GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyoxalase - GlyoxalaseBleomycin resistance proteinDioxygenase superfamily
Pfam: PF00903 (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: CL0104
Length: 128
Sequences: 22126
Seq/Len: 172.86
HH_delta: 0.059 (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
17_D21_D2.691723.429
11_D14_K2.348582.992
93_R97_Q2.333942.973
91_Y95_K2.15312.743
92_E96_A1.951172.485
16_I20_T1.745862.224
102_V119_R1.697732.163
15_A122_D1.674122.132
90_A93_R1.644192.094
94_L99_V1.627192.073
16_I27_L1.548131.972
100_E119_R1.526341.944
86_D89_A1.478171.883
20_T27_L1.468461.870
9_V15_A1.452831.851
120_D124_N1.452131.850
27_L30_E1.424731.815
89_A93_R1.393361.775
95_K101_I1.324061.687
17_D20_T1.30181.658
16_I30_E1.300021.656
10_K122_D1.292581.646
21_D97_Q1.289941.643
94_L118_F1.261621.607
92_E95_K1.232071.569
13_E17_D1.181131.504
52_I56_L1.14771.462
14_K122_D1.143411.456
91_Y101_I1.135271.446
83_D86_D1.132781.443
93_R96_A1.124011.432
119_R125_L1.11341.418
88_D92_E1.100491.402
82_F86_D1.052651.341
14_K17_D1.042541.328
22_V97_Q1.030361.312
16_I43_A1.009881.286
90_A128_F1.003861.279
28_V46_R0.994241.266
88_D113_G0.979571.248
84_V90_A0.957341.219
19_Y120_D0.949971.210
95_K104_E0.942651.201
91_Y105_P0.936531.193
79_F82_F0.933181.189
118_F126_I0.9111.160
102_V125_L0.883991.126
13_E16_I0.875671.115
12_L16_I0.868661.106
76_H79_F0.839241.069
89_A92_E0.827381.054
101_I104_E0.796531.015
91_Y104_E0.793621.011
20_T26_R0.786041.001
41_R44_F0.77020.981
46_R49_E0.765570.975
26_R46_R0.764910.974
22_V99_V0.761370.970
118_F128_F0.726270.925
12_L56_L0.709530.904
76_H127_E0.706650.900
88_D91_Y0.702240.894
99_V118_F0.689910.879
84_V88_D0.689740.879
41_R56_L0.689580.878
87_L91_Y0.688020.876
118_F121_P0.685430.873
79_F127_E0.684030.871
25_F47_I0.683730.871
87_L105_P0.681770.868
78_A81_A0.673720.858
18_F22_V0.662420.844
10_K14_K0.659340.840
110_F114_Y0.65810.838
107_R113_G0.654850.834
41_R45_L0.64070.816
15_A19_Y0.639010.814
50_G56_L0.637780.812
103_E106_D0.630810.804
9_V122_D0.624930.796
42_I53_E0.621590.792
20_T45_L0.621270.791
18_F99_V0.614120.782
15_A124_N0.612960.781
13_E30_E0.608570.775
12_L15_A0.599010.763
91_Y103_E0.591720.754
76_H82_F0.577680.736
107_R110_F0.569430.725
15_A121_P0.567430.723
14_K121_P0.562120.716
17_D22_V0.559260.712
25_F45_L0.55540.707
119_R123_G0.552780.704
22_V94_L0.552490.704
64_A67_H0.551790.703
58_P61_P0.544250.693
22_V25_F0.543170.692
107_R112_S0.537280.684
6_A55_F0.53560.682
48_G51_H0.530850.676
81_A127_E0.530410.676
46_R51_H0.527870.672
47_I50_G0.525520.669
11_D17_D0.525410.669
19_Y126_I0.52470.668
40_L45_L0.522260.665
102_V105_P0.519280.661
77_I82_F0.519180.661
5_I50_G0.513720.654
120_D123_G0.512660.653
4_H81_A0.512550.653
11_D15_A0.510630.650
51_H56_L0.500030.637
9_V12_L0.495480.631
53_E57_N0.494540.630
18_F121_P0.492710.628
56_L59_S0.489050.623
28_V51_H0.483490.616
7_I124_N0.476510.607
42_I46_R0.475540.606
95_K99_V0.469320.598
88_D105_P0.468890.597
57_N60_P0.462280.589
9_V54_L0.462150.589
9_V124_N0.461760.588
27_L43_A0.457460.583
108_Y114_Y0.455870.581
90_A94_L0.454090.578
77_I80_L0.449160.572
41_R46_R0.448320.571
53_E56_L0.448060.571
44_F53_E0.446770.569
40_L43_A0.446030.568
103_E108_Y0.443420.565
6_A79_F0.440360.561
43_A47_I0.438370.558
40_L44_F0.438240.558
87_L128_F0.436830.556
81_A128_F0.434460.553
94_L97_Q0.42940.547
85_D89_A0.429170.547
110_F113_G0.422920.539
30_E41_R0.422850.539
6_A78_A0.422120.538
20_T25_F0.420310.535
21_D93_R0.41950.534
4_H76_H0.419310.534
30_E42_I0.417260.531
12_L30_E0.416580.531
63_R66_G0.416410.530
88_D112_S0.414930.529
10_K15_A0.412050.525
84_V87_L0.410780.523
7_I15_A0.409440.522
76_H124_N0.404490.515
76_H80_L0.401470.511
30_E43_A0.400860.511
114_Y127_E0.400850.511
105_P113_G0.399750.509
101_I105_P0.397270.506
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
4g6xA0.960999.60.059
3oa4A0.960999.50.131
3vb0A0.921999.50.134
3l7tA0.945399.50.137
3rheA0.890699.50.14
3kolA0.960999.50.142
3lm4A0.921999.50.145
3vw9A0.968899.50.148
3hpyA0.921999.50.148
3hdpA0.953199.50.148

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