GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SNase - Staphylococcal nuclease homologue
Pfam: PF00565 (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: 108
Sequences: 2030
Seq/Len: 18.8
HH_delta: 0.069 (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
67_E94_A0.850132.723
30_L65_I0.750932.405
4_L66_N0.63632.038
64_D91_L0.618191.980
68_E71_E0.617171.977
8_D11_E0.609351.952
67_E90_S0.597561.914
29_F69_L0.586391.878
97_E101_A0.578791.854
4_L30_L0.569131.823
29_F72_E0.568491.821
68_E72_E0.56161.799
95_E99_R0.550631.764
57_Y64_D0.54091.733
5_A55_L0.535081.714
77_V95_E0.527471.690
27_K31_R0.517321.657
96_E100_K0.467071.496
71_E97_E0.466411.494
79_R95_E0.453171.452
63_E68_E0.431771.383
95_E106_W0.426651.367
70_L77_V0.42611.365
77_V92_L0.423581.357
43_V54_L0.423551.357
41_V58_V0.423191.356
29_F33_L0.421951.352
12_T27_K0.419221.343
33_L65_I0.419211.343
41_V56_A0.418381.340
70_L91_L0.410141.314
59_Y64_D0.403571.293
11_E51_Y0.396621.270
9_A30_L0.390411.251
67_E71_E0.3881.243
69_L75_A0.381761.223
34_L65_I0.37441.199
30_L69_L0.367051.176
9_A26_A0.366281.173
22_Y74_L0.361991.160
73_G98_A0.358161.147
44_D57_Y0.357741.146
3_R51_Y0.356361.142
31_R35_L0.351711.127
3_R11_E0.350791.124
5_A57_Y0.349261.119
70_L75_A0.347861.114
43_V56_A0.345791.108
76_R105_I0.345751.108
33_L68_E0.344451.103
26_A69_L0.343281.100
88_Y92_L0.341111.093
29_F68_E0.337661.082
57_Y91_L0.332851.066
79_R92_L0.332421.065
12_T24_Q0.331731.063
11_E53_R0.32921.055
93_Q96_E0.321481.030
96_E99_R0.317481.017
49_D53_R0.313211.003
59_Y87_Y0.310940.996
5_A44_D0.308370.988
22_Y58_V0.306970.983
3_R49_D0.301140.965
28_E31_R0.297150.952
42_E59_Y0.287680.922
7_I69_L0.286620.918
3_R8_D0.286070.916
2_V56_A0.2840.910
60_V63_E0.273130.875
57_Y66_N0.269370.863
34_L39_V0.261660.838
3_R53_R0.261440.837
22_Y41_V0.260730.835
9_A75_A0.25560.819
29_F32_E0.255530.819
24_Q28_E0.250610.803
72_E103_K0.249620.800
28_E32_E0.247340.792
77_V82_P0.245810.787
97_E100_K0.245410.786
8_D78_Y0.240710.771
20_E76_R0.231740.742
91_L94_A0.231640.742
40_V59_Y0.231480.742
21_P25_E0.230670.739
9_A23_G0.229920.737
42_E86_E0.229690.736
7_I75_A0.229560.735
99_R106_W0.228410.732
3_R78_Y0.227430.729
73_G104_G0.225750.723
45_D55_L0.225730.723
2_V41_V0.224720.720
66_N91_L0.224140.718
33_L63_E0.220520.706
29_F74_L0.220410.706
8_D51_Y0.220390.706
71_E101_A0.21960.703
49_D55_L0.219510.703
87_Y90_S0.217130.696
24_Q27_K0.216650.694
71_E94_A0.216520.694
51_Y78_Y0.214620.687
27_K30_L0.212610.681
8_D53_R0.21210.679
6_G57_Y0.211240.677
59_Y62_G0.208610.668
97_E103_K0.208360.667
90_S94_A0.204430.655
6_G88_Y0.204340.655
78_Y81_Y0.203750.653
64_D67_E0.201490.645
43_V46_I0.20080.643
57_Y87_Y0.199230.638
36_G39_V0.198980.637
66_N70_L0.195990.628
37_R60_V0.195940.628
77_V91_L0.195250.625
42_E57_Y0.191780.614
66_N75_A0.190030.609
30_L34_L0.188680.604
13_N27_K0.187960.602
92_L96_E0.186350.597
8_D20_E0.186090.596
104_G107_S0.185150.593
55_L82_P0.184510.591
97_E102_K0.184010.589
4_L7_I0.183110.587
33_L60_V0.181090.580
11_E55_L0.179950.576
67_E91_L0.17940.575
33_L72_E0.179030.573
1_K77_V0.178470.572
20_E58_V0.176970.567
25_E28_E0.176160.564
40_V61_D0.174630.559
44_D55_L0.17440.559
21_P74_L0.173460.556
90_S93_Q0.173180.555
26_A74_L0.172090.551
21_P56_A0.171460.549
37_R61_D0.169530.543
5_A43_V0.166490.533
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
3bdlA199.90.069
3bdlA0.972299.90.069
4eqpA0.944499.90.073
2wacA0.907499.50.331
2hqxA0.907499.40.386
4b9wA0.629697.10.72
4b9xA0.861196.70.74
3ntkA0.546393.30.794
3m9wA0.796312.10.899
4gmfA0.879611.60.9

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