GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cyc-maltodext_C - Cyclo-malto-dextrinase C-terminal domain
Pfam: PF10438 (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: CL0369
Length: 78
Sequences: 4101
Seq/Len: 52.58
HH_delta: 0.21 (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
27_L73_V1.249742.996
69_P72_S1.181712.833
14_Y25_V1.104042.647
15_F22_T1.095352.626
21_K77_E1.052072.522
17_Y22_T0.899482.156
10_G30_N0.841532.017
13_V26_I0.806741.934
35_T65_N0.774211.856
53_D74_L0.748541.795
35_T67_T0.705941.692
33_E67_T0.673251.614
53_D56_T0.673231.614
53_D57_G0.600061.439
23_V77_E0.591321.418
37_D65_N0.579251.389
30_N34_Q0.536951.287
68_L72_S0.528181.266
8_Q34_Q0.528081.266
27_L75_I0.523551.255
55_L73_V0.519451.245
29_K71_K0.517271.240
33_E69_P0.517181.240
15_F24_M0.508261.219
30_N71_K0.488751.172
18_Y21_K0.476421.142
23_V54_I0.475851.141
51_A76_L0.470981.129
25_V75_I0.458231.099
12_Y27_L0.448951.076
53_D76_L0.447471.073
10_G34_Q0.441441.058
31_D71_K0.44041.056
50_S59_T0.412910.990
10_G29_K0.408670.980
17_Y20_G0.385550.924
11_V36_L0.384110.921
13_V24_M0.383970.921
23_V75_I0.37980.911
10_G75_I0.365870.877
26_I74_L0.360.863
51_A62_L0.357910.858
52_K59_T0.35540.852
10_G32_K0.353560.848
53_D60_I0.331360.794
23_V27_L0.330950.793
12_Y75_I0.322770.774
53_D58_K0.317270.761
12_Y73_V0.316710.759
56_T60_I0.302020.724
60_I76_L0.298080.715
16_R25_V0.295240.708
15_F18_Y0.292550.701
14_Y73_V0.292340.701
8_Q14_Y0.287820.690
31_D70_P0.28730.689
26_I36_L0.286240.686
16_R73_V0.285420.684
19_D49_T0.279870.671
74_L77_E0.27830.667
37_D50_S0.272440.653
53_D59_T0.269260.646
11_V34_Q0.266010.638
50_S63_S0.265380.636
51_A54_I0.263750.632
37_D64_K0.262920.630
12_Y29_K0.254970.611
33_E70_P0.254140.609
66_L76_L0.251590.603
26_I66_L0.247770.594
17_Y51_A0.242160.581
40_R71_K0.239920.575
13_V25_V0.239650.575
8_Q11_V0.23910.573
60_I65_N0.238630.572
10_G61_D0.238230.571
11_V68_L0.237390.569
14_Y75_I0.236230.566
36_L66_L0.235970.566
52_K77_E0.235370.564
16_R27_L0.234940.563
58_K62_L0.23370.560
49_T64_K0.232550.558
40_R61_D0.231550.555
14_Y27_L0.2280.547
33_E58_K0.227670.546
52_K63_S0.22640.543
26_I68_L0.225630.541
57_G73_V0.224250.538
12_Y15_F0.224240.538
13_V36_L0.21970.527
26_I76_L0.21920.526
60_I64_K0.217320.521
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
3edfA198.60.21
3ucqA0.974498.50.239
4aieA0.884698.50.249
4e2oA0.974498.30.301
1m53A0.923198.20.321
1uokA0.948798.10.324
3zssA198.10.332
4aeeA0.923198.10.334
1ea9C0.923198.10.337
1j0hA0.948798.10.343

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