GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF983 - Protein of unknown function (DUF983)
Pfam: PF06170 (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: 86
Sequences: 423
Seq/Len: 4.92
HH_delta: 0.85 (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
16_L20_H0.25472.018
10_R15_G0.239731.899
52_P56_V0.239521.898
24_D29_Y0.237571.882
62_L66_L0.20621.634
29_Y33_L0.196021.553
22_R29_Y0.192971.529
8_A12_P0.190471.509
24_D37_H0.182371.445
6_K74_R0.182031.442
7_V18_Y0.180911.433
39_V42_L0.179771.424
4_Y74_R0.178181.412
23_A81_I0.174091.379
47_E57_H0.172691.368
44_L48_M0.169341.342
71_L75_P0.168341.334
29_Y37_H0.166981.323
26_G30_F0.164121.300
4_Y31_V0.163271.294
2_R9_P0.162421.287
72_L76_V0.15761.249
42_L45_W0.148111.173
27_P30_F0.146131.158
31_V35_V0.143191.134
12_P18_Y0.14251.129
42_L46_V0.142061.126
30_F80_L0.138571.098
2_R8_A0.13841.097
2_R6_K0.137361.088
5_L25_D0.136281.080
45_W49_A0.135011.070
9_P15_G0.134371.065
21_A29_Y0.134221.063
7_V77_K0.132381.049
23_A27_P0.132011.046
25_D77_K0.13171.043
57_H64_L0.131491.042
73_L77_K0.131471.042
68_L72_L0.131471.042
43_A46_V0.131151.039
46_V50_F0.129511.026
3_G6_K0.128861.021
45_W79_A0.127631.011
48_M51_R0.125950.998
10_R51_R0.124540.987
6_K58_L0.124140.984
30_F33_L0.123520.979
53_P56_V0.122730.972
61_W65_T0.122710.972
27_P32_I0.122370.970
3_G74_R0.121590.963
1_F75_P0.121190.960
7_V21_A0.119670.948
17_D25_D0.119610.948
23_A29_Y0.119460.946
34_I37_H0.119150.944
4_Y73_L0.1190.943
35_V44_L0.116880.926
5_L73_L0.113860.902
6_K60_I0.113430.899
31_V75_P0.11340.898
40_V76_V0.113350.898
59_A63_P0.112540.892
40_V54_L0.112520.891
8_A18_Y0.112340.890
29_Y32_I0.112250.889
46_V49_A0.111750.885
64_L68_L0.111450.883
12_P66_L0.11080.878
26_G74_R0.109980.871
25_D78_G0.109480.867
35_V65_T0.109340.866
33_L48_M0.108810.862
30_F34_I0.107850.854
53_P57_H0.107320.850
8_A15_G0.107250.850
34_I69_S0.107020.848
56_V79_A0.106720.846
53_P65_T0.106670.845
39_V68_L0.106620.845
46_V61_W0.106580.844
69_S72_L0.106280.842
23_A73_L0.106220.842
22_R82_A0.106210.841
38_I68_L0.105970.840
23_A37_H0.105340.835
60_I63_P0.104960.832
5_L36_G0.10420.826
58_L81_I0.104180.825
57_H61_W0.104160.825
19_S23_A0.102890.815
34_I76_V0.101680.806
2_R59_A0.101210.802
74_R80_L0.101180.802
39_V70_L0.10050.796
51_R67_A0.100470.796
27_P80_L0.100120.793
26_G33_L0.100120.793
59_A62_L0.099820.791
66_L75_P0.099750.790
36_G40_V0.099510.788
47_E52_P0.099480.788
66_L82_A0.099150.786
26_G82_A0.099050.785
24_D74_R0.098990.784
29_Y79_A0.098840.783
3_G13_H0.09870.782
13_H54_L0.098530.781
17_D21_A0.098390.780
24_D32_I0.098050.777
76_V79_A0.097890.776
8_A83_L0.097850.775
47_E66_L0.097150.770
34_I55_W0.097110.769
33_L61_W0.096570.765
7_V81_I0.096080.761
41_P44_L0.095330.755
44_L53_P0.095130.754
39_V71_L0.094620.750
18_Y81_I0.094450.748
5_L70_L0.094110.746
1_F63_P0.093860.744
56_V60_I0.09310.738
10_R13_H0.092940.736
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
3nw0A0.337280.20.85
2ct0A0.348879.40.851
3rfuA0.965158.60.871
2gmgA0.337240.60.884
1k82A0.418636.60.886
2kizA0.302332.60.889
3u6pA0.418631.60.89
2xzfA0.430230.30.891
2ectA0.395329.70.891
2ecyA0.279128.40.892
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