GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAN_4 - PAN domain
Pfam: PF14295 (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: CL0168
Length: 51
Sequences: 650
Seq/Len: 12.75
HH_delta: 0.06 (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
7_D51_K0.402481.876
9_R28_D0.373351.741
18_P34_F0.372051.735
2_D7_D0.369121.721
8_L28_D0.364681.700
22_Q33_A0.332191.549
20_E24_A0.305631.425
23_A27_A0.286731.337
22_Q34_F0.284031.324
18_P22_Q0.280531.308
31_C48_C0.280431.307
26_A34_F0.261041.217
17_S20_E0.256831.197
25_C31_C0.246841.151
3_Y34_F0.245881.146
2_D51_K0.245341.144
3_Y8_L0.242751.132
9_R13_V0.242191.129
14_T47_R0.235161.096
37_N49_Y0.2321.082
21_C25_C0.228511.065
4_P7_D0.225571.052
14_T44_S0.225151.050
2_D5_G0.222321.036
15_A20_E0.219381.023
5_G21_C0.218761.020
25_C48_C0.21731.013
16_S19_E0.216131.008
38_P47_R0.210570.982
23_A29_P0.209890.979
21_C31_C0.209720.978
6_G15_A0.204820.955
21_C48_C0.20460.954
37_N45_S0.197860.922
3_Y22_Q0.197650.921
7_D10_S0.194760.908
10_S47_R0.193270.901
19_E26_A0.192890.899
19_E27_A0.189460.883
5_G51_K0.188870.881
37_N46_G0.188510.879
25_C51_K0.187420.874
38_P44_S0.18470.861
10_S50_L0.179520.837
36_F46_G0.176410.822
1_T38_P0.173230.808
13_V32_Q0.172560.804
48_C51_K0.172010.802
16_S46_G0.170850.797
22_Q26_A0.160680.749
7_D49_Y0.159980.746
1_T22_Q0.157990.737
9_R19_E0.154430.720
19_E23_A0.154250.719
33_A49_Y0.151310.705
45_S50_L0.149740.698
14_T23_A0.149320.696
20_E32_Q0.148220.691
44_S49_Y0.144950.676
37_N47_R0.144410.673
17_S33_A0.142660.665
4_P32_Q0.142560.665
9_R29_P0.142340.664
28_D46_G0.142150.663
14_T38_P0.140570.655
23_A30_G0.139250.649
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
2f83A0.960898.60.06
2f83A0.960898.60.062
4a5vA0.882498.40.149
4a5vA0.882498.30.157
2yilA0.862798.20.193
2yilA0.90298.10.229
2ll3A0.882497.60.322
1hkyA0.843193.50.549
4durA0.8627880.605
3hmsA0.843186.90.612

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