GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Gp_dh_N - Glyceraldehyde 3-phosphate dehydrogenase NAD binding domain
Pfam: PF00044 (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: CL0063
Length: 151
Sequences: 8091
Seq/Len: 53.58
HH_delta: 0.07 (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
2_K26_E1.701124.270
76_E81_E1.539813.865
106_E110_D1.349983.388
78_D81_E1.342373.369
4_G89_V1.048462.632
104_N107_A1.007662.529
132_M136_H0.991822.489
102_R106_E0.906942.276
140_D143_H0.766151.923
26_E69_K0.747231.875
37_P41_A0.732431.838
101_T104_N0.720571.809
8_F44_L0.709511.781
16_L27_V0.702551.763
79_P99_F0.678191.702
15_V93_V0.66771.676
16_L44_L0.665511.670
19_A27_V0.661821.661
2_K90_D0.651671.636
74_T87_L0.648161.627
103_E107_A0.64531.620
92_V113_A0.622991.564
37_P73_V0.61931.554
80_E110_D0.60391.516
2_K28_V0.603581.515
14_L50_H0.593321.489
80_E107_A0.58761.475
41_A45_K0.583611.465
4_G92_V0.577381.449
115_K144_H0.576551.447
107_A110_D0.569861.430
100_R118_I0.546271.371
106_E109_L0.533831.340
122_S125_D0.532841.337
40_L73_V0.531631.334
39_Y42_Y0.519031.303
128_P138_D0.51561.294
122_S129_T0.511531.284
2_K88_G0.498021.250
103_E106_E0.497631.249
39_Y70_K0.484091.215
105_A118_I0.477681.199
28_V89_V0.477191.198
42_Y46_Y0.474811.192
8_F30_I0.460911.157
95_C119_S0.456341.145
101_T123_K0.455911.144
20_L69_K0.455631.144
14_L17_R0.445591.118
90_D114_K0.440171.105
125_D128_P0.434861.091
130_F143_H0.428821.076
14_L18_A0.427321.073
94_E105_A0.425321.068
102_R121_P0.42321.062
6_N94_E0.421261.057
38_E42_Y0.42021.055
107_A111_A0.418791.051
89_V92_V0.412111.034
128_P143_H0.40971.028
29_A89_V0.40831.025
29_A74_T0.407961.024
131_V149_A0.400211.004
41_A44_L0.400021.004
123_K127_D0.388020.974
8_F16_L0.383430.962
32_D40_L0.383030.961
34_A40_L0.377390.947
132_M148_N0.372660.935
99_F121_P0.361360.907
3_V25_I0.359070.901
39_Y72_K0.35890.901
100_R104_N0.358040.899
24_D27_V0.356390.895
18_A22_Q0.355130.891
34_A38_E0.353740.888
100_R103_E0.353420.887
10_R13_R0.351190.881
20_L49_V0.34940.877
19_A25_I0.345540.867
130_F138_D0.343040.861
40_L75_E0.342480.860
115_K139_Y0.342080.859
82_I87_L0.329980.828
13_R17_R0.328420.824
108_H113_A0.32760.822
4_G82_I0.323220.811
82_I111_A0.322140.809
3_V91_I0.321880.808
117_I146_I0.319270.801
79_P104_N0.318890.800
33_P78_D0.315590.792
137_D140_D0.315070.791
91_I117_I0.312390.784
18_A21_D0.312150.783
5_I27_V0.310730.780
92_V108_H0.308640.775
17_R21_D0.307340.771
3_V19_A0.306460.769
139_Y146_I0.306130.768
15_V19_A0.302180.758
44_L47_D0.30090.755
2_K25_I0.299370.751
16_L71_I0.298310.749
103_E124_D0.298140.748
16_L20_L0.297240.746
29_A87_L0.296990.745
39_Y43_L0.295420.741
76_E82_I0.293170.736
101_T124_D0.292020.733
9_G12_G0.291110.731
81_E88_G0.289780.727
37_P70_K0.288970.725
28_V77_R0.287980.723
104_N108_H0.284610.714
6_N100_R0.284550.714
94_E97_G0.283810.712
34_A39_Y0.281730.707
105_A109_L0.281670.707
72_K87_L0.280350.704
139_Y144_H0.279360.701
138_D143_H0.279260.701
96_T120_A0.27610.693
102_R127_D0.275070.690
22_Q25_I0.274720.690
133_G136_H0.274340.689
91_I115_K0.274050.688
44_L75_E0.273440.686
109_L145_I0.271440.681
34_A37_P0.271240.681
101_T105_A0.270490.679
78_D107_A0.269510.676
143_H146_I0.268770.675
124_D127_D0.267520.671
26_E74_T0.267270.671
33_P76_E0.266420.669
97_G120_A0.266150.668
2_K89_V0.265650.667
8_F32_D0.264570.664
96_T101_T0.263590.662
114_K144_H0.263140.660
32_D39_Y0.261230.656
130_F139_Y0.260380.654
3_V93_V0.258930.650
28_V88_G0.257190.646
141_P144_H0.255950.642
28_V87_L0.25390.637
40_L44_L0.2530.635
6_N96_T0.249950.627
5_I12_G0.247960.622
21_D72_K0.247540.621
30_I73_V0.247380.621
101_T106_E0.24660.619
82_I89_V0.245130.615
33_P96_T0.244410.613
34_A49_V0.243610.611
102_R125_D0.242490.609
87_L111_A0.240460.604
38_E44_L0.240280.603
6_N92_V0.239280.601
19_A93_V0.23880.599
23_P69_K0.23880.599
102_R122_S0.238420.598
68_G71_I0.237850.597
91_I114_K0.236690.594
118_I122_S0.236020.592
79_P108_H0.235090.590
42_Y49_V0.234410.588
25_I91_I0.234260.588
96_T119_S0.234180.588
133_G148_N0.234170.588
8_F13_R0.233840.587
78_D82_I0.233480.586
43_L75_E0.232860.584
69_K146_I0.232720.584
73_V132_M0.230270.578
77_R81_E0.229920.577
101_T119_S0.229550.576
118_I148_N0.229110.575
28_V31_N0.228190.573
76_E98_K0.225740.567
95_C99_F0.224540.564
5_I13_R0.223180.560
28_V82_I0.222670.559
11_I95_C0.22250.558
140_D144_H0.222480.558
94_E108_H0.222120.558
100_R105_A0.218620.549
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
3pymA0.986899.90.07
3v1yO0.986899.90.077
3lvfP0.986899.90.079
4dibA0.986899.90.08
3docA0.986899.90.082
3idsC0.993499.90.083
3h9eO0.980199.90.092
3hjaA0.980199.90.115
1u8fO0.986899.90.126
2b4rO0.993499.90.132

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