GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Trehalose_PPase - Trehalose-phosphatase
Pfam: PF02358 (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: CL0137
Length: 235
Sequences: 7287
Seq/Len: 31.01
HH_delta: 0.306 (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
180_A185_D1.338834.019
189_Y203_L1.16043.483
200_F212_G1.145773.440
2_L39_V1.103683.313
174_L187_V1.014293.045
10_P19_V0.994062.984
43_S50_L0.937582.815
171_R202_A0.873112.621
189_Y199_A0.842662.530
30_A33_A0.83782.515
22_P26_E0.804782.416
165_N198_D0.804312.415
180_A186_F0.781922.347
184_P202_A0.768392.307
214_K218_V0.740272.222
172_R175_E0.719282.159
1_F170_V0.71232.138
4_Y9_A0.70762.124
2_L190_I0.701522.106
30_A34_D0.677622.034
189_Y200_F0.666742.002
12_V19_V0.662351.988
28_L39_V0.653561.962
62_A169_A0.641531.926
171_R175_E0.636161.910
168_S171_R0.617371.853
180_A184_P0.610681.833
172_R176_E0.57531.727
167_G202_A0.570951.714
43_S63_G0.549951.651
38_T177_L0.548161.646
85_D88_W0.543421.631
26_E30_A0.540131.621
23_E27_L0.519961.561
40_A173_L0.518931.558
1_F42_V0.516121.549
174_L184_P0.508631.527
40_A60_G0.505171.517
135_A139_R0.499691.500
67_A161_P0.49291.480
21_P24_L0.492011.477
29_R33_A0.48581.458
25_R56_I0.483861.453
197_E201_R0.480691.443
174_L179_F0.476571.431
24_L27_L0.465251.397
75_S78_T0.463621.392
184_P187_V0.455111.366
170_V199_A0.447881.345
88_W91_E0.445661.338
203_L212_G0.438261.316
167_G198_D0.434741.305
25_R29_R0.423061.270
137_Q140_E0.422661.269
165_N168_S0.420931.264
31_L39_V0.412021.237
213_I216_G0.406071.219
67_A164_V0.401391.205
174_L202_A0.399941.201
136_E140_E0.399031.198
147_G162_P0.398881.197
187_V203_L0.396221.189
60_G177_L0.395071.186
46_S64_E0.394081.183
3_D192_D0.384371.154
10_P21_P0.380761.143
161_P164_V0.37971.140
91_E94_E0.379671.140
26_E29_R0.37891.137
69_I172_R0.377491.133
153_G156_V0.376371.130
93_R97_E0.368911.107
173_L177_L0.366951.102
188_L213_I0.366511.100
132_R136_E0.364371.094
63_G68_E0.363581.091
149_E163_G0.361511.085
69_I169_A0.360981.084
64_E68_E0.359761.080
1_F187_V0.359071.078
94_E98_Y0.357471.073
4_Y53_F0.355941.069
29_R32_A0.35521.066
170_V203_L0.355031.066
47_L63_G0.352321.058
8_L28_L0.351321.055
170_V189_Y0.351221.054
179_F186_F0.349531.049
32_A59_I0.347471.043
160_R165_N0.346591.040
139_R143_A0.346561.040
91_E145_H0.342131.027
140_E143_A0.340741.023
1_F40_A0.340161.021
95_I99_F0.34011.021
22_P25_R0.333221.000
142_L145_H0.332420.998
42_V199_A0.331530.995
194_R197_E0.328360.986
2_L31_L0.327660.984
71_R75_S0.327570.983
214_K217_S0.320670.963
27_L31_L0.319220.958
187_V202_A0.318410.956
50_L61_L0.318160.955
167_G171_R0.315560.947
1_F173_L0.315150.946
24_L190_I0.314340.944
62_A173_L0.312490.938
89_K93_R0.311050.934
65_H158_E0.309760.930
71_R74_G0.305640.918
42_V62_A0.304150.913
149_E198_D0.301920.906
32_A58_N0.301670.906
87_E91_E0.300050.901
64_E158_E0.296710.891
74_G77_W0.296430.890
164_V168_S0.294910.885
192_D218_V0.294390.884
69_I173_L0.289440.869
203_L211_F0.289340.869
8_L20_P0.288440.866
6_G215_V0.287360.863
42_V189_Y0.286380.860
86_L90_D0.286040.859
179_F187_V0.285370.857
91_E147_G0.284940.855
171_R174_L0.283730.852
2_L8_L0.283520.851
171_R184_P0.283390.851
50_L53_F0.283110.850
38_T179_F0.283050.850
133_E136_E0.282620.848
163_G168_S0.281190.844
156_V193_D0.280040.841
62_A66_G0.279920.840
65_H195_T0.279820.840
197_E200_F0.278120.835
42_V65_H0.276890.831
99_F137_Q0.275840.828
64_E156_V0.275430.827
133_E137_Q0.275010.826
32_A39_V0.273810.822
153_G193_D0.273480.821
215_V218_V0.271710.816
63_G70_R0.27130.814
190_I213_I0.269510.809
97_E101_E0.269480.809
7_T195_T0.268450.806
43_S61_L0.266120.799
46_S49_D0.265340.797
90_D94_E0.265290.796
4_Y41_I0.261980.786
189_Y212_G0.261970.786
95_I98_Y0.261740.786
8_L24_L0.260420.782
179_F185_D0.258220.775
188_L211_F0.258120.775
4_Y24_L0.257210.772
47_L70_R0.256150.769
38_T60_G0.254840.765
73_G76_E0.254570.764
160_R198_D0.254390.764
54_G61_L0.253720.762
160_R164_V0.253570.761
43_S49_D0.253060.760
49_D64_E0.252360.758
168_S172_R0.251810.756
91_E95_I0.251480.755
137_Q141_I0.251190.754
72_P75_S0.246990.741
50_L54_G0.246640.740
4_Y13_D0.246260.739
94_E97_E0.244780.735
98_Y141_I0.243510.731
4_Y50_L0.24280.729
3_D7_T0.241510.725
72_P76_E0.240810.723
136_E139_R0.240420.722
20_P25_R0.240380.722
3_D44_G0.237990.714
153_G158_E0.236750.711
20_P24_L0.236530.710
64_E67_A0.2360.708
69_I176_E0.234890.705
6_G153_G0.231940.696
107_F110_D0.230720.693
24_L28_L0.229590.689
2_L41_I0.226870.681
5_D45_R0.226810.681
44_G167_G0.225720.678
21_P45_R0.223170.670
166_K196_D0.22190.666
41_I50_L0.221420.665
42_V198_D0.220850.663
104_P107_F0.220150.661
23_E26_E0.219680.659
70_R75_S0.219050.658
60_G173_L0.218680.656
62_A69_I0.21830.655
190_I211_F0.218120.655
44_G195_T0.2180.654
60_G71_R0.216580.650
7_T192_D0.215340.646
106_S109_E0.213220.640
78_T172_R0.212960.639
213_I217_S0.212960.639
149_E165_N0.212690.638
41_I59_I0.211860.636
176_E180_A0.210660.632
96_L101_E0.210440.632
103_T106_S0.210310.631
40_A170_V0.209980.630
100_A116_A0.208820.627
65_H151_V0.208430.626
166_K192_D0.207970.624
31_L34_D0.207670.623
49_D156_V0.20740.623
149_E160_R0.206580.620
169_A173_L0.205950.618
192_D215_V0.203490.611
6_G193_D0.203410.611
24_L64_E0.202770.609
200_F203_L0.202370.608
47_L51_E0.201450.605
27_L30_A0.201350.604
115_V119_Y0.200380.602
2_L28_L0.199250.598
173_L176_E0.199240.598
4_Y8_L0.198990.597
111_K118_H0.197370.592
50_L63_G0.197060.592
88_W92_V0.196280.589
8_L39_V0.193790.582
131_A135_A0.193790.582
60_G72_P0.193580.581
77_W172_R0.19320.580
202_A212_G0.1930.579
132_R135_A0.192930.579
44_G192_D0.191610.575
68_E75_S0.191220.574
46_S193_D0.191170.574
7_T44_G0.190460.572
95_I142_L0.189940.570
40_A174_L0.189860.570
51_E54_G0.189620.569
122_A125_E0.189220.568
174_L186_F0.189120.568
71_R76_E0.188880.567
152_P156_V0.188430.566
151_V155_K0.187710.563
200_F214_K0.186960.561
141_I145_H0.186170.559
56_I59_I0.185420.557
20_P53_F0.185150.556
20_P45_R0.184410.554
156_V194_R0.183270.550
159_V162_P0.182760.549
168_S198_D0.182040.546
100_A104_P0.181930.546
110_D114_S0.180390.542
98_Y101_E0.179620.539
76_E79_N0.179520.539
70_R170_V0.179420.539
51_E55_G0.178970.537
87_E90_D0.178750.537
88_W148_L0.178630.536
41_I61_L0.17860.536
167_G200_F0.178040.534
39_V213_I0.177620.533
44_G47_L0.177480.533
192_D196_D0.177210.532
40_A62_A0.17680.531
149_E162_P0.176720.531
41_I54_G0.176380.529
44_G158_E0.176010.528
93_R110_D0.175940.528
19_V22_P0.175630.527
135_A152_P0.175090.526
138_L141_I0.174840.525
111_K114_S0.17460.524
48_D51_E0.173840.522
8_L41_I0.173820.522
117_F131_A0.173810.522
200_F213_I0.173180.520
103_T130_Q0.172960.519
84_E88_W0.172090.517
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
3daoA0.91911000.306
1u02A0.87661000.308
3pgvA0.91491000.311
3mpoA0.91491000.318
4dw8A0.91491000.319
3l7yA0.91491000.321
3r4cA0.91911000.322
3dnpA0.91061000.327
2amyA0.89361000.33
2fueA0.91061000.335

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