GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Acyltransferase - Acyltransferase
Pfam: PF01553 (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: CL0228
Length: 132
Sequences: 10217
Seq/Len: 77.4
HH_delta: 0.193 (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
6_G9_N1.310333.142
14_G125_P1.119892.685
49_D70_D1.114022.671
85_K89_R1.046812.510
85_K121_K0.907232.176
52_F68_P0.889272.132
16_V93_S0.84612.029
16_V127_V0.837522.008
18_F93_S0.82731.984
18_F127_V0.787221.888
87_I92_G0.763721.831
86_E90_K0.758741.819
83_D86_E0.75821.818
58_G62_R0.737251.768
16_V125_P0.733041.758
83_D87_I0.723261.734
88_L124_V0.691951.659
85_K122_A0.688051.650
20_S97_F0.676781.623
19_V115_A0.676111.621
119_A126_I0.662851.590
44_R92_G0.65271.565
84_I118_I0.64021.535
87_I90_K0.633741.520
20_S95_V0.628061.506
20_S129_V0.618141.482
59_W63_R0.616521.478
84_I94_I0.616361.478
15_G91_G0.614791.474
49_D53_K0.609691.462
4_V7_L0.584541.402
89_R122_A0.583231.399
79_K83_D0.579211.389
59_W62_R0.570371.368
44_R87_I0.56851.363
117_H121_K0.564881.355
43_P95_V0.545091.307
52_F62_R0.543821.304
48_K71_R0.535361.284
103_S106_G0.525211.259
55_P58_G0.525051.259
76_K79_K0.519291.245
82_K85_K0.517811.242
47_A52_F0.513391.231
48_K101_T0.508811.220
20_S31_L0.507791.218
7_L11_P0.504741.210
113_K117_H0.502741.206
18_F35_L0.49991.199
31_L97_F0.498351.195
15_G124_V0.489971.175
47_A66_F0.481681.155
103_S109_L0.47531.140
11_P14_G0.47081.129
78_R82_K0.465111.115
46_V67_I0.445391.068
47_A51_L0.437011.048
18_F129_V0.432131.036
48_K51_L0.427031.024
117_H120_L0.425271.020
115_A119_A0.42471.018
116_F120_L0.419931.007
100_G114_G0.418391.003
54_I57_L0.41751.001
82_K86_E0.401430.963
49_D52_F0.387390.929
114_G117_H0.386210.926
71_R101_T0.38560.925
46_V84_I0.382290.917
50_E71_R0.381340.914
67_I87_I0.377910.906
15_G88_L0.376770.903
99_E108_L0.375830.901
17_I119_A0.375490.900
9_N127_V0.366940.880
17_I124_V0.364520.874
76_K80_A0.360220.864
9_N12_K0.359640.862
88_L91_G0.357650.858
75_K78_R0.356050.854
119_A123_K0.35260.846
65_G92_G0.351750.843
81_L85_K0.351680.843
119_A122_A0.350740.841
119_A125_P0.35050.840
98_P111_F0.348850.837
55_P59_W0.344920.827
100_G112_K0.344330.826
23_Q102_R0.344130.825
86_E89_R0.34010.816
45_F95_V0.339650.814
85_K118_I0.338580.812
46_V69_I0.335350.804
24_S102_R0.333890.801
111_F116_F0.33280.798
48_K102_R0.332760.798
102_R106_G0.332190.797
10_L127_V0.331890.796
21_N99_E0.331770.796
97_F131_I0.329190.789
79_K82_K0.329050.789
99_E111_F0.327350.785
57_L61_L0.326690.783
8_E11_P0.326560.783
21_N111_F0.321440.771
17_I126_I0.320450.768
47_A61_L0.320320.768
17_I115_A0.319950.767
3_E7_L0.319580.766
31_L129_V0.3190.765
70_D76_K0.316290.758
99_E103_S0.314260.754
23_Q103_S0.313340.751
31_L131_I0.311840.748
21_N98_P0.308990.741
105_S109_L0.308030.739
101_T109_L0.306030.734
13_G16_V0.304510.730
94_I118_I0.302750.726
56_F59_W0.302390.725
61_L68_P0.300920.722
32_M45_F0.300430.720
21_N27_D0.299650.719
127_V131_I0.299640.719
81_L84_I0.293370.703
21_N97_F0.293140.703
51_L57_L0.292570.702
115_A126_I0.292120.701
23_Q115_A0.290040.696
29_F32_M0.287360.689
88_L118_I0.287180.689
8_E12_K0.286150.686
53_K62_R0.285560.685
15_G93_S0.283720.680
77_N81_L0.281550.675
104_R109_L0.280560.673
75_K79_K0.277910.666
29_F64_L0.277310.665
30_A33_A0.27720.665
28_G32_M0.275090.660
61_L66_F0.274990.659
29_F57_L0.273760.656
14_G93_S0.273380.656
11_P16_V0.272480.653
14_G41_R0.272050.652
3_E6_G0.271740.652
4_V34_L0.271230.650
70_D77_N0.270750.649
23_Q28_G0.270390.648
96_I115_A0.269670.647
14_G124_V0.266640.639
77_N80_A0.266570.639
80_A83_D0.266350.639
54_I58_G0.266310.639
35_L92_G0.265640.637
118_I122_A0.265480.637
78_R117_H0.265230.636
19_V98_P0.265170.636
88_L122_A0.265140.636
78_R121_K0.264750.635
5_E9_N0.261360.627
81_L121_K0.260320.624
97_F100_G0.257330.617
32_M35_L0.256670.615
43_P93_S0.256640.615
30_A131_I0.256530.615
64_L68_P0.256260.615
81_L118_I0.255850.614
46_V118_I0.253380.608
46_V96_I0.252850.606
60_F64_L0.251740.604
12_K16_V0.248610.596
124_V127_V0.248130.595
5_E8_E0.246450.591
62_R68_P0.246350.591
17_I96_I0.245520.589
17_I94_I0.245140.588
88_L94_I0.243710.584
15_G92_G0.2430.583
44_R67_I0.24290.582
4_V8_E0.241540.579
116_F119_A0.241350.579
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
1iuqA199.70.193
4eo7A0.772717.70.883
2e11A0.575813.60.888
3ivzA0.5682130.889
2w1vA0.5758110.892
1emsA0.65919.70.895
3lxzA0.757.50.899
1snnA0.41677.30.9
3ragA0.35615.90.904
1f89A0.63645.70.905

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