GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DapB_C - Dihydrodipicolinate reductase C-terminus
Pfam: PF05173 (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. )
Length: 132
Sequences: 1564
Seq/Len: 11.85
HH_delta: 0.008 (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
7_K11_Q0.623792.896
10_K49_E0.620132.879
44_A71_V0.539392.504
84_E97_T0.52112.419
8_L12_A0.509272.364
1_G98_H0.471752.190
25_I74_V0.448842.084
5_L96_L0.44692.075
27_S79_I0.432052.006
95_E99_R0.418751.944
84_E95_E0.40071.860
42_M46_S0.391491.818
61_G64_E0.391171.816
123_P126_Y0.388491.804
93_T101_H0.381461.771
9_A43_L0.379271.761
3_N128_M0.377451.752
11_Q14_K0.374211.737
65_Q68_E0.373191.733
54_D57_E0.360731.675
100_A106_F0.337021.565
82_E99_R0.334781.554
6_M46_S0.334451.553
111_L115_R0.330181.533
5_L94_I0.32291.499
53_R58_V0.322331.497
42_M45_E0.32071.489
3_N6_M0.318511.479
6_M42_M0.312941.453
22_I47_I0.310111.440
31_Q78_G0.30691.425
10_K50_A0.298991.388
25_I86_I0.295251.371
10_K14_K0.290311.348
10_K129_D0.288951.342
116_W131_V0.287621.335
7_K129_D0.284981.323
59_A64_E0.282371.311
100_A105_I0.280361.302
74_V86_I0.279471.298
5_L43_L0.275431.279
78_G101_H0.2671.240
24_I44_A0.264571.228
8_L96_L0.262811.220
90_P104_S0.257471.195
4_L15_L0.254671.182
65_Q70_G0.253971.179
9_A47_I0.250861.165
60_R63_R0.249281.157
62_G73_S0.246651.145
31_Q90_P0.242331.125
78_G91_G0.24111.119
81_G103_R0.240131.115
76_G88_G0.237061.101
7_K10_K0.231231.074
89_S108_E0.230721.071
47_I85_V0.228141.059
83_H98_H0.227811.058
60_R68_E0.226711.053
9_A96_L0.226451.051
6_M43_L0.226121.050
127_S131_V0.223881.039
112_R115_R0.223791.039
5_L83_H0.2211.026
116_W119_G0.219561.019
59_A63_R0.219231.018
27_S74_V0.216771.006
107_A110_A0.216551.005
16_L89_S0.215130.999
1_G83_H0.211170.980
62_G72_H0.210680.978
28_H83_H0.207820.965
79_I82_E0.206490.959
76_G89_S0.203580.945
79_I88_G0.202970.942
76_G82_E0.20230.939
22_I87_F0.201650.936
23_E88_G0.201020.933
9_A12_A0.200140.929
128_M131_V0.198680.922
17_P51_R0.198290.921
53_R67_N0.192370.893
29_H103_R0.192350.893
27_S82_E0.192250.893
18_N54_D0.189460.880
111_L114_A0.187940.873
25_I72_H0.187820.872
46_S49_E0.183770.853
86_I93_T0.183670.853
10_K46_S0.182130.846
60_R64_E0.180680.839
44_A48_A0.180160.836
30_R77_G0.180140.836
57_E60_R0.179040.831
41_L44_A0.178750.830
45_E56_S0.17560.815
78_G93_T0.174920.812
60_R73_S0.174150.809
14_K50_A0.172420.801
2_V6_M0.172360.800
128_M132_L0.170780.793
25_I88_G0.17070.793
113_A131_V0.170530.792
88_G93_T0.170430.791
55_L71_V0.16970.788
41_L45_E0.168410.782
47_I50_A0.168290.781
5_L85_V0.16760.778
103_R110_A0.167480.778
27_S97_T0.166950.775
91_G95_E0.163680.760
33_K101_H0.163540.759
29_H75_R0.15870.737
85_V89_S0.157970.733
30_R69_I0.157850.733
23_E72_H0.157330.730
93_T99_R0.157310.730
76_G79_I0.157090.729
17_P123_P0.156930.729
43_L47_I0.154810.719
9_A85_V0.154650.718
108_E123_P0.153990.715
77_G124_G0.152710.709
2_V39_T0.152120.706
3_N132_L0.151950.705
23_E76_G0.151080.701
3_N125_L0.14980.695
42_M126_Y0.149250.693
110_A114_A0.148770.691
72_H88_G0.148630.690
77_G107_A0.148350.689
29_H34_D0.148050.687
18_N66_E0.147750.686
4_L112_R0.147420.684
32_K38_G0.147070.683
5_L11_Q0.146360.680
39_T75_R0.146350.679
32_K39_T0.145630.676
78_G88_G0.145320.675
25_I73_S0.144750.672
22_I69_I0.144040.669
24_I40_A0.144040.669
126_Y131_V0.143860.668
34_D98_H0.143420.666
12_A132_L0.143380.666
23_E70_G0.143340.665
28_H39_T0.143090.664
49_E54_D0.142730.663
29_H81_G0.142260.660
10_K13_A0.141990.659
57_E67_N0.141890.659
28_H32_K0.141720.658
4_L24_I0.141610.657
33_K111_L0.141330.656
28_H38_G0.141280.656
46_S83_H0.141230.656
116_W128_M0.139510.648
79_I86_I0.139220.646
4_L8_L0.138490.643
52_D58_V0.137570.639
106_F110_A0.136220.632
31_Q77_G0.135690.630
108_E115_R0.135560.629
42_M83_H0.134970.627
115_R118_A0.134220.623
89_S116_W0.134020.622
53_R65_Q0.133850.621
62_G68_E0.133740.621
17_P77_G0.133680.621
1_G29_H0.133270.619
11_Q90_P0.132670.616
40_A81_G0.132640.616
112_R116_W0.132530.615
97_T104_S0.132110.613
42_M87_F0.131560.611
2_V13_A0.131430.610
18_N104_S0.131030.608
88_G101_H0.130880.608
44_A69_I0.13030.605
90_P113_A0.130230.605
26_E81_G0.129880.603
45_E48_A0.129650.602
23_E86_I0.129630.602
23_E74_V0.129620.602
52_D119_G0.129580.602
6_M105_I0.129380.601
79_I92_E0.129370.601
28_H103_R0.12920.600
48_A69_I0.128980.599
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
4f3yA0.99241000.008
3ijpA0.99241000.01
3qy9A0.96971000.033
1dihA0.99241000.042
1vm6A0.84851000.058
1p9lA0.95451000.091
1f06A0.977396.50.859
2m4gA0.272712.20.943
2ca5A0.22738.90.947
1wh9A0.28037.60.948

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