GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GRAM - GRAM domain
Pfam: PF02893 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0266
Length: 69
Sequences: 978
Seq/Len: 14.17
HH_delta: 0.606 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
3_F37_T0.484032.785
32_G43_F0.426182.452
18_E33_R0.417312.401
34_L41_L0.347121.997
13_E39_N0.316261.820
21_C34_L0.286031.646
59_L62_I0.268291.544
62_I67_K0.255041.468
41_L59_L0.248161.428
3_F16_I0.240571.384
22_A28_I0.221291.273
4_R9_L0.220921.271
10_P65_I0.219741.264
44_Y51_K0.211461.217
22_A29_P0.210761.213
21_C55_F0.21021.209
6_L44_Y0.209841.207
58_P61_D0.204431.176
44_Y48_F0.199841.150
31_Q47_K0.192561.108
13_E38_N0.192351.107
36_I59_L0.190211.094
25_K37_T0.189831.092
46_N49_G0.186821.075
42_C56_V0.185571.068
33_R46_N0.185091.065
21_C32_G0.184391.061
35_Y48_F0.180581.039
60_S64_S0.177331.020
61_D65_I0.176591.016
39_N60_S0.171510.987
10_P39_N0.171470.987
37_T42_C0.170550.981
4_R27_K0.168540.970
28_I54_K0.167150.962
44_Y54_K0.166970.961
11_E14_R0.166710.959
24_F29_P0.166070.956
31_Q34_L0.165440.952
40_Y66_E0.165220.951
55_F58_P0.164180.945
13_E37_T0.163670.942
5_K59_L0.16090.926
20_S33_R0.160170.922
60_S63_K0.158760.914
8_K56_V0.158190.910
59_L65_I0.15760.907
16_I27_K0.155570.895
22_A31_Q0.15220.876
15_L37_T0.151280.870
6_L9_L0.15090.868
15_L25_K0.149030.858
30_V52_T0.148390.854
12_E39_N0.148280.853
7_F42_C0.146010.840
4_R63_K0.144880.834
9_L12_E0.144320.830
11_E60_S0.14420.830
13_E40_Y0.144050.829
35_Y67_K0.142020.817
57_I62_I0.141640.815
56_V63_K0.14110.812
9_L43_F0.140790.810
5_K51_K0.140750.810
27_K66_E0.139750.804
5_K21_C0.137480.791
51_K66_E0.137060.789
19_Y35_Y0.136290.784
6_L19_Y0.135730.781
19_Y25_K0.135180.778
3_F15_L0.133220.767
5_K66_E0.132790.764
29_P38_N0.131060.754
24_F28_I0.130470.751
10_P38_N0.13040.750
8_K52_T0.130350.750
10_P60_S0.130330.750
57_I60_S0.129840.747
16_I59_L0.128520.740
9_L44_Y0.128170.737
4_R51_K0.127690.735
21_C27_K0.127060.731
27_K38_N0.126590.728
8_K12_E0.12640.727
12_E60_S0.126260.727
19_Y66_E0.125780.724
30_V51_K0.125470.722
18_E46_N0.12420.715
23_L42_C0.123610.711
10_P66_E0.121930.702
20_S66_E0.121480.699
45_S57_I0.120780.695
8_K60_S0.11980.689
12_E19_Y0.119760.689
3_F63_K0.119460.687
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
1lw3A0.985597.10.606
1zsqA0.956596.90.626
2hthB0.97195.70.672
2cayA0.956595.60.674
1w7pD0.956595.20.684
2yf0A0.869693.30.712
1t77A0.826191.30.729
1pfjA0.826171.70.785
1zyiA0.927559.80.8
3hsaA0.855143.30.818
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0313 seconds.