GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GlutR_dimer - Glutamyl-tRNAGlu reductase dimerisation domain
Pfam: PF00745 (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: 101
Sequences: 1140
Seq/Len: 11.29
HH_delta: 0.191 (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
52_D55_D0.515982.936
38_R63_T0.497612.832
35_E38_R0.412182.346
31_R68_N0.380642.166
41_E69_K0.379092.157
14_F17_W0.372052.117
45_A58_V0.369312.102
10_E13_E0.361172.055
41_E44_R0.350421.994
31_R75_I0.349671.990
41_E65_S0.345971.969
46_L56_E0.301691.717
61_K65_S0.28461.620
45_A62_L0.282281.606
90_Y97_L0.261391.488
33_K73_P0.253151.441
34_A70_L0.252831.439
86_D89_E0.245581.398
31_R72_H0.239991.366
3_A6_I0.236731.347
38_R64_R0.232341.322
30_L98_F0.231311.316
35_E39_D0.229451.306
45_A63_T0.221071.258
34_A71_L0.22061.255
11_V14_F0.216851.234
57_E61_K0.20831.185
29_A95_R0.207951.183
92_E96_K0.205121.167
17_W24_D0.203851.160
38_R60_E0.202231.151
21_R24_D0.20131.146
51_L55_D0.19611.116
94_L97_L0.195781.114
48_K51_L0.194221.105
63_T66_L0.189461.078
33_K43_E0.188621.073
41_E61_K0.187491.067
36_E40_E0.186891.064
17_W20_S0.183031.042
32_E36_E0.179741.023
49_L58_V0.179361.021
80_E84_E0.179261.020
17_W27_I0.178241.014
2_K17_W0.177631.011
8_E12_D0.174910.995
25_P30_L0.174520.993
16_R19_K0.172380.981
70_L74_P0.170960.973
32_E73_P0.170590.971
77_N80_E0.169090.962
12_D19_K0.167990.956
74_P97_L0.167550.954
39_D42_L0.165530.942
26_V29_A0.164870.938
5_E8_E0.164730.937
55_D101_D0.164030.934
59_I62_L0.163920.933
17_W21_R0.161680.920
12_D16_R0.160670.914
67_V70_L0.15960.908
23_V79_R0.159290.907
30_L100_L0.158960.905
3_A99_G0.158730.903
55_D59_I0.158130.900
30_L94_L0.157910.899
39_D60_E0.157740.898
27_I72_H0.156640.891
73_P99_G0.156570.891
14_F20_S0.15640.890
77_N97_L0.156180.889
30_L71_L0.154170.877
56_E60_E0.153930.876
52_D59_I0.153680.875
48_K53_E0.152170.866
19_K82_A0.150660.857
47_K59_I0.150310.855
8_E11_V0.148680.846
63_T69_K0.14810.843
42_L72_H0.145820.830
4_E8_E0.145460.828
58_V63_T0.145330.827
1_R7_I0.144160.820
38_R45_A0.143940.819
60_E63_T0.143780.818
82_A86_D0.143420.816
3_A20_S0.142750.812
54_D59_I0.141630.806
78_L94_L0.140470.799
13_E53_E0.138630.789
21_R43_E0.1380.785
26_V100_L0.137350.782
14_F18_L0.136970.780
44_R72_H0.136890.779
5_E43_E0.136390.776
1_R4_E0.136050.774
5_E9_E0.135620.772
16_R83_E0.134890.768
60_E64_R0.134690.767
33_K36_E0.134660.766
45_A52_D0.134550.766
78_L96_K0.134130.763
79_R84_E0.134070.763
24_D29_A0.133280.759
81_A85_G0.13210.752
39_D57_E0.131230.747
21_R60_E0.131190.747
3_A58_V0.131050.746
38_R68_N0.130520.743
34_A67_V0.13040.742
31_R74_P0.130270.741
84_E93_A0.130240.741
44_R65_S0.130050.740
31_R70_L0.129780.739
26_V95_R0.129320.736
32_E39_D0.128890.734
76_S80_E0.128540.732
52_D58_V0.128260.730
50_D56_E0.128060.729
5_E12_D0.128060.729
19_K85_G0.128030.729
85_G89_E0.128010.729
94_L98_F0.127630.726
2_K5_E0.126860.722
71_L74_P0.126670.721
19_K86_D0.125910.717
35_E46_L0.125530.714
89_E92_E0.12460.709
38_R71_L0.124580.709
20_S83_E0.124310.707
24_D31_R0.123110.701
37_I75_I0.122520.697
38_R66_L0.122430.697
23_V91_L0.121520.692
28_K96_K0.121480.691
42_L74_P0.12140.691
65_S69_K0.120660.687
45_A65_S0.120430.685
53_E83_E0.119950.683
20_S72_H0.119920.682
54_D57_E0.119740.681
56_E59_I0.11960.681
75_I79_R0.119280.679
70_L75_I0.118590.675
81_A84_E0.117850.671
11_V57_E0.117820.671
92_E99_G0.117470.669
28_K32_E0.117030.666
57_E64_R0.116740.664
23_V68_N0.11670.664
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
1gpjA0.980299.60.191
1nytA0.346555.10.844
2w6bA0.5545350.861
1p77A0.346526.10.869
3sgiA0.920815.60.881
4glxA0.920812.90.885
4b9qA0.465312.10.887
4a8eA0.722811.80.887
2ck3A0.712910.80.889
2owoA0.920810.40.89

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