GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CobT_C - Cobalamin biosynthesis protein CobT VWA domain
Pfam: PF11775 (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. )
Clan: CL0128
Length: 219
Sequences: 2899
Seq/Len: 13.24
HH_delta: 0.387 (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
126_A172_I0.482742.874
118_D141_V0.430352.562
30_I34_A0.41832.490
14_V137_K0.413822.463
14_V50_P0.407742.427
24_S144_D0.379972.262
201_D204_E0.368452.193
38_D108_M0.343132.042
116_N145_G0.335461.997
21_C55_G0.330861.969
25_M29_P0.323391.925
125_A139_L0.317891.892
16_T52_E0.310171.846
124_W127_E0.308591.837
128_R131_A0.301771.796
31_E34_A0.288451.717
122_L139_L0.287331.710
117_I120_E0.280811.672
130_L176_S0.277321.651
17_L37_A0.269511.604
19_I37_A0.266021.583
60_A124_W0.264441.574
14_V134_E0.259981.548
170_A174_T0.257431.532
116_N144_D0.251181.495
168_V172_I0.250761.493
167_Q171_E0.248561.480
17_L140_I0.245671.462
20_D24_S0.243771.451
18_L139_L0.242671.444
122_L141_V0.236181.406
38_D42_R0.233771.392
117_I149_D0.232171.382
41_A51_V0.22841.360
25_M33_A0.225541.343
28_R31_E0.225231.341
58_T114_K0.224641.337
25_M202_V0.223821.332
18_L121_A0.223371.330
140_I183_I0.222761.326
181_I212_Q0.222311.323
21_C30_I0.219731.308
118_D147_P0.217661.296
21_C57_T0.21761.295
138_I181_I0.216341.288
16_T128_R0.215561.283
56_F118_D0.212031.262
29_P33_A0.20971.248
136_R179_E0.20921.245
18_L125_A0.203221.210
16_T54_L0.202511.205
169_I172_I0.200961.196
89_V92_D0.199481.187
14_V132_R0.19831.180
169_I180_L0.196381.169
60_A121_A0.196181.168
122_L172_I0.192961.149
36_C209_L0.189761.130
121_A125_A0.188351.121
52_E55_G0.188071.119
182_A196_A0.187961.119
16_T125_A0.185491.104
91_K95_T0.183761.094
204_E207_G0.183071.090
21_C110_E0.182211.085
197_V209_L0.182211.085
23_G144_D0.181741.082
117_I148_A0.181281.079
123_R127_E0.180681.075
169_I192_Y0.180381.074
54_L121_A0.180331.073
23_G114_K0.179361.068
168_V180_L0.178391.062
91_K97_W0.178361.062
119_G149_D0.176911.053
38_D104_L0.17631.049
52_E128_R0.176171.049
123_R171_E0.173771.034
15_V138_I0.169181.007
202_V205_L0.167951.000
142_I209_L0.166680.992
112_L115_E0.166410.991
142_I183_I0.166310.990
129_L139_L0.165180.983
166_R170_A0.164350.978
183_I212_Q0.163880.975
45_E48_G0.163410.973
126_A178_V0.163140.971
21_C25_M0.162420.967
119_G147_P0.162330.966
28_R105_G0.161790.963
24_S116_N0.159940.952
31_E35_L0.159330.948
123_R126_A0.157630.938
56_F93_A0.156710.933
107_M110_E0.156030.929
202_V206_G0.155850.928
20_D23_G0.155560.926
22_S145_G0.155130.923
33_A37_A0.154280.918
52_E121_A0.15420.918
36_C202_V0.154040.917
183_I197_V0.151950.904
120_E124_W0.15150.902
25_M30_I0.15080.898
200_D204_E0.150250.894
34_A107_M0.149950.893
60_A117_I0.149590.890
140_I212_Q0.147910.880
13_T136_R0.146470.872
20_D25_M0.145170.864
138_I213_L0.145150.864
127_E171_E0.143360.853
165_L168_V0.143180.852
45_E170_A0.142990.851
123_R168_V0.142380.848
208_A211_E0.142250.847
104_L107_M0.142170.846
33_A142_I0.142150.846
22_S25_M0.142040.845
120_E123_R0.140380.836
181_I205_L0.140260.835
37_A53_V0.139160.828
29_P148_A0.138830.826
119_G123_R0.138490.824
121_A128_R0.137780.820
59_R131_A0.137770.820
32_V35_L0.136740.814
127_E131_A0.136050.810
182_A186_G0.135780.808
14_V135_Q0.135640.807
30_I110_E0.1350.804
122_L126_A0.134890.803
34_A110_E0.13420.799
10_F45_E0.134170.799
17_L53_V0.132360.788
28_R201_D0.131620.783
59_R109_R0.131350.782
124_W139_L0.131250.781
17_L33_A0.131170.781
106_L114_K0.13110.780
15_V40_L0.130750.778
16_T137_K0.129610.772
58_T148_A0.12960.771
59_R127_E0.127930.762
132_R137_K0.127760.760
91_K94_D0.127680.760
147_P150_D0.127440.759
105_G109_R0.126940.756
40_L44_L0.126730.754
106_L110_E0.126540.753
116_N121_A0.126310.752
184_G198_T0.12610.751
115_E148_A0.1260.750
167_Q201_D0.125990.750
169_I173_E0.125450.747
110_E114_K0.1250.744
89_V94_D0.124760.743
167_Q170_A0.124720.742
34_A108_M0.124240.740
137_K177_D0.124140.739
25_M36_C0.123810.737
42_R134_E0.123750.737
117_I147_P0.123630.736
166_R171_E0.123550.735
197_V208_A0.123460.735
31_E109_R0.123350.734
123_R131_A0.123190.733
165_L169_I0.123180.733
38_D105_G0.123090.733
59_R207_G0.12230.728
199_I204_E0.121850.725
142_I185_I0.121510.723
57_T117_I0.121430.723
33_A205_L0.120930.720
37_A142_I0.12080.719
18_L141_V0.120530.717
141_V182_A0.120530.717
46_R111_G0.120270.716
190_S198_T0.119940.714
28_R32_V0.118980.708
127_E130_L0.118830.707
145_G184_G0.118660.706
126_A168_V0.117810.701
121_A147_P0.117650.700
105_G191_R0.117190.698
135_Q138_I0.117040.697
36_C185_I0.116670.694
44_L49_V0.116640.694
50_P132_R0.116020.691
30_I33_A0.115990.690
37_A57_T0.115820.689
27_G142_I0.115640.688
35_L42_R0.115420.687
56_F147_P0.115270.686
15_V142_I0.114490.682
15_V35_L0.114340.681
49_V56_F0.11360.676
35_L38_D0.113550.676
139_L172_I0.113380.675
41_A47_C0.113140.673
48_G167_Q0.11310.673
189_V194_R0.113070.673
133_P171_E0.112990.673
176_S204_E0.112990.673
53_V56_F0.11280.671
205_L212_Q0.112710.671
137_K178_V0.112570.670
107_M113_L0.112440.669
127_E133_P0.112430.669
89_V106_L0.112190.668
145_G185_I0.111940.666
60_A196_A0.111840.666
207_G211_E0.11180.665
170_A173_E0.111240.662
55_G90_Y0.111120.661
129_L137_K0.110880.660
43_A46_R0.110790.659
16_T139_L0.110320.657
18_L54_L0.11030.657
176_S203_E0.110250.656
32_V112_L0.109890.654
13_T49_V0.109820.654
36_C142_I0.10960.652
56_F142_I0.109590.652
22_S116_N0.109480.652
185_I202_V0.109480.652
56_F143_S0.109380.651
37_A43_A0.10910.649
166_R169_I0.109070.649
179_E189_V0.109070.649
137_K172_I0.108790.648
19_I210_F0.10860.646
128_R140_I0.108550.646
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
4fx5A0.840299.90.387
3hrzD0.86399.90.391
4hqoA0.831199.90.396
3k6sA0.821999.90.405
1mf7A0.785499.90.414
1ijbA0.817499.80.424
2b2xA0.799199.80.424
4hqfA0.831199.80.426
2odpA0.849399.80.428
1q0pA0.86399.80.428

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