GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Ala_racemase_C - Alanine racemase C-terminal domain
Pfam: PF00842 (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: 129
Sequences: 2044
Seq/Len: 15.84
HH_delta: -0.018 (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
19_T24_R1.096693.094
13_E33_R0.962672.716
54_Y61_R0.957892.702
5_K89_E0.878082.477
19_T27_R0.874712.467
35_A77_V0.870312.455
15_P31_D0.845472.385
91_T96_Q0.826422.331
21_G69_C0.825112.328
8_I35_A0.819342.311
25_T67_R0.811442.289
26_Y32_T0.792882.237
103_E113_P0.780982.203
61_R104_D0.769582.171
120_L124_V0.724782.045
102_A117_L0.719252.029
4_L39_I0.710292.004
34_I65_V0.698451.970
62_C80_I0.684331.930
13_E31_D0.656851.853
30_R79_D0.649461.832
45_F92_L0.648461.829
71_D123_R0.647851.828
16_K31_D0.635961.794
6_A37_V0.625931.766
55_V75_V0.62581.765
58_N88_D0.606141.710
36_V74_M0.591661.669
14_V28_A0.591111.667
46_P119_R0.568441.604
69_C74_M0.562611.587
15_P18_E0.527961.489
45_F105_L0.521161.470
8_I84_V0.513931.450
85_K88_D0.508641.435
57_I62_C0.484511.367
32_T76_D0.481011.357
56_L91_T0.47081.328
56_L61_R0.46151.302
56_L100_I0.459211.295
2_M93_F0.45571.285
11_V77_V0.450611.271
4_L124_V0.435041.227
32_T78_T0.434481.226
15_P28_A0.431751.218
37_V90_V0.431461.217
37_V73_T0.428721.209
7_R89_E0.425211.199
29_P32_T0.407681.150
93_F102_A0.398021.123
57_I75_V0.394531.113
106_A111_T0.393121.109
53_G64_I0.391251.104
28_A32_T0.376681.063
25_T51_N0.373971.055
68_V73_T0.372431.051
20_V34_I0.369771.043
18_E28_A0.361921.021
39_I92_L0.361271.019
6_A38_P0.35671.006
56_L96_Q0.355231.002
54_Y63_P0.349950.987
10_Q36_V0.348590.983
45_F64_I0.340970.962
62_C78_T0.336310.949
19_T28_A0.333580.941
21_G74_M0.33290.939
10_Q86_V0.331820.936
47_R112_I0.330210.931
101_S104_D0.3280.925
43_D123_R0.326090.920
9_I72_M0.321730.908
46_P49_L0.314730.888
34_I74_M0.313720.885
2_M120_L0.313440.884
55_V73_T0.313150.883
43_D71_D0.307760.868
42_A71_D0.306460.864
93_F116_I0.302640.854
113_P117_L0.301540.851
9_I38_P0.298120.841
8_I11_V0.294040.829
109_S116_I0.293060.827
6_A73_T0.287320.810
94_G100_I0.286750.809
54_Y108_Q0.286260.808
11_V86_V0.284480.802
46_P109_S0.281890.795
30_R78_T0.281430.794
36_V72_M0.281090.793
48_A110_G0.280810.792
5_K91_T0.280770.792
3_S95_R0.279640.789
79_D82_P0.278840.787
3_S91_T0.278010.784
4_L120_L0.277350.782
37_V75_V0.2770.781
32_T65_V0.274480.774
17_G31_D0.269960.762
55_V92_L0.269260.760
106_A112_I0.268640.758
8_I77_V0.268460.757
21_G67_R0.265070.748
33_R83_D0.263730.744
93_F120_L0.261270.737
39_I73_T0.260340.734
42_A121_G0.25540.720
23_G67_R0.25380.716
69_C73_T0.253020.714
102_A113_P0.252940.714
62_C84_V0.252070.711
45_F93_F0.249580.704
49_L108_Q0.248910.702
14_V20_V0.246480.695
41_Y70_M0.246470.695
4_L93_F0.246460.695
60_K82_P0.245360.692
58_N85_K0.24470.690
45_F53_G0.242920.685
25_T50_S0.240860.679
71_D124_V0.240140.677
121_G124_V0.239960.677
77_V80_I0.238710.673
114_Y118_T0.238140.672
57_I90_V0.237970.671
20_V32_T0.237110.669
30_R76_D0.236690.668
14_V18_E0.235280.664
42_A123_R0.231820.654
60_K79_D0.230460.650
8_I57_I0.229550.648
2_M102_A0.221850.626
11_V33_R0.22180.626
20_V28_A0.221340.624
58_N80_I0.22120.624
77_V84_V0.220860.623
62_C79_D0.220270.621
4_L105_L0.219280.619
104_D107_K0.219060.618
48_A109_S0.217350.613
20_V74_M0.217210.613
17_G28_A0.216820.612
106_A114_Y0.215940.609
47_R115_E0.215850.609
93_F100_I0.214530.605
49_L109_S0.213650.603
60_K80_I0.20820.587
102_A112_I0.208130.587
103_E107_K0.206520.583
50_S53_G0.206060.581
62_C75_V0.205860.581
45_F73_T0.20190.570
41_Y114_Y0.201190.568
60_K83_D0.200780.566
29_P63_P0.199980.564
111_T116_I0.19960.563
75_V90_V0.19840.560
100_I104_D0.198010.559
56_L95_R0.197460.557
69_C72_M0.197420.557
93_F105_L0.196030.553
53_G108_Q0.194450.549
45_F100_I0.194080.547
87_G90_V0.192890.544
84_V88_D0.191570.540
62_C82_P0.190070.536
65_V76_D0.189950.536
96_Q100_I0.189540.535
48_A115_E0.189030.533
111_T114_Y0.188890.533
23_G47_R0.187930.530
57_I77_V0.186830.527
21_G50_S0.186160.525
68_V119_R0.185440.523
73_T92_L0.184640.521
2_M117_L0.184530.521
28_A31_D0.18430.520
33_R77_V0.183610.518
32_T79_D0.183090.516
59_G100_I0.182680.515
16_K29_P0.181090.511
49_L53_G0.181030.511
120_L126_R0.179480.506
11_V35_A0.178190.503
106_A113_P0.177710.501
14_V26_Y0.176590.498
37_V55_V0.175070.494
58_N83_D0.174810.493
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
4dyjA0.9922100-0.018
3kw3A0.969100-0.015
4eclA0.9922100-0.014
3hurA0.969100-0.001
4a3qA0.9691000.002
3mubA0.9691000.008
3e5pA0.9691000.013
4dzaA0.99221000.016
2rjgA0.9691000.137
1bd0A0.9691000.163

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