GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GIDA_assoc_3 - GidA associated domain 3
Pfam: PF13932 (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: 72
Sequences: 1491
Seq/Len: 20.71
HH_delta: -0.051 (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
32_S46_E1.601614.972
30_D33_K0.901582.799
41_A66_A0.889792.762
11_Q15_E0.768122.385
4_E8_E0.749762.328
41_A62_V0.590971.835
44_K59_I0.585771.818
10_Q13_E0.556981.729
24_K51_R0.55631.727
63_T66_A0.555171.723
54_G58_R0.521761.620
32_S42_R0.520121.615
8_E11_Q0.507481.575
39_N42_R0.507051.574
68_S71_L0.501351.556
46_E49_R0.474241.472
53_I71_L0.463611.439
39_N43_E0.456031.416
21_E58_R0.454071.410
27_E51_R0.453291.407
42_R46_E0.450261.398
68_S72_V0.447651.390
53_I67_I0.418081.298
43_E47_K0.40611.261
21_E54_G0.398771.238
17_L54_G0.396981.232
25_I46_E0.379551.178
26_P49_R0.377731.173
38_S63_T0.369171.146
57_S67_I0.367231.140
27_E49_R0.359341.116
25_I29_F0.359061.115
15_E18_R0.354191.100
41_A63_T0.346631.076
62_V66_A0.33881.052
48_I55_Q0.332531.032
36_G69_L0.323251.004
35_P42_R0.316860.984
38_S41_A0.308970.959
28_D49_R0.303170.941
39_N60_P0.301820.937
2_K6_Y0.297770.924
48_I59_I0.295970.919
1_I20_D0.282630.877
16_R20_D0.268490.834
29_F34_I0.267470.830
44_K60_P0.263640.818
18_R54_G0.261670.812
55_Q58_R0.261260.811
24_K27_E0.259970.807
22_S33_K0.259790.806
8_E12_Q0.25680.797
28_D33_K0.249570.775
38_S66_A0.24940.774
31_Y37_L0.249340.774
17_L20_D0.246930.767
40_E44_K0.240490.747
22_S35_P0.234560.728
2_K5_G0.233070.724
4_E47_K0.232830.723
2_K16_R0.232030.720
50_P56_A0.230480.716
63_T69_L0.229050.711
12_Q15_E0.22580.701
59_I62_V0.223510.694
5_G8_E0.222750.692
10_Q14_I0.222750.692
9_R69_L0.222460.691
11_Q51_R0.222220.690
13_E17_L0.221110.686
11_Q18_R0.218510.678
2_K7_I0.217220.674
15_E19_K0.217220.674
20_D23_L0.214790.667
36_G39_N0.214640.666
13_E16_R0.212370.659
43_E62_V0.211390.656
48_I51_R0.209950.652
1_I4_E0.205840.639
24_K52_T0.203280.631
19_K36_G0.202830.630
6_Y40_E0.201360.625
26_P29_F0.200940.624
32_S39_N0.199580.620
1_I72_V0.198640.617
12_Q19_K0.196840.611
1_I48_I0.19590.608
3_Y7_I0.194040.602
25_I70_L0.193220.600
55_Q70_L0.188840.586
22_S36_G0.187480.582
14_I17_L0.186050.578
25_I31_Y0.185940.577
13_E68_S0.184940.574
31_Y45_L0.183790.571
1_I8_E0.183670.570
35_P69_L0.183370.569
20_D24_K0.183060.568
10_Q52_T0.181270.563
6_Y34_I0.181240.563
9_R44_K0.180060.559
41_A44_K0.179050.556
31_Y49_R0.177650.551
6_Y9_R0.177490.551
11_Q22_S0.176370.548
33_K46_E0.175850.546
32_S35_P0.174860.543
20_D71_L0.174690.542
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
3cp8A199.9-0.051
3cesA199.9-0.049
2zxiA199.9-0.047
2z43A0.763932.80.88
2rrdA0.916730.70.882
3jvdA0.388929.90.882
2kv2A0.819429.10.883
1jyeA0.347227.60.884
2ja2A0.944426.70.885
3e3mA0.472226.60.885

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