GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CW_binding_2 - Putative cell wall binding repeat 2
Pfam: PF04122 (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: 92
Sequences: 1538
Seq/Len: 16.72
HH_delta: 0.865 (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
14_K17_K1.02833.191
78_I90_E0.867542.692
87_D90_E0.800722.485
9_Y33_G0.795542.469
42_A79_I0.792622.460
82_E87_D0.75342.338
26_D74_K0.717442.227
78_I85_I0.641521.991
9_Y34_D0.638291.981
12_S16_A0.629381.953
67_F70_S0.620331.925
27_K77_Y0.610071.893
27_K75_K0.590081.831
62_S66_A0.574991.785
10_E14_K0.560351.739
65_K69_K0.52431.627
87_D91_N0.523351.624
28_V73_I0.5231.623
7_D10_E0.517291.605
16_A67_F0.511841.589
16_A70_S0.50961.582
28_V68_L0.472561.467
38_D81_G0.44711.388
56_V85_I0.421171.307
5_G11_T0.417881.297
56_V60_L0.417391.295
3_I18_K0.417091.294
21_P24_K0.410251.273
17_K70_S0.408941.269
13_A64_V0.393521.221
10_E63_S0.392151.217
8_R11_T0.379541.178
45_L51_A0.379141.177
4_S14_K0.374271.162
62_S65_K0.36931.146
13_A67_F0.368291.143
29_Y77_Y0.365011.133
67_F71_L0.357121.108
73_I76_V0.357071.108
6_A10_E0.345891.073
57_N61_P0.341891.061
60_L65_K0.33971.054
31_A79_I0.338011.049
8_R33_G0.336331.044
5_G8_R0.328171.018
42_A45_L0.323151.003
31_A39_A0.322831.002
3_I15_V0.31960.992
88_S91_N0.318380.988
3_I14_K0.312940.971
34_D57_N0.311380.966
19_F42_A0.307350.954
32_S84_A0.303030.940
2_R36_F0.30040.932
12_S64_V0.296730.921
61_P64_V0.296630.921
27_K49_N0.285320.886
42_A51_A0.284850.884
17_K67_F0.28390.881
27_K51_A0.281440.873
29_Y45_L0.280920.872
35_N84_A0.27330.848
32_S79_I0.273150.848
32_S35_N0.270380.839
9_Y61_P0.267890.831
32_S36_F0.267220.829
13_A17_K0.261590.812
29_Y79_I0.260330.808
44_P47_A0.258930.804
36_F40_L0.253920.788
68_L73_I0.251160.779
30_I56_V0.250640.778
29_Y46_A0.247820.769
29_Y51_A0.247270.767
29_Y49_N0.247170.767
28_V31_A0.242530.753
2_R39_A0.237570.737
29_Y78_I0.236630.734
7_D63_S0.235490.731
13_A54_L0.233850.726
31_A55_L0.232530.722
16_A54_L0.231120.717
11_T38_D0.230330.715
65_K88_S0.229670.713
60_L64_V0.22910.711
13_A61_P0.228890.710
29_Y42_A0.218730.679
45_L48_K0.218010.677
16_A52_P0.215230.668
18_K21_P0.215040.667
31_A40_L0.212730.660
28_V76_V0.211970.658
13_A63_S0.211380.656
30_I76_V0.210860.654
85_I89_V0.20930.650
47_A50_N0.2080.646
56_V89_V0.205450.638
29_Y47_A0.203920.633
27_K73_I0.20110.624
59_S62_S0.198480.616
58_N86_S0.19580.608
6_A83_G0.195080.605
41_S77_Y0.192890.599
49_N77_Y0.191270.594
8_R83_G0.189560.588
66_A70_S0.188460.585
43_S47_A0.187670.582
11_T33_G0.187460.582
5_G55_L0.186510.579
4_S62_S0.185280.575
20_Y25_S0.184920.574
54_L64_V0.181930.565
30_I89_V0.181860.564
66_A69_K0.18030.560
25_S43_S0.175650.545
28_V72_N0.174510.542
59_S90_E0.174170.541
59_S86_S0.173910.540
54_L68_L0.171150.531
9_Y32_S0.170920.530
11_T43_S0.170430.529
41_S79_I0.169550.526
13_A16_A0.169220.525
37_A81_G0.167830.521
57_N74_K0.167790.521
45_L77_Y0.167120.519
60_L89_V0.163990.509
41_S44_P0.163540.508
59_S88_S0.163470.507
3_I16_A0.16260.505
30_I85_I0.160960.500
6_A66_A0.160870.499
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
2cunA0.9783500.865
2p8tA0.695749.90.865
3av3A0.945744.10.869
1vpeA0.978342.80.87
3rg9A0.9565420.871
4dg5A0.978341.50.871
1phpA0.978340.10.872
3q3vA0.967438.60.873
4f06A0.967435.70.875
1v6sA0.9674350.876
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