GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ThuA - Trehalose utilisation
Pfam: PF06283 (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: CL0014
Length: 217
Sequences: 6907
Seq/Len: 31.83
HH_delta: 0.142 (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
28_L57_V0.948032.753
134_P204_D0.890392.586
207_R210_R0.855042.483
101_Y188_V0.849332.466
77_Y82_G0.805932.340
25_A29_E0.79742.316
37_T53_Y0.795922.311
119_T136_S0.690072.004
66_L103_E0.686071.992
210_R214_R0.677891.969
110_K147_L0.664471.930
121_R159_T0.663051.926
204_D207_R0.63991.858
119_T138_T0.623471.811
76_D79_E0.610781.774
31_S206_R0.610691.773
160_A177_V0.606731.762
26_Q29_E0.597961.736
91_A190_Y0.596831.733
182_E186_G0.582051.690
74_L100_E0.575941.673
132_G211_N0.572411.662
120_V158_L0.570581.657
159_T174_D0.565271.642
75_R79_E0.557941.620
156_V176_P0.557661.619
137_F204_D0.549381.595
24_L87_L0.544861.582
72_A75_R0.541391.572
182_E185_K0.538411.564
129_I189_F0.534681.553
127_H157_L0.533141.548
158_L178_A0.525631.526
207_R211_N0.52231.517
75_R104_L0.512311.488
155_T182_E0.50951.480
121_R136_S0.508491.477
156_V159_T0.5071.472
121_R161_D0.496611.442
113_P175_H0.494881.437
55_V213_I0.483011.403
180_T189_F0.482571.401
58_F84_L0.47811.388
25_A38_V0.466541.355
78_V84_L0.452161.313
129_I211_N0.450241.308
138_T203_P0.449231.305
56_V82_G0.438421.273
27_L206_R0.433731.260
72_A76_D0.431991.255
33_G36_V0.431691.254
58_F70_Q0.424451.233
41_D49_N0.422851.228
127_H180_T0.421171.223
71_R104_L0.420881.222
157_L180_T0.41191.196
110_K145_Y0.408031.185
130_T178_A0.407151.182
51_K76_D0.400911.164
39_T49_N0.398781.158
76_D80_N0.398721.158
84_L188_V0.396841.152
181_R187_R0.39541.148
108_Y147_L0.390931.135
161_D174_D0.388211.127
124_D155_T0.387631.126
67_T71_R0.387621.126
49_N53_Y0.386531.122
182_E187_R0.385941.121
34_F213_I0.382121.110
189_F212_G0.380951.106
32_E210_R0.37631.093
48_E51_K0.37371.085
85_V191_T0.372821.083
155_T180_T0.372521.082
25_A36_V0.369321.073
88_H195_H0.364631.059
133_L207_R0.362761.053
29_E35_E0.361191.049
128_P189_F0.360041.046
206_R210_R0.355151.031
85_V212_G0.352331.023
131_R214_R0.352321.023
29_E36_V0.351611.021
160_A175_H0.349311.014
117_P138_T0.347411.009
57_V85_V0.345741.004
50_L53_Y0.339160.985
37_T49_N0.332150.965
28_L213_I0.332140.965
90_A195_H0.325380.945
112_H145_Y0.324750.943
127_H189_F0.3240.941
71_R100_E0.321630.934
87_L209_L0.320250.930
178_A191_T0.319680.928
78_V186_G0.318680.925
76_D81_G0.316690.920
157_L181_R0.316370.919
71_R103_E0.313860.911
92_T192_T0.308660.896
83_G187_R0.308570.896
55_V212_G0.306720.891
50_L117_P0.303940.883
28_L32_E0.303530.881
55_V83_G0.303290.881
34_F55_V0.301990.877
32_E214_R0.300640.873
154_V179_W0.299530.870
91_A146_F0.29840.867
78_V188_V0.296940.862
125_P157_L0.295840.859
108_Y148_R0.295520.858
130_T158_L0.293060.851
132_G207_R0.29070.844
71_R75_R0.290050.842
24_L209_L0.287280.834
102_N107_G0.283770.824
139_I202_D0.283150.822
56_V73_A0.282920.822
56_V77_Y0.281530.818
26_Q31_S0.280250.814
39_T53_Y0.279510.812
106_G155_T0.279480.812
64_D67_T0.279150.811
49_N52_G0.277640.806
28_L34_F0.275570.800
119_T161_D0.274710.798
47_P77_Y0.273340.794
78_V104_L0.272760.792
134_P137_F0.272720.792
134_P203_P0.272370.791
74_L78_V0.270630.786
145_Y176_P0.270470.785
133_L211_N0.270140.784
127_H155_T0.269890.784
47_P50_L0.269210.782
81_G186_G0.269060.781
126_D131_R0.268850.781
120_V138_T0.267960.778
117_P140_Y0.266960.775
152_P182_E0.263880.766
47_P51_K0.263350.765
121_R124_D0.263060.764
191_T212_G0.262690.763
48_E52_G0.261760.760
88_H196_D0.261630.760
86_G196_D0.261590.760
22_K25_A0.261560.760
125_P135_E0.260050.755
74_L77_Y0.259710.754
77_Y80_N0.259620.754
22_K26_Q0.259080.752
133_L204_D0.258860.752
61_T86_G0.257060.747
138_T204_D0.256830.746
70_Q73_A0.256270.744
157_L189_F0.255840.743
121_R174_D0.255640.742
120_V160_A0.254180.738
79_E82_G0.251990.732
66_L71_R0.24980.725
60_N90_A0.24960.725
63_G66_L0.249290.724
112_H175_H0.249210.724
69_E73_A0.248840.723
121_R135_E0.247720.719
32_E209_L0.247680.719
60_N88_H0.247150.718
61_T90_A0.245210.712
130_T157_L0.244890.711
129_I208_L0.244010.709
150_P153_N0.243820.708
138_T208_L0.243220.706
133_L137_F0.242780.705
133_L208_L0.241740.702
105_L188_V0.241060.700
86_G92_T0.240090.697
61_T89_G0.239420.695
151_R174_D0.239220.695
26_Q202_D0.238160.692
157_L178_A0.237460.690
32_E206_R0.237390.689
120_V137_F0.237360.689
61_T91_A0.236860.688
28_L55_V0.233820.679
124_D136_S0.23340.678
70_Q74_L0.23290.676
86_G195_H0.232740.676
79_E186_G0.231560.672
32_E213_I0.231110.671
178_A189_F0.229880.668
120_V139_I0.22870.664
81_G188_V0.228180.663
59_Y62_G0.226210.657
73_A76_D0.225750.656
47_P73_A0.225510.655
24_L28_L0.224470.652
60_N86_G0.222410.646
130_T211_N0.221160.642
124_D127_H0.221120.642
192_T197_E0.220920.642
124_D135_E0.219960.639
88_H197_E0.219850.638
111_G148_R0.21940.637
100_E104_L0.218770.635
197_E205_F0.218580.635
86_G197_E0.218340.634
81_G187_R0.217530.632
47_P76_D0.217380.631
87_L196_D0.21720.631
150_P156_V0.21720.631
86_G90_A0.216710.629
105_L186_G0.216420.628
32_E36_V0.216310.628
34_F214_R0.216010.627
62_G192_T0.21570.626
92_T190_Y0.215210.625
126_D135_E0.215190.625
67_T70_Q0.213580.620
60_N196_D0.2130.619
62_G90_A0.212050.616
50_L73_A0.211620.615
162_E174_D0.211140.613
130_T193_L0.210520.611
71_R74_L0.210280.611
128_P131_R0.20930.608
59_Y143_W0.209110.607
68_D71_R0.208580.606
109_F179_W0.206580.600
179_W190_Y0.206440.600
135_E204_D0.206040.598
92_T197_E0.205510.597
37_T52_G0.205290.596
26_Q198_E0.204560.594
102_N179_W0.203680.591
51_K81_G0.202850.589
145_Y175_H0.202670.589
39_T50_L0.200470.582
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
4jqsA0.9771000.142
4e5vA0.95391000.147
1t0bA0.917199.90.295
3rhtA0.944799.80.431
3sozA0.926399.80.464
2gk3A0.926399.80.467
2zuvA0.907899.70.501
3ttyA0.866499.30.642
4gudA0.811199.30.646
3tqiA0.834199.20.654

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