GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gly_acyl_tr_C - Aralkyl acyl-CoAamino acid N-acyltransferase C-terminal region
Pfam: PF08444 (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: CL0257
Length: 89
Sequences: 40138
Seq/Len: 450.99
HH_delta: 0.148 (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
38_S73_L3.279352.558
45_A75_F3.268342.549
14_S44_L2.919512.277
57_G70_S2.553291.991
38_S72_S2.236121.744
67_Q71_K2.20231.718
43_H47_Y2.182141.702
31_Y34_Q2.17181.694
43_H46_Q2.059481.606
12_S27_T2.017821.574
11_V31_Y2.015461.572
71_K77_F1.957341.527
67_Q77_F1.934361.509
42_Y73_L1.922291.499
47_Y51_L1.899511.482
68_R71_K1.86421.454
5_G10_P1.842541.437
41_M73_L1.838421.434
59_V67_Q1.826421.425
20_G53_F1.826341.424
16_M44_L1.78671.394
6_P31_Y1.76071.373
66_S70_S1.739951.357
14_S40_V1.702321.328
38_S42_Y1.686171.315
47_Y50_K1.68311.313
28_L31_Y1.666471.300
6_P11_V1.615421.260
39_Q43_H1.610131.256
37_M69_L1.542611.203
41_M70_S1.517191.183
41_M75_F1.493361.165
63_N66_S1.488681.161
9_N31_Y1.482221.156
36_L39_Q1.407921.098
19_T56_Y1.388311.083
64_E67_Q1.387811.082
59_V70_S1.358551.060
16_M48_L1.347641.051
69_L73_L1.312451.024
9_N30_E1.294351.010
35_G38_S1.2790.998
45_A73_L1.250480.975
45_A55_F1.244650.971
21_E24_M1.208470.943
39_Q42_Y1.201660.937
21_E58_H1.194250.931
21_E56_Y1.175040.916
42_Y45_A1.165390.909
15_L23_R1.164840.909
60_D63_N1.159480.904
64_E68_R1.159430.904
29_P32_R1.157290.903
32_R65_A1.14710.895
22_M41_M1.140.889
16_M47_Y1.134320.885
9_N28_L1.130770.882
57_G75_F1.125780.878
48_L53_F1.112850.868
48_L55_F1.105890.863
46_Q49_H1.10270.860
59_V66_S1.097310.856
59_V63_N1.093920.853
20_G48_L1.083790.845
6_P9_N1.074960.838
45_A49_H1.073180.837
27_T32_R1.062710.829
42_Y46_Q1.025560.800
65_A68_R1.01970.795
68_R72_S1.019420.795
13_W26_Y1.001680.781
56_Y78_M0.997060.778
13_W24_M0.993890.775
27_T36_L0.987050.770
70_S75_F0.980290.765
15_L24_M0.971180.757
33_G65_A0.969120.756
46_Q50_K0.965690.753
23_R26_Y0.954890.745
31_Y36_L0.947370.739
5_G8_G0.932790.728
40_V43_H0.922490.720
6_P34_Q0.909660.710
27_T37_M0.906120.707
23_R58_H0.882920.689
24_M58_H0.878660.685
5_G9_N0.877130.684
12_S36_L0.870390.679
22_M70_S0.860510.671
27_T40_V0.854220.666
16_M20_G0.837660.653
25_G70_S0.822340.641
11_V36_L0.81590.636
25_G41_M0.813870.635
5_G11_V0.805870.629
15_L26_Y0.801760.625
41_M45_A0.795820.621
11_V28_L0.779610.608
38_S69_L0.776760.606
10_P13_W0.774740.604
14_S43_H0.730040.569
22_M75_F0.729090.569
23_R60_D0.719440.561
41_M69_L0.718630.561
25_G37_M0.718440.560
24_M60_D0.716210.559
66_S69_L0.710890.554
48_L51_L0.709110.553
49_H52_G0.704730.550
6_P36_L0.697130.544
48_L52_G0.695460.542
63_N67_Q0.691640.539
55_F75_F0.650160.507
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
1sqhA0.977599.20.148
3ec4A0.988899.20.158
3fynA199.10.171
1tiqA199.10.174
3jvnA0.988899.10.177
4e2aA199.10.179
2pdoA199.10.181
3fixA199.10.183
1u6mA199.10.184
3pp9A199.10.185

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