GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Succ_CoA_lig - Succinyl-CoA ligase like flavodoxin domain
Pfam: PF13607 (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: CL0506
Length: 138
Sequences: 3399
Seq/Len: 24.63
HH_delta: 0.03 (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
3_G56_R1.577024.973
115_A119_Q1.162013.664
19_D23_D0.873892.756
59_V131_L0.844932.664
72_L116_A0.702492.215
114_D124_R0.700282.208
29_S55_T0.669622.112
117_L122_V0.668032.107
86_V117_L0.641982.024
22_Q27_G0.624211.968
113_Y117_L0.62271.964
57_V135_A0.597371.884
52_D55_T0.557431.758
4_V57_V0.554411.748
73_E76_R0.553791.746
50_A81_R0.548441.729
1_P54_D0.54361.714
58_I80_R0.543031.712
40_V45_L0.532861.680
47_E51_E0.532561.679
112_V115_A0.521981.646
125_V134_A0.497941.570
118_R126_D0.467151.473
111_A115_A0.466491.471
125_V130_E0.463591.462
32_V45_L0.461181.454
14_G31_V0.454061.432
91_R126_D0.448821.415
115_A118_R0.447291.410
8_S14_G0.441711.393
74_A78_A0.427431.348
5_A55_T0.423221.335
116_A120_A0.416041.312
6_L28_F0.410881.296
24_R133_D0.410161.293
123_V134_A0.408211.287
114_D126_D0.406841.283
75_A122_V0.396351.250
59_V135_A0.391111.233
46_L58_I0.391061.233
112_V116_A0.388581.225
43_A47_E0.383821.210
130_E133_D0.381861.204
22_Q28_F0.379921.198
5_A29_S0.372761.175
44_D47_E0.372171.174
71_F75_A0.370971.170
73_E77_R0.368291.161
91_R114_D0.367531.159
50_A80_R0.364771.150
114_D118_R0.357411.127
6_L21_A0.356791.125
57_V85_V0.347111.095
127_D130_E0.346421.092
72_L76_R0.343811.084
21_A28_F0.338311.067
67_D71_F0.337571.064
40_V73_E0.336041.060
60_L86_V0.331581.046
4_V135_A0.322211.016
71_F76_R0.313840.990
20_W129_D0.311580.983
86_V122_V0.310140.978
30_Y48_Y0.304650.961
2_G27_G0.304490.960
67_D70_R0.29780.939
85_V134_A0.296660.935
5_A49_L0.296120.934
7_I49_L0.293130.924
30_Y49_L0.292270.922
75_A80_R0.292210.921
12_A15_T0.292190.921
69_R73_E0.290790.917
20_W132_L0.290380.916
43_A77_R0.290220.915
71_F74_A0.288890.911
75_A79_A0.285320.900
24_R129_D0.285310.900
89_A93_E0.28490.898
42_F62_L0.28420.896
85_V125_V0.283660.894
125_V131_L0.283270.893
50_A58_I0.281570.888
126_D130_E0.281430.887
30_Y55_T0.281070.886
21_A132_L0.28090.886
37_E66_G0.279630.882
11_G36_N0.274120.864
47_E77_R0.272770.860
7_I34_V0.271920.857
20_W24_R0.267240.843
18_L31_V0.265370.837
44_D70_R0.255390.805
7_I45_L0.253310.799
13_L128_L0.249550.787
46_L60_L0.24740.780
18_L28_F0.243250.767
35_G90_G0.242080.763
28_F31_V0.241070.760
76_R79_A0.236790.747
11_G63_E0.234490.739
87_L131_L0.231660.731
51_E77_R0.231520.730
51_E81_R0.230450.727
50_A78_A0.230350.726
34_V42_F0.229510.724
12_A19_D0.229440.724
7_I60_L0.227780.718
69_R72_L0.226970.716
37_E42_F0.226120.713
18_L22_Q0.225550.711
49_L55_T0.221760.699
6_L18_L0.221370.698
12_A132_L0.220940.697
26_I135_A0.21830.688
78_A81_R0.217380.685
53_P82_K0.215760.680
50_A74_A0.20970.661
67_D91_R0.209070.659
75_A84_V0.207790.655
66_G93_E0.20740.654
52_D83_P0.2060.650
19_D134_A0.20580.649
47_E80_R0.205430.648
7_I46_L0.204460.645
59_V85_V0.204230.644
40_V77_R0.203990.643
34_V37_E0.203030.640
21_A26_I0.199250.628
5_A30_Y0.19840.626
35_G63_E0.197310.622
47_E74_A0.196180.619
84_V122_V0.195820.617
38_A66_G0.193770.611
13_L16_A0.192630.607
118_R124_R0.192520.607
13_L61_Y0.19050.601
62_L86_V0.189210.597
13_L113_Y0.188350.594
47_E50_A0.187520.591
7_I42_F0.185560.585
14_G33_S0.184880.583
9_Q88_K0.184680.582
2_G35_G0.184250.581
128_L135_A0.184250.581
92_T112_V0.184140.581
17_I61_Y0.183950.580
46_L50_A0.183830.580
19_D31_V0.183340.578
43_A74_A0.182470.575
42_F60_L0.181630.573
15_T33_S0.181560.573
65_I113_Y0.181480.572
38_A67_D0.180840.570
32_V49_L0.180140.568
43_A70_R0.179440.566
118_R123_V0.179190.565
10_S63_E0.178350.562
64_G113_Y0.177640.560
78_A123_V0.176550.557
1_P27_G0.17560.554
15_T31_V0.175490.553
54_D133_D0.175040.552
91_R124_R0.174470.550
44_D63_E0.17290.545
76_R80_R0.171970.542
4_V56_R0.171040.539
15_T61_Y0.169620.535
50_A75_A0.169290.534
75_A78_A0.16910.533
56_R76_R0.168830.532
116_A119_Q0.168380.531
41_D44_D0.168330.531
43_A78_A0.168230.530
61_Y64_G0.168070.530
72_L75_A0.165920.523
80_R111_A0.165430.522
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
2csuA11000.03
3mwdB0.99281000.038
1oi7A0.99281000.056
2yv2A0.99281000.061
3pffA0.98551000.062
2fp4A0.98551000.066
2yv1A0.98551000.071
2nu8A0.985599.90.089
3dmyA0.833399.90.219
2csuA0.884199.60.442

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