GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ub-RnfH - RnfH family Ubiquitin
Pfam: PF03658 (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. )
Clan: CL0072
Length: 84
Sequences: 2426
Seq/Len: 28.88
HH_delta: 0.242 (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_F66_D1.341013.837
7_Y16_L0.997782.855
63_R66_D0.882912.526
29_A62_L0.797042.281
25_T28_Q0.76152.179
53_G67_R0.732112.095
4_E17_T0.671161.920
29_A68_V0.597881.711
27_A31_E0.583171.669
56_V60_T0.583081.668
51_I68_V0.581841.665
24_T28_Q0.57881.656
51_I60_T0.574981.645
4_E15_I0.572531.638
3_V65_G0.5461.562
26_V49_V0.534051.528
50_G55_L0.526771.507
49_V70_I0.466451.335
36_L41_E0.446861.279
30_I70_I0.440151.259
71_Y75_T0.439451.257
50_G69_E0.41721.194
49_V58_L0.417191.194
32_A37_E0.416891.193
6_A67_R0.414831.187
26_V56_V0.414181.185
32_A38_Q0.406641.164
71_Y74_L0.400691.147
27_A58_L0.398111.139
9_L71_Y0.392551.123
26_V68_V0.373761.069
39_F42_I0.372921.067
50_G73_P0.369831.058
24_T61_V0.368861.055
48_K55_L0.361371.034
8_A71_Y0.358941.027
30_I58_L0.355741.018
69_E73_P0.346380.991
6_A69_E0.343930.984
13_Q16_L0.338010.967
50_G53_G0.33520.959
28_Q31_E0.330280.945
27_A59_D0.33010.945
26_V60_T0.322360.922
31_E37_E0.319920.915
10_P70_I0.319010.913
52_F72_R0.318380.911
21_P32_A0.314940.901
55_L74_L0.296430.848
7_Y13_Q0.295070.844
51_I63_R0.291360.834
9_L47_N0.282610.809
13_Q39_F0.277480.794
28_Q32_A0.273510.783
54_K57_K0.271280.776
3_V64_D0.269460.771
69_E74_L0.268970.770
4_E19_E0.267840.766
57_K60_T0.266350.762
50_G71_Y0.265010.758
10_P47_N0.262020.750
30_I49_V0.260750.746
17_T31_E0.259040.741
4_E67_R0.258930.741
55_L71_Y0.257150.736
5_V18_L0.255390.731
55_L75_T0.250350.716
31_E36_L0.248360.711
53_G69_E0.247590.708
50_G74_L0.246620.706
47_N74_L0.245740.703
36_L43_D0.24550.702
10_P71_Y0.245350.702
24_T32_A0.244430.699
11_E72_R0.242320.693
7_Y70_I0.236630.677
8_A73_P0.236180.676
25_T59_D0.233220.667
9_L48_K0.23310.667
48_K71_Y0.232450.665
7_Y42_I0.229220.656
23_G61_V0.228540.654
31_E43_D0.226420.648
6_A50_G0.225590.646
50_G72_R0.22430.642
7_Y11_E0.221120.633
51_I56_V0.220240.630
40_P43_D0.216940.621
12_R15_I0.215220.616
58_L61_V0.212410.608
37_E43_D0.210510.602
20_V24_T0.208360.596
8_A50_G0.205490.588
8_A74_L0.204140.584
23_G37_E0.203440.582
9_L74_L0.202610.580
22_E32_A0.202160.578
30_I68_V0.201060.575
46_K49_V0.200120.573
37_E63_R0.198170.567
12_R16_L0.197880.566
44_L47_N0.197680.566
37_E61_V0.197460.565
36_L39_F0.195580.560
5_V68_V0.190820.546
45_E57_K0.189470.542
3_V20_V0.188560.540
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
2hj1A199.60.242
1vjkA0.892999.40.318
3po0A0.892999.40.339
3dwgC0.86999.40.35
2qjlA0.892999.40.353
3rpfC0.833399.30.363
2q5wD0.86999.30.389
1fm0D0.86999.30.39
2l52A0.88199.20.393
2g1eA0.88199.20.4

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