GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Fasciclin - Fasciclin domain
Pfam: PF02469 (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: 128
Sequences: 2849
Seq/Len: 22.26
HH_delta: 0.082 (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
111_D120_H0.953193.703
4_S33_D0.862443.351
3_L121_I0.857793.333
38_K124_D0.794993.089
68_T71_D0.74922.911
29_F63_V0.577812.245
50_S53_Q0.553462.150
6_F30_A0.488381.898
28_V62_I0.4811.869
105_A124_D0.449381.746
106_R123_D0.449151.745
29_F101_V0.448191.741
98_T106_R0.444751.728
100_Y106_R0.436221.695
68_T118_V0.432451.680
56_S84_N0.412321.602
69_S120_H0.404551.572
7_S11_E0.397561.545
55_K59_K0.394521.533
68_T113_E0.393791.530
80_E87_P0.393651.529
11_E16_A0.365171.419
78_T87_P0.362331.408
34_D37_Q0.35691.387
69_S111_D0.353841.375
60_Y84_N0.344711.339
66_S113_E0.340531.323
10_L13_A0.339481.319
91_S100_Y0.33931.318
31_P35_A0.330741.285
46_S50_S0.330471.284
32_T108_V0.329171.279
61_H126_L0.3291.278
9_L48_A0.324241.260
46_S49_D0.316111.228
5_T36_F0.315531.226
63_V79_L0.29991.165
6_F58_L0.296971.154
32_T121_I0.296971.154
18_L59_K0.295991.150
8_R12_Q0.294421.144
5_T8_R0.293951.142
46_S53_Q0.291631.133
30_A119_I0.290631.129
74_N77_Q0.287011.115
59_K83_L0.283461.101
90_V101_V0.281091.092
79_L90_V0.275731.071
122_I126_L0.275061.069
67_I75_G0.274741.067
23_D26_Y0.273391.062
42_E45_S0.272381.058
39_L42_E0.265191.030
3_L119_I0.263941.025
32_T35_A0.263571.024
69_S72_L0.262311.019
56_S59_K0.259361.008
9_L54_L0.256730.997
60_Y86_Q0.255530.993
40_S44_N0.255030.991
18_L83_L0.252930.983
105_A123_D0.249480.969
99_I107_I0.249030.968
69_S110_S0.248790.967
57_L125_V0.247550.962
63_V81_T0.247250.961
9_L36_F0.246560.958
29_F122_I0.246410.957
13_A55_K0.246190.957
6_F28_V0.245570.954
89_R93_S0.244940.952
39_L47_L0.244560.950
78_T89_R0.243610.946
60_Y128_P0.241490.938
2_D33_D0.240550.935
12_Q51_K0.240210.933
93_S100_Y0.239690.931
31_P61_H0.239640.931
81_T84_N0.236910.920
39_L127_I0.236480.919
5_T37_Q0.235040.913
66_S71_D0.233520.907
56_S86_Q0.232520.903
15_L58_L0.231840.901
5_T33_D0.229210.891
47_L50_S0.228840.889
14_G17_D0.228520.888
81_T88_L0.226910.882
114_A117_G0.226550.880
113_E118_V0.225690.877
92_S99_I0.218540.849
38_K123_D0.216890.843
15_L59_K0.21640.841
36_F58_L0.215860.839
3_L7_S0.21580.838
29_F120_H0.215060.836
43_T46_S0.214460.833
105_A108_V0.214220.832
34_D38_K0.213970.831
7_S10_L0.20930.813
114_A119_I0.2090.812
89_R102_N0.208550.810
110_S120_H0.208170.809
27_T120_H0.206960.804
10_L16_A0.206650.803
52_E56_S0.205220.797
51_K55_K0.204140.793
13_A54_L0.203340.790
103_G124_D0.201560.783
26_Y116_N0.199550.775
13_A51_K0.199470.775
18_L62_I0.198870.773
10_L19_L0.198840.773
52_E55_K0.198630.772
107_I110_S0.198250.770
3_L6_F0.198250.770
39_L44_N0.197930.769
19_L26_Y0.197850.769
93_S96_N0.197060.766
12_Q48_A0.196020.762
111_D118_V0.193380.751
2_D34_D0.192010.746
6_F36_F0.191180.743
60_Y126_L0.190670.741
18_L26_Y0.189270.735
35_A125_V0.189210.735
46_S88_L0.187710.729
91_S103_G0.185770.722
72_L90_V0.185230.720
81_T86_Q0.184350.716
31_P125_V0.181320.704
51_K54_L0.180310.701
28_V114_A0.178470.693
44_N50_S0.178380.693
31_P122_I0.175940.684
4_S109_K0.17540.681
14_G51_K0.17450.678
10_L112_I0.173830.675
61_H122_I0.173210.673
112_I119_I0.173080.672
45_S49_D0.172830.671
36_F39_L0.172590.671
53_Q56_S0.171210.665
88_L101_V0.17050.662
70_S113_E0.170330.662
5_T9_L0.169360.658
28_V119_I0.167460.651
101_V126_L0.166890.648
25_N66_S0.166620.647
6_F9_L0.164750.640
66_S118_V0.164740.640
45_S48_A0.164670.640
117_G120_H0.163290.634
17_D21_D0.163280.634
25_N65_G0.162720.632
89_R92_S0.162420.631
75_G89_R0.161670.628
57_L128_P0.161260.627
31_P36_F0.161180.626
32_T36_F0.160770.625
43_T49_D0.160630.624
37_Q41_Q0.159570.620
109_K112_I0.159010.618
22_S70_S0.158140.614
54_L61_H0.157590.612
74_N92_S0.157310.611
88_L92_S0.157270.611
44_N49_D0.157220.611
54_L57_L0.156920.610
100_Y103_G0.156460.608
36_F125_V0.154490.600
3_L30_A0.154060.599
40_S43_T0.152510.593
73_R77_Q0.151330.588
74_N89_R0.150840.586
109_K121_I0.150630.585
91_S98_T0.149630.581
39_L124_D0.149140.579
43_T47_L0.148090.575
58_L110_S0.147780.574
67_I102_N0.147230.572
53_Q57_L0.147020.571
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
1w7dA0.945399.90.082
1nyoA0.929799.90.103
2vxpA0.945399.90.105
1o70A0.984499.90.166
1o70A0.960999.90.172
2kd2A0.492237.10.89
1s29A0.67979.40.915
2j63A0.63288.80.917
3v32B0.35948.20.917
1o22A0.56258.20.918

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