GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mur_ligase_C - Mur ligase family glutamate ligase domain
Pfam: PF02875 (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: 91
Sequences: 9380
Seq/Len: 103.08
HH_delta: 0.118 (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
7_V15_T1.767273.086
45_A72_A1.656472.893
7_V17_I1.35642.369
29_A32_E1.30162.273
44_I74_V1.223372.137
42_R74_V1.096391.915
28_R67_L1.017611.777
28_R32_E1.005911.757
3_G18_D1.000941.748
10_E14_P0.963791.683
5_M17_I0.959761.676
10_E15_T0.95241.663
42_R73_D0.941511.644
60_F63_E0.909221.588
57_D81_N0.85981.502
7_V10_E0.850811.486
44_I76_I0.844891.476
51_G80_D0.794541.388
66_E70_Q0.786731.374
5_M33_A0.783081.368
46_V78_T0.779761.362
32_E67_L0.776821.357
25_D29_A0.767471.340
34_L43_I0.762961.332
62_E66_E0.741081.294
58_K62_E0.729261.274
22_H27_I0.717371.253
49_A63_E0.703951.229
56_K59_D0.676541.182
23_N26_S0.675731.180
2_P6_E0.664931.161
44_I75_V0.649071.134
63_E66_E0.636831.112
27_I31_L0.607651.061
60_F64_I0.600211.048
6_E18_D0.598221.045
56_K60_F0.597411.043
66_E69_A0.596551.042
9_R14_P0.587621.026
1_V20_Y0.576991.008
17_I34_L0.571630.998
5_M34_L0.565690.988
22_H26_S0.559860.978
50_M79_G0.541380.945
15_T41_G0.54010.943
68_A75_V0.524290.916
24_P28_R0.514990.899
28_R70_Q0.511450.893
28_R66_E0.503920.880
47_F77_L0.50160.876
59_D63_E0.501580.876
10_E13_G0.500110.873
2_P8_V0.492980.861
21_A26_S0.492150.860
7_V37_L0.491270.858
29_A33_A0.490280.856
37_L40_K0.487990.852
31_L45_A0.486720.850
9_R15_T0.485280.848
61_H65_G0.484620.846
65_G69_A0.482980.844
63_E67_L0.476190.832
67_L70_Q0.4680.817
33_A37_L0.456230.797
57_D62_E0.454510.794
46_V76_I0.44770.782
57_D60_F0.439760.768
21_A30_L0.438270.765
35_K43_I0.429190.750
49_A82_P0.41980.733
26_S29_A0.41880.731
31_L35_K0.417620.729
21_A27_I0.415590.726
20_Y23_N0.402990.704
8_V18_D0.402670.703
62_E65_G0.401880.702
2_P18_D0.400120.699
31_L66_E0.397110.694
24_P63_E0.385760.674
52_D81_N0.385370.673
35_K70_Q0.384990.672
52_D60_F0.384740.672
50_M81_N0.384290.671
27_I63_E0.378840.662
19_D22_H0.37720.659
15_T37_L0.373870.653
25_D28_R0.369360.645
49_A81_N0.368470.644
49_A64_I0.366360.640
61_H64_I0.360710.630
27_I47_F0.353360.617
27_I45_A0.352410.615
48_G78_T0.35070.612
58_K63_E0.349690.611
65_G82_P0.348530.609
27_I67_L0.347930.608
48_G79_G0.345990.604
40_K43_I0.344110.601
19_D30_L0.340590.595
35_K40_K0.338450.591
15_T40_K0.334590.584
32_E36_E0.332350.580
26_S48_G0.327870.573
5_M19_D0.325990.569
35_K73_D0.323250.565
44_I73_D0.320350.559
23_N60_F0.319540.558
51_G81_N0.318180.556
3_G51_G0.316050.552
64_I68_A0.315670.551
70_Q74_V0.31480.550
5_M18_D0.313520.548
26_S50_M0.312470.546
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
1e8cA0.95699.50.118
2wtzA0.945199.50.127
3nrsA0.912199.50.142
2vosA0.912199.40.172
3hn7A0.97899.30.209
3mvnA0.97899.30.209
1p3dA0.96799.30.212
2am1A0.97899.30.22
2f00A0.96799.30.22
1j6uA0.95699.30.222

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