GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ldh_1_C - lactatemalate dehydrogenase alphabeta C-terminal domain
Pfam: PF02866 (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: CL0341
Length: 174
Sequences: 2889
Seq/Len: 16.6
HH_delta: 0.073 (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
153_Q157_K0.7723.075
69_E73_K0.723482.882
133_V141_K0.668092.661
70_R77_E0.625492.491
161_K165_K0.590052.350
61_E65_E0.588472.344
128_F156_L0.571592.277
106_R135_G0.561072.235
154_E158_E0.531092.115
150_E153_Q0.501721.998
66_E70_R0.495121.972
128_F160_A0.492071.960
114_Y127_Y0.483791.927
157_K161_K0.475891.896
99_E103_K0.465281.853
36_V152_E0.45621.817
1_T129_S0.451941.800
150_E154_E0.447991.784
135_G140_E0.441821.760
121_I157_K0.434471.731
121_I156_L0.431561.719
40_S149_S0.428451.707
106_R140_E0.427791.704
115_L130_V0.421641.679
15_K63_E0.404131.610
115_L118_E0.401811.600
21_S105_E0.400131.594
113_V132_V0.397091.582
155_K158_E0.388171.546
16_L44_V0.379771.513
19_N22_S0.374351.491
2_M93_A0.373341.487
40_S152_E0.370751.477
132_V139_V0.369861.473
34_S162_E0.365721.457
117_G120_G0.36041.436
60_S63_E0.356761.421
65_E69_E0.354981.414
116_D122_P0.354021.410
164_K168_E0.352961.406
27_V37_P0.351691.401
25_A42_A0.350061.394
137_N140_E0.34791.386
69_E72_R0.34751.384
13_A23_V0.347361.384
73_K76_Y0.340411.356
37_P68_T0.340251.355
75_G79_I0.339021.350
158_E161_K0.336071.339
151_E154_E0.335361.336
77_E81_A0.334661.333
133_V143_V0.329971.314
28_I38_D0.327571.305
165_K169_K0.325241.295
165_K168_E0.324321.292
22_S45_G0.314951.254
162_E166_E0.313211.248
118_E144_E0.308881.230
108_I133_V0.308851.230
2_M109_L0.308511.229
7_R31_H0.305711.218
104_D136_K0.305681.218
79_I85_S0.304171.212
113_V139_V0.301441.201
24_N43_K0.289741.154
130_V142_I0.288921.151
18_V23_V0.284441.133
75_G85_S0.281061.119
77_E80_K0.278811.111
156_L160_A0.278341.109
47_V51_S0.276971.103
11_F70_R0.270811.079
59_L63_E0.269471.073
10_Y14_E0.269331.073
96_R107_R0.26891.071
73_K80_K0.268171.068
121_I160_A0.265471.057
111_V132_V0.263411.049
8_F36_V0.263351.049
157_K160_A0.26271.046
158_E162_E0.257931.027
76_Y80_K0.255341.017
13_A20_P0.254931.015
95_A98_V0.252751.007
62_E66_E0.252311.005
9_R24_N0.252281.005
4_D7_R0.250560.998
154_E157_K0.250020.996
15_K66_E0.249680.995
60_S64_L0.249610.994
8_F25_A0.24860.990
94_A98_V0.246010.980
82_K86_T0.245720.979
97_I111_V0.243860.971
91_A95_A0.243790.971
34_S159_S0.241190.961
151_E155_K0.240970.960
108_I143_V0.235070.936
50_L71_V0.23370.931
148_L156_L0.23120.921
30_E86_T0.231140.921
118_E142_I0.23040.918
99_E105_E0.229750.915
101_I134_I0.228010.908
141_K144_E0.227020.904
68_T151_E0.226640.903
79_I86_T0.223540.890
110_P129_S0.222420.886
4_D31_H0.222070.885
98_V102_L0.220010.876
161_K168_E0.219970.876
54_K147_P0.219490.874
76_Y79_I0.218970.872
48_P51_S0.218950.872
164_K167_I0.217830.868
89_S92_A0.216310.862
117_G122_P0.21620.861
27_V68_T0.214190.853
166_E169_K0.213960.852
63_E66_E0.21340.850
126_V164_K0.212780.848
104_D135_G0.21260.847
3_L7_R0.212250.845
122_P160_A0.211330.842
100_A109_L0.210660.839
65_E151_E0.209650.835
111_V134_I0.208030.829
31_H75_G0.205970.820
6_A89_S0.204520.815
51_S147_P0.204210.813
86_T90_I0.201920.804
38_D41_H0.201920.804
119_Y144_E0.199420.794
75_G86_T0.198970.793
109_L134_I0.198730.792
112_S121_I0.198020.789
98_V101_I0.19590.780
34_S158_E0.195270.778
2_M97_I0.195260.778
78_I89_S0.193830.772
18_V22_S0.193080.769
111_V115_L0.193020.769
82_K90_I0.192980.769
74_A89_S0.192860.768
50_L64_L0.192580.767
33_D76_Y0.190650.759
16_L59_L0.189780.756
28_I36_V0.189750.756
61_E151_E0.188940.753
5_S9_R0.188770.752
122_P164_K0.188690.752
96_R105_E0.188390.750
1_T90_I0.185460.739
18_V44_V0.18530.738
47_V52_Y0.185080.737
161_K164_K0.18490.736
11_F74_A0.184420.735
118_E123_D0.183380.730
16_L23_V0.182450.727
66_E69_E0.182220.726
113_V127_Y0.181660.724
97_I109_L0.181340.722
23_V44_V0.181060.721
32_G166_E0.18050.719
12_L16_L0.178990.713
135_G141_K0.178610.711
43_K46_G0.178550.711
39_W64_L0.177620.707
35_Q90_I0.177560.707
35_Q86_T0.175270.698
12_L23_V0.174930.697
12_L59_L0.173860.693
92_A96_R0.173850.692
4_D33_D0.173210.690
8_F37_P0.172970.689
112_S127_Y0.171750.684
11_F14_E0.171510.683
8_F27_V0.171120.682
1_T35_Q0.169780.676
81_A85_S0.169180.674
94_A112_S0.169050.673
73_K77_E0.167240.666
148_L157_K0.163780.652
85_S89_S0.163190.650
116_D119_Y0.163190.650
148_L152_E0.16280.648
137_N141_K0.162210.646
112_S115_L0.161240.642
8_F67_L0.161010.641
79_I87_S0.16070.640
1_T27_V0.159620.636
118_E121_I0.158740.632
121_I126_V0.157820.629
35_Q75_G0.157710.628
10_Y92_A0.156040.622
53_A59_L0.155730.620
30_E34_S0.155170.618
78_I87_S0.15510.618
34_S37_P0.154990.617
138_G152_E0.154940.617
26_Y108_I0.154640.616
74_A85_S0.154460.615
119_Y146_L0.154240.614
96_R109_L0.154180.614
102_L138_G0.154070.614
123_D126_V0.153970.613
75_G93_A0.153920.613
78_I81_A0.15360.612
44_V52_Y0.153570.612
31_H86_T0.153410.611
8_F42_A0.152410.607
150_E157_K0.152250.606
1_T34_S0.151230.602
167_I170_G0.151130.602
2_M92_A0.151060.602
86_T89_S0.150130.598
156_L159_S0.150040.598
11_F71_V0.149960.597
106_R133_V0.149910.597
7_R32_G0.149770.597
2_M100_A0.14940.595
59_L64_L0.148170.590
116_D121_I0.147870.589
103_K108_I0.14760.588
14_E66_E0.14670.584
126_V160_A0.146680.584
59_L62_E0.14620.582
144_E147_P0.146190.582
43_K48_P0.14490.577
42_A49_L0.144640.576
50_L60_S0.144130.574
149_S152_E0.144110.574
121_I128_F0.143470.571
38_D93_A0.143330.571
72_R88_Y0.143320.571
115_L121_I0.143310.571
117_G121_I0.143250.571
113_V118_E0.142570.568
10_Y20_P0.142310.567
1_T4_D0.142260.567
115_L120_G0.142240.567
5_S26_Y0.141990.566
50_L63_E0.141640.564
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
3vkuA0.9771000.073
3pqeA0.9771000.077
4aj2A0.97131000.086
3tl2A0.92531000.111
3nepX0.94831000.112
4bgtA0.93681000.112
3p7mA0.9771000.113
3gviA0.9771000.117
7mdhA0.9541000.135
1ojuA0.86781000.14

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