GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CobW_C - Cobalamin synthesis protein cobW C-terminal domain
Pfam: PF07683 (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: 94
Sequences: 2661
Seq/Len: 28.31
HH_delta: 0.151 (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
83_K87_R1.134534.182
6_F91_D0.798272.943
20_W89_A0.730652.693
31_A46_F0.707622.608
87_R91_D0.585492.158
7_E73_R0.565882.086
17_L37_V0.529511.952
82_D85_A0.522941.928
13_D16_R0.449451.657
31_A48_G0.4441.637
4_V86_L0.436231.608
4_V87_R0.432821.595
45_V58_A0.422771.558
78_G81_L0.409761.510
43_R58_A0.404251.490
84_E88_E0.400851.478
9_D71_D0.395941.459
48_G53_Y0.386171.423
85_A89_A0.38381.415
15_E19_A0.359641.326
4_V83_K0.354231.306
6_F12_F0.352561.300
36_W70_R0.349641.289
32_K77_I0.339251.251
11_P36_W0.336721.241
13_D38_A0.332721.226
42_R57_P0.33141.222
7_E71_D0.330151.217
42_R60_R0.325061.198
18_E22_Q0.316481.167
34_I45_V0.309681.142
14_P18_E0.307391.133
35_V72_S0.303711.120
19_A23_E0.302511.115
20_W93_C0.296571.093
40_G44_L0.295371.089
85_A88_E0.29431.085
45_V56_E0.29421.084
16_R93_C0.287851.061
14_P37_V0.284411.048
8_F72_S0.280461.034
2_S83_K0.280061.032
88_E91_D0.278431.026
27_D80_N0.277161.022
36_W68_E0.271571.001
14_P90_L0.266570.983
20_W25_P0.262330.967
29_L79_K0.259640.957
84_E87_R0.258670.953
9_D36_W0.257040.947
8_F87_R0.256020.944
35_V46_F0.252150.929
31_A76_F0.250580.924
36_W43_R0.250110.922
40_G57_P0.24950.920
46_F53_Y0.245390.905
13_D39_D0.245330.904
38_A41_P0.245310.904
9_D69_D0.245110.904
23_E89_A0.244190.900
85_A92_A0.238590.879
44_L55_I0.237520.876
17_L33_G0.235040.866
6_F90_L0.232780.858
89_A92_A0.230940.851
8_F90_L0.229380.846
57_P86_L0.221330.816
27_D79_K0.220540.813
46_F74_L0.219710.810
20_W86_L0.219540.809
37_V44_L0.215150.793
1_I77_I0.214190.790
43_R47_Q0.214160.789
59_G68_E0.207150.764
88_E92_A0.20630.760
24_L28_V0.205390.757
33_G46_F0.203930.752
25_P51_G0.203430.750
29_L34_I0.202040.745
31_A52_R0.199840.737
23_E92_A0.197130.727
8_F91_D0.194660.718
45_V48_G0.19410.715
5_T8_F0.193430.713
33_G78_G0.191510.706
25_P28_V0.188930.696
57_P60_R0.188860.696
20_W54_D0.188510.695
2_S5_T0.188250.694
15_E18_E0.187010.689
13_D72_S0.186960.689
33_G50_G0.186110.686
12_F90_L0.185380.683
14_P39_D0.184860.681
12_F17_L0.182710.673
4_V76_F0.180380.665
3_S79_K0.180160.664
6_F87_R0.178240.657
49_V75_V0.178080.656
8_F12_F0.176070.649
18_E53_Y0.176050.649
55_I59_G0.175910.648
74_L82_D0.175730.648
81_L86_L0.175490.647
44_L54_D0.175270.646
17_L91_D0.174150.642
24_L85_A0.173980.641
6_F11_P0.172690.637
35_V40_G0.172220.635
22_Q51_G0.170950.630
17_L90_L0.170610.629
38_A93_C0.170050.627
56_E59_G0.169530.625
14_P57_P0.169190.624
42_R71_D0.166880.615
28_V76_F0.166660.614
43_R60_R0.165530.610
44_L51_G0.165220.609
21_L46_F0.165210.609
1_I48_G0.164920.608
38_A80_N0.164550.607
1_I52_R0.164270.606
17_L35_V0.163910.604
32_K47_Q0.163830.604
28_V31_A0.163680.603
14_P17_L0.163070.601
32_K75_V0.163070.601
11_P69_D0.162540.599
43_R70_R0.162050.597
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
1nijA0.957499.50.151
3os4A0.883230.854
1vs3A0.957420.20.857
1dj0A0.957419.70.858
1vlpA0.88317.10.862
2g82O0.808516.10.863
2im5A0.88315.70.864
4hl7A0.88313.60.867
1yirA0.88313.50.867
1ybeA0.883120.87

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