GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
B12-binding - B12 binding domain
Pfam: PF02310 (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. )
Length: 121
Sequences: 64238
Seq/Len: 530.89
HH_delta: -0.091 (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_L33_I3.283982.489
17_L38_V3.2542.466
41_E64_N3.051482.312
61_M90_H3.020112.289
44_V74_A2.782812.109
21_A33_I2.676832.028
57_I71_L2.674072.026
32_D52_P2.661032.017
48_R78_R2.63371.996
65_L74_A2.562141.942
39_P64_N2.551361.933
46_A50_E2.353231.783
40_P65_L2.344671.777
72_A84_I2.327581.764
38_V42_E2.176751.650
21_A25_R2.082111.578
46_A49_A2.008331.522
55_V82_I1.991311.509
39_P42_E1.99091.509
74_A78_R1.98561.505
76_K106_D1.920941.456
32_D46_A1.915541.452
86_V105_I1.912551.449
67_E70_R1.908681.446
32_D50_E1.895731.437
74_A77_E1.825021.383
65_L70_R1.813941.375
46_A52_P1.742941.321
40_P71_L1.738481.317
59_V69_K1.717861.302
34_L46_A1.655341.254
12_V58_S1.634071.238
42_E46_A1.615821.224
72_A86_V1.590861.206
41_E65_L1.58761.203
47_L75_I1.580431.198
41_E45_E1.565521.186
86_V98_I1.53211.161
44_V71_L1.521341.153
14_P18_L1.520241.152
57_I84_I1.498931.136
70_R73_R1.482071.123
43_L71_L1.460451.107
69_K98_I1.448891.098
18_L21_A1.39611.058
90_H95_P1.369921.038
59_V86_V1.363671.033
69_K97_E1.361021.031
45_E49_A1.355851.027
16_G19_Y1.354951.027
97_E100_R1.335671.012
13_H16_G1.332561.010
70_R74_A1.329541.008
20_L87_G1.308050.991
96_E100_R1.270880.963
42_E45_E1.268110.961
92_T95_P1.24520.944
107_Y111_G1.223660.927
44_V48_R1.22350.927
18_L22_A1.223010.927
15_L19_Y1.21840.923
93_A96_E1.216650.922
47_L79_N1.216170.922
55_V84_I1.202620.911
59_V67_E1.202520.911
45_E48_R1.20180.911
57_I72_A1.193420.904
72_A105_I1.177720.892
14_P17_L1.164240.882
47_L82_I1.159750.879
44_V65_L1.146670.869
11_E17_L1.1460.868
73_R103_P1.145290.868
56_G87_G1.139060.863
107_Y110_R1.128570.855
34_L43_L1.115470.845
19_Y22_A1.1150.845
22_A26_K1.0950.830
79_N82_I1.088970.825
23_Y27_A1.088330.825
14_P38_V1.088280.825
97_E103_P1.078230.817
104_G107_Y1.064060.806
55_V75_I1.052670.798
43_L47_L1.024650.776
69_K73_R1.011850.767
31_V34_L0.996070.755
83_P106_D0.986730.748
19_Y23_Y0.982390.744
72_A103_P0.978740.742
21_A31_V0.96920.734
56_G85_V0.944280.716
40_P44_V0.940780.713
108_V111_G0.934430.708
72_A76_K0.92840.704
16_G20_L0.900470.682
13_H89_P0.896380.679
76_K82_I0.890040.674
15_L22_A0.888880.674
59_V98_I0.886810.672
91_A110_R0.88270.669
54_V85_V0.881790.668
61_M89_P0.879330.666
73_R97_E0.871820.661
11_E111_G0.866530.657
94_D97_E0.847530.642
73_R77_E0.846990.642
48_R74_A0.842150.638
71_L75_I0.837830.635
57_I86_V0.827970.627
29_H33_I0.817280.619
58_S62_T0.811410.615
13_H19_Y0.803650.609
15_L18_L0.792050.600
96_E99_L0.787520.597
42_E64_N0.784030.594
59_V105_I0.779160.590
12_V62_T0.77720.589
85_V107_Y0.777070.589
98_I108_V0.777040.589
24_L31_V0.770890.584
40_P62_T0.769810.583
25_R31_V0.768870.583
34_L42_E0.767740.582
51_R79_N0.76550.580
44_V47_L0.762590.578
86_V104_G0.756540.573
59_V90_H0.754070.571
76_K83_P0.752380.570
39_P43_L0.746530.566
28_G31_V0.741620.562
12_V89_P0.738910.560
48_R79_N0.722430.547
57_I75_I0.720610.546
22_A25_R0.719440.545
12_V63_P0.715160.542
99_L103_P0.712450.540
11_E62_T0.711320.539
103_P107_Y0.709570.538
16_G87_G0.702570.532
27_A31_V0.702520.532
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
3to5A0.909199.2-0.091
3dzdA0.909199.2-0.064
3eq2A0.909199.2-0.056
3n0rA0.892699.1-0.042
1ny5A0.909199.1-0.04
3rqiA0.909199.1-0.038
4eukA0.917499.1-0.035
2lpmA0.87699.1-0.025
3r0jA0.909199.1-0.024
2ayxA0.909199.1-0.014

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