GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Copper-bind - Copper binding proteins plastocyaninazurin family
Pfam: PF00127 (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: CL0026
Length: 99
Sequences: 6713
Seq/Len: 67.81
HH_delta: 0.141 (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
82_Y94_G1.647473.668
26_T73_T1.616173.598
28_T71_S1.485183.306
84_C87_H1.312722.923
22_K25_D1.256762.798
37_H84_C1.071872.386
28_T73_T1.026052.284
79_T97_I1.025142.282
65_A68_E0.974622.170
21_V27_V0.948422.111
30_V69_T0.933982.079
84_C92_M0.916172.040
40_V85_T0.896921.997
18_E95_T0.892481.987
42_V83_Y0.787681.754
79_T95_T0.778741.734
23_A77_P0.772891.721
20_T97_I0.762771.698
26_T75_T0.756491.684
18_E97_I0.735211.637
37_H87_H0.639391.423
38_N85_T0.602361.341
81_E95_T0.582531.297
38_N41_F0.565371.259
49_G52_S0.55011.225
19_I96_I0.525741.170
23_A76_K0.514441.145
40_V83_Y0.510861.137
30_V71_S0.491961.095
43_A46_M0.490321.092
46_M61_S0.487011.084
88_Y93_V0.481431.072
40_V43_A0.463961.033
83_Y88_Y0.444110.989
27_V74_F0.435190.969
64_L68_E0.429060.955
80_Y98_V0.429030.955
19_I94_G0.425950.948
32_N69_T0.401350.894
61_S70_Y0.384250.855
36_P63_L0.381170.849
64_L70_Y0.379420.845
81_E93_V0.378990.844
31_N39_V0.376060.837
42_V81_E0.375190.835
21_V26_T0.375170.835
34_S67_G0.374330.833
21_V74_F0.374180.833
38_N43_A0.371470.827
74_F96_I0.366380.816
23_A80_Y0.365360.813
31_N34_S0.364290.811
62_P70_Y0.363460.809
31_N68_E0.353040.786
29_F82_Y0.348150.775
60_S63_L0.332630.741
88_Y91_G0.329910.734
16_P93_V0.311820.694
44_D50_A0.308660.687
87_H92_M0.308470.687
37_H43_A0.307040.684
81_E88_Y0.301680.672
62_P65_A0.299220.666
41_F44_D0.294430.655
37_H41_F0.291640.649
31_N35_M0.281670.627
77_P92_M0.278410.620
24_G78_G0.277540.618
76_K98_V0.27740.618
17_S82_Y0.277150.617
35_M64_L0.27630.615
39_V43_A0.271260.604
78_G98_V0.271160.604
45_G49_G0.267690.596
23_A75_T0.265110.590
45_G76_K0.262310.584
45_G51_D0.261340.582
31_N64_L0.258470.575
61_S72_V0.25770.574
42_V85_T0.257020.572
21_V98_V0.251150.559
21_V25_D0.249170.555
24_G75_T0.247980.552
72_V82_Y0.247850.552
36_P50_A0.246250.548
76_K88_Y0.244460.544
46_M90_A0.243940.543
15_D81_E0.243410.542
16_P96_I0.241420.537
77_P98_V0.240250.535
32_N68_E0.240090.535
37_H92_M0.239210.533
15_D18_E0.237020.528
16_P94_G0.23390.521
89_E92_M0.232830.518
36_P65_A0.231670.516
17_S94_G0.23110.515
39_V82_Y0.22820.508
46_M49_G0.223720.498
87_H91_G0.223370.497
76_K90_A0.22290.496
17_S91_G0.221870.494
32_N67_G0.221460.493
16_P82_Y0.221430.493
31_N69_T0.221290.493
27_V89_E0.220690.491
77_P80_Y0.220040.490
34_S87_H0.219950.490
46_M52_S0.219720.489
76_K80_Y0.219220.488
26_T71_S0.217880.485
44_D80_Y0.215450.480
80_Y90_A0.212590.473
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
3cvbA0.979899.70.141
1b3iA0.959699.70.145
1pcsA0.969799.70.149
2gimA0.979899.70.155
1bypA199.70.157
1plcA0.979899.70.158
3erxA0.89999.70.159
3ef4A0.89999.60.164
3tu6A0.89999.60.164
2pltA0.969799.60.169

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