GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
MoCF_biosynth - Probable molybdopterin binding domain
Pfam: PF00994 (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: 144
Sequences: 5590
Seq/Len: 38.82
HH_delta: 0.044 (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
47_K80_E1.538653.410
26_L31_I1.446833.206
43_P80_E1.344132.978
1_A57_A1.294462.868
25_L135_E1.038932.302
43_P77_A1.022142.265
78_L122_G0.964772.138
47_K51_R0.857811.901
49_A52_R0.834631.849
91_E94_R0.818991.815
43_P47_K0.797091.766
42_D45_A0.784081.737
3_I53_A0.77571.719
40_P45_A0.770991.708
23_A27_E0.755011.673
52_R56_R0.751221.665
7_D71_D0.746121.653
96_V99_R0.729551.617
134_L138_V0.728511.614
22_L134_L0.72721.611
2_I23_A0.717751.590
1_A53_A0.716811.588
37_G49_A0.713211.580
121_F138_V0.693361.536
51_R81_A0.684561.517
37_G52_R0.680591.508
16_D19_G0.677131.500
47_K81_A0.669471.483
21_F131_K0.655031.451
39_V49_A0.651491.444
34_I57_A0.630951.398
23_A36_Y0.629431.395
43_P73_V0.623541.382
43_P76_E0.608371.348
9_L14_I0.598651.327
25_L134_L0.598321.326
45_A48_E0.587251.301
2_I33_V0.57371.271
48_E52_R0.570731.265
47_K77_A0.570381.264
45_A49_A0.561311.244
65_G74_T0.549421.217
25_L28_E0.525761.165
44_D48_E0.514181.139
5_T39_V0.511661.134
18_N63_T0.509141.128
54_L120_V0.505241.120
59_L121_F0.500841.110
8_E14_I0.498991.106
44_D47_K0.498131.104
20_P24_A0.497521.102
124_P129_A0.492411.091
62_T122_G0.492371.091
10_L13_Q0.490851.088
15_R20_P0.48871.083
105_G122_G0.487021.079
96_V137_L0.485241.075
39_V45_A0.485211.075
121_F141_L0.483291.071
61_I123_L0.483131.071
98_M137_L0.47811.059
49_A53_A0.47571.054
4_S16_D0.474771.052
26_L33_V0.474381.051
3_I39_V0.474291.051
29_L134_L0.472851.048
3_I49_A0.470141.042
5_T46_I0.464971.030
63_T130_A0.454761.008
78_L120_V0.454531.007
7_D40_P0.451531.001
1_A56_R0.446860.990
26_L134_L0.437430.969
59_L142_L0.4290.951
17_S127_P0.421360.934
37_G53_A0.419290.929
54_L118_K0.411620.912
106_L121_F0.403220.894
97_S101_G0.40070.888
51_R54_L0.397060.880
19_G35_R0.396850.879
92_L95_G0.396190.878
21_F130_A0.395150.876
53_A57_A0.393650.872
21_F24_A0.393530.872
75_P94_R0.39250.870
43_P46_I0.390010.864
4_S38_I0.388310.860
93_F97_S0.386250.856
4_S63_T0.385110.853
104_T133_M0.38470.852
46_I77_A0.384330.852
16_D20_P0.383940.851
51_R55_D0.383710.850
25_L29_L0.381980.846
4_S19_G0.378880.840
77_A81_A0.377880.837
50_L78_L0.375060.831
19_G36_Y0.372970.826
46_I73_V0.37220.825
94_R98_M0.370660.821
76_E79_A0.369240.818
123_L134_L0.368940.818
26_L61_I0.367530.814
24_A28_E0.366340.812
41_D65_G0.359840.797
128_V132_V0.35890.795
92_L108_P0.358460.794
22_L63_T0.357260.792
109_G113_S0.356910.791
95_G98_M0.354610.786
72_D125_G0.353980.784
76_E80_E0.351180.778
98_M133_M0.347710.770
50_L60_V0.345970.767
94_R97_S0.345560.766
59_L119_P0.343240.761
5_T62_T0.343230.761
84_R108_P0.342210.758
25_L131_K0.341620.757
104_T137_L0.340760.755
126_N129_A0.334630.742
1_A35_R0.334070.740
1_A36_Y0.333180.738
8_E41_D0.331920.736
108_P113_S0.330480.732
3_I37_G0.328080.727
62_T66_T0.327130.725
5_T74_T0.324770.720
54_L60_V0.32440.719
77_A80_E0.322060.714
41_D125_G0.320480.710
102_K129_A0.320310.710
21_F25_L0.316730.702
66_T75_P0.315670.699
131_K135_E0.315630.699
42_D46_I0.314490.697
123_L133_M0.314420.697
61_I134_L0.31310.694
6_G9_L0.312830.693
34_I56_R0.312640.693
25_L138_V0.312290.692
63_T123_L0.311220.690
62_T120_V0.31120.690
27_E33_V0.309960.687
48_E55_D0.309510.686
35_R52_R0.308640.684
2_I26_L0.307790.682
94_R105_G0.306850.680
44_D51_R0.306750.680
2_I22_L0.306260.679
23_A33_V0.30540.677
19_G23_A0.304960.676
100_P132_V0.303360.672
36_Y53_A0.303130.672
10_L15_R0.302910.671
46_I50_L0.30260.671
52_R55_D0.302190.670
4_S36_Y0.301910.669
4_S37_G0.30150.668
60_V118_K0.300520.666
2_I19_G0.298770.662
50_L62_T0.298620.662
62_T74_T0.296040.656
12_G15_R0.295230.654
4_S18_N0.294650.653
53_A60_V0.294270.652
22_L61_I0.289170.641
48_E51_R0.287670.637
84_R113_S0.284990.632
36_Y56_R0.284920.631
31_I142_L0.284250.630
103_P137_L0.284040.629
36_Y57_A0.283830.629
123_L130_A0.283450.628
126_N132_V0.282810.627
20_P36_Y0.282640.626
123_L138_V0.28130.623
12_G16_D0.280920.622
75_P79_A0.280880.622
18_N130_A0.280350.621
44_D80_E0.279450.619
27_E32_E0.2790.618
22_L130_A0.278550.617
67_G103_P0.276260.612
3_I62_T0.275630.611
24_A131_K0.273420.606
95_G99_R0.270260.599
130_A134_L0.268160.594
66_T105_G0.268070.594
35_R53_A0.264750.587
136_V140_P0.264310.586
109_G133_M0.264030.585
84_R92_L0.263820.585
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
3rfqA0.98611000.044
2pjkA0.99311000.05
2ftsA0.94441000.066
1g8lA0.90971000.067
3pzyA0.97921000.069
1uz5A0.90971000.07
1y5eA0.97921000.082
2g2cA0.98611000.092
1mkzA0.97921000.098
1jljA0.95141000.102

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