GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PAX - Paired box domain
Pfam: PF00292 (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: CL0123
Length: 125
Sequences: 3919
Seq/Len: 31.35
HH_delta: 0.21 (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
34_V38_D0.850232.343
36_P51_S0.767542.115
30_A39_I0.740892.042
26_I50_V0.725181.998
37_C47_H0.716081.973
34_V42_Q0.699691.928
22_L45_V0.698181.924
36_P54_L0.695531.917
83_K87_Y0.688161.896
29_L42_Q0.688091.896
30_A54_L0.687871.896
118_S122_R0.676391.864
81_V123_I0.657851.813
40_S50_V0.652261.797
29_L34_V0.644791.777
118_S121_N0.643041.772
48_G52_K0.569311.569
47_H51_S0.562811.551
39_I43_L0.556391.533
48_G51_S0.552911.524
76_A80_V0.527961.455
29_L43_L0.5241.444
25_R29_L0.518471.429
35_R38_D0.518241.428
77_T80_V0.516441.423
102_R106_D0.511821.410
39_I50_V0.506361.395
94_I98_E0.506361.395
57_Y63_I0.496161.367
82_E86_Q0.485091.337
45_V50_V0.480731.325
102_R105_A0.475931.312
37_C41_R0.469341.293
85_E89_R0.462541.275
116_S119_S0.456451.258
38_D41_R0.453321.249
100_R120_I0.453171.249
95_F98_E0.444841.226
24_Q28_E0.444061.224
25_R28_E0.425921.174
96_A121_N0.412231.136
84_I123_I0.408071.125
76_A123_I0.401951.108
46_S49_C0.400211.103
26_I53_I0.395521.090
38_D42_Q0.391841.080
119_S122_R0.389691.074
53_I56_R0.389551.074
36_P47_H0.384461.059
20_N24_Q0.379421.046
81_V85_E0.378741.044
117_V121_N0.374281.031
29_L39_I0.370671.021
94_I97_W0.370561.021
40_S45_V0.364881.006
54_L58_R0.364771.005
49_C53_I0.363391.001
23_R53_I0.346740.956
101_D104_I0.346550.955
26_I39_I0.339160.935
99_I121_N0.335520.925
49_C52_K0.334060.921
83_K86_Q0.333110.918
43_L50_V0.330540.911
21_E24_Q0.328860.906
100_R104_I0.323340.891
100_R117_V0.320480.883
55_S59_E0.319270.880
98_E103_L0.317170.874
22_L25_R0.315540.870
23_R27_V0.315210.869
86_Q90_E0.312340.861
76_A81_V0.309750.854
84_I99_I0.307710.848
88_K124_L0.307340.847
40_S47_H0.30650.845
80_V123_I0.305640.842
69_G73_P0.304820.840
83_K106_D0.304050.838
29_L32_E0.301710.831
119_S123_I0.297880.821
96_A99_I0.296840.818
78_P82_E0.296750.818
94_I102_R0.296150.816
28_E32_E0.294330.811
52_K55_S0.289560.798
39_I54_L0.28860.795
66_G69_G0.287950.794
27_V57_Y0.283570.781
21_E25_R0.283390.781
30_A36_P0.281680.776
28_E31_K0.281010.774
99_I124_L0.279690.771
97_W101_D0.267130.736
34_V39_I0.265720.732
88_K99_I0.264210.728
120_I123_I0.263580.726
97_W117_V0.262980.725
46_S51_S0.262140.722
98_E102_R0.254380.701
99_I103_L0.253150.698
65_P69_G0.250.689
27_V63_I0.248810.686
24_Q57_Y0.248260.684
97_W100_R0.248210.684
46_S52_K0.247190.681
20_N23_R0.245050.675
85_E123_I0.243490.671
80_V103_L0.241690.666
24_Q27_V0.240550.663
94_I99_I0.234830.647
26_I43_L0.233250.643
51_S55_S0.229650.633
22_L26_I0.227750.628
91_N97_W0.226480.624
79_E82_E0.225210.621
70_G73_P0.22240.613
37_C51_S0.221270.610
31_K57_Y0.219360.605
96_A124_L0.216920.598
80_V84_I0.215330.593
99_I120_I0.21520.593
91_N94_I0.214350.591
73_P89_R0.213630.589
87_Y102_R0.21250.586
77_T81_V0.211790.584
20_N64_R0.211110.582
59_E62_S0.210440.580
78_P81_V0.208330.574
57_Y62_S0.207870.573
87_Y91_N0.204780.564
55_S58_R0.203460.561
27_V31_K0.201290.555
74_R81_V0.19950.550
67_P108_V0.198650.547
74_R78_P0.198640.547
104_I108_V0.196790.542
72_K81_V0.196230.541
45_V49_C0.195310.538
53_I63_I0.195060.538
33_G39_I0.193280.533
96_A100_R0.192450.530
22_L53_I0.190720.526
95_F103_L0.190110.524
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
1pdnC199.70.21
1k78A199.70.217
2k27A199.70.237
1u78A0.80899.40.367
3hotA0.899.30.417
2lvsA0.78499.20.43
4fcyA0.96898.50.587
1hlvA0.8898.10.635
2elhA0.65697.80.66
1tc3C0.40897.80.661

Page generated in 0.0253 seconds.