GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fn3-like - Fibronectin type III-like domain
Pfam: PF14310 (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. )
Length: 71
Sequences: 3159
Seq/Len: 44.49
HH_delta: -0.09 (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
1_E69_D1.398742.884
10_P64_T1.224412.524
23_G39_F1.183952.441
50_D57_V1.153022.377
42_P45_D1.121542.312
5_L39_F1.087972.243
8_S64_T1.087682.243
49_W56_W1.081692.230
2_V26_R1.069162.204
19_K66_S1.023452.110
7_V22_V0.989252.040
30_A33_E0.979532.020
8_S66_S0.918361.893
16_R20_Q0.874821.804
9_D63_Y0.86851.791
16_R48_Y0.837641.727
27_V37_V0.805011.660
47_A58_I0.77261.593
29_L35_K0.770711.589
47_A56_W0.73991.525
29_L33_E0.710271.464
49_W54_G0.69221.427
27_V35_K0.671281.384
7_V65_L0.613941.266
12_S16_R0.609641.257
13_S59_E0.595011.227
48_Y59_E0.564891.165
5_L67_V0.562821.160
44_E47_A0.537691.109
17_P20_Q0.532651.098
23_G45_D0.510661.053
9_D61_G0.496381.023
59_E63_Y0.492781.016
22_V45_D0.491091.013
22_V41_L0.478640.987
41_L46_L0.465270.959
10_P62_T0.461010.950
13_S48_Y0.459520.947
51_E54_G0.452770.934
8_S19_K0.452620.933
12_S59_E0.4430.913
25_E37_V0.440010.907
7_V46_L0.435350.898
14_V48_Y0.413030.852
68_G71_S0.403940.833
16_R59_E0.390090.804
9_D12_S0.389360.803
25_E35_K0.387740.799
28_S31_P0.385270.794
50_D55_K0.383520.791
29_L37_V0.381940.787
4_Q68_G0.381180.786
6_Y71_S0.363680.750
46_L58_I0.362440.747
41_L45_D0.360420.743
52_D62_T0.359290.741
46_L65_L0.355230.732
5_L22_V0.35370.729
4_Q70_S0.348840.719
43_P47_A0.346060.713
28_S35_K0.342670.707
9_D59_E0.341080.703
9_D48_Y0.33610.693
5_L65_L0.3310.682
49_W71_S0.31750.655
9_D20_Q0.315060.650
18_V66_S0.310750.641
9_D13_S0.303120.625
6_Y68_G0.299870.618
10_P61_G0.299030.617
18_V71_S0.298460.615
5_L41_L0.298220.615
41_L65_L0.294990.608
14_V51_E0.293410.605
14_V59_E0.290060.598
3_V25_E0.287470.593
42_P58_I0.286620.591
19_K71_S0.286270.590
4_Q71_S0.285650.589
20_Q48_Y0.285340.588
66_S71_S0.281360.580
40_T43_P0.280490.578
25_E28_S0.279090.575
4_Q21_L0.275890.569
11_Q62_T0.274310.566
1_E70_S0.271620.560
36_T62_T0.271040.559
29_L34_S0.270710.558
11_Q15_Q0.267150.551
11_Q14_V0.26710.551
5_L23_G0.258490.533
2_V6_Y0.257720.531
31_P34_S0.25580.527
7_V63_Y0.247590.510
48_Y63_Y0.244170.503
3_V69_D0.240630.496
7_V41_L0.239270.493
35_K62_T0.238760.492
3_V27_V0.235630.486
3_V67_V0.229370.473
50_D54_G0.226910.468
23_G37_V0.225790.466
15_Q52_D0.221690.457
6_Y21_L0.220670.455
25_E38_S0.220190.454
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
3zyzA199.8-0.09
3u48A0.985999.8-0.08
4iibA0.971899.8-0.073
4i3gA199.8-0.071
3abzA199.8-0.062
2x41A0.971899.8-0.06
3kmhA0.845158.30.819
2kllA0.591541.80.835
3iduA0.66226.80.851
2x3cA0.760622.80.855

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