GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cupredoxin_1 - Cupredoxin-like domain
Pfam: PF13473 (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: 104
Sequences: 3213
Seq/Len: 30.89
HH_delta: 0.194 (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
46_T79_T1.114263.552
90_F100_G0.913562.912
48_T77_T0.868382.768
39_V45_V0.790192.519
24_T48_T0.683642.179
87_E101_T0.661522.109
26_T52_N0.659432.102
36_T103_I0.649592.071
46_T77_T0.627111.999
41_A85_P0.592671.889
38_T103_I0.586721.870
40_K43_Q0.555121.770
89_E101_T0.549081.750
87_E103_I0.544761.737
92_C98_M0.530921.692
48_T75_T0.526491.678
47_L80_F0.519691.657
58_E93_T0.504251.607
22_T48_T0.503721.606
71_P74_E0.497361.585
50_T75_T0.489941.562
24_T50_T0.472851.507
37_I102_L0.469461.497
21_Q43_Q0.467891.492
36_T101_T0.466631.487
22_T46_T0.441331.407
51_N72_P0.437831.396
85_P88_Y0.436561.392
23_V37_I0.426671.360
60_V93_T0.422931.348
41_A88_Y0.417251.330
39_V80_F0.385081.228
37_I100_G0.383381.222
42_G86_G0.371561.184
26_T33_S0.371351.184
28_T52_N0.369891.179
57_H98_M0.36391.160
57_H92_C0.360271.148
34_P100_G0.359841.147
49_F59_F0.357671.140
45_V80_F0.343491.095
49_F78_V0.343071.094
89_E99_K0.329121.049
23_V43_Q0.327131.043
27_V30_F0.297040.947
34_P37_I0.287850.918
91_Y96_P0.276560.882
47_L78_V0.276420.881
28_T31_G0.275320.878
53_D57_H0.269210.858
61_I66_I0.266210.849
32_F92_C0.264490.843
29_D53_D0.262420.837
23_V39_V0.25540.814
56_P69_V0.252880.806
70_L76_A0.252610.805
25_I34_P0.250850.800
43_Q82_P0.247930.790
45_V82_P0.242140.772
60_V91_Y0.239770.764
41_A83_L0.23650.754
39_V104_V0.234480.747
20_A23_V0.231360.738
39_V102_L0.230810.736
67_S76_A0.226660.723
34_P102_L0.222680.710
61_I64_L0.220350.702
38_T41_A0.219760.701
92_C95_H0.215460.687
42_G83_L0.215160.686
45_V49_F0.214580.684
91_Y99_K0.213290.680
34_P99_K0.209240.667
86_G104_V0.207310.661
45_V102_L0.206480.658
63_D88_Y0.206390.658
76_A90_F0.206370.658
49_F70_L0.205370.655
66_I78_V0.204230.651
25_I37_I0.203380.648
62_P71_P0.202970.647
27_V51_N0.201840.643
26_T50_T0.200910.640
56_P71_P0.199860.637
25_I32_F0.195430.623
37_I90_F0.195210.622
90_F102_L0.194940.621
61_I78_V0.194750.621
52_N74_E0.19460.620
55_R70_L0.194570.620
22_T43_Q0.193650.617
51_N71_P0.193170.616
47_L51_N0.191310.610
32_F94_M0.188070.600
51_N59_F0.187030.596
64_L67_S0.186490.594
29_D55_R0.185960.593
35_S90_F0.185580.592
41_A65_G0.184850.589
66_I94_M0.184630.589
51_N57_H0.184490.588
31_G54_S0.184330.588
78_V90_F0.184180.587
39_V100_G0.182630.582
62_P91_Y0.179360.572
31_G35_S0.178910.570
69_V74_E0.178250.568
29_D54_S0.177990.567
55_R97_N0.177370.565
80_F102_L0.173020.552
57_H93_T0.172690.550
28_T54_S0.171410.546
30_F69_V0.171170.546
56_P84_K0.171130.546
43_Q46_T0.170410.543
68_K76_A0.170010.542
24_T75_T0.16920.539
51_N70_L0.166370.530
69_V93_T0.166280.530
33_S89_E0.166160.530
62_P89_E0.165880.529
68_K90_F0.165650.528
24_T73_G0.165380.527
79_T82_P0.164670.525
39_V82_P0.159550.509
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
4hciA0.932799.70.194
3c75A0.961599.70.237
4f2eA0.913599.70.262
4f2fA0.923199.60.306
3ay2A0.990499.60.309
1cuoA0.826999.60.316
2ov0A0.942399.60.318
1id2A0.903899.60.319
2ccwA0.826999.50.327
1ibyA0.980899.50.329

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