GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HAMP - HAMP domain
Pfam: PF00672 (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: 70
Sequences: 33191
Seq/Len: 474.16
HH_delta: -0.043 (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
31_S56_Q2.784712.453
52_D55_G2.185711.925
16_A20_A2.184291.924
31_S35_Q2.177331.918
37_I65_A2.167191.909
51_P55_G2.146411.891
36_R44_T2.066291.820
31_S60_A2.000851.763
35_Q60_A1.956731.724
36_R41_D1.888521.664
34_M61_F1.747591.539
13_L17_W1.728371.523
62_N65_A1.716811.512
14_L18_L1.706491.503
34_M64_M1.651011.454
28_R31_S1.643351.448
20_A24_T1.598291.408
30_L58_A1.582341.394
38_A63_Q1.562121.376
65_A69_R1.541381.358
34_M60_A1.525071.343
33_A44_T1.477991.302
48_V59_R1.443131.271
45_R62_N1.433771.263
45_R65_A1.419661.251
41_D44_T1.410091.242
20_A23_I1.406831.239
62_N66_D1.37371.210
45_R69_R1.371821.208
35_Q56_Q1.344721.185
45_R66_D1.311621.155
50_G55_G1.310251.154
33_A46_I1.24841.100
17_W21_R1.21091.067
38_A67_R1.184711.044
29_R33_A1.181661.041
43_S69_R1.180211.040
38_A60_A1.162051.024
64_M68_L1.130970.996
63_Q67_R1.121130.988
21_R25_R1.105650.974
58_A62_N1.103450.972
22_R26_P1.096440.966
37_I64_M1.074520.947
48_V58_A1.050830.926
55_G59_R1.048180.923
56_Q59_R1.046680.922
27_L54_I1.039760.916
35_Q38_A1.014120.893
47_P62_N0.993990.876
27_L57_L0.982750.866
35_Q39_Q0.98050.864
6_L10_L0.979940.863
34_M57_L0.971870.856
60_A63_Q0.967380.852
33_A36_R0.962560.848
48_V55_G0.961470.847
30_L61_F0.956560.843
30_L57_L0.923030.813
28_R32_D0.914850.806
35_Q63_Q0.908920.801
26_P50_G0.891240.785
24_T28_R0.890960.785
3_V7_I0.888730.783
46_I58_A0.883290.778
46_I62_N0.861820.759
18_L22_R0.852690.751
14_L17_W0.850540.749
33_A65_A0.809710.713
34_M37_I0.806450.710
4_L8_I0.799750.705
42_L68_L0.78130.688
37_I61_F0.775570.683
18_L21_R0.774540.682
36_R39_Q0.769770.678
23_I26_P0.766160.675
44_T48_V0.766070.675
29_R32_D0.724270.638
32_D36_R0.722240.636
29_R47_P0.71740.632
30_L34_M0.715090.630
42_L65_A0.710690.626
48_V62_N0.710670.626
19_L23_I0.705310.621
32_D35_Q0.704720.621
21_R28_R0.703810.620
7_I11_L0.702580.619
25_R29_R0.680480.599
5_F8_I0.671370.591
44_T65_A0.666830.587
33_A47_P0.659890.581
26_P29_R0.657870.580
49_S55_G0.645260.568
59_R63_Q0.642360.566
24_T54_I0.639140.563
39_Q67_R0.628560.554
25_R28_R0.625740.551
37_I42_L0.625310.551
54_I58_A0.623580.549
33_A62_N0.621450.547
37_I40_G0.612470.540
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
4gycB198.3-0.043
2f95B198.2-0.022
4i5sA198.10.035
4i3mA0.842997.50.167
3zrxA0.771497.30.209
3zccA0.771497.30.219
2aswA0.742997.20.224
3lnrA0.842997.20.228
3zx6A0.728696.90.267
2f93B0.857193.60.436

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