GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cytochrom_B_C - Cytochrome b(C-terminal)b6petD
Pfam: PF00032 (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: 102
Sequences: 3404
Seq/Len: 33.37
HH_delta: -0.047 (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
74_S100_F1.023463.395
88_Y92_W0.932943.095
81_L94_G0.900142.986
77_V97_F0.830672.756
19_P79_T0.825252.738
23_I36_A0.698052.316
38_G42_L0.6652.206
46_L50_L0.606922.013
74_S97_F0.554071.838
88_Y91_I0.493241.636
92_W96_I0.492841.635
81_L93_I0.484711.608
91_I95_Q0.473761.572
86_P94_G0.46931.557
29_N32_G0.468511.554
61_R64_F0.460611.528
53_S56_R0.456661.515
27_I36_A0.449361.491
71_F75_F0.443211.470
58_P64_F0.442621.468
12_K83_S0.439561.458
70_L100_F0.437841.453
96_I100_F0.424951.410
3_N6_K0.416751.383
7_T11_I0.414841.376
55_V61_R0.411621.366
10_H85_P0.410681.362
47_L50_L0.410361.361
8_P11_I0.394351.308
70_L74_S0.391041.297
35_I39_L0.384321.275
26_S94_G0.382771.270
77_V93_I0.37491.244
42_L45_F0.374511.242
66_A70_L0.356871.184
20_F37_M0.353561.173
71_F74_S0.350831.164
8_P33_G0.344061.141
91_I94_G0.340761.130
80_W84_Q0.340361.129
92_W95_Q0.340191.129
96_I99_I0.339321.126
69_W73_I0.339221.125
37_M41_I0.332131.102
42_L46_L0.33151.100
87_E90_F0.327531.087
98_T101_Y0.324721.077
9_A12_K0.318581.057
65_R69_W0.306471.017
64_F67_A0.301911.002
14_E18_L0.301671.001
93_I97_F0.299130.992
20_F79_T0.299020.992
63_I66_A0.298840.991
67_A70_L0.298420.990
38_G41_I0.297130.986
91_I97_F0.293760.975
39_L46_L0.282790.938
11_I21_Y0.279770.928
19_P40_S0.278730.925
19_P37_M0.27860.924
41_I101_Y0.277930.922
75_F84_Q0.277130.919
68_F72_V0.27690.919
6_K66_A0.267990.889
37_M40_S0.265610.881
61_R97_F0.265230.880
13_P21_Y0.262270.870
20_F23_I0.260150.863
38_G45_F0.25850.858
80_W93_I0.256410.851
58_P66_A0.254730.845
24_L33_G0.254090.843
92_W99_I0.251160.833
51_D55_V0.249790.829
56_R60_F0.249740.829
75_F99_I0.248520.824
14_E30_K0.247120.820
86_P91_I0.247060.820
70_L73_I0.246880.819
11_I33_G0.244940.813
7_T10_H0.24170.802
51_D56_R0.241070.800
59_R73_I0.24050.798
34_V37_M0.238970.793
22_A78_L0.237170.787
31_L35_I0.236630.785
58_P65_R0.236380.784
72_V75_F0.236220.784
15_W24_L0.234080.777
67_A74_S0.233430.774
50_L93_I0.229840.762
1_P9_A0.2250.746
90_F93_I0.223990.743
60_F71_F0.223780.742
4_P62_P0.221510.735
45_F50_L0.218180.724
46_L49_F0.217840.723
49_F92_W0.215270.714
12_K32_G0.215040.713
11_I30_K0.214960.713
53_S61_R0.213280.708
22_A26_S0.213080.707
22_A83_S0.212790.706
92_W97_F0.211770.703
52_R64_F0.211640.702
27_I32_G0.21160.702
30_K33_G0.21080.699
53_S67_A0.210520.698
43_I101_Y0.20980.696
89_P94_G0.209580.695
49_F59_R0.208930.693
66_A72_V0.207850.690
97_F100_F0.207210.687
70_L88_Y0.203770.676
22_A57_S0.203140.674
71_F97_F0.202690.672
53_S57_S0.201470.668
52_R88_Y0.199470.662
20_F40_S0.198980.660
40_S43_I0.198620.659
47_L92_W0.197730.656
18_L79_T0.196130.651
54_P57_S0.196090.651
37_M86_P0.196070.650
88_Y97_F0.196010.650
28_P31_L0.193310.641
4_P36_A0.191040.634
78_L81_L0.190470.632
6_K99_I0.190050.630
75_F79_T0.18940.628
5_L37_M0.1870.620
70_L75_F0.186610.619
6_K39_L0.186220.618
45_F100_F0.186160.618
8_P14_E0.184290.611
3_N31_L0.183020.607
34_V78_L0.179970.597
22_A34_V0.179440.595
67_A100_F0.176580.586
70_L92_W0.175470.582
73_I77_V0.175020.581
24_L34_V0.174850.580
4_P85_P0.174550.579
1_P100_F0.173720.576
58_P63_I0.172740.573
22_A82_G0.172730.573
73_I97_F0.172570.573
7_T21_Y0.172060.571
57_S61_R0.171840.570
50_L55_V0.171190.568
46_L96_I0.170120.564
23_I28_P0.17010.564
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
1pp9C1100-0.047
3cx5C1100-0.045
2qjyA1100-0.035
1vf5B0.931499.90.095
4h44B0.931499.90.125
3effK0.70594.70.929
2k1eA0.69613.40.934
3qhoA0.42163.10.935
3arcI0.37253.10.935
2hi7B0.5492.60.937

Page generated in 0.0336 seconds.