GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ig - Immunoglobulin domain
Pfam: PF00047 (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: CL0011
Length: 64
Sequences: 24700
Seq/Len: 385.94
HH_delta: -0.157 (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
22_S63_V2.089273.203
3_S48_T1.629142.498
5_T48_T1.591892.441
3_S50_S1.560332.392
22_S61_T1.478462.267
23_K58_G1.442122.211
24_N28_L1.394992.139
8_C62_C1.368212.098
13_G17_T1.326992.035
24_N61_T1.241911.904
10_V19_V1.228431.883
20_T63_V1.148711.761
21_W47_L0.953291.462
54_P57_S0.935211.434
26_Q29_P0.905851.389
4_V49_I0.790361.212
25_G28_L0.768641.179
49_I52_V0.751961.153
3_S51_N0.725771.113
33_T36_R0.716711.099
52_V57_S0.708431.086
32_S35_N0.701861.076
53_T56_D0.695851.067
14_P17_T0.680781.044
49_I56_D0.652271.000
22_S27_S0.651710.999
39_N42_S0.645070.989
24_N27_S0.635030.974
38_T41_V0.624930.958
4_V52_V0.621140.952
32_S36_R0.617470.947
20_T27_S0.598210.917
38_T42_S0.595260.913
36_R39_N0.593850.911
34_T38_T0.592660.909
36_R40_S0.59120.906
12_S17_T0.581920.892
31_G35_N0.556270.853
34_T37_S0.554420.850
23_K60_Y0.549570.843
49_I60_Y0.542530.832
30_E33_T0.532750.817
15_P18_T0.524050.803
36_R41_V0.517780.794
31_G34_T0.506310.776
30_E34_T0.501570.769
35_N38_T0.499430.766
29_P32_S0.49920.765
28_L31_G0.498020.764
24_N59_T0.493440.757
29_P33_T0.490160.752
37_S40_S0.489840.751
52_V62_C0.488780.749
3_S49_I0.474920.728
37_S41_V0.463940.711
31_G36_R0.462030.708
13_G16_P0.449750.690
49_I53_T0.447620.686
17_T20_T0.439810.674
35_N39_N0.436010.669
23_K26_Q0.434550.666
24_N29_P0.428210.657
12_S41_V0.427680.656
33_T38_T0.424210.650
52_V58_G0.42260.648
52_V56_D0.417350.640
19_V47_L0.416450.639
10_V15_P0.412360.632
6_L19_V0.4060.622
23_K28_L0.403380.618
10_V17_T0.399790.613
1_G53_T0.392780.602
57_S60_Y0.389090.597
35_N41_V0.38740.594
35_N40_S0.381960.586
12_S16_P0.381390.585
13_G19_V0.381070.584
19_V57_S0.375350.576
6_L60_Y0.366240.562
30_E36_R0.36310.557
1_G51_N0.362460.556
25_G59_T0.35680.547
9_S13_G0.35410.543
29_P34_T0.35380.542
33_T37_S0.351730.539
1_G52_V0.35060.538
23_K29_P0.34820.534
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
3knbA0.984497.9-0.157
2lqrA0.984497.8-0.137
3knbB0.953197.8-0.133
3b43A0.953197.7-0.128
3v2aR0.921997.7-0.118
2lvcA0.937597.7-0.113
2lu7A0.937597.6-0.109
3rbsA197.6-0.107
3rbsA0.921997.6-0.102
2id5A0.953197.6-0.101

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