GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
BMC - BMC domain
Pfam: PF00936 (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: 75
Sequences: 1291
Seq/Len: 17.21
HH_delta: -0.014 (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
21_A44_I0.869583.610
47_D50_A0.580562.410
56_D60_E0.53052.203
52_K56_D0.51742.148
14_A42_V0.516532.145
60_E64_K0.387441.609
34_L37_G0.37281.548
18_A29_L0.372111.545
60_E63_G0.360461.497
46_G51_V0.359821.494
27_V44_I0.341.412
57_A61_A0.31991.328
25_A53_A0.302851.257
5_I43_I0.297691.236
9_K39_K0.296351.230
20_A61_A0.294861.224
30_V45_T0.293341.218
26_N49_S0.287961.196
11_I36_C0.281741.170
8_T14_A0.280681.165
31_E43_I0.280061.163
32_I37_G0.27741.152
20_A57_A0.276161.147
21_A58_A0.275761.145
4_G55_V0.275281.143
61_A65_K0.261311.085
13_A65_K0.259561.078
3_L43_I0.258881.075
59_E63_G0.258571.074
14_A32_I0.254791.058
33_E41_T0.252751.049
57_A60_E0.252331.048
20_A58_A0.252291.047
6_I58_A0.250041.038
6_I55_V0.249591.036
49_S53_A0.247231.026
35_I39_K0.242271.006
20_A24_A0.242011.005
22_L29_L0.240410.998
58_A62_A0.240310.998
8_T62_A0.238890.992
7_E39_K0.232280.964
11_I15_I0.225290.935
2_A45_T0.223730.929
18_A42_V0.22250.924
4_G19_D0.217830.904
14_A40_V0.217650.904
28_E57_A0.217080.901
26_N50_A0.216140.897
17_A62_A0.212440.882
19_D23_K0.209580.870
16_V47_D0.204890.851
5_I40_V0.203570.845
55_V59_E0.19370.804
13_A61_A0.19370.804
5_I41_T0.192610.800
10_G39_K0.19210.798
16_V64_K0.191840.796
9_K13_A0.188670.783
5_I35_I0.188010.781
10_G13_A0.186510.774
1_K52_K0.1860.772
61_A64_K0.183330.761
37_G40_V0.182960.760
52_K64_K0.182850.759
28_E45_T0.182130.756
53_A56_D0.181910.755
24_A57_A0.179750.746
42_V49_S0.179410.745
1_K45_T0.176440.733
17_A61_A0.175120.727
13_A37_G0.169820.705
11_I22_L0.169520.704
10_G33_E0.168720.700
25_A57_A0.168070.698
17_A48_V0.167240.694
36_C43_I0.167240.694
29_L54_A0.167090.694
8_T13_A0.166420.691
21_A39_K0.165990.689
11_I14_A0.165960.689
2_A48_V0.165860.689
3_L31_E0.164320.682
3_L45_T0.163440.679
9_K12_A0.163360.678
11_I38_G0.162990.677
29_L41_T0.161770.672
19_D55_V0.161760.672
12_A40_V0.161690.671
4_G27_V0.161430.670
21_A40_V0.160890.668
52_K59_E0.160230.665
26_N47_D0.160.664
28_E50_A0.159880.664
18_A30_V0.15950.662
36_C40_V0.159210.661
45_T50_A0.156820.651
13_A38_G0.156380.649
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
3ngkA199.8-0.014
3mpyA199.8-0.014
3ssrB199.8-0.014
2a10A199.8-0.01
4axjA199.8-0.01
3bn4A199.8-0.01
3ssqA199.8-0.009
2a1bA199.8-0.008
3cimA199.8-0.006
3gv2A199.80.004

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