GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CARDB - CARDB
Pfam: PF07705 (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: CL0159
Length: 101
Sequences: 1936
Seq/Len: 19.17
HH_delta: 0.072 (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
34_D59_P0.644533.013
58_A61_E0.614382.872
28_K62_S0.573762.682
26_T62_S0.521612.439
25_V65_V0.45282.117
43_Y82_V0.43392.029
41_R82_V0.422211.974
42_L79_I0.405881.898
45_D77_Y0.392811.836
38_V83_I0.385981.805
15_V21_V0.369291.727
34_D58_A0.361731.691
22_T66_T0.353761.654
24_T66_T0.328391.535
26_T64_T0.324231.516
21_V71_P0.292831.369
25_V42_L0.289271.352
57_L63_E0.274971.286
27_V81_V0.2671.248
24_T64_T0.260861.220
45_D78_T0.253031.183
25_V40_V0.246061.150
52_V65_V0.243051.136
42_L67_F0.239911.122
22_T68_T0.23981.121
41_R51_T0.237321.110
38_V84_D0.235381.100
57_L62_S0.233731.093
43_Y80_R0.233721.093
39_T51_T0.229751.074
45_D80_R0.228191.067
20_P68_T0.226261.058
45_D48_S0.222181.039
73_S77_Y0.220311.030
42_L81_V0.218321.021
44_L79_I0.218141.020
20_P70_T0.214531.003
23_I69_W0.208930.977
43_Y48_S0.206150.964
36_E56_S0.204860.958
74_P77_Y0.200470.937
57_L61_E0.198590.928
31_G35_A0.198590.928
22_T86_D0.195440.914
34_D56_S0.19390.907
44_L47_N0.193050.903
29_N59_P0.192770.901
26_T69_W0.191820.897
67_F81_V0.189490.886
71_P83_I0.189050.884
77_Y80_R0.18710.875
23_I79_I0.186670.873
38_V56_S0.18650.872
37_N56_S0.185230.866
16_V19_E0.179630.840
21_V69_W0.17910.837
30_N60_G0.178130.833
35_A85_P0.177260.829
24_T68_T0.175220.819
10_V15_V0.175020.818
67_F71_P0.174450.816
37_N46_G0.174310.815
43_Y84_D0.174180.814
40_V67_F0.174060.814
44_L86_D0.174010.814
18_G72_P0.172890.808
25_V64_T0.171440.802
46_G72_P0.171170.800
32_T72_P0.169480.792
11_S15_V0.168620.788
40_V83_I0.168380.787
40_V63_E0.168090.786
27_V57_L0.167450.783
10_V22_T0.166990.781
17_P72_P0.166740.780
40_V52_V0.16630.777
41_R73_S0.165960.776
18_G21_V0.163070.762
47_N78_T0.162520.760
9_T15_V0.16220.758
41_R48_S0.161510.755
52_V63_E0.160740.751
41_R61_E0.159260.745
17_P74_P0.158660.742
48_S51_T0.158010.739
37_N53_T0.157630.737
39_T86_D0.156630.732
38_V54_I0.15660.732
9_T19_E0.156480.732
84_D87_N0.155830.729
12_P21_V0.15530.726
28_K60_G0.155030.725
20_P48_S0.153220.716
13_S21_V0.152550.713
63_E66_T0.152390.712
53_T56_S0.15110.706
52_V55_P0.149730.700
68_T71_P0.149360.698
14_N49_V0.149270.698
39_T67_F0.148740.695
54_I65_V0.146080.683
42_L51_T0.146040.683
80_R86_D0.145160.679
36_E84_D0.145110.678
25_V67_F0.144350.675
35_A38_V0.14320.669
19_E75_G0.142710.667
42_L50_S0.142220.665
14_N78_T0.141550.662
9_T12_P0.140960.659
48_S68_T0.140620.657
16_V58_A0.140480.657
15_V22_T0.140160.655
27_V40_V0.139970.654
13_S24_T0.139150.651
17_P71_P0.138520.648
15_V23_I0.138330.647
42_L85_P0.138110.646
41_R84_D0.137510.643
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
3iduA0.980299.50.072
2l0dA0.990199.40.114
2kutA0.970399.20.22
1vjjA0.960496.70.633
2q3zA0.960496.60.641
1ex0A0.960496.50.643
2hr0B0.970396.40.65
1g0dA0.960496.40.65
3prxB0.910996.20.655
3cu7A0.960496.20.656

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