GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gp_dh_C - Glyceraldehyde 3-phosphate dehydrogenase C-terminal domain
Pfam: PF02800 (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: CL0139
Length: 157
Sequences: 2976
Seq/Len: 18.96
HH_delta: 0.023 (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
9_D66_E1.652584.184
6_K10_D1.414113.580
15_E93_E1.388573.515
118_G134_H1.368433.464
48_N127_S1.080082.734
11_N107_Q1.062442.690
25_Y46_A1.055182.671
95_P149_N1.045472.647
82_N130_N1.024482.594
136_S155_A0.992332.512
16_K91_E0.932962.362
12_F104_A0.927762.349
105_L138_F0.895832.268
123_P141_E0.850862.154
101_V151_V0.826312.092
49_I76_V0.812122.056
103_E107_Q0.809232.049
61_G68_N0.795312.013
24_A80_T0.781151.978
76_V85_L0.753941.909
95_P148_G0.747511.892
5_L67_L0.740431.875
83_V129_F0.73451.860
92_L151_V0.718311.819
94_K100_E0.702941.780
124_L129_F0.696671.764
106_K121_E0.692541.753
44_A47_Q0.691171.750
15_E91_E0.691161.750
41_R52_T0.669541.695
47_Q81_P0.666561.688
72_T144_I0.661061.674
98_K143_T0.655651.660
119_Y140_A0.647051.638
97_T100_E0.630891.597
118_G132_D0.626931.587
38_D41_R0.612181.550
62_K68_N0.607751.539
15_E149_N0.586711.485
106_K110_R0.573641.452
11_N104_A0.567961.438
132_D137_I0.563461.426
31_L45_A0.556711.409
104_A107_Q0.543781.377
27_D34_G0.533731.351
127_S130_N0.528091.337
46_A81_P0.523631.326
120_T124_L0.511281.294
102_N143_T0.510681.293
91_E149_N0.509721.290
120_T129_F0.508911.288
44_A81_P0.506871.283
8_L105_L0.506461.282
30_K34_G0.503611.275
17_G71_I0.499571.265
134_H137_I0.499271.264
7_V117_L0.488421.237
27_D32_V0.482691.222
92_L96_V0.479981.215
4_V105_L0.478521.211
12_F92_L0.478041.210
16_K147_N0.473991.200
106_K119_Y0.468791.187
145_V148_G0.465851.179
5_L14_I0.462431.171
4_V136_S0.460311.165
4_V155_A0.450891.142
11_N15_E0.450331.140
28_P36_H0.449711.139
4_V153_L0.448861.136
121_E140_A0.439851.114
100_E103_E0.439761.113
9_D64_L0.435241.102
8_L92_L0.431031.091
28_P41_R0.427571.082
98_K102_N0.424611.075
96_V145_V0.421521.067
107_Q111_G0.416561.055
74_M154_F0.411361.041
103_E106_K0.409791.037
8_L153_L0.406741.030
13_G92_L0.404851.025
113_L117_L0.399111.010
102_N138_F0.398351.008
102_N140_A0.396441.004
9_D93_E0.393680.997
22_I76_V0.392830.995
40_R139_D0.391070.990
142_A154_F0.385340.976
107_Q112_P0.384770.974
25_Y81_P0.384540.974
12_F96_V0.38370.971
120_T141_E0.382990.970
99_E102_N0.373710.946
25_Y31_L0.366930.929
85_L154_F0.365310.925
96_V100_E0.363650.921
145_V151_V0.355820.901
7_V104_A0.355790.901
90_V153_L0.353490.895
20_T89_T0.350750.888
16_K150_L0.349260.884
99_E103_E0.34750.880
18_R74_M0.341080.864
109_A112_P0.34050.862
16_K149_N0.333280.844
81_P127_S0.328880.833
13_G93_E0.328320.831
39_W42_G0.32820.831
120_T140_A0.317650.804
5_L71_I0.315410.799
105_L153_L0.31530.798
74_M152_K0.315110.798
125_V128_D0.315010.798
8_L90_V0.313950.795
27_D30_K0.312410.791
12_F101_V0.310370.786
87_D152_K0.306860.777
18_R152_K0.306320.776
11_N94_K0.30170.764
118_G137_I0.298890.757
40_R142_A0.296230.750
10_D64_L0.294350.745
80_T83_V0.292770.741
32_V81_P0.28940.733
104_A108_A0.287680.728
47_Q130_N0.287630.728
107_Q110_R0.286020.724
38_D52_T0.285850.724
83_V130_N0.28340.717
1_L19_M0.272720.690
25_Y47_Q0.268270.679
96_V151_V0.2650.671
76_V154_F0.264980.671
117_L136_S0.264130.669
96_V104_A0.263380.667
106_K109_A0.261940.663
1_L5_L0.261620.662
96_V101_V0.26070.660
34_G50_I0.260630.660
25_Y45_A0.257920.653
18_R72_T0.256750.650
83_V86_H0.255550.647
43_R128_D0.255510.647
103_E110_R0.254460.644
116_I135_S0.252770.640
6_K112_P0.251980.638
90_V151_V0.251490.637
110_R114_K0.251490.637
36_H42_G0.25140.636
19_M88_L0.250830.635
27_D50_I0.249110.631
91_E150_L0.242480.614
11_N108_A0.241570.612
55_G84_S0.241240.611
110_R119_Y0.240330.608
47_Q127_S0.239960.608
8_L14_I0.237530.601
18_R146_V0.2370.600
54_T84_S0.236680.599
40_R43_R0.234890.595
5_L64_L0.233340.591
105_L119_Y0.233060.590
31_L34_G0.233010.590
74_M144_I0.231940.587
29_Q33_D0.231280.586
119_Y138_F0.230530.584
20_T87_D0.23020.583
120_T139_D0.230180.583
9_D13_G0.229650.581
102_N119_Y0.22850.578
53_S58_K0.228090.577
98_K138_F0.226890.574
30_K42_G0.225220.570
25_Y44_A0.225120.570
124_L139_D0.225110.570
17_G88_L0.220290.558
92_L145_V0.220240.558
20_T76_V0.219280.555
30_K36_H0.217680.551
25_Y135_S0.217240.550
4_V138_F0.216730.549
89_T150_L0.216690.549
19_M73_G0.215930.547
23_H26_T0.215280.545
108_A112_P0.214260.542
27_D35_P0.213950.542
9_D67_L0.213650.541
24_A44_A0.212990.539
49_I80_T0.210250.532
122_D129_F0.209730.531
58_K61_G0.207830.526
18_R88_L0.206620.523
28_P32_V0.205950.521
7_V113_L0.20420.517
21_T54_T0.204140.517
14_I90_V0.203140.514
111_G114_K0.202940.514
38_D42_G0.202880.514
18_R89_T0.20280.513
49_I154_F0.20210.512
47_Q82_N0.201880.511
20_T152_K0.200140.507
7_V108_A0.199490.505
27_D31_L0.199440.505
145_V149_N0.199390.505
17_G90_V0.198410.502
66_E93_E0.197640.500
1_L86_H0.19690.498
57_A73_G0.195530.495
144_I150_L0.195470.495
74_M89_T0.194970.494
74_M142_A0.194890.493
8_L88_L0.192980.489
58_K88_L0.192670.488
70_K93_E0.191790.486
36_H41_R0.191280.484
43_R77_R0.190580.482
60_V71_I0.18980.481
11_N93_E0.189680.480
97_T148_G0.189310.479
102_N105_L0.188430.477
35_P120_T0.187650.475
105_L117_L0.18760.475
91_E147_N0.187170.474
93_E149_N0.183680.465
21_T84_S0.183480.465
39_W123_P0.183320.464
89_T146_V0.18270.463
12_F94_K0.182460.462
28_P42_G0.181860.460
5_L90_V0.181570.460
62_K66_E0.181480.459
11_N100_E0.18090.458
96_V149_N0.180410.457
4_V86_H0.179390.454
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
4dibA11000.023
3idsC11000.03
3pymA11000.03
3docA11000.03
3h9eO11000.03
3hjaA11000.032
3v1yO11000.039
1obfO0.99361000.049
2ep7A0.99361000.055
2b4rO11000.058

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