GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
VanW - VanW like protein
Pfam: PF04294 (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: 132
Sequences: 677
Seq/Len: 5.13
HH_delta: 0.931 (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
24_T78_V0.482893.114
26_S104_D0.468163.019
76_E110_P0.384542.480
35_T38_N0.373392.408
70_A105_L0.357742.307
70_A107_F0.334822.159
2_N41_K0.329312.123
27_F31_V0.327842.114
76_E108_R0.320182.065
20_M114_P0.316652.042
45_V54_G0.313142.019
78_V108_R0.309091.993
27_F98_V0.28581.843
70_A77_I0.272951.760
10_A62_V0.271161.748
13_A40_Y0.254841.643
68_N94_R0.254481.641
10_A59_I0.252991.631
118_Q129_E0.239161.542
14_I25_F0.233891.508
81_H103_L0.233821.508
119_A128_V0.232851.501
24_T106_K0.227321.466
24_T108_R0.223441.441
75_L110_P0.222731.436
79_E106_K0.218681.410
64_S90_V0.215691.391
5_H41_K0.214871.386
11_A119_A0.211741.365
14_I62_V0.208941.347
28_N34_R0.203191.310
15_N118_Q0.200661.294
36_A55_I0.198651.281
66_L117_I0.198631.281
97_T103_L0.196641.268
60_C95_D0.195721.262
20_M23_E0.195321.259
17_T30_T0.193671.249
31_V98_V0.192261.240
80_R96_A0.191041.232
68_N90_V0.190471.228
117_I130_I0.189081.219
11_A126_L0.185431.196
67_Y71_L0.179651.158
28_N59_I0.178191.149
27_F63_S0.178081.148
120_S127_T0.175551.132
32_G39_G0.17411.123
5_H8_R0.17281.114
42_P53_P0.171991.109
13_A38_N0.171561.106
67_Y105_L0.169131.091
120_S129_E0.166161.071
44_P51_L0.164341.060
9_L12_Q0.162861.050
65_T69_A0.162821.050
36_A42_P0.162521.048
28_N32_G0.160711.036
60_C83_H0.160281.034
61_Q65_T0.160151.033
107_F117_I0.159421.028
31_V34_R0.157781.017
3_R62_V0.15631.008
46_I51_L0.15621.007
67_Y74_G0.15551.003
44_P53_P0.154930.999
19_V23_E0.154220.994
46_I87_V0.152390.983
116_L131_W0.152380.983
33_P101_G0.152120.981
17_T25_F0.15210.981
33_P100_Y0.150640.971
115_I130_I0.149810.966
99_A102_Y0.147770.953
10_A34_R0.146890.947
19_V122_D0.146860.947
32_G100_Y0.146620.945
86_P89_Y0.144990.935
60_C80_R0.144320.931
80_R95_D0.143880.928
63_S105_L0.143460.925
43_A54_G0.142740.920
40_Y43_A0.140790.908
66_L107_F0.140140.904
81_H106_K0.138910.896
15_N121_V0.136780.882
114_P131_W0.136720.882
38_N100_Y0.136330.879
89_Y95_D0.134220.865
75_L111_T0.132980.857
75_L115_I0.132040.851
56_G83_H0.131330.847
68_N72_R0.130270.840
69_A130_I0.130010.838
46_I85_Y0.129680.836
39_G84_S0.129630.836
34_R100_Y0.128790.830
25_F30_T0.127760.824
67_Y80_R0.126650.817
82_P98_V0.126450.815
8_R117_I0.125990.812
4_T8_R0.12570.811
9_L66_L0.124680.804
67_Y96_A0.124610.804
122_D127_T0.12420.801
58_G83_H0.12370.798
23_E36_A0.123330.795
12_Q15_N0.122960.793
65_T128_V0.122650.791
8_R121_V0.122560.790
77_I80_R0.122460.790
4_T121_V0.122440.790
18_V114_P0.121190.781
72_R94_R0.120980.780
85_Y99_A0.119960.774
120_S123_G0.119810.773
60_C89_Y0.119770.772
34_R59_I0.119580.771
11_A127_T0.119330.769
80_R89_Y0.118910.767
86_P92_P0.118650.765
48_N103_L0.118610.765
63_S98_V0.118430.764
48_N52_V0.118180.762
47_V52_V0.117790.760
54_G103_L0.117330.757
49_G52_V0.117210.756
41_K45_V0.116770.753
16_G116_L0.116630.752
27_F60_C0.116080.749
68_N91_P0.115460.745
18_V81_H0.115210.743
53_P97_T0.115140.742
65_T90_V0.114890.741
39_G57_G0.114850.741
29_Q37_E0.114460.738
8_R12_Q0.11440.738
9_L32_G0.113810.734
45_V52_V0.113810.734
9_L14_I0.11370.733
3_R64_S0.113640.733
84_S112_D0.113420.731
14_I27_F0.113110.729
111_T114_P0.112980.729
74_G115_I0.112960.728
54_G99_A0.112850.728
18_V77_I0.11210.723
46_I54_G0.111630.720
74_G111_T0.110860.715
43_A53_P0.110640.713
70_A130_I0.110610.713
67_Y86_P0.110470.712
80_R87_V0.110370.712
23_E108_R0.110020.709
8_R112_D0.109790.708
14_I19_V0.109480.706
73_A115_I0.108520.700
65_T68_N0.108340.699
31_V100_Y0.107970.696
121_V126_L0.107790.695
15_N125_K0.107360.692
19_V76_E0.107360.692
42_P55_I0.107290.692
28_N31_V0.106470.687
45_V87_V0.105330.679
11_A62_V0.104760.676
37_E125_K0.104440.673
44_P68_N0.104360.673
41_K76_E0.104340.673
9_L13_A0.104260.672
61_Q80_R0.103960.670
122_D125_K0.102880.663
3_R65_T0.102850.663
73_A130_I0.102670.662
77_I111_T0.101890.657
44_P84_S0.10180.656
3_R7_I0.101790.656
67_Y90_V0.101510.655
57_G83_H0.101360.654
51_L87_V0.101350.654
71_L77_I0.101220.653
10_A31_V0.101080.652
87_V97_T0.100840.650
48_N55_I0.100740.650
72_R82_P0.100390.647
18_V124_G0.098690.636
48_N106_K0.098530.635
64_S95_D0.09840.635
43_A88_S0.098370.634
33_P37_E0.098210.633
111_T115_I0.09810.633
3_R63_S0.09780.631
65_T89_Y0.09710.626
2_N23_E0.097060.626
79_E82_P0.097020.626
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
2f8aA0.416749.90.931
4a17E0.393917.80.945
3vynA0.939416.50.945
3u5eH0.393916.10.946
3iz5F0.393914.10.947
2qjvA0.825813.20.948
3j39H0.3939130.948
2zkre0.39399.80.95
3j21F0.40159.50.951
4aslA0.40159.20.951
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