GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ParA - ParAMinD ATPase like
Pfam: PF10609 (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: CL0023
Length: 81
Sequences: 9561
Seq/Len: 118.04
HH_delta: 0.177 (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
33_T63_M2.807245.822
27_G57_L1.372672.847
34_P61_E1.173112.433
27_G58_G1.083432.247
1_L4_L0.956471.984
35_Q38_A0.954831.980
30_V45_A0.924781.918
29_I60_V0.877451.820
46_I50_R0.875771.816
33_T38_A0.84851.760
27_G55_P0.823691.708
31_V62_N0.77871.615
32_T59_V0.711511.476
28_A49_F0.69261.436
34_P64_S0.626731.300
36_E40_A0.623921.294
14_D17_L0.591741.227
43_R46_I0.560831.163
47_D51_K0.544181.129
39_L43_R0.53361.107
29_I58_G0.524771.088
61_E64_S0.521041.081
14_D18_T0.513131.064
39_L42_V0.502641.042
13_G16_H0.493211.023
38_A41_D0.485031.006
47_D50_R0.482391.000
17_L48_M0.482291.000
28_A54_V0.472350.980
15_E19_L0.465360.965
37_L40_A0.456010.946
14_D21_Q0.44960.932
8_L19_L0.446220.925
18_T22_Y0.443110.919
32_T42_V0.432240.896
21_Q52_L0.431710.895
7_D10_P0.430490.893
28_A31_V0.428960.890
44_R47_D0.419250.869
45_A49_F0.410120.851
31_V41_D0.405490.841
20_M49_F0.397460.824
30_V46_I0.391490.812
43_R47_D0.38890.806
36_E44_R0.383110.794
16_H20_M0.379780.788
8_L18_T0.379450.787
15_E18_T0.378790.786
10_P41_D0.376630.781
26_D53_N0.376390.781
27_G56_I0.376240.780
49_F54_V0.375370.778
28_A56_I0.373890.775
42_V46_I0.369330.766
3_Y6_I0.366210.759
6_I19_L0.362690.752
47_D57_L0.362440.752
20_M28_A0.354310.735
19_L22_Y0.35250.731
28_A41_D0.351270.728
44_R61_E0.347150.720
31_V37_L0.345690.717
48_M52_L0.338280.702
31_V60_V0.335840.696
37_L41_D0.331840.688
34_P62_N0.331650.688
11_G63_M0.324750.673
32_T61_E0.323550.671
13_G18_T0.319440.662
18_T21_Q0.317350.658
34_P41_D0.316720.657
44_R48_M0.316620.657
22_Y47_D0.315280.654
8_L16_H0.314590.652
36_E39_L0.314130.651
8_L28_A0.313570.650
40_A43_R0.307690.638
41_D49_F0.306530.636
11_G44_R0.305030.633
34_P37_L0.304320.631
9_P13_G0.302470.627
17_L21_Q0.301710.626
38_A63_M0.301560.625
10_P13_G0.30150.625
40_A47_D0.301430.625
9_P37_L0.301060.624
42_V45_A0.299320.621
32_T37_L0.299080.620
40_A44_R0.297290.617
30_V42_V0.289440.600
20_M52_L0.288810.599
16_H21_Q0.286920.595
18_T54_V0.285510.592
6_I16_H0.285330.592
12_T17_L0.284580.590
16_H45_A0.28260.586
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
3pg5A0.9753990.177
2ozeA0.975398.90.208
1wcv10.975398.90.218
3k9gA0.96398.80.231
3kjhA0.96398.80.242
3cwqA0.96398.80.25
3ea0A0.975398.80.25
3q9lA0.975398.80.256
4dzzA0.950698.70.258
1hyqA0.975398.70.265

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