GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DsbC_N - Disulfide bond isomerase protein N-terminus
Pfam: PF10411 (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: 57
Sequences: 627
Seq/Len: 11
HH_delta: 0.128 (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
52_D55_T0.487182.561
26_Y40_E0.374941.971
30_L34_G0.367681.933
2_K6_K0.340061.787
39_D42_G0.331261.741
22_I50_L0.289321.521
27_E35_I0.276531.454
17_V28_V0.262751.381
43_R52_D0.258391.358
25_L46_I0.257051.351
28_V38_V0.252151.325
1_I5_L0.251891.324
21_P52_D0.238041.251
3_Q7_K0.234471.232
52_D56_K0.232841.224
18_S48_G0.219281.153
36_L47_Q0.218681.149
36_L51_Y0.217751.145
34_G51_Y0.216171.136
40_E49_Q0.214811.129
46_I50_L0.214711.129
4_A54_K0.213591.123
43_R54_K0.209821.103
20_S25_L0.206921.088
1_I43_R0.202471.064
11_G51_Y0.200061.052
25_L38_V0.198641.044
14_V26_Y0.193271.016
5_L24_G0.186670.981
21_P37_Y0.184640.971
20_S26_Y0.182660.960
8_A36_L0.182390.959
35_I51_Y0.177790.935
14_V33_G0.177420.933
27_E55_T0.174170.915
12_L33_G0.173810.914
4_A38_V0.172420.906
7_K13_K0.172040.904
22_I25_L0.170090.894
19_P23_P0.169510.891
36_L49_Q0.167040.878
45_L49_Q0.164020.862
12_L30_L0.16380.861
43_R53_L0.163320.858
27_E50_L0.162980.857
1_I38_V0.162770.856
12_L45_L0.159670.839
12_L34_G0.15870.834
23_P44_Y0.158170.831
4_A13_K0.157890.830
19_P47_Q0.157460.828
16_S27_E0.155060.815
1_I42_G0.15430.811
3_Q41_D0.152520.802
26_Y49_Q0.152320.801
19_P43_R0.151810.798
8_A34_G0.151420.796
17_V39_D0.149380.785
17_V27_E0.149030.783
3_Q6_K0.148730.782
16_S29_V0.14620.768
22_I39_D0.146010.767
3_Q33_G0.145420.764
38_V42_G0.144660.760
49_Q54_K0.143470.754
5_L42_G0.142240.748
28_V36_L0.141230.742
16_S50_L0.140730.740
38_V44_Y0.140290.737
8_A39_D0.139280.732
3_Q13_K0.138730.729
14_V28_V0.138260.727
2_K56_K0.137160.721
2_K5_L0.136680.718
16_S26_Y0.135280.711
6_K14_V0.133640.702
15_E29_V0.132970.699
42_G47_Q0.131940.694
29_V34_G0.131920.693
2_K16_S0.128860.677
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
1t3bA0.947499.20.128
1eejA0.947499.20.129
3tdgA199.10.172
1v58A0.964998.80.277
3u1wA0.771987.20.721
3elgA0.8246810.742
3db7A0.824678.80.747
4dsdA0.8246750.755
2ljkA0.947471.50.761
4hbrA157.80.78

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