GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RimM - RimM N-terminal domain
Pfam: PF01782 (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: 84
Sequences: 1718
Seq/Len: 20.45
HH_delta: -0.007 (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
66_D69_A0.915252.902
46_K62_E0.875542.776
48_E60_K0.860052.727
46_K63_G0.799252.534
8_P67_R0.783482.484
64_I70_A0.70612.239
68_E71_E0.65162.066
8_P71_E0.633192.008
60_K65_D0.586681.860
67_R71_E0.576571.828
1_V79_Y0.559421.774
9_H58_I0.526551.669
32_Q44_P0.510251.618
5_I15_V0.505611.603
48_E62_E0.498831.582
23_F26_R0.497751.578
30_L33_V0.492831.563
1_V77_E0.466731.480
14_E60_K0.463761.470
14_E51_R0.46291.468
7_K74_R0.459191.456
71_E74_R0.449451.425
15_V61_F0.44381.407
65_D69_A0.442181.402
15_V59_V0.439151.392
4_R18_R0.427231.355
81_P84_D0.421771.337
4_R77_E0.417961.325
36_E77_E0.383111.215
15_V70_A0.382451.213
69_A72_A0.376481.194
36_E79_Y0.372651.182
45_L61_F0.36611.161
6_G74_R0.352121.116
9_H14_E0.350921.113
21_T27_L0.333331.057
8_P74_R0.329931.046
11_L67_R0.329391.044
3_G17_V0.328061.040
9_H51_R0.324961.030
52_P57_L0.318631.010
7_K16_K0.317331.006
6_G75_G0.312790.992
53_H58_I0.310720.985
9_H16_K0.309770.982
14_E49_S0.300890.954
17_V59_V0.300480.953
33_V78_L0.299080.948
27_L30_L0.293890.932
19_P27_L0.291590.925
2_V27_L0.290940.922
49_S60_K0.289850.919
70_A73_L0.287180.911
5_I61_F0.277330.879
11_L66_D0.277260.879
11_L68_E0.264870.840
34_Y44_P0.264150.838
47_V50_V0.259460.823
36_E76_C0.259270.822
20_F77_E0.255990.812
3_G27_L0.254890.808
5_I35_L0.249340.791
34_Y47_V0.247910.786
18_R56_S0.24580.779
65_D68_E0.243920.773
15_V73_L0.243410.772
6_G18_R0.242780.770
47_V61_F0.240770.763
4_R20_F0.239990.761
32_Q46_K0.237820.754
64_I67_R0.234950.745
6_G16_K0.234290.743
35_L78_L0.232920.738
57_L82_R0.231120.733
16_K56_S0.226980.720
3_G20_F0.226740.719
6_G56_S0.225010.713
64_I73_L0.222810.706
21_T26_R0.222490.705
22_D26_R0.221070.701
35_L76_C0.217660.690
11_L14_E0.216730.687
5_I76_C0.216050.685
32_Q84_D0.214470.680
1_V4_R0.214310.679
36_E39_N0.213050.675
45_L64_I0.212720.674
3_G16_K0.212420.673
2_V26_R0.208160.660
34_Y84_D0.20450.648
19_P57_L0.204140.647
30_L59_V0.203880.646
2_V21_T0.201410.639
50_V57_L0.200550.636
33_V45_L0.195940.621
33_V59_V0.195730.621
28_F52_P0.193960.615
5_I17_V0.190460.604
28_F33_V0.190280.603
45_L78_L0.188130.596
3_G6_G0.179930.570
35_L45_L0.179350.569
3_G53_H0.178590.566
39_N75_G0.177670.563
43_R69_A0.177270.562
12_K58_I0.176660.560
26_R29_N0.175890.558
32_Q49_S0.173970.552
3_G10_G0.173390.550
24_P70_A0.172740.548
28_F31_K0.172730.548
21_T80_V0.17160.544
69_A73_L0.171190.543
1_V20_F0.169240.537
26_R30_L0.168920.536
33_V47_V0.168270.534
11_L16_K0.167320.531
4_R75_G0.166040.526
9_H53_H0.164870.523
48_E65_D0.163910.520
19_P30_L0.163910.520
43_R76_C0.161450.512
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
3h9nA0.988199.8-0.007
2qggA0.988199.80
2f1lA0.988199.80.003
2dyiA0.904899.70.142
3izcj0.654880.10.814
3j3bf0.63175.80.821
3j21c0.4167690.83
4a18H0.4762640.835
3j39f0.476260.60.839
3iz5j0.476258.50.84

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