GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Laminin_G_3 - Concanavalin A-like lectinglucanases superfamily
Pfam: PF13385 (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: CL0004
Length: 157
Sequences: 6697
Seq/Len: 42.66
HH_delta: 0.175 (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
88_H104_N1.256134.200
100_T107_L1.102093.685
27_S91_A1.049143.508
31_K140_Y1.016043.397
29_W89_H0.933713.122
84_D88_H0.857642.868
147_Y151_L0.821662.747
27_S145_R0.805552.694
107_L110_S0.800342.676
27_S89_H0.767332.566
31_K87_W0.738652.470
83_P88_H0.646892.163
23_S95_D0.625552.092
29_W142_D0.594781.989
64_F92_L0.588121.967
28_F144_L0.586011.960
30_V90_L0.583491.951
32_P137_F0.571881.912
100_T110_S0.564351.887
41_F44_M0.543771.818
93_T150_A0.543081.816
127_I144_L0.540271.807
29_W143_D0.530591.774
137_F141_I0.490991.642
93_T102_Y0.467261.562
32_P88_H0.463841.551
28_F90_L0.45431.519
25_T93_T0.451331.509
83_P86_K0.448641.500
32_P84_D0.448161.499
55_F63_R0.440271.472
33_D138_N0.438231.465
126_F129_G0.436481.460
27_S147_Y0.423651.417
33_D85_N0.420731.407
98_T110_S0.412171.378
27_S151_L0.403911.351
24_F94_Y0.397921.331
29_W87_W0.389641.303
40_S43_F0.383531.282
31_K85_N0.383521.282
111_S114_P0.375521.256
92_L99_V0.361331.208
27_S143_D0.358771.200
101_L109_G0.356761.193
39_Q43_F0.355171.188
102_Y107_L0.353161.181
25_T91_A0.352241.178
45_D50_G0.351491.175
129_G136_P0.349311.168
93_T100_T0.346881.160
23_S150_A0.332581.112
57_N63_R0.331931.110
90_L103_V0.329681.102
82_L88_H0.324431.085
87_W142_D0.323011.080
54_L92_L0.316851.059
113_I116_N0.312891.046
37_S40_S0.311741.042
28_F54_L0.310541.038
91_A151_L0.309321.034
23_S94_Y0.30461.019
50_G67_G0.30441.018
46_S50_G0.298150.997
25_T150_A0.296750.992
78_S108_V0.295980.990
56_I62_L0.294070.983
128_G139_G0.289160.967
32_P83_P0.286530.958
26_I144_L0.282140.943
86_K104_N0.281180.940
26_I92_L0.281080.940
40_S44_M0.279780.936
39_Q42_V0.276920.926
80_S106_E0.275650.922
45_D49_S0.273640.915
89_H105_G0.2730.913
91_A102_Y0.272490.911
38_S43_F0.26750.894
111_S116_N0.264370.884
102_Y105_G0.263680.882
35_P84_D0.263070.880
47_S50_G0.262310.877
14_I127_I0.261470.874
82_L103_V0.257140.860
89_H93_T0.2570.859
63_R75_S0.255790.855
12_I16_N0.255210.853
16_N19_F0.252440.844
111_S115_S0.250620.838
79_D108_V0.248720.832
89_H143_D0.247980.829
62_L90_L0.247420.827
103_V108_V0.245320.820
94_Y99_V0.245020.819
25_T102_Y0.244480.817
52_F55_F0.241440.807
80_S108_V0.240940.806
60_G81_N0.239550.801
38_S41_F0.237710.795
34_S138_N0.234320.784
12_I15_P0.232580.778
63_R77_S0.231980.776
32_P35_P0.231650.775
93_T98_T0.23150.774
61_R78_S0.231290.773
11_Y129_G0.230560.771
16_N20_P0.228670.765
145_R149_R0.227650.761
13_S124_P0.226160.756
98_T112_T0.225820.755
140_Y147_Y0.224820.752
147_Y152_T0.224360.750
30_V82_L0.223870.749
30_V88_H0.220630.738
29_W91_A0.220160.736
44_M52_F0.218960.732
28_F141_I0.218520.731
64_F99_V0.217240.726
149_R152_T0.215820.722
88_H103_V0.214280.717
39_Q44_M0.214230.716
24_F28_F0.212760.711
51_G55_F0.212150.709
79_D109_G0.208970.699
52_F64_F0.208820.698
145_R151_L0.208030.696
57_N77_S0.205630.688
62_L82_L0.205550.687
113_I117_I0.205040.686
92_L101_L0.204520.684
32_P56_I0.201590.674
45_D53_G0.200280.670
64_F94_Y0.199740.668
91_A147_Y0.199310.666
33_D140_Y0.198740.665
30_V137_F0.198270.663
85_N88_H0.198060.662
48_G53_G0.197960.662
95_D100_T0.197160.659
112_T115_S0.194090.649
105_G128_G0.192570.644
77_S80_S0.190950.638
30_V62_L0.189630.634
27_S142_D0.189310.633
61_R79_D0.187540.627
53_G65_Y0.187530.627
62_L81_N0.187070.626
91_A105_G0.1870.625
127_I141_I0.185820.621
126_F131_G0.185810.621
55_F65_Y0.184580.617
95_D98_T0.184110.616
129_G140_Y0.183180.613
78_S81_N0.182630.611
78_S109_G0.181940.608
99_V111_S0.181260.606
59_N62_L0.17960.601
56_I82_L0.179150.599
10_D15_P0.178990.599
51_G94_Y0.178830.598
15_P124_P0.178750.598
22_G86_K0.17840.597
52_F56_I0.178180.596
18_D48_G0.177340.593
109_G112_T0.177090.592
53_G56_I0.177060.592
115_S118_S0.177010.592
108_V111_S0.176720.591
20_P52_F0.17590.588
48_G57_N0.175840.588
78_S82_L0.175170.586
10_D14_I0.174370.583
13_S16_N0.172930.578
25_T147_Y0.172920.578
87_W140_Y0.172170.576
76_F79_D0.171510.573
91_A145_R0.170940.572
26_I146_I0.170720.571
114_P118_S0.169960.568
11_Y126_F0.169150.566
143_D147_Y0.169020.565
30_V139_G0.167330.560
65_Y75_S0.166590.557
64_F101_L0.166370.556
50_G69_G0.166290.556
76_F80_S0.165960.555
61_R77_S0.164590.550
13_S126_F0.163670.547
11_Y15_P0.162880.545
28_F103_V0.161680.541
66_I74_Y0.161430.540
45_D48_G0.16120.539
122_N125_L0.160910.538
81_N106_E0.160420.536
132_G135_S0.160340.536
97_S112_T0.160330.536
18_D123_G0.159740.534
31_K86_K0.159470.533
54_L64_F0.15940.533
68_N117_I0.158830.531
106_E115_S0.158730.531
95_D150_A0.158150.529
142_D145_R0.157730.527
14_I126_F0.15760.527
57_N61_R0.156910.525
11_Y14_I0.156650.524
51_G54_L0.155150.519
56_I60_G0.1550.518
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
3pvnA0.968299.80.175
3kqrA0.961899.80.176
4avsA0.961899.80.176
3flpA0.980999.80.177
4dqaA0.923699.70.21
2sliA0.993699.60.309
1a8dA0.993699.60.317
2jkbA0.980999.60.318
2nyyA0.993699.60.322
1epwA0.993699.50.343

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