GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Amastin - Amastin surface glycoprotein
Pfam: PF07344 (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: CL0375
Length: 155
Sequences: 1686
Seq/Len: 10.88
HH_delta: 0.894 (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
8_L12_P0.338852.610
21_G25_G0.316052.435
21_G57_Q0.314372.422
13_L137_G0.303922.341
92_C126_A0.300892.318
67_A71_I0.276242.128
25_G57_Q0.260392.006
25_G92_C0.259762.001
39_C55_C0.243191.873
139_A143_A0.241051.857
83_G101_N0.230031.772
25_G126_A0.226651.746
11_T69_A0.216751.670
10_G141_F0.213571.645
70_I74_F0.211761.631
31_T39_C0.209781.616
10_G144_A0.208121.603
114_L118_V0.202111.557
60_S64_A0.192491.483
6_F144_A0.191751.477
18_V135_G0.185461.429
122_G125_G0.183091.410
4_F76_Y0.179991.387
4_F77_G0.176061.356
112_W144_A0.174731.346
62_F66_Q0.174531.344
138_F142_V0.172971.332
115_M119_Y0.170161.311
6_F140_L0.169971.309
117_V120_Y0.166621.284
39_C135_G0.165911.278
15_M29_C0.163481.259
78_A81_V0.162511.252
16_F31_T0.162031.248
116_V120_Y0.156021.202
73_I82_L0.155321.197
9_V13_L0.153381.182
102_I152_I0.153251.181
134_Y142_V0.151311.166
69_A112_W0.15131.166
104_G107_T0.149751.154
21_G127_L0.148811.146
84_V107_T0.147741.138
123_F133_K0.140921.086
117_V121_G0.140881.085
69_A87_L0.139691.076
119_Y132_Y0.139611.075
13_L31_T0.139221.072
120_Y139_A0.139111.072
63_R90_C0.137891.062
15_M136_A0.136971.055
13_L136_A0.136431.051
16_F115_M0.136261.050
72_S78_A0.136121.049
99_V103_V0.135771.046
57_Q126_A0.135121.041
74_F80_F0.134931.039
74_F78_A0.134491.036
7_V76_Y0.134481.036
100_L108_L0.134181.034
112_W145_W0.134071.033
11_T70_I0.133641.029
61_R65_A0.133141.026
62_F124_C0.132451.020
18_V150_I0.131791.015
85_L89_C0.131721.015
92_C95_W0.131251.011
16_F141_F0.131051.010
110_V114_L0.13051.005
5_L12_P0.130011.002
10_G85_L0.129560.998
21_G92_C0.128350.989
6_F21_G0.128040.986
10_G69_A0.124810.961
149_I153_I0.123130.949
114_L153_I0.123110.948
95_W100_L0.122230.942
13_L17_R0.122180.941
8_L73_I0.122090.941
5_L9_V0.120930.932
81_V84_V0.120890.931
62_F86_L0.120830.931
102_I105_I0.120340.927
17_R119_Y0.120090.925
5_L8_L0.120060.925
150_I153_I0.119670.922
102_I135_G0.118770.915
82_L87_L0.118540.913
102_I109_L0.118320.911
100_L104_G0.117930.908
11_T21_G0.117650.906
19_K119_Y0.117460.905
4_F41_S0.117120.902
115_M148_D0.117080.902
10_G137_G0.116560.898
45_S55_C0.116170.895
63_R67_A0.116140.895
14_D34_G0.115980.893
100_L103_V0.115960.893
25_G43_S0.115910.893
65_A115_M0.115270.888
120_Y142_V0.114390.881
109_L149_I0.114330.881
66_Q113_A0.113150.872
72_S112_W0.113050.871
113_A145_W0.113020.871
6_F147_L0.112880.870
57_Q150_I0.112740.868
110_V145_W0.112620.868
75_V91_S0.112380.866
30_Y38_D0.112130.864
74_F91_S0.112080.863
12_P15_M0.111610.860
90_C101_N0.111590.860
57_Q61_R0.110810.854
134_Y145_W0.110550.852
9_V12_P0.110520.851
72_S76_Y0.110350.850
138_F151_N0.109710.845
11_T87_L0.109660.845
14_D29_C0.109410.843
84_V91_S0.109260.842
85_L151_N0.109220.841
11_T15_M0.109060.840
11_T72_S0.108450.835
6_F134_Y0.10810.833
100_L153_I0.107710.830
82_L101_N0.107570.829
96_V99_V0.107440.828
143_A146_C0.107020.824
86_L89_C0.106920.824
123_F129_S0.106810.823
21_G26_N0.106790.823
3_A152_I0.106660.822
120_Y144_A0.106490.820
73_I150_I0.106370.819
14_D31_T0.10630.819
73_I97_C0.106090.817
75_V80_F0.105870.816
71_I74_F0.10580.815
95_W103_V0.10560.813
133_K148_D0.105470.812
84_V146_C0.105270.811
121_G138_F0.104950.808
83_G99_V0.104310.804
111_V119_Y0.104190.803
31_T137_G0.10410.802
45_S51_L0.103920.801
34_G134_Y0.103640.798
44_Y50_D0.103220.795
12_P76_Y0.103130.794
73_I147_L0.102910.793
28_G40_G0.102840.792
7_V72_S0.102790.792
39_C102_I0.102230.788
75_V107_T0.101960.785
84_V98_L0.10180.784
106_V152_I0.101250.780
33_W145_W0.101090.779
32_L98_L0.10090.777
83_G98_L0.10060.775
25_G95_W0.100330.773
66_Q109_L0.099160.764
112_W116_V0.099050.763
20_G124_C0.098730.761
139_A142_V0.098730.761
122_G140_L0.098620.760
42_V45_S0.098480.759
3_A148_D0.097810.753
8_L134_Y0.09780.753
20_G133_K0.097680.752
58_R126_A0.097610.752
104_G146_C0.097090.748
5_L60_S0.096640.744
7_V10_G0.096430.743
64_A147_L0.096410.743
79_A111_V0.096180.741
7_V144_A0.096010.740
29_C136_A0.0960.740
8_L147_L0.095930.739
88_C105_I0.095820.738
65_A72_S0.095690.737
42_V54_N0.095680.737
121_G146_C0.095670.737
7_V145_W0.095460.735
88_C138_F0.095130.733
132_Y137_G0.094820.730
73_I99_V0.094750.730
75_V150_I0.094730.730
77_G80_F0.094720.730
3_A78_A0.094690.729
124_C137_G0.094550.728
60_S122_G0.094530.728
82_L143_A0.094480.728
21_G128_K0.094230.726
8_L91_S0.094230.726
62_F111_V0.094230.726
25_G127_L0.09410.725
74_F112_W0.093930.724
127_L131_G0.093550.721
41_S127_L0.093360.719
3_A6_F0.092910.716
27_K41_S0.092890.716
4_F17_R0.092830.715
34_G140_L0.092760.715
103_V107_T0.092590.713
86_L90_C0.092580.713
9_V28_G0.092540.713
10_G58_R0.09250.713
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
4ib4A0.767742.60.894
1q8dA0.348430.20.901
2ks1B0.283915.40.914
3pblA0.82587.70.924
2jwaA0.277470.925
2yevA0.97426.30.927
3emlA0.69684.70.931
2v5eA0.36774.50.931
3uonA0.71613.60.934
4grvA0.79353.40.935
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

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