GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SH3_5 - Bacterial SH3 domain
Pfam: PF08460 (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: CL0010
Length: 65
Sequences: 772
Seq/Len: 11.88
HH_delta: 0.11 (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
20_G25_S0.893044.130
16_N27_V0.510382.360
22_S25_S0.446562.065
32_P35_Q0.395641.830
25_S62_Y0.384181.777
15_I63_V0.375681.737
18_R27_V0.340441.574
16_N64_A0.330821.530
17_I53_Y0.299871.387
14_T30_T0.291581.348
14_T32_P0.2791.290
39_Y51_I0.269521.246
13_T33_K0.255511.182
53_Y60_R0.253411.172
18_R50_W0.249121.152
54_I60_R0.24671.141
31_Y62_Y0.245441.135
16_N30_T0.243771.127
19_N28_V0.237891.100
17_I29_G0.234851.086
29_G35_Q0.233341.079
31_Y35_Q0.23141.070
22_S64_A0.218721.011
44_K49_V0.210950.975
19_N26_P0.209070.967
23_T64_A0.202940.938
31_Y37_V0.19890.920
17_I63_V0.197870.915
11_F15_I0.197290.912
35_Q57_S0.197280.912
55_S60_R0.197110.911
53_Y61_R0.196640.909
37_V54_I0.193330.894
13_T26_P0.193070.893
21_P43_I0.190760.882
19_N38_N0.186140.861
18_R64_A0.18540.857
21_P62_Y0.185260.857
16_N23_T0.18310.847
35_Q56_Y0.182890.846
32_P37_V0.181950.841
18_R23_T0.181640.840
55_S58_G0.1810.837
42_V51_I0.177710.822
12_N15_I0.174260.806
39_Y62_Y0.169590.784
39_Y49_V0.169410.783
39_Y61_R0.168490.779
24_S59_Q0.167160.773
53_Y56_Y0.166060.768
55_S61_R0.164260.760
31_Y53_Y0.163760.757
28_V61_R0.162420.751
11_F31_Y0.162250.750
20_G45_A0.161170.745
39_Y53_Y0.160620.743
56_Y59_Q0.160370.742
13_T16_N0.159850.739
26_P42_V0.159350.737
43_I51_I0.158970.735
47_G51_I0.158760.734
51_I63_V0.158250.732
11_F35_Q0.157480.728
17_I32_P0.157090.726
17_I61_R0.155220.718
42_V62_Y0.153810.711
41_Q54_I0.14940.691
45_A49_V0.146920.679
18_R28_V0.146470.677
26_P60_R0.144590.669
29_G55_S0.144230.667
17_I43_I0.143140.662
17_I54_I0.143080.662
14_T36_S0.142910.661
19_N55_S0.142420.659
30_T46_D0.141880.656
42_V57_S0.140690.651
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
1r77A199.40.11
2kt8A0.892398.50.387
2kq8A0.861598.40.408
2krsA0.861598.40.419
3npfA0.907797.90.495
3npfA0.938597.50.553
3h41A0.938597.30.573
1xovA0.892397.10.59
2hbwA0.938596.90.601
3h41A0.923196.20.637

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