GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cu_amine_oxidN1 - Copper amine oxidase N-terminal domain
Pfam: PF07833 (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: 93
Sequences: 1537
Seq/Len: 16.53
HH_delta: 0.099 (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
13_A31_I0.728672.926
4_K57_S0.662312.660
72_R76_E0.655522.632
36_K50_N0.641082.574
41_K44_S0.627422.519
10_R14_E0.570722.292
47_A73_F0.566282.274
9_L31_I0.540642.171
46_E53_K0.519192.085
28_T39_K0.5112.052
6_Y61_V0.509672.047
38_I49_V0.488411.961
42_V67_T0.48771.958
47_A56_L0.46651.873
18_A33_K0.442721.778
84_W89_K0.414611.665
6_Y58_A0.411121.651
85_D88_T0.397931.598
42_V62_I0.396051.590
48_T53_K0.390911.570
23_D26_T0.380731.529
47_A54_I0.365381.467
61_V68_Y0.32721.314
29_V67_T0.312611.255
29_V40_L0.311341.250
30_T37_S0.309931.245
8_P11_F0.309561.243
9_L69_V0.296361.190
23_D30_T0.293721.179
62_I67_T0.293091.177
4_K66_R0.290711.167
10_R22_W0.276911.112
45_N55_T0.27081.087
73_F77_A0.270371.086
11_F14_E0.269221.081
86_N89_K0.268741.079
56_L73_F0.26191.052
45_N59_P0.256461.030
27_K43_G0.25561.026
72_R82_V0.254571.022
21_S32_T0.252821.015
41_K60_P0.24951.002
72_R75_S0.247010.992
6_Y63_I0.243140.976
22_W27_K0.241990.972
62_I65_G0.238450.958
8_P12_I0.238020.956
57_S73_F0.232930.935
28_T41_K0.232540.934
12_I80_Y0.226620.910
10_R29_V0.226140.908
23_D28_T0.226120.908
30_T39_K0.225760.907
14_E20_V0.225510.906
10_R72_R0.225470.905
10_R20_V0.220070.884
46_E55_T0.21580.867
73_F76_E0.215130.864
12_I74_L0.210760.846
11_F15_A0.210640.846
24_N86_N0.210570.846
9_L29_V0.210310.845
42_V60_P0.209110.840
27_K89_K0.207070.831
40_L47_A0.205550.825
44_S56_L0.20530.824
19_K32_T0.204580.822
22_W26_T0.201950.811
38_I78_F0.201230.808
26_T64_N0.200940.807
71_L75_S0.200660.806
76_E82_V0.19810.795
6_Y56_L0.196710.790
27_K44_S0.196030.787
70_P73_F0.191680.770
3_G65_G0.191410.769
13_A20_V0.187050.751
18_A80_Y0.186760.750
5_T79_G0.185770.746
40_L74_L0.184490.741
39_K48_T0.184460.741
11_F66_R0.182490.733
63_I68_Y0.178910.718
56_L59_P0.177930.714
31_I78_F0.175410.704
57_S66_R0.173450.696
49_V54_I0.17280.694
13_A18_A0.171910.690
10_R13_A0.171660.689
36_K49_V0.168750.678
14_E67_T0.166370.668
5_T30_T0.165720.665
48_T51_G0.165650.665
16_L80_Y0.163320.656
18_A78_F0.16330.656
11_F69_V0.16230.652
46_E52_K0.161630.649
27_K65_G0.15920.639
16_L37_S0.158670.637
17_G34_G0.156640.629
7_V16_L0.152720.613
11_F31_I0.152480.612
9_L13_A0.152410.612
4_K58_A0.152230.611
19_K81_K0.150780.605
58_A61_V0.149890.602
45_N57_S0.148460.596
16_L78_F0.147340.592
72_R84_W0.145850.586
71_L74_L0.145660.585
45_N52_K0.145290.583
2_D64_N0.145040.582
52_K55_T0.144590.581
20_V31_I0.144390.580
21_S78_F0.143290.575
5_T8_P0.143150.575
32_T39_K0.143120.575
40_L70_P0.142440.572
23_D39_K0.141710.569
32_T37_S0.140860.566
9_L15_A0.14070.565
9_L82_V0.140670.565
15_A75_S0.140250.563
75_S82_V0.140180.563
22_W66_R0.140050.562
13_A16_L0.140030.562
23_D27_K0.139560.560
40_L60_P0.139480.560
4_K84_W0.139090.559
35_K50_N0.138890.558
4_K72_R0.138880.558
19_K86_N0.138840.558
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
1spuA199.60.099
1spuA0.344196.90.667
4k3lA0.95724.10.857
3p16A0.946219.40.863
3d1gA0.957190.863
4gdzA0.645212.80.873
1vpkA0.946212.70.873
3t0pA0.9462120.874
2oynA0.516111.80.875
3ge2A0.76348.40.882

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