GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Lum_binding - Lumazine binding domain
Pfam: PF00677 (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: CL0076
Length: 85
Sequences: 3599
Seq/Len: 42.34
HH_delta: -0.003 (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_I25_E1.354082.654
9_K25_E1.324172.595
9_K79_R1.147242.248
43_N74_L1.132542.220
64_E68_R1.107982.171
74_L78_D1.0952.146
23_R58_E1.076772.110
51_D58_E1.076082.109
23_R56_W1.052042.062
8_G24_I1.047622.053
53_N56_W0.939391.841
25_E55_D0.904971.774
42_V80_V0.832511.632
45_V71_L0.80331.574
7_T79_R0.799761.567
15_K20_Q0.769921.509
13_I20_Q0.760131.490
10_I74_L0.749841.470
71_L74_L0.749831.470
35_K38_G0.735941.442
63_P67_R0.730061.431
50_T60_D0.723791.418
25_E56_W0.721861.415
21_R58_E0.72111.413
34_L49_V0.716881.405
22_L61_L0.7061.384
11_I56_W0.702011.376
20_Q66_L0.687531.347
42_V57_F0.668831.311
66_L72_G0.655671.285
34_L40_I0.646721.267
13_I22_L0.63731.249
6_G27_P0.631861.238
43_N70_T0.622341.220
12_S23_R0.61981.215
8_G82_L0.619711.214
45_V70_T0.619241.214
75_K78_D0.595231.167
6_G26_I0.583961.144
45_V69_T0.58021.137
33_D37_G0.5781.133
19_S60_D0.572791.123
21_R60_D0.571541.120
12_S76_V0.554221.086
5_D84_R0.543411.065
45_V61_L0.541341.061
16_N21_R0.537451.053
30_I33_D0.532751.044
38_G85_D0.52741.034
10_I24_I0.505470.991
21_R50_T0.498150.976
4_I41_A0.491850.964
24_I59_V0.489680.960
6_G30_I0.464090.910
42_V82_L0.456410.894
26_I82_L0.456280.894
10_I80_V0.455860.893
42_V59_V0.439770.862
39_S45_V0.436320.855
34_L37_G0.431940.847
70_T74_L0.423450.830
14_E21_R0.420110.823
30_I34_L0.419440.822
64_E67_R0.416310.816
3_I85_D0.404180.792
37_G46_C0.401770.787
3_I46_C0.399160.782
13_I75_K0.398240.780
5_D38_G0.395640.775
50_T58_E0.393720.772
33_D84_R0.38970.764
34_L84_R0.387850.760
31_L34_L0.382740.750
61_L66_L0.377910.741
13_I76_V0.376270.737
46_C85_D0.372270.730
26_I57_F0.367870.721
34_L52_I0.367230.720
47_L65_T0.365530.716
19_S62_I0.362910.711
16_N19_S0.35550.697
30_I37_G0.354180.694
66_L69_T0.346980.680
47_L61_L0.346820.680
10_I13_I0.341660.670
5_D35_K0.339440.665
8_G42_V0.338120.663
22_L66_L0.331620.650
3_I38_G0.32980.646
12_S56_W0.327350.642
61_L71_L0.324710.636
33_D36_I0.320810.629
10_I22_L0.320180.627
63_P69_T0.319810.627
46_C84_R0.315650.619
26_I30_I0.314470.616
11_I76_V0.312880.613
53_N58_E0.312390.612
32_S37_G0.308640.605
42_V47_L0.304940.598
39_S69_T0.303330.594
66_L71_L0.301760.591
23_R53_N0.300690.589
11_I23_R0.296250.581
1_T4_I0.29550.579
22_L71_L0.295470.579
49_V52_I0.292720.574
19_S66_L0.292060.572
35_K46_C0.284710.558
6_G29_K0.284460.557
14_E58_E0.279940.549
18_D63_P0.278760.546
39_S46_C0.276720.542
32_S55_D0.275660.540
10_I78_D0.274710.538
18_D67_R0.27450.538
8_G26_I0.270850.531
36_I51_D0.268370.526
45_V74_L0.268360.526
34_L38_G0.266420.522
42_V74_L0.255540.501
38_G84_R0.251740.493
43_N78_D0.248440.487
40_I57_F0.24560.481
62_I65_T0.244750.480
1_T85_D0.24350.477
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
1i8dA199.9-0.003
1i8dA199.90.004
1kzlA0.988299.90.007
3a35A199.90.009
3ddyA0.988299.90.021
1kzlA199.90.023
3ddyA199.90.03
3a35A0.988299.90.032
3vo2A0.976548.70.875
1fnbA0.976548.30.875

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