GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PHD - PHD-finger
Pfam: PF00628 (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: CL0390
Length: 51
Sequences: 4875
Seq/Len: 95.59
HH_delta: -0.023 (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
19_S44_Y1.406933.026
45_C48_C1.268642.728
16_Q23_W1.238072.662
13_D26_Q1.229362.644
24_Y29_V1.224982.634
14_M23_W0.910951.959
29_V46_P0.849011.826
16_Q21_N0.840881.808
20_C25_H0.781881.681
17_C20_C0.704741.516
24_Y43_W0.66631.433
4_V24_Y0.580481.248
29_V43_W0.567241.220
10_D27_E0.523141.125
7_Q11_D0.508211.093
22_R47_N0.506351.089
6_G22_R0.505071.086
5_C20_C0.489151.052
13_D27_E0.485491.044
25_H28_C0.479411.031
17_C25_H0.455120.979
15_I18_D0.420910.905
18_D21_N0.415510.894
9_D19_S0.398370.857
8_S13_D0.396210.852
12_G27_E0.392210.843
30_G34_K0.391530.842
31_P43_W0.384370.827
5_C25_H0.37760.812
46_P49_R0.369720.795
16_Q22_R0.364350.784
14_M18_D0.359190.772
9_D40_S0.357550.769
10_D13_D0.356320.766
29_V33_E0.348080.749
5_C17_C0.34020.732
44_Y49_R0.337570.726
8_S14_M0.337220.725
25_H45_C0.335350.721
6_G14_M0.333620.717
28_C48_C0.331460.713
18_D42_D0.330570.711
27_E47_N0.327330.704
8_S12_G0.317950.684
34_K47_N0.310060.667
34_K37_E0.309480.666
4_V7_Q0.304030.654
34_K49_R0.300270.646
15_I23_W0.29720.639
26_Q38_I0.295550.636
26_Q33_E0.293940.632
41_G49_R0.292580.629
37_E40_S0.290320.624
28_C45_C0.287610.618
37_E42_D0.286890.617
44_Y47_N0.277180.596
38_I41_G0.273060.587
4_V10_D0.271870.585
26_Q44_Y0.265490.571
32_P39_P0.261770.563
15_I26_Q0.260440.560
14_M26_Q0.257420.554
20_C45_C0.257410.554
26_Q31_P0.253270.545
12_G16_Q0.250690.539
26_Q29_V0.249920.537
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
2k16A0.960898.4-0.023
3kv5D0.960898.4-0.019
3kv4A0.960898.4-0.015
2e6rA0.960898.40.002
3askA0.960898.40.003
2lv9A0.921698.30.019
3u5nA0.90298.30.019
3o36A0.90298.30.033
2ri7A0.960898.30.033
1f62A0.960898.30.033

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