GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cu-oxidase_3 - Multicopper oxidase
Pfam: PF07732 (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: 117
Sequences: 5476
Seq/Len: 46.8
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
29_R114_E1.984774.902
37_R83_E1.702564.205
39_T81_T1.608953.974
35_T83_E1.387693.427
41_T79_S1.213012.996
95_Y109_G0.983952.430
35_T85_T0.961722.375
31_R114_E0.95872.368
75_A78_E0.946922.339
32_E115_P0.910372.248
51_H98_H0.874822.161
37_R81_T0.842952.082
53_H96_H0.813422.009
30_V36_V0.793511.960
39_T79_S0.785761.941
48_T97_S0.767141.895
31_R34_D0.733811.812
18_T23_F0.726721.795
27_T110_A0.704821.741
47_P75_A0.69871.726
57_Q60_S0.657561.624
97_S102_Q0.652891.612
53_H98_H0.616921.524
48_T102_Q0.564081.393
40_V74_I0.55891.380
40_V82_Y0.554021.368
74_I80_F0.552661.365
17_W105_M0.545361.347
30_V86_A0.53631.324
63_M80_F0.52211.289
40_V50_I0.518071.279
92_T112_I0.508891.257
92_T110_A0.497411.228
32_E88_Q0.473761.170
52_W84_F0.453181.119
29_R112_I0.445891.101
17_W107_L0.441851.091
97_S107_L0.439911.086
103_Q108_Y0.425781.052
56_H88_Q0.417341.031
44_L48_T0.415971.027
94_W108_Y0.410141.013
51_H96_H0.404010.998
36_V84_F0.395370.976
38_I82_Y0.393890.973
14_R105_M0.382340.944
46_E102_Q0.380020.939
19_Y50_I0.370880.916
48_T107_L0.362640.896
47_P73_P0.361310.892
26_P109_G0.359720.888
60_S63_M0.359010.887
16_V23_F0.353050.872
45_D76_P0.348050.860
19_Y107_L0.343560.848
43_N79_S0.339850.839
32_E87_N0.338090.835
55_L113_V0.336960.832
66_V69_V0.335240.828
23_F108_Y0.334960.827
71_Q80_F0.331520.819
32_E90_A0.330080.815
36_V86_A0.327710.809
82_Y95_Y0.325310.803
28_I111_I0.318410.786
51_H64_D0.31770.785
49_S97_S0.317480.784
33_G87_N0.315740.780
25_G95_Y0.313910.775
43_N77_G0.310450.767
88_Q93_Y0.310430.767
28_I109_G0.310250.766
49_S99_V0.302480.747
44_L76_P0.301730.745
27_T112_I0.297940.736
19_Y95_Y0.297610.735
40_V48_T0.294180.727
93_Y113_V0.292270.722
67_P99_V0.290280.717
100_H103_Q0.283790.701
64_D68_G0.282440.698
86_A111_I0.280620.693
17_W45_D0.276680.683
68_G73_P0.272560.673
101_G105_M0.272180.672
56_H87_N0.271960.672
49_S71_Q0.271750.671
88_Q113_V0.271320.670
24_P108_Y0.266990.659
22_Q25_G0.26580.656
101_G107_L0.264370.653
26_P95_Y0.264210.653
51_H54_G0.263960.652
32_E93_Y0.263620.651
72_C75_A0.257920.637
30_V111_I0.257570.636
52_W55_L0.257520.636
52_W57_Q0.254970.630
38_I84_F0.252880.625
14_R17_W0.25160.621
30_V34_D0.249810.617
68_G71_Q0.248740.614
54_G93_Y0.248410.613
73_P99_V0.246310.608
17_W23_F0.243720.602
94_W103_Q0.24310.600
38_I95_Y0.240950.595
50_I82_Y0.240620.594
17_W44_L0.239450.591
42_N45_D0.237450.586
49_S52_W0.237390.586
55_L93_Y0.236660.584
63_M66_V0.234410.579
68_G104_V0.23360.577
59_P71_Q0.229230.566
20_N26_P0.227750.562
74_I79_S0.227130.561
45_D77_G0.226770.560
20_N24_P0.226340.559
63_M68_G0.224310.554
86_A90_A0.220960.546
40_V52_W0.220620.545
82_Y112_I0.220270.544
57_Q72_C0.219450.542
101_G104_V0.21890.541
55_L84_F0.218870.541
84_F111_I0.21840.539
72_C80_F0.216440.535
58_P63_M0.2160.533
49_S98_H0.212930.526
15_K18_T0.209840.518
46_E101_G0.209070.516
58_P85_T0.208420.515
42_N64_D0.20470.506
18_T21_G0.202190.499
94_W98_H0.201520.498
48_T99_V0.201360.497
57_Q84_F0.200580.495
99_V102_Q0.200580.495
63_M84_F0.199070.492
39_T43_N0.196540.485
38_I52_W0.196330.485
15_K43_N0.195230.482
34_D86_A0.194760.481
59_P70_T0.194760.481
87_N90_A0.194740.481
64_D67_P0.194480.480
75_A115_P0.192950.477
60_S105_M0.191530.473
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
1aozA0.9915100-0.069
3sqrA0.9915100-0.068
3t6vA1100-0.06
1zpuA1100-0.058
3pxlA1100-0.057
1v10A1100-0.049
2q9oA0.9915100-0.043
1hfuA0.9915100-0.022
2uxtA0.9573100-0.001
4f7kA0.974499.90.011

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