GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
FabA - FabA-like domain
Pfam: PF07977 (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: CL0050
Length: 138
Sequences: 2282
Seq/Len: 16.54
HH_delta: -0.019 (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
95_G132_E0.937562.953
17_D21_G0.935772.947
29_A62_A0.872872.749
28_V105_R0.869992.740
59_M106_I0.856692.698
90_N138_E0.764282.407
88_I91_V0.755032.378
30_R103_T0.74572.348
28_V107_E0.694892.188
39_F50_M0.682372.149
107_E128_Y0.669552.109
55_L104_L0.661192.082
109_E124_D0.657152.069
128_Y133_L0.64382.027
14_L30_R0.637842.009
124_D138_E0.634661.999
58_A106_I0.623981.965
126_T133_L0.618691.948
107_E126_T0.616261.941
91_V137_A0.606011.908
63_A123_F0.589541.857
108_V125_G0.571621.800
12_R30_R0.5591.760
47_D96_P0.548431.727
128_Y131_G0.519371.636
15_E28_V0.500921.577
17_D22_S0.497641.567
47_D82_V0.496021.562
111_K124_D0.492581.551
21_G109_E0.486961.534
38_P41_D0.485891.530
15_E22_S0.471981.486
55_L135_A0.467061.471
27_I66_L0.461991.455
13_V29_A0.440611.388
30_R105_R0.437381.377
1_L64_G0.430831.357
105_R128_Y0.422481.330
13_V65_F0.418321.317
66_L70_S0.403971.272
31_K37_E0.396421.248
22_S109_E0.395871.247
47_D98_Y0.393011.238
22_S107_E0.38391.209
3_H45_P0.383071.206
101_D129_V0.374071.178
49_V84_F0.371571.170
84_F96_P0.370061.165
27_I62_A0.367451.157
133_L136_E0.364461.148
44_F52_G0.364281.147
110_I121_A0.361361.138
59_M137_A0.358211.128
95_G134_V0.357091.125
32_N103_T0.353511.113
43_H52_G0.353481.113
5_Y41_D0.348031.096
50_M54_L0.346331.091
10_V62_A0.336481.060
33_V50_M0.336291.059
85_L88_I0.323581.019
94_R136_E0.323121.018
55_L127_A0.322951.017
47_D84_F0.32121.012
20_G70_S0.319411.006
106_I127_A0.318011.001
17_D20_G0.316370.996
22_S28_V0.311830.982
56_I91_V0.311240.980
56_I88_I0.308560.972
116_R119_G0.307020.967
50_M58_A0.301710.950
111_K122_I0.298490.940
5_Y35_P0.298220.939
112_K118_G0.2980.938
68_G121_A0.295920.932
16_V27_I0.295350.930
16_V69_Y0.290750.916
63_A108_V0.285940.900
104_L127_A0.285170.898
111_K138_E0.28370.893
97_V134_V0.283610.893
5_Y36_D0.283570.893
127_A135_A0.280790.884
59_M125_G0.277490.874
27_I108_V0.277250.873
27_I63_A0.277120.873
105_R131_G0.275960.869
103_T130_D0.271460.855
14_L105_R0.270260.851
116_R121_A0.257780.812
12_R32_N0.257620.811
3_H9_L0.248070.781
13_V27_I0.247150.778
109_E126_T0.245820.774
59_M135_A0.242630.764
92_K136_E0.241140.759
16_V22_S0.240680.758
13_V62_A0.24060.758
83_P121_A0.239630.755
126_T136_E0.234610.739
42_G53_V0.232280.731
83_P86_A0.230860.727
49_V52_G0.229810.724
14_L28_V0.228390.719
10_V106_I0.227210.716
86_A120_M0.225790.711
67_A123_F0.224860.708
32_N35_P0.223360.703
39_F54_L0.219910.693
125_G137_A0.219670.692
48_P51_P0.208570.657
83_P123_F0.205920.648
97_V127_A0.205380.647
6_P10_V0.204250.643
75_G81_K0.203560.641
43_H49_V0.201690.635
33_V39_F0.200860.633
28_V45_P0.200350.631
68_G116_R0.198470.625
67_A70_S0.197490.622
66_L123_F0.197280.621
44_F49_V0.196710.619
5_Y32_N0.195080.614
43_H48_P0.192960.608
68_G83_P0.192820.607
43_H53_V0.19230.606
86_A94_R0.191610.603
63_A125_G0.19150.603
97_V104_L0.190410.600
12_R103_T0.189950.598
71_G75_G0.189940.598
57_E61_Q0.18920.596
4_R8_L0.189040.595
89_R122_I0.188350.593
7_F54_L0.188340.593
34_T37_E0.187970.592
44_F83_P0.187950.592
68_G71_G0.187920.592
52_G94_R0.187150.589
51_P93_F0.186540.587
21_G110_I0.185610.585
88_I93_F0.185520.584
77_G87_G0.184420.581
9_L31_K0.183610.578
87_G92_K0.182870.576
42_G52_G0.182140.574
40_F99_P0.182060.573
94_R133_L0.181550.572
16_V19_P0.181070.570
124_D136_E0.180540.569
83_P118_G0.180080.567
71_G77_G0.179440.565
68_G75_G0.179240.564
98_Y101_D0.179230.564
52_G93_F0.179210.564
27_I65_F0.177920.560
14_L103_T0.172790.544
56_I85_L0.172210.542
116_R122_I0.171850.541
27_I68_G0.170790.538
50_M104_L0.170740.538
3_H7_F0.169950.535
95_G129_V0.169650.534
40_F52_G0.169440.534
57_E60_A0.16860.531
110_I123_F0.168150.530
9_L54_L0.168020.529
77_G81_K0.166080.523
110_I116_R0.164180.517
63_A83_P0.164080.517
11_D34_T0.164010.516
81_K118_G0.163990.516
51_P99_P0.163690.515
66_L110_I0.163490.515
20_G124_D0.163150.514
64_G83_P0.162150.511
71_G81_K0.162010.510
86_A121_A0.16190.510
55_L93_F0.161690.509
112_K122_I0.159480.502
60_A64_G0.159110.501
70_S76_T0.158750.500
5_Y34_T0.15870.500
42_G45_P0.15870.500
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
4h4gA0.9203100-0.019
4i83A0.9131000.043
2gllA0.93481000.085
3q62A0.92751000.092
2cf2C0.93481000.099
4b8uA0.9421000.103
4b0bA0.92751000.106
2cf2C0.9421000.122
3d6xA0.92751000.122
1u1zA0.92031000.13

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