GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FAD_binding_5 - FAD binding domain in molybdopterin dehydrogenase
Pfam: PF00941 (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: CL0077
Length: 171
Sequences: 9281
Seq/Len: 54.27
HH_delta: 0.05 (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
133_E165_S1.873083.723
67_R165_S1.688363.356
131_R142_T1.645613.271
67_R167_R1.391682.766
11_L133_E1.330442.644
133_E142_T1.226782.438
131_R167_R1.162922.311
72_V77_L1.157092.300
133_E140_T1.032222.052
6_F17_L1.002831.993
65_G167_R0.981281.950
135_A164_T0.964631.917
136_S141_R0.9621.912
112_L166_I0.923161.835
6_F46_V0.916151.821
73_T76_E0.907371.804
133_E167_R0.892371.774
7_R52_R0.876891.743
7_R49_D0.87221.734
55_E69_G0.852961.695
125_L132_V0.844731.679
10_S13_E0.839341.668
11_L15_L0.838061.666
131_R144_P0.836351.662
68_I77_L0.833761.657
140_T164_T0.828341.646
75_S79_E0.823511.637
14_A164_T0.811681.613
9_K13_E0.803361.597
69_G165_S0.796251.583
144_P147_D0.794451.579
9_K52_R0.784641.560
12_E16_E0.783231.557
53_I69_G0.782781.556
57_N69_G0.781991.554
69_G72_V0.757351.505
26_I162_L0.749721.490
134_I161_E0.74971.490
126_L169_P0.743451.478
134_I143_V0.73611.463
142_T167_R0.727991.447
80_S85_Q0.711931.415
15_L19_A0.706741.405
14_A162_L0.674861.341
132_V152_P0.661711.315
113_C163_I0.653831.300
27_V47_L0.650811.294
68_I168_I0.645811.284
54_P76_E0.644221.280
4_E46_V0.639441.271
132_V163_I0.624051.240
141_R161_E0.617691.228
23_D45_D0.609951.212
24_A48_I0.600721.194
15_L135_A0.59581.184
65_G126_L0.591171.175
50_L162_L0.584531.162
5_Y49_D0.58171.156
12_E15_L0.578011.149
135_A139_G0.576911.147
60_S67_R0.574151.141
58_G72_V0.573661.140
108_I166_I0.570131.133
15_L140_T0.569331.132
135_A140_T0.568411.130
61_E86_Y0.564081.121
18_L24_A0.551721.097
94_A97_I0.540881.075
148_F157_L0.537651.069
7_R51_S0.535661.065
27_V30_G0.534011.061
8_P13_E0.522571.039
134_I141_R0.514861.023
80_S84_Q0.505891.006
22_P46_V0.50551.005
17_L46_V0.504221.002
11_L14_A0.503291.000
8_P17_L0.497910.990
76_E79_E0.496230.986
120_D123_P0.493410.981
11_L164_T0.491780.977
67_R133_E0.48620.966
68_I108_I0.4690.932
60_S63_D0.467010.928
8_P50_L0.466730.928
28_A71_A0.466290.927
50_L70_A0.465030.924
11_L140_T0.464470.923
29_G73_T0.463380.921
133_E164_T0.461870.918
14_A48_I0.453840.902
70_A109_G0.449860.894
64_G169_P0.448970.892
151_G154_K0.448390.891
14_A135_A0.447440.889
28_A107_T0.444380.883
65_G169_P0.443730.882
56_L80_S0.442060.879
74_L121_L0.440720.876
16_E19_A0.439880.874
72_V76_E0.439810.874
111_N115_A0.437140.869
50_L53_I0.436850.868
74_L106_A0.426370.847
96_R100_P0.421490.838
66_L81_P0.421350.837
112_L125_L0.417970.831
57_N76_E0.41770.830
59_I80_S0.403720.802
14_A53_I0.403570.802
32_D36_Q0.400950.797
95_R100_P0.399430.794
111_N121_L0.395950.787
107_T110_G0.394040.783
126_L131_R0.390020.775
114_N117_P0.389940.775
150_T156_D0.389060.773
79_E84_Q0.388770.773
50_L71_A0.388450.772
18_L135_A0.386510.768
13_E16_E0.385950.767
66_L77_L0.384580.764
4_E22_P0.384050.763
134_I157_L0.38290.761
68_I72_V0.382340.760
55_E72_V0.381840.759
66_L168_I0.379790.755
101_Q106_A0.379770.755
97_I100_P0.378470.752
99_S106_A0.377660.751
35_V38_R0.376910.749
61_E80_S0.375380.746
81_P85_Q0.374480.744
11_L69_G0.368390.732
108_I111_N0.368140.732
76_E80_S0.367770.731
96_R99_S0.362840.721
16_E20_K0.357990.712
59_I72_V0.357610.711
116_S153_R0.357010.710
15_L136_S0.356770.709
27_V33_L0.356350.708
74_L94_A0.356060.708
109_G163_I0.355130.706
138_D141_R0.352830.701
60_S65_G0.351490.699
74_L78_E0.349140.694
106_A111_N0.348610.693
61_E85_Q0.346680.689
121_L124_A0.3460.688
17_L48_I0.34480.685
106_A121_L0.344660.685
149_F154_K0.342820.681
119_S122_A0.341940.680
51_S73_T0.341640.679
115_A155_T0.339710.675
132_V166_I0.336570.669
97_I106_A0.335970.668
24_A46_V0.335580.667
25_R47_L0.335090.666
28_A50_L0.332730.661
126_L145_L0.331390.659
56_L69_G0.331070.658
74_L77_L0.329780.655
27_V49_D0.327570.651
8_P14_A0.327270.650
126_L167_R0.327110.650
4_E20_K0.326220.648
12_E135_A0.326020.648
136_S139_G0.325780.648
43_S47_L0.32560.647
18_L26_I0.323250.642
54_P72_V0.322760.642
8_P48_I0.320920.638
56_L72_V0.318260.633
28_A70_A0.317380.631
62_D65_G0.316240.629
66_L83_I0.314280.625
32_D114_N0.311760.620
58_G67_R0.311430.619
108_I168_I0.311370.619
25_R43_S0.311130.618
154_K159_P0.308690.614
86_Y89_A0.307680.612
18_L162_L0.306060.608
100_P106_A0.302650.602
57_N71_A0.302070.600
83_I86_Y0.299890.596
31_T111_N0.299640.596
121_L168_I0.296720.590
106_A114_N0.296460.589
74_L111_N0.296010.588
26_I48_I0.295710.588
6_F13_E0.295020.586
138_D160_G0.2930.582
58_G61_E0.291810.580
121_L125_L0.288890.574
12_E140_T0.288730.574
157_L163_I0.288270.573
148_F155_T0.288010.572
145_L149_F0.287040.571
70_A166_I0.286470.569
14_A50_L0.286360.569
132_V143_V0.286090.569
110_G115_A0.284740.566
74_L97_I0.2840.564
66_L80_S0.283770.564
149_F156_D0.283420.563
158_E161_E0.283030.563
134_I152_P0.281910.560
58_G69_G0.278920.554
53_I56_L0.276340.549
99_S116_S0.276320.549
26_I50_L0.273220.543
150_T155_T0.272340.541
150_T154_K0.269520.536
5_Y47_L0.269180.535
58_G165_S0.268770.534
143_V146_E0.26860.534
143_V156_D0.26760.532
132_V149_F0.267160.531
151_G160_G0.266250.529
62_D67_R0.266090.529
96_R101_Q0.264130.525
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
3hrdC11000.05
1t3qC11000.052
3zyvA11000.062
1n62C11000.064
3uncA11000.068
3nvzB11000.071
1ffvC11000.076
2w3sA0.98831000.077
1rm6B0.99421000.101
1hskA0.888999.80.335

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