GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DXPR_C - DXP reductoisomerase C-terminal domain
Pfam: PF13288 (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: 121
Sequences: 1577
Seq/Len: 13.03
HH_delta: -0.012 (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
82_S85_D0.860963.212
28_D31_K0.817123.048
74_E78_E0.78572.931
85_D88_D0.706982.638
73_V77_L0.689142.571
106_S109_D0.640612.390
91_E95_E0.609062.272
114_D118_R0.594942.220
60_T97_F0.575862.148
93_V121_A0.575832.148
42_F52_Y0.553982.067
42_F49_K0.549042.048
40_P48_L0.544762.032
49_K53_E0.525231.960
47_C87_P0.514491.919
93_V117_A0.511371.908
96_R120_Y0.479051.787
61_A94_L0.473561.767
93_V120_Y0.458671.711
53_E95_E0.448881.675
105_N109_D0.440971.645
75_A80_K0.435511.625
31_K39_E0.427831.596
25_E31_K0.416231.553
89_I121_A0.405171.512
47_C90_I0.404021.507
38_E45_F0.403791.506
54_A94_L0.394141.470
71_V121_A0.384151.433
97_F116_W0.380671.420
115_A119_R0.373381.393
92_K95_E0.371071.384
60_T113_I0.370281.381
81_I85_D0.364951.362
15_S20_L0.363461.356
71_V75_A0.357551.334
64_V97_F0.350851.309
57_K61_A0.350481.308
11_A15_S0.348081.299
66_N69_N0.346011.291
117_A121_A0.345651.290
71_V114_D0.341241.273
112_E115_A0.333631.245
1_L35_L0.329061.228
46_P91_E0.320641.196
41_D44_R0.320511.196
107_L111_L0.31921.191
112_E116_W0.317631.185
116_W119_R0.306771.144
52_Y55_L0.305991.142
47_C65_L0.304411.136
73_V86_I0.303721.133
72_A90_I0.301471.125
53_E57_K0.295661.103
63_I110_I0.295091.101
8_L24_V0.292021.089
30_T39_E0.288891.078
52_Y56_R0.288021.075
2_S8_L0.286321.068
49_K91_E0.276011.030
92_K96_R0.272391.016
71_V74_E0.265560.991
30_T33_G0.265410.990
108_E112_E0.259040.966
50_L65_L0.256340.956
53_E56_R0.251530.938
55_L59_G0.251250.937
42_F48_L0.247440.923
75_A121_A0.244750.913
116_W120_Y0.243550.909
113_I117_A0.241380.901
67_A114_D0.240660.898
20_L23_P0.236950.884
63_I113_I0.235820.880
43_E49_K0.234610.875
29_F33_G0.233510.871
59_G63_I0.231210.863
88_D92_K0.230660.861
38_E44_R0.23010.858
66_N114_D0.229490.856
29_F32_L0.227010.847
72_A89_I0.22660.845
69_N73_V0.226180.844
113_I116_W0.2250.839
18_E21_P0.224390.837
54_A62_P0.224050.836
46_P88_D0.215440.804
69_N86_I0.213810.798
83_F87_P0.213380.796
3_P24_V0.211790.790
45_F48_L0.207750.775
87_P90_I0.207220.773
49_K56_R0.205540.767
58_G61_A0.203060.758
71_V118_R0.200270.747
54_A65_L0.200090.746
5_D24_V0.198030.739
50_L91_E0.1980.739
11_A20_L0.196060.731
27_L33_G0.195290.729
97_F120_Y0.195130.728
55_L62_P0.193450.722
100_S105_N0.19330.721
1_L27_L0.192290.717
62_P90_I0.191460.714
3_P26_P0.191320.714
60_T104_P0.191170.713
89_I92_K0.190450.711
52_Y59_G0.190290.710
9_P74_E0.190260.710
57_K99_N0.189230.706
13_A66_N0.189180.706
47_C86_I0.189080.705
61_A97_F0.18830.703
8_L55_L0.187920.701
3_P7_R0.186770.697
85_D89_I0.185430.692
65_L94_L0.18520.691
58_G62_P0.184880.690
13_A113_I0.184570.689
9_P69_N0.184170.687
29_F35_L0.181790.678
60_T109_D0.180850.675
57_K60_T0.18020.672
54_A58_G0.179380.669
36_T39_E0.176840.660
2_S23_P0.176110.657
61_A99_N0.174670.652
88_D104_P0.174610.651
55_L58_G0.172280.643
27_L81_I0.171870.641
46_P49_K0.171390.639
100_S113_I0.171390.639
64_V93_V0.171360.639
33_G39_E0.170920.638
64_V113_I0.169440.632
104_P110_I0.16930.632
50_L87_P0.167380.624
90_I94_L0.165670.618
44_R87_P0.165610.618
41_D45_F0.165250.617
103_N109_D0.163270.609
39_E120_Y0.162860.608
8_L11_A0.162680.607
107_L113_I0.160540.599
30_T55_L0.160030.597
81_I89_I0.158530.591
104_P109_D0.156450.584
40_P87_P0.155130.579
55_L61_A0.153680.573
72_A86_I0.153580.573
106_S115_A0.153060.571
110_I113_I0.15280.570
11_A16_Y0.151970.567
3_P32_L0.15110.564
96_R100_S0.149880.559
65_L87_P0.149050.556
23_P47_C0.148750.555
14_L72_A0.148230.553
54_A91_E0.147630.551
75_A89_I0.146690.547
89_I93_V0.146370.546
16_Y35_L0.145610.543
65_L77_L0.145020.541
26_P104_P0.144950.541
59_G113_I0.144910.541
3_P45_F0.144740.540
36_T40_P0.144620.540
53_E91_E0.144140.538
43_E46_P0.143870.537
11_A24_V0.14280.533
39_E43_E0.142370.531
100_S112_E0.141470.528
60_T90_I0.140190.523
32_L39_E0.139850.522
97_F117_A0.139810.522
59_G62_P0.139650.521
54_A61_A0.139150.519
43_E82_S0.137340.512
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
1q0qA0.9835100-0.012
3au8A1100-0.005
2y1eA0.9835100-0.005
1r0kA0.98351000.024
3a06A0.95871000.056
3e39A0.33068.30.948
3vwxA0.53727.70.949
1vq8Y0.4386.40.95
4ifdA0.93395.60.951
1jcuA0.62815.60.951

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