GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1091 - Protein of unknown function (DUF1091)
Pfam: PF06477 (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: CL0532
Length: 81
Sequences: 886
Seq/Len: 10.94
HH_delta: 0.479 (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_C51_C0.419493.104
46_N61_R0.218611.617
49_H53_F0.216831.604
25_K29_S0.200851.486
26_F38_Y0.194221.437
23_F47_L0.191851.419
11_G15_F0.191661.418
44_Y64_T0.187711.389
45_S53_F0.186961.383
65_I69_F0.186021.376
21_V35_K0.18311.355
8_R17_F0.182731.352
22_D25_K0.182481.350
53_F80_R0.177951.317
9_D36_I0.172691.278
45_S49_H0.168881.249
15_F18_N0.16811.244
48_P58_Y0.167511.239
35_K39_K0.166341.231
57_N60_L0.164951.220
47_L62_N0.163931.213
27_L53_F0.163111.207
33_L36_I0.158961.176
38_Y42_K0.154531.143
22_D33_L0.153931.139
7_K80_R0.150981.117
13_K23_F0.149251.104
77_G80_R0.149121.103
58_Y80_R0.148641.100
19_I33_L0.145981.080
53_F58_Y0.144311.068
7_K10_N0.142791.056
34_F37_V0.142381.053
26_F34_F0.141331.046
6_F58_Y0.139481.032
78_D81_I0.13791.020
45_S48_P0.137091.014
67_E76_E0.136731.012
69_F78_D0.136711.011
11_G18_N0.136481.010
67_E81_I0.136391.009
72_S79_Y0.136211.008
45_S60_L0.135571.003
57_N62_N0.135521.003
43_K63_F0.134980.999
16_L75_P0.132590.981
70_L76_E0.132110.977
17_F40_S0.130180.963
17_F34_F0.127850.946
39_K59_Y0.127810.946
48_P53_F0.12770.945
13_K16_L0.12750.943
8_R79_Y0.127120.941
63_F68_K0.126330.935
28_R50_T0.126110.933
11_G14_P0.123690.915
68_K71_P0.123340.913
25_K55_K0.123230.912
6_F80_R0.123130.911
6_F78_D0.122880.909
35_K67_E0.12190.902
9_D37_V0.120960.895
11_G45_S0.120930.895
66_D70_L0.119910.887
27_L58_Y0.119190.882
33_L60_L0.119180.882
47_L50_T0.11880.879
56_G65_I0.118790.879
40_S81_I0.118750.879
6_F35_K0.116950.865
55_K68_K0.116430.861
28_R42_K0.115850.857
11_G41_L0.115540.855
43_K80_R0.115190.852
5_L39_K0.114760.849
25_K47_L0.114390.846
31_N36_I0.113680.841
46_N59_Y0.113650.841
43_K66_D0.113020.836
16_L22_D0.112660.834
36_I70_L0.112120.830
23_F40_S0.110960.821
25_K31_N0.10980.812
24_C52_P0.109410.809
65_I68_K0.109220.808
12_Y78_D0.108990.806
19_I29_S0.108830.805
12_Y75_P0.108210.801
38_Y47_L0.108090.800
32_P37_V0.10760.796
9_D60_L0.107390.795
18_N66_D0.107270.794
8_R16_L0.107090.792
64_T80_R0.10690.791
27_L74_L0.106120.785
10_N13_K0.105970.784
5_L8_R0.105570.781
58_Y81_I0.105220.778
31_N55_K0.104750.775
32_P75_P0.104160.771
39_K66_D0.103960.769
12_Y29_S0.103880.769
46_N49_H0.103640.767
7_K36_I0.103550.766
17_F74_L0.103450.765
5_L56_G0.103420.765
5_L9_D0.103260.764
9_D76_E0.102640.759
58_Y74_L0.102140.756
11_G60_L0.101720.753
12_Y15_F0.101590.752
5_L71_P0.101530.751
26_F35_K0.101260.749
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
2ag4A0.987798.70.479
3m7oA0.728476.90.812
3mtxA0.740753.40.838
1xwvA0.67937.10.853
1nepA0.6914360.854
4ar2A0.925912.80.88
3hbeX0.62967.30.892
1x9pA0.81485.30.898
3w3eA0.65434.70.901
3vq2C0.97534.20.903

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