GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DsbC - Disulphide bond corrector protein DsbC
Pfam: PF11412 (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: 117
Sequences: 1240
Seq/Len: 10.6
HH_delta: 0.095 (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
59_E74_E0.562933.042
62_Y69_E0.481572.602
60_R69_E0.450132.432
51_G82_P0.442042.389
36_S58_P0.400462.164
33_H61_K0.370342.001
28_I76_Q0.358621.938
25_T76_Q0.346271.871
27_T76_Q0.332481.797
36_S71_E0.324571.754
25_T78_T0.318681.722
23_V78_T0.316461.710
21_E82_P0.314741.701
62_Y67_G0.300481.624
33_H74_E0.280881.518
31_G100_S0.278061.502
96_Y111_K0.272641.473
91_K112_T0.266321.439
23_V80_T0.262661.419
43_L53_V0.260941.410
63_D70_V0.257271.390
26_F34_L0.256491.386
26_F94_L0.254051.373
53_V79_F0.251161.357
98_G106_Y0.244821.323
22_L81_Q0.242381.310
58_P71_E0.233321.261
74_E101_D0.227491.229
97_Q107_P0.225721.220
32_W106_Y0.220311.190
18_D21_E0.219841.188
49_V83_L0.212711.149
61_K74_E0.209031.129
62_Y65_F0.208271.125
100_S106_Y0.204951.107
21_E80_T0.203981.102
56_P77_V0.201811.090
17_G20_Y0.199141.076
100_S104_I0.192891.042
97_Q106_Y0.192271.039
36_S73_Y0.191791.036
36_S55_Y0.191361.034
96_Y100_S0.190251.028
34_L98_G0.18681.009
93_K110_T0.186261.006
28_I77_V0.185731.004
33_H98_G0.184370.996
35_Y63_D0.183720.993
60_R71_E0.181610.981
54_Q84_K0.180470.975
97_Q108_P0.173480.937
96_Y109_Q0.173420.937
31_G101_D0.172870.934
19_T84_K0.17130.926
53_V82_P0.166810.901
95_R109_Q0.165670.895
63_D107_P0.164740.890
54_Q82_P0.16150.873
51_G81_Q0.16050.867
37_D55_Y0.159590.862
96_Y101_D0.158670.857
51_G83_L0.158560.857
84_K89_T0.158080.854
98_G104_I0.157420.851
67_G70_V0.157230.850
24_L38_N0.156430.845
61_K72_V0.156160.844
29_A104_I0.15550.840
43_L46_P0.153840.831
54_Q80_T0.153160.828
94_L108_P0.153160.828
18_D84_K0.152590.825
44_E93_K0.1520.821
39_P71_E0.151850.821
46_P86_P0.150470.813
60_R79_F0.149410.807
57_E110_T0.148310.801
70_V108_P0.147620.798
56_P73_Y0.147220.795
36_S56_P0.14710.795
41_G88_G0.146050.789
28_I75_G0.145420.786
33_H71_E0.144680.782
56_P71_E0.143850.777
53_V81_Q0.142850.772
49_V88_G0.142840.772
28_I34_L0.142470.770
54_Q57_E0.141640.765
44_E87_D0.141330.764
35_Y98_G0.141070.762
22_L92_L0.140770.761
35_Y67_G0.140220.758
48_G86_P0.139820.756
39_P55_Y0.139710.755
17_G94_L0.139360.753
26_F106_Y0.139310.753
32_W100_S0.13870.749
36_S72_V0.137190.741
29_A32_W0.136650.738
16_A19_T0.136080.735
34_L39_P0.135590.733
48_G87_D0.134540.727
16_A48_G0.134370.726
34_L94_L0.134170.725
26_F79_F0.133660.722
32_W63_D0.133110.719
62_Y72_V0.133030.719
95_R108_P0.132650.717
100_S108_P0.132650.717
61_K101_D0.131820.712
93_K111_K0.131510.711
37_D73_Y0.131410.710
42_E93_K0.131010.708
83_L88_G0.130910.707
31_G44_E0.130820.707
24_L81_Q0.130550.705
95_R110_T0.130460.705
39_P109_Q0.130260.704
77_V80_T0.129510.700
54_Q94_L0.129410.699
43_L97_Q0.129150.698
41_G94_L0.128970.697
20_Y32_W0.128340.693
33_H39_P0.126870.686
85_V88_G0.126210.682
92_L104_I0.124760.674
39_P106_Y0.124470.673
44_E111_K0.123180.666
99_C105_C0.122660.663
16_A52_E0.122010.659
91_K101_D0.121830.658
55_Y72_V0.120890.653
37_D98_G0.120530.651
27_T89_T0.119850.648
23_V30_P0.119140.644
96_Y108_P0.118720.641
96_Y110_T0.118680.641
26_F96_Y0.118660.641
47_D89_T0.118510.640
27_T78_T0.118230.639
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
3pfuA0.974499.90.095
2k0rA0.982999.90.096
1jpeA0.974499.90.097
1l6pA0.974499.90.105
1imhC0.837625.30.902
1ej6A0.923120.90.906
2ebfX0.90613.50.913
3tawA0.897411.60.916
1svcP0.86328.40.921
1iq8A0.87186.70.924

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