GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CysG_dimeriser - Sirohaem synthase dimerisation region
Pfam: PF10414 (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: 60
Sequences: 761
Seq/Len: 12.68
HH_delta: 0.113 (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_D50_E0.546642.653
12_R52_E0.406851.975
4_G7_A0.351631.707
23_D26_E0.351131.704
9_L39_F0.346871.684
21_L30_F0.318151.544
39_F43_V0.299171.452
7_A28_R0.292981.422
10_A31_W0.287241.394
42_L47_D0.286621.391
16_R56_E0.275431.337
15_E19_Q0.272561.323
10_A35_F0.269891.310
2_S44_L0.269191.307
41_E45_A0.257281.249
6_L10_A0.253411.230
54_L57_Q0.249651.212
6_L40_A0.248041.204
37_G40_A0.24321.180
18_K31_W0.242441.177
43_V51_A0.238471.157
28_R32_E0.237951.155
46_G51_A0.236931.150
49_E57_Q0.230771.120
21_L27_R0.229921.116
50_E53_A0.226811.101
3_L36_D0.225491.094
38_P44_L0.222551.080
34_F58_A0.221321.074
2_S5_R0.213051.034
17_V32_E0.212921.033
14_R31_W0.212251.030
49_E53_A0.210581.022
3_L40_A0.207411.007
10_A30_F0.205590.998
21_L26_E0.203210.986
34_F39_F0.202390.982
13_F39_F0.197560.959
18_K34_F0.196980.956
6_L9_L0.195920.951
12_R26_E0.194180.942
2_S16_R0.185740.902
11_G35_F0.185730.901
31_W35_F0.185490.900
54_L58_A0.182210.884
27_R30_F0.181630.882
52_E55_L0.180940.878
14_R28_R0.179830.873
45_A56_E0.179490.871
13_F30_F0.173340.841
5_R48_E0.172950.839
37_G51_A0.170770.829
17_V39_F0.170440.827
42_L50_E0.169330.822
15_E22_P0.168290.817
22_P27_R0.167390.812
35_F58_A0.167310.812
31_W34_F0.165830.805
5_R46_G0.164940.801
9_L13_F0.163970.796
26_E29_R0.162640.789
13_F37_G0.160810.781
32_E35_F0.160790.780
25_A29_R0.160460.779
5_R8_E0.159880.776
6_L39_F0.159770.775
29_R41_E0.158660.770
1_Q46_G0.158470.769
13_F55_L0.155930.757
49_E54_L0.155430.754
6_L17_V0.155350.754
22_P25_A0.155210.753
3_L41_E0.155090.753
24_F32_E0.154640.751
22_P52_E0.154150.748
3_L44_L0.153430.745
2_S7_A0.152770.741
17_V31_W0.152520.740
42_L51_A0.152260.739
5_R12_R0.150750.732
5_R25_A0.148770.722
15_E20_R0.147290.715
29_R53_A0.145440.706
37_G46_G0.145130.704
45_A53_A0.145040.704
33_R58_A0.143370.696
41_E44_L0.142840.693
52_E56_E0.142520.692
8_E24_F0.141010.684
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
1pjqA198.30.113
3dfzA0.9597.80.24
1kyqA1950.478
3fysA0.96675.70.795
3bldA0.63335.50.796
3sxmA0.96675.30.798
2pjwV0.83335.20.798
3qwwA0.933350.8
3sxyA0.96674.70.803
2di3A0.96674.70.803

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