GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Response_reg - Response regulator receiver domain
Pfam: PF00072 (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: CL0304
Length: 112
Sequences: 80522
Seq/Len: 718.95
HH_delta: -0.284 (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
11_R28_T4.500343.052
11_R30_S3.909522.652
15_E28_T3.830252.598
27_T44_P3.472472.355
4_V35_A3.346492.270
33_E55_D3.166232.148
52_E80_E2.930551.988
36_L64_Q2.861361.941
56_G64_Q2.849391.933
40_K68_I2.766651.877
31_S55_D2.735461.855
32_G56_G2.728341.851
49_I61_L2.668831.810
29_A38_L2.636431.788
30_S34_E2.629641.784
27_T38_L2.601021.764
76_V94_A2.548181.728
96_D110_A2.525721.713
17_L104_P2.506891.700
21_A108_R2.428951.647
27_T42_H2.409791.634
2_L29_A2.392161.623
62_L74_I2.309151.566
66_R95_D2.283261.549
15_E19_E2.210161.499
31_S34_E2.100971.425
64_Q68_I2.009791.363
56_G60_E2.0071.361
57_D60_E1.983251.345
38_L42_H1.96891.335
80_E85_E1.871581.269
64_Q67_Q1.851831.256
63_E92_A1.847511.253
38_L41_K1.8441.251
47_I72_I1.83081.242
32_G61_L1.807141.226
51_L59_L1.784291.210
33_E56_G1.762481.195
36_L61_L1.750721.187
38_L44_P1.742791.182
83_S87_Q1.722191.168
39_L65_I1.712841.162
106_E110_A1.709311.159
87_Q91_R1.669911.133
82_D85_E1.575481.069
59_L88_E1.568411.064
33_E37_E1.55431.054
77_V102_F1.544221.047
76_V89_A1.538711.044
62_L76_V1.529811.038
8_P30_S1.507951.023
12_E15_E1.50651.022
1_I23_Y1.495241.014
60_E63_E1.491651.012
2_L35_A1.484081.007
49_I74_I1.482631.006
6_D50_D1.482471.006
29_A35_A1.462620.992
5_D11_R1.461750.991
18_L111_I1.461420.991
2_L44_P1.460660.991
46_L111_I1.447920.982
88_E92_A1.447510.982
59_L89_A1.445140.980
5_D100_K1.428770.969
4_V53_L1.425390.967
34_E38_L1.420960.964
37_E41_K1.3930.945
36_L56_G1.390680.943
49_I62_L1.381570.937
35_A61_L1.365380.926
51_L76_V1.364290.925
108_R112_N1.352230.917
9_E13_L1.345980.913
75_I110_A1.344160.912
106_E109_A1.342140.910
8_P12_E1.335140.906
3_I14_L1.320050.895
14_L77_V1.312070.890
7_D10_I1.306420.886
51_L57_D1.28860.874
10_I13_L1.277430.866
103_S106_E1.270490.862
34_E37_E1.269920.861
83_S103_S1.266450.859
12_E16_K1.263710.857
62_L92_A1.256270.852
29_A34_E1.252050.849
47_I74_I1.243960.844
84_D88_E1.243330.843
86_V106_E1.236770.839
88_E91_R1.231810.836
62_L94_A1.231590.835
60_E64_Q1.224520.831
39_L69_N1.203980.817
47_I65_I1.198390.813
23_Y112_N1.189190.807
85_E88_E1.182490.802
8_P11_R1.173860.796
12_E28_T1.16770.792
2_L38_L1.165250.790
48_I77_V1.161510.788
35_A39_L1.153140.782
104_P108_R1.148540.779
4_V47_I1.146680.778
10_I102_F1.126640.764
36_L40_K1.12450.763
39_L72_I1.110410.753
37_E40_K1.109870.753
83_S86_V1.09910.745
32_G36_L1.088140.738
15_E26_V1.08740.738
63_E88_E1.084710.736
13_L17_L1.084650.736
89_A93_G1.083160.735
69_N72_I1.064510.722
1_I46_L1.054850.715
86_V99_S1.046380.710
81_D99_S1.035570.702
89_A97_Y1.034160.701
13_L16_K1.017450.690
16_K20_R1.015920.689
4_V61_L1.014760.688
73_P95_D1.009210.685
61_L65_I0.976370.662
105_E109_A0.973650.660
48_I107_L0.973210.660
86_V90_L0.961970.652
1_I18_L0.956480.649
4_V29_A0.951620.645
63_E67_Q0.950520.645
50_D100_K0.945910.642
89_A94_A0.92840.630
52_E79_D0.926960.629
14_L102_F0.921250.625
9_E12_E0.920120.624
49_I76_V0.909820.617
23_Y108_R0.909770.617
51_L85_E0.894790.607
48_I75_I0.893980.606
2_L39_L0.890270.604
5_D53_L0.881140.598
7_D79_D0.862760.585
9_E16_K0.860950.584
49_I65_I0.853950.579
75_I96_D0.850250.577
32_G53_L0.848960.576
3_I11_R0.84220.571
66_R72_I0.84090.570
40_K64_Q0.838710.569
51_L94_A0.838240.569
56_G61_L0.836360.567
17_L21_A0.832110.564
16_K19_E0.828680.562
6_D53_L0.825820.560
2_L27_T0.825760.560
90_L96_D0.825330.560
59_L92_A0.820510.557
51_L89_A0.819530.556
87_Q90_L0.817480.554
21_A112_N0.815190.553
59_L63_E0.81110.550
53_L58_G0.804830.546
36_L39_L0.804760.546
18_L23_Y0.803350.545
84_D87_Q0.802230.544
59_L85_E0.797920.541
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
3to5A199.5-0.284
3dzdA0.991199.5-0.262
4eukA0.991199.4-0.248
3rqiA0.991199.4-0.237
3eq2A0.991199.4-0.234
1ny5A0.991199.4-0.233
3n0rA0.964399.4-0.233
3r0jA0.991199.4-0.229
1w25A0.991199.4-0.217
2ayxA0.991199.4-0.21

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