYTE 59 (74)
T ss_pred CCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6677899999985 469999999999999999998999999988774
No 22
>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=90.14 E-value=0.38 Score=31.48 Aligned_cols=46 Identities=20% Similarity=0.275 Sum_probs=40.7
Q ss_pred ccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 34 FPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 34 FpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
+|..-|.|+.+.+. ..|||..+..-+..+||.+..+|+.-|..++.
T Consensus 14 i~k~~I~RLarr~G-vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~ 59 (85)
T cd00076 14 ITKPAIRRLARRGG-VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTE 59 (85)
T ss_pred CCHHHHHHHHHHcC-cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67778999999875 89999999999999999999999999887765
No 23
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=87.96 E-value=0.69 Score=35.23 Aligned_cols=52 Identities=21% Similarity=0.277 Sum_probs=43.3
Q ss_pred cccccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 29 KAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 29 ragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
-.-..||++||.+.+|......-|.+.|||.++-.+|+...|+=..|...+.
T Consensus 70 ~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Te 121 (236)
T KOG1657|consen 70 FKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTE 121 (236)
T ss_pred hhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhc
Confidence 3456799999999999988889999999999999999997777665554443
No 24
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=80.32 E-value=2.3 Score=33.12 Aligned_cols=51 Identities=24% Similarity=0.376 Sum_probs=41.7
Q ss_pred ccccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhcc
Q 034732 32 LQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACN 82 (85)
Q Consensus 32 LqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~ 82 (85)
+.+|..||.+++|...--.-|++.+||.+|-+-|-+.+|+--.|--.|..|
T Consensus 108 h~LPlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~N 158 (286)
T COG5208 108 HNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEEN 158 (286)
T ss_pred ccCcHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHh
Confidence 458999999999988777899999999999999988888766664444433
No 25
>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=73.39 E-value=6.1 Score=24.44 Aligned_cols=45 Identities=13% Similarity=0.091 Sum_probs=37.7
Q ss_pred ccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 36 VGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 36 V~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
-..+..++++..-..|++..+...|..+.|=+..+|++.|...|+
T Consensus 4 k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAk 48 (72)
T cd07981 4 KRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAK 48 (72)
T ss_pred HHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667777765568999999999999999999999999988876
No 26
>PF12096 DUF3572: Protein of unknown function (DUF3572); InterPro: IPR021955 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 100 amino acids in length.
Probab=65.68 E-value=3.4 Score=27.34 Aligned_cols=32 Identities=41% Similarity=0.696 Sum_probs=22.9
Q ss_pred chhhhhccCCcc---ccccCchhHHHHHHHHHHHH
Q 034732 38 RIGRYLKKGRYS---QRVGTGAPVYLAAVLEYLAA 69 (85)
Q Consensus 38 rv~r~Lr~~~~~---~Rv~a~a~VYLaAVLEYLta 69 (85)
++.|+|-..-.. -|-.++-|.||++||+||..
T Consensus 23 ~l~rFLa~TG~~p~~LR~~a~dp~FL~~VLdFl~~ 57 (88)
T PF12096_consen 23 RLPRFLALTGLSPDDLRAAAGDPAFLAAVLDFLLM 57 (88)
T ss_pred HHHHHHHHhCCCHHHHHHHccChHHHHHHHHHHHc
Confidence 445555433333 47778899999999999984
No 27
>PTZ00463 histone H2B; Provisional
Probab=63.30 E-value=28 Score=24.32 Aligned_cols=43 Identities=9% Similarity=-0.047 Sum_probs=27.6
Q ss_pred chhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 38 RIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 38 rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
.|++.|++-.-..-|+..+.-.|...+.=+...|...|..-|+
T Consensus 33 YI~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~ 75 (117)
T PTZ00463 33 YIFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCK 75 (117)
T ss_pred HHHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7899999866667788777665555555555555444544444
No 28
>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=55.49 E-value=19 Score=24.32 Aligned_cols=42 Identities=14% Similarity=-0.032 Sum_probs=35.2
Q ss_pred chhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 38 RIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 38 rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
-|++.|++. -..+++..++..|.-.++-.+.+||+-|-.+|.
T Consensus 6 ~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~ 47 (117)
T cd07979 6 VIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSE 47 (117)
T ss_pred HHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467888873 346899999999999999999999999987775
No 29
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=46.53 E-value=9 Score=28.80 Aligned_cols=45 Identities=22% Similarity=0.289 Sum_probs=38.5
Q ss_pred cccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHh
Q 034732 33 QFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFY 78 (85)
Q Consensus 33 qFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~ 78 (85)
-||-+.|.+++..- ..+-|+....|.++++-+-+..||+|+|--.
T Consensus 112 ~f~Ka~iKkL~~~i-tg~~v~~nv~Ia~~GiaKvFVGEvVEeAl~V 156 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSI-TGQSVSENVAIAMAGIAKVFVGEVVEEALDV 156 (195)
T ss_pred cCCHHHHHHHHHHH-hCCccCcceeeeecchhhHhHHHHHHHHHHH
Confidence 38899999999873 4445999999999999999999999999644
No 30
>PLN00158 histone H2B; Provisional
Probab=46.19 E-value=36 Score=23.66 Aligned_cols=46 Identities=13% Similarity=0.023 Sum_probs=32.9
Q ss_pred cchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhhcc
Q 034732 37 GRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAACN 82 (85)
Q Consensus 37 ~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~~ 82 (85)
..|++.|++-.-..-|+..+.--|...+.-+...|..-|..-++-|
T Consensus 31 ~YI~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~n 76 (116)
T PLN00158 31 IYIYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYN 76 (116)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3799999987666788888877777777666666666666665543
No 31
>COG4905 Predicted membrane protein [Function unknown]
Probab=45.89 E-value=22 Score=27.37 Aligned_cols=20 Identities=20% Similarity=0.599 Sum_probs=17.1
Q ss_pred hHHHHHHHHHHHHHHHHHhh
Q 034732 57 PVYLAAVLEYLAAEVVLLVL 76 (85)
Q Consensus 57 ~VYLaAVLEYLtaeILELAg 76 (85)
++++..|+||+|+-|||---
T Consensus 71 si~ivTv~Eyvt~~ILEa~F 90 (243)
T COG4905 71 SIFIVTVLEYVTGFILEAIF 90 (243)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 57889999999999998643
No 32
>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=44.09 E-value=41 Score=21.71 Aligned_cols=46 Identities=20% Similarity=0.242 Sum_probs=38.3
Q ss_pred ccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 34 FPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 34 FpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
||-..+.+++.. ...+.++....+-++++-.-+..||.|.|-..-.
T Consensus 17 f~k~~iKr~~~~-~~~~~v~~~v~i~v~glaKvFVGeivE~A~~V~~ 62 (85)
T cd08048 17 FPKAAIKRLIQS-VTGQSVSQNVVIAVAGIAKVFVGEIVEEARDVQE 62 (85)
T ss_pred ccHHHHHHHHHH-HcCCCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666778888775 4558999999999999999999999999976543
No 33
>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=40.01 E-value=18 Score=23.83 Aligned_cols=46 Identities=15% Similarity=0.184 Sum_probs=33.9
Q ss_pred ccccchhhhhccCCcc-ccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 34 FPVGRIGRYLKKGRYS-QRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 34 FpV~rv~r~Lr~~~~~-~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
||=.-|.+++.. ... +.|+....+-++++-..+..||.|.|-....
T Consensus 24 ~~k~~ikkli~~-~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~ 70 (90)
T PF04719_consen 24 FNKAAIKKLINQ-VLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQE 70 (90)
T ss_dssp --HHHHHHHHHH-HHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHH-HcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 666678888877 345 7999999999999999999999999976543
No 34
>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=38.86 E-value=40 Score=26.43 Aligned_cols=33 Identities=15% Similarity=0.158 Sum_probs=29.7
Q ss_pred cccccCchhHHHHHHHHHHHHHHHHHhhHhhhc
Q 034732 49 SQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAAC 81 (85)
Q Consensus 49 ~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~ 81 (85)
..|++..+...|+..+||-..+|++.|.+.++-
T Consensus 14 i~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~h 46 (343)
T cd08050 14 IDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRH 46 (343)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 369999999999999999999999999887754
No 35
>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=38.70 E-value=86 Score=19.62 Aligned_cols=47 Identities=21% Similarity=0.162 Sum_probs=33.8
Q ss_pred cccchhhhhccC--CccccccCchhHHHHHHHHHHHHHHHHHhhHhhhc
Q 034732 35 PVGRIGRYLKKG--RYSQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAAC 81 (85)
Q Consensus 35 pV~rv~r~Lr~~--~~~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~ 81 (85)
|..-|.|+|+.. +-.-||+..|---++..|+-++.|-+..|-.+|.+
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~ 49 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEA 49 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444567777742 23369999999999999999999998888776654
No 36
>PF09377 SBDS_C: SBDS protein C-terminal domain; InterPro: IPR018978 This entry represents the C-terminal domain of proteins that are highly conserved in species ranging from archaea to vertebrates and plants []. The family contains several Shwachman-Bodian-Diamond syndrome (SBDS, OMIM 260400) proteins from both mouse and humans. Shwachman-Diamond syndrome is an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, haematological dysfunction and skeletal abnormalities. It is characterised by bone marrow failure and leukemia predisposition. Members of this family play a role in RNA metabolism [, ]. In yeast Sdo1 is involved in the biogenesis of the 60S ribosomal subunit and translational activation of ribosomes. Together with the EF-2-like GTPase RIA1 (EfI1), it triggers the GTP-dependent release of TIF6 from 60S pre-ribosomes in the cytoplasm, thereby activating ribosomes for translation competence by allowing 80S ribosome assembly and facilitating TIF6 recycling to the nucleus, where it is required for 60S rRNA processing and nuclear export. This data links defective late 60S subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition []. A number of uncharacterised hydrophilic proteins of about 30 kDa share regions of similarity. These include, Mouse protein 22A3. Saccharomyces cerevisiae chromosome XII hypothetical protein YLR022c. Caenorhabditis elegans hypothetical protein W06E11.4. Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ0592. ; GO: 0042254 ribosome biogenesis; PDB: 2KDO_A 2L9N_A 2WBM_B 1P9Q_C 1T95_A.
Probab=34.41 E-value=41 Score=22.79 Aligned_cols=39 Identities=21% Similarity=0.325 Sum_probs=26.6
Q ss_pred cccccccccchhhhhccCCccccccCchhHHHHHHHHHH
Q 034732 29 KAGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYL 67 (85)
Q Consensus 29 ragLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYL 67 (85)
+.+..+|+++|++.|++-.++-....++---.-.++.-|
T Consensus 18 ~T~rP~p~~~IE~Am~e~~~~v~p~ksak~QalevIk~L 56 (125)
T PF09377_consen 18 RTNRPYPPTRIEKAMKEAHFSVDPNKSAKQQALEVIKKL 56 (125)
T ss_dssp TTTBTT-HHHHHHHHHHTTS-SSTTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHhCCcccCCCCCHHHHHHHHHHHH
Confidence 568889999999999998888666666655554454444
No 37
>PF11208 DUF2992: Protein of unknown function (DUF2992); InterPro: IPR016787 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=28.05 E-value=27 Score=24.41 Aligned_cols=44 Identities=23% Similarity=0.155 Sum_probs=35.2
Q ss_pred cccccchhhhhccCCccccccCchhHHHHHHHHHHHHHHHHHhh
Q 034732 33 QFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYLAAEVVLLVL 76 (85)
Q Consensus 33 qFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYLtaeILELAg 76 (85)
+|+||-+++.-...-...||.=++-.--.=|++||.....+|-.
T Consensus 8 ~FWvGv~E~~~~~~~~v~rv~FG~EP~d~Ei~~fi~~~~~~L~f 51 (132)
T PF11208_consen 8 PFWVGVFERHEDGKYKVARVTFGAEPKDPEIYEFILKHWYKLRF 51 (132)
T ss_pred CcEEEEEEEEECCEEEEEEEeeCCCCCcHHHHHHHHHHHHHhcC
Confidence 79999999986554444899888888888899999888877643
No 38
>PF06541 DUF1113: Protein of unknown function (DUF1113); InterPro: IPR010540 This family consists of several bacterial proteins of unknown function.
Probab=27.59 E-value=61 Score=22.60 Aligned_cols=21 Identities=19% Similarity=0.268 Sum_probs=16.4
Q ss_pred hHHHHHHHHHHHHHHHHHhhH
Q 034732 57 PVYLAAVLEYLAAEVVLLVLF 77 (85)
Q Consensus 57 ~VYLaAVLEYLtaeILELAgn 77 (85)
...++.++||++..++|..-+
T Consensus 65 ~~i~~t~lEyi~g~~le~~~~ 85 (157)
T PF06541_consen 65 GMILITALEYITGWILEKLFG 85 (157)
T ss_pred HHHHHHHHHHHHHHHHHHHHC
Confidence 345677899999999997643
No 39
>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=26.55 E-value=1e+02 Score=19.04 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=25.5
Q ss_pred cccCchhHHHHHHHHHHHHHHHHHhhHhhhc
Q 034732 51 RVGTGAPVYLAAVLEYLAAEVVLLVLFYAAC 81 (85)
Q Consensus 51 Rv~a~a~VYLaAVLEYLtaeILELAgn~A~~ 81 (85)
-++..+.-.||--+||-..||++-|.+..+-
T Consensus 20 ~l~de~a~~La~dveyrlreiiq~a~kfm~h 50 (66)
T PF02969_consen 20 NLSDEAAKALAEDVEYRLREIIQEALKFMRH 50 (66)
T ss_dssp -B-HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677888999999999999999999877653
No 40
>PF10093 DUF2331: Uncharacterized protein conserved in bacteria (DUF2331); InterPro: IPR016633 This entry describes a conserved hypothetical protein that typically is encoded next to the gene efp for translation elongation factor P. The function is unknown.
Probab=24.81 E-value=31 Score=28.09 Aligned_cols=14 Identities=71% Similarity=1.028 Sum_probs=11.6
Q ss_pred hHHHHHH-----------HHHHHHH
Q 034732 57 PVYLAAV-----------LEYLAAE 70 (85)
Q Consensus 57 ~VYLaAV-----------LEYLtae 70 (85)
+.|++++ ||||++|
T Consensus 90 ~~y~~~ma~~~~~p~WiNLEYLSAE 114 (374)
T PF10093_consen 90 ESYLAAMAARRPPPLWINLEYLSAE 114 (374)
T ss_pred HHHHHHHhccCCCCeEEEccccCHh
Confidence 4688887 9999988
No 41
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=24.18 E-value=41 Score=17.56 Aligned_cols=36 Identities=28% Similarity=0.354 Sum_probs=21.6
Q ss_pred ccccccchhhhhccCCcc-ccccCchhHHHHHHHHHH
Q 034732 32 LQFPVGRIGRYLKKGRYS-QRVGTGAPVYLAAVLEYL 67 (85)
Q Consensus 32 LqFpV~rv~r~Lr~~~~~-~Rv~a~a~VYLaAVLEYL 67 (85)
|.++.+.|.+++++|... .+++...-+--..+.+|+
T Consensus 11 lgis~~ti~~~~~~g~i~~~~~g~~~~~~~~~l~~~~ 47 (49)
T TIGR01764 11 LGVSKDTVYRLIHEGELPAYRVGRHYRIPREDVDEYL 47 (49)
T ss_pred HCCCHHHHHHHHHcCCCCeEEeCCeEEEeHHHHHHHH
Confidence 456777888888888765 455543333344444444
No 42
>PF11850 DUF3370: Protein of unknown function (DUF3370); InterPro: IPR021801 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 452 to 532 amino acids in length.
Probab=23.51 E-value=45 Score=27.94 Aligned_cols=38 Identities=26% Similarity=0.413 Sum_probs=29.7
Q ss_pred ccccccccchhhhhccCCccccccCchhHHHHHHHHHH
Q 034732 30 AGLQFPVGRIGRYLKKGRYSQRVGTGAPVYLAAVLEYL 67 (85)
Q Consensus 30 agLqFpV~rv~r~Lr~~~~~~Rv~a~a~VYLaAVLEYL 67 (85)
-.|.+||.-+...|--+..--|+.++.+||+|.+--|=
T Consensus 180 ~nlpIPv~gl~p~lNGRstllRl~S~Gpvy~AslA~~a 217 (441)
T PF11850_consen 180 LNLPIPVRGLDPPLNGRSTLLRLRSSGPVYMASLAMYA 217 (441)
T ss_pred EeccccCCCCCCCCCcceeEEEEecCCcchHHHHHhhh
Confidence 35678888888777555666899999999999876554
No 43
>PF11486 DUF3212: Protein of unknown function (DUF3212); InterPro: IPR021579 Members in this family of proteins are annotated as YfmB however currently no function for this protein is known. ; PDB: 2EUC_B.
Probab=23.45 E-value=63 Score=22.63 Aligned_cols=32 Identities=22% Similarity=0.431 Sum_probs=22.9
Q ss_pred cccccCchhHHHHHHHHHHHHHHHHHhhHhhh
Q 034732 49 SQRVGTGAPVYLAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 49 ~~Rv~a~a~VYLaAVLEYLtaeILELAgn~A~ 80 (85)
+.-+-..-+-||+|++-|++++.++-+-..|+
T Consensus 66 a~~ie~~LSsyl~al~p~it~dm~~~S~~na~ 97 (120)
T PF11486_consen 66 AVEIENKLSSYLTALLPFITADMLKVSKFNAN 97 (120)
T ss_dssp SSHHHHHHHHHHHHHGGG--HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566789999999999999998765554
No 44
>COG1694 MazG Predicted pyrophosphatase [General function prediction only]
Probab=22.86 E-value=1e+02 Score=19.63 Aligned_cols=21 Identities=19% Similarity=0.104 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHhhHhhh
Q 034732 60 LAAVLEYLAAEVVLLVLFYAA 80 (85)
Q Consensus 60 LaAVLEYLtaeILELAgn~A~ 80 (85)
+.+.+-||+.|+.|+|--..+
T Consensus 28 ~~~~~~~l~eE~gEv~eai~~ 48 (102)
T COG1694 28 PESLLLYLVEEAGEVAEAIRK 48 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 567788999999999854433
No 45
>KOG1585 consensus Protein required for fusion of vesicles in vesicular transport, gamma-SNAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.89 E-value=74 Score=25.48 Aligned_cols=40 Identities=25% Similarity=0.265 Sum_probs=31.8
Q ss_pred hhccCCccccccCchhH---HHHHHHHHHHHHHHHHhhHhhhc
Q 034732 42 YLKKGRYSQRVGTGAPV---YLAAVLEYLAAEVVLLVLFYAAC 81 (85)
Q Consensus 42 ~Lr~~~~~~Rv~a~a~V---YLaAVLEYLtaeILELAgn~A~~ 81 (85)
+||+++....+.++..+ |+++||=||..+=+.+|-..-++
T Consensus 173 ~lKe~~~~~~~~~y~~~~k~~va~ilv~L~~~Dyv~aekc~r~ 215 (308)
T KOG1585|consen 173 FLKEGVAADKCDAYNSQCKAYVAAILVYLYAHDYVQAEKCYRD 215 (308)
T ss_pred HHHhhhHHHHHhhcccHHHHHHHHHHHHhhHHHHHHHHHHhcc
Confidence 56888888888888888 99999999998777766554443
Done!