GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DbpA - DbpA RNA binding domain
Pfam: PF03880 (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: 74
Sequences: 1726
Seq/Len: 23.32
HH_delta: 0.089 (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
14_T17_D0.604782.251
18_I43_S0.599412.231
20_G24_N0.539932.010
17_D65_K0.527281.963
64_I69_V0.493371.837
32_D51_V0.441791.645
22_I45_V0.43961.636
10_K40_D0.39011.452
37_D42_F0.388551.446
19_V33_I0.385051.433
32_D48_P0.382351.423
21_A24_N0.372111.385
53_E57_E0.349291.300
54_K57_E0.347681.294
52_A56_L0.345961.288
29_P32_D0.3321.236
38_I43_S0.327651.220
19_V36_I0.325141.210
57_E60_N0.324881.209
60_N68_K0.32331.203
47_V55_V0.323111.203
21_A59_L0.320811.194
11_D67_K0.319281.188
10_K41_N0.317551.182
19_V23_C0.314681.171
24_N33_I0.312971.165
23_C30_G0.312211.162
17_D20_G0.305891.139
39_F42_F0.305661.138
54_K58_A0.295061.098
26_A29_P0.290371.081
22_I33_I0.289831.079
21_A64_I0.279961.042
51_V54_K0.279621.041
47_V52_A0.277681.034
59_L71_V0.267530.996
29_P50_E0.263970.983
48_P51_V0.258010.960
36_I39_F0.251290.935
33_I55_V0.250970.934
39_F44_F0.24860.925
52_A55_V0.247630.922
26_A30_G0.246910.919
22_I46_E0.241680.900
26_A55_V0.24140.899
9_R40_D0.238440.888
13_L18_I0.234660.874
63_K68_K0.230340.857
16_R20_G0.22950.854
17_D21_A0.227850.848
47_V51_V0.227420.847
26_A54_K0.225740.840
19_V25_E0.225560.840
34_G46_E0.22350.832
16_R19_V0.218720.814
42_F72_E0.218720.814
56_L71_V0.216330.805
60_N71_V0.213820.796
49_E54_K0.213490.795
13_L17_D0.209110.778
50_E57_E0.208460.776
11_D43_S0.206860.770
11_D40_D0.206130.767
16_R24_N0.204450.761
23_C33_I0.204170.760
11_D41_N0.203560.758
13_L20_G0.202120.752
37_D53_E0.201310.749
41_N70_R0.20120.749
21_A25_E0.200580.747
27_G40_D0.20050.746
32_D47_V0.200380.746
31_R53_E0.199280.742
55_V72_E0.196550.732
20_G34_G0.191950.715
22_I28_I0.191020.711
35_R65_K0.189440.705
32_D50_E0.188560.702
9_R15_P0.18820.701
28_I33_I0.187430.698
49_E53_E0.186110.693
10_K68_K0.185870.692
15_P21_A0.184790.688
36_I46_E0.182960.681
60_N70_R0.182690.680
16_R30_G0.181830.677
68_K72_E0.181350.675
18_I22_I0.180450.672
11_D18_I0.179760.669
36_I43_S0.178890.666
26_A58_A0.177810.662
33_I43_S0.176870.658
20_G23_C0.176030.655
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
2g0cA199.50.089
2fphX0.97398.90.348
3i32A0.783897.80.554
2wbrA0.945995.20.69
3thtA0.959592.40.725
2dgtA0.918991.80.73
3q2sC0.945991.50.732
2bz2A0.918991.40.733
1x5pA0.918990.90.736
2jvrA0.932490.50.739

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