GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF385 - Domain of unknown function (DUF385)
Pfam: PF04075 (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: CL0336
Length: 132
Sequences: 1746
Seq/Len: 13.23
HH_delta: 0.095 (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
93_R131_E0.663863.176
79_V90_V0.630423.016
93_R129_V0.546742.616
53_R129_V0.515752.467
31_T42_R0.497652.381
33_T76_N0.460422.203
29_L42_R0.441252.111
32_T72_N0.429992.057
79_V130_L0.406991.947
94_E128_V0.390911.870
95_V103_L0.375991.799
78_E91_R0.367261.757
58_A70_Y0.360871.726
90_V130_L0.353761.692
95_V129_V0.348141.665
50_D102_R0.339261.623
78_E89_R0.337711.616
80_T87_R0.331151.584
55_V103_L0.327241.565
47_Y83_V0.326331.561
33_T40_P0.317081.517
31_T80_T0.304211.455
70_Y128_V0.293481.404
68_D71_R0.293441.404
74_R94_E0.28941.384
66_H70_Y0.287371.375
28_L81_V0.282411.351
70_Y74_R0.272631.304
30_L79_V0.266031.273
94_E126_P0.264131.264
54_L81_V0.260731.247
79_V92_A0.260031.244
39_R78_E0.259071.239
73_L92_A0.253361.212
53_R131_E0.248561.189
56_V90_V0.246981.182
28_L47_Y0.246111.177
92_A128_V0.24571.175
29_L84_G0.245341.174
73_L79_V0.244351.169
28_L56_V0.230581.103
28_L90_V0.230231.101
92_A130_L0.229711.099
106_R109_A0.22671.085
54_L88_R0.221721.061
40_P80_T0.216241.034
81_V90_V0.214541.026
35_R71_R0.212961.019
80_T89_R0.212731.018
102_R106_R0.212631.017
97_D101_A0.210531.007
41_R68_D0.208560.998
58_A67_P0.207760.994
35_R76_N0.20740.992
93_R99_E0.205230.982
54_L83_V0.204790.980
56_V130_L0.200160.958
22_F113_G0.196270.939
32_T79_V0.194170.929
33_T38_G0.193020.923
30_L45_L0.192930.923
66_H124_R0.192090.919
49_R52_G0.191680.917
77_P92_A0.191070.914
29_L44_P0.190470.911
42_R82_E0.189890.908
28_L130_L0.188950.904
91_R131_E0.188750.903
104_W127_V0.187940.899
100_R124_R0.180810.865
59_S125_I0.179490.859
117_Y127_V0.179250.858
25_M83_V0.178560.854
114_Y123_R0.176440.844
37_S72_N0.175510.840
74_R128_V0.175190.838
96_T99_E0.174170.833
70_Y94_E0.173650.831
27_V44_P0.171040.818
46_V107_L0.17070.817
46_V59_S0.170550.816
69_W72_N0.170370.815
44_P82_E0.169960.813
81_V88_R0.169760.812
32_T43_T0.16910.809
31_T87_R0.164720.788
85_G112_P0.163430.782
37_S75_A0.163340.781
105_A109_A0.162660.778
58_A69_W0.162620.778
43_T72_N0.162330.777
82_E87_R0.161950.775
103_L110_A0.161580.773
67_P104_W0.160840.769
43_T69_W0.160570.768
70_Y126_P0.160.765
48_V107_L0.158040.756
47_Y54_L0.157890.755
114_Y117_Y0.157870.755
22_F25_M0.15780.755
104_W108_V0.157620.754
97_D124_R0.156880.750
44_P55_V0.155910.746
23_A113_G0.153370.734
82_E85_G0.152790.731
104_W122_G0.152250.728
97_D105_A0.152130.728
101_A105_A0.15160.725
106_R110_A0.149790.717
95_V100_R0.149750.716
29_L82_E0.149580.716
76_N92_A0.148840.712
31_T82_E0.148780.712
121_T125_I0.14760.706
32_T77_P0.146990.703
98_D101_A0.146920.703
113_G116_D0.146330.700
33_T39_R0.145960.698
83_V88_R0.145520.696
24_G97_D0.143450.686
35_R75_A0.143140.685
22_F109_A0.143020.684
58_A126_P0.142790.683
41_R89_R0.141650.678
46_V104_W0.141520.677
65_R71_R0.140570.672
21_R128_V0.139890.669
115_A119_A0.13830.662
33_T77_P0.137890.660
31_T40_P0.137560.658
79_V91_R0.136690.654
81_V130_L0.136540.653
101_A104_W0.134390.643
27_V82_E0.134220.642
59_S67_P0.134060.641
77_P91_R0.132440.634
100_R104_W0.132210.632
28_L88_R0.132020.632
45_L76_N0.131510.629
103_L127_V0.131390.629
67_P114_Y0.131080.627
71_R74_R0.131040.627
119_A122_G0.130360.624
71_R75_A0.129830.621
105_A119_A0.128650.615
114_Y118_Q0.128350.614
118_Q122_G0.1280.612
59_S124_R0.127910.612
48_V106_R0.127810.611
47_Y67_P0.127790.611
97_D100_R0.127270.609
86_R90_V0.127040.608
53_R98_D0.126440.605
50_D106_R0.126350.604
118_Q125_I0.126350.604
49_R54_L0.12620.604
76_N89_R0.125680.601
22_F107_L0.125440.600
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
3r5yA199.90.095
3r5zA199.90.096
3h96A199.90.112
3r5lA0.924299.90.169
1rfeA0.931899.70.385
3f7eA0.878899.60.39
3db0A0.848599.60.408
2furA0.939499.60.409
2fg9A0.954599.60.409
2vpaA0.931899.60.41

Page generated in 0.0192 seconds.