GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SmpA_OmlA - SmpA OmlA family
Pfam: PF04355 (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: CL0320
Length: 71
Sequences: 1300
Seq/Len: 18.31
HH_delta: -0.004 (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
59_V67_V0.64563.106
12_I67_V0.516462.485
16_M20_Q0.514652.476
6_Q10_A0.363121.747
5_T8_Q0.347161.670
11_Q24_L0.324521.561
20_Q23_A0.313621.509
32_D35_D0.29951.441
38_R60_Y0.276271.329
44_S52_N0.276251.329
62_D66_V0.276241.329
22_R27_S0.274961.323
16_M25_L0.272871.313
39_W61_F0.264921.275
8_Q24_L0.251071.208
48_G53_E0.250121.203
12_I25_L0.246471.186
21_V61_F0.245161.180
16_M24_L0.231111.112
39_W57_L0.229781.106
59_V66_V0.229431.104
19_D66_V0.229371.104
40_Y56_Q0.228861.101
19_D22_R0.228091.097
19_D23_A0.227781.096
33_P36_P0.227141.093
8_Q11_Q0.226761.091
12_I16_M0.225951.087
7_E64_D0.218131.050
4_L8_Q0.215011.035
17_T23_A0.214591.033
18_K64_D0.210961.015
12_I21_V0.210161.011
29_S43_Y0.208381.003
47_R52_N0.206290.993
4_L7_E0.204190.982
42_V56_Q0.202820.976
4_L9_L0.201330.969
60_Y69_S0.200480.965
17_T66_V0.20040.964
22_R31_R0.199610.960
9_L57_L0.198340.954
4_L57_L0.197220.949
27_S33_P0.19560.941
10_A14_P0.19550.941
16_M21_V0.193430.931
17_T20_Q0.191860.923
5_T43_Y0.188060.905
40_Y58_K0.187580.903
33_P42_V0.180190.867
34_F39_W0.179240.862
59_V69_S0.177450.854
21_V59_V0.174980.842
43_Y48_G0.174640.840
14_P68_K0.173320.834
38_R58_K0.172370.829
20_Q24_L0.172180.828
65_G69_S0.170760.822
23_A43_Y0.170760.822
16_M40_Y0.167010.804
30_L60_Y0.166970.803
18_K37_N0.165870.798
65_G68_K0.165670.797
44_S54_Q0.163620.787
13_K39_W0.163540.787
28_P31_R0.163330.786
62_D68_K0.161860.779
18_K22_R0.161670.778
15_G19_D0.160720.773
8_Q12_I0.160660.773
33_P37_N0.160630.773
42_V54_Q0.159290.766
43_Y55_R0.159070.765
33_P45_K0.158610.763
27_S34_F0.156010.751
32_D46_R0.15570.749
32_D54_Q0.154280.742
30_L55_R0.153990.741
54_Q60_Y0.151570.729
28_P45_K0.151570.729
29_S42_V0.147840.711
14_P69_S0.14770.711
18_K39_W0.147530.710
18_K65_G0.146730.706
36_P42_V0.145820.702
31_R52_N0.145560.700
11_Q55_R0.145280.699
35_D40_Y0.142950.688
18_K31_R0.142890.688
21_V67_V0.142190.684
18_K63_D0.141490.681
22_R28_P0.140870.678
9_L27_S0.140050.674
29_S32_D0.138550.667
43_Y56_Q0.137460.661
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
2km7A199.5-0.004
2yh9A199.5-0.001
2pxgA0.985999.50.028
4dm5A0.929698.40.393
3d4eA0.957797.90.487
3gmxB0.915596.90.59
3gmvX0.929696.40.615
3d4eA0.901496.40.617
3n4iB0.957796.40.618
3gmxB0.943793.70.681

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