GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SNAP - Soluble NSF attachment protein SNAP
Pfam: PF14938 (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: CL0020
Length: 282
Sequences: 21792
Seq/Len: 77.28
HH_delta: 0.006 (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
170_R173_E2.582173.368
130_D133_K2.577653.362
211_D214_A2.489743.248
50_D53_K2.452143.199
89_D92_E2.432293.173
252_A255_E2.429353.169
162_A178_Y1.842222.403
121_A138_Y1.731112.258
117_L137_Y1.668132.176
158_L177_I1.606942.096
82_A97_Y1.597982.084
203_I219_L1.565442.042
42_A58_Y1.559532.034
199_F218_A1.552692.025
78_Y96_C1.525931.990
202_A218_A1.473641.922
94_I98_E1.444021.884
55_A59_E1.431851.868
120_L137_Y1.394341.819
179_E202_A1.392491.816
161_A177_I1.377071.796
81_A96_C1.31291.713
38_Y57_A1.305951.703
165_Y177_I1.289141.682
135_I139_Q1.274061.662
98_E120_L1.269871.656
216_R220_E1.254361.636
124_Y137_Y1.243891.623
165_Y170_R1.242331.620
165_Y173_E1.229331.604
45_F57_A1.212531.582
206_H218_A1.204711.571
124_Y133_K1.192651.556
206_H211_D1.157191.509
206_H214_A1.131671.476
58_Y80_E1.125911.469
139_Q161_A1.118851.459
59_E81_A1.114381.454
85_Y96_C1.11091.449
45_F53_K1.10851.446
97_Y119_E1.074051.401
85_Y92_E1.070761.397
175_I179_E1.045051.363
175_I209_M1.039791.356
178_Y201_K1.023831.335
173_E176_E0.994371.297
45_F50_D0.990891.293
117_L140_K0.989491.291
53_K56_E0.989341.290
257_V261_D0.987721.288
214_A217_K0.982461.282
138_Y160_K0.980461.279
158_L180_E0.976311.273
120_L124_Y0.969321.264
41_A57_A0.951011.240
124_Y130_D0.948881.238
92_E95_E0.930441.214
203_I222_Y0.929481.212
44_C48_A0.927691.210
127_Q130_D0.92581.208
180_E184_K0.910641.188
172_E209_M0.909241.186
238_L259_E0.900491.175
85_Y89_D0.897111.170
202_A206_H0.892351.164
181_V198_Y0.878431.146
81_A85_Y0.878181.145
133_K136_E0.877551.145
135_I168_L0.874931.141
162_A181_V0.870791.136
140_K144_L0.87041.135
175_I206_H0.860191.122
135_I165_Y0.859911.122
199_F221_R0.859581.121
94_I127_Q0.855771.116
161_A165_Y0.849141.108
118_K157_C0.847921.106
141_A157_C0.836991.092
94_I124_Y0.826821.078
114_A141_A0.818471.068
78_Y99_K0.811551.059
110_F113_A0.799551.043
35_A39_E0.796351.039
175_I205_C0.794161.036
79_E119_E0.787711.027
60_K64_C0.782231.020
259_E262_S0.782011.020
75_A100_A0.780841.019
42_A54_A0.780391.018
79_E116_C0.776331.013
185_C188_N0.774031.010
203_I215_A0.768441.002
163_D201_K0.765050.998
262_S265_R0.761310.993
55_A85_Y0.760290.992
121_A134_A0.751050.980
217_K221_R0.750620.979
55_A88_G0.745550.972
118_K160_K0.742240.968
131_Y164_L0.73810.963
65_Y73_E0.735720.960
241_L245_Y0.727140.948
91_D127_Q0.726060.947
135_I161_A0.725750.947
100_A116_C0.719950.939
255_E258_A0.718750.938
175_I202_A0.718250.937
99_K103_I0.717330.936
61_A77_A0.710410.927
207_L244_A0.708990.925
176_E180_E0.704890.919
121_A141_A0.704370.919
199_F222_Y0.703560.918
123_I127_Q0.702510.916
137_Y140_K0.702390.916
90_P123_I0.702050.916
94_I120_L0.700220.913
41_A45_F0.697260.909
101_I117_L0.696620.909
136_E140_K0.692740.904
83_N119_E0.692550.903
52_E88_G0.688060.897
159_L201_K0.68730.897
38_Y60_K0.685670.894
171_Y205_C0.685190.894
175_I211_D0.683340.891
132_E168_L0.677890.884
242_L245_Y0.669460.873
84_C88_G0.667420.871
180_E183_K0.66580.868
216_R250_V0.664520.867
94_I123_I0.663590.866
65_Y77_A0.661620.863
164_L168_L0.659580.860
86_K119_E0.657850.858
242_L260_Y0.657320.857
155_A181_V0.653870.853
122_E160_K0.653630.853
42_A61_A0.651720.850
241_L259_E0.649370.847
57_A60_K0.648310.846
39_E80_E0.648110.845
135_I164_L0.647620.845
62_A78_Y0.645770.842
179_E183_K0.64410.840
222_Y225_Q0.642260.838
86_K123_I0.641680.837
39_E43_N0.64080.836
96_C99_K0.640320.835
240_D243_E0.638950.833
125_E138_Y0.633750.827
133_K137_Y0.633420.826
125_E164_L0.633110.826
238_L242_L0.6310.823
117_L141_A0.629480.821
162_A174_A0.628930.820
98_E102_E0.626040.817
256_A260_Y0.625620.816
78_Y100_A0.62390.814
218_A221_R0.623220.813
60_K63_D0.61960.808
92_E96_C0.61850.807
158_L181_V0.616970.805
204_L208_A0.616880.805
43_N80_E0.614860.802
207_L219_L0.614320.801
55_A81_A0.613290.800
160_K163_D0.609290.795
59_E63_D0.608350.794
82_A100_A0.607530.792
166_A201_K0.607220.792
199_F225_Q0.607160.792
201_K204_L0.606470.791
142_A161_A0.606030.790
38_Y61_A0.604430.788
99_K102_E0.604150.788
35_A61_A0.60410.788
140_K143_E0.603720.787
65_Y74_A0.600510.783
131_Y168_L0.597020.779
142_A158_L0.596590.778
205_C209_M0.596570.778
151_P154_A0.59430.775
258_A262_S0.593120.774
221_R224_S0.592530.773
93_A97_Y0.592120.772
62_A77_A0.589160.768
135_I170_R0.588770.768
37_L41_A0.587690.767
159_L198_Y0.584810.763
82_A93_A0.58420.762
122_E126_E0.583940.762
221_R225_Q0.583890.762
38_Y41_A0.583430.761
79_E82_A0.582820.760
125_E131_Y0.582640.760
222_Y226_D0.582040.759
125_E160_K0.577180.753
100_A103_I0.571830.746
101_I116_C0.570920.745
182_A202_A0.570610.744
166_A208_A0.569910.743
239_E243_E0.569360.743
118_K122_E0.568910.742
59_E62_A0.564160.736
255_E259_E0.563410.735
46_K54_A0.563360.735
214_A218_A0.561010.732
158_L184_K0.55990.730
243_E247_E0.558420.728
53_K57_A0.553190.722
186_L189_N0.552480.721
51_W84_C0.551580.719
260_Y264_S0.550510.718
43_N47_L0.549730.717
182_A199_F0.549020.716
200_L204_L0.548890.716
177_I180_E0.548540.716
46_K84_C0.548520.715
86_K93_A0.545380.711
37_L40_K0.542180.707
55_A84_C0.541830.707
212_Y216_R0.540320.705
166_A178_Y0.539830.704
258_A261_D0.538870.703
79_E83_N0.538870.703
245_Y255_E0.536230.699
91_D95_E0.536130.699
119_E122_E0.535970.699
251_E256_A0.53570.699
173_E177_I0.534210.697
74_A77_A0.531570.693
259_E263_I0.530140.692
93_A123_I0.529190.690
74_A113_A0.528260.689
46_K51_W0.527480.688
181_V184_K0.526390.687
253_F256_A0.524290.684
200_L240_D0.523490.683
166_A171_Y0.5220.681
219_L240_D0.521820.681
56_E60_K0.521140.680
55_A89_D0.520670.679
174_A205_C0.517040.674
56_E59_E0.512830.669
171_Y209_M0.512280.668
204_L219_L0.511810.668
79_E100_A0.511420.667
101_I120_L0.510110.665
207_L212_Y0.509190.664
200_L237_F0.50860.663
113_A154_A0.506410.661
171_Y208_A0.505220.659
62_A81_A0.504990.659
39_E77_A0.503540.657
235_Y242_L0.502790.656
159_L163_D0.50230.655
131_Y167_R0.501090.654
118_K141_A0.500610.653
172_E176_E0.498320.650
95_E99_K0.497660.649
220_E241_L0.496780.648
139_Q143_E0.496370.647
254_T258_A0.496290.647
86_K97_Y0.495140.646
36_D40_K0.494120.645
235_Y239_E0.493070.643
213_V250_V0.491750.641
141_A144_L0.48890.638
131_Y135_I0.48610.634
237_F240_D0.486090.634
166_A205_C0.485120.633
46_K80_E0.482920.630
83_N87_K0.479490.625
90_P127_Q0.478720.624
239_E242_L0.478220.624
54_A58_Y0.477610.623
247_E250_V0.477320.623
74_A154_A0.476960.622
46_K58_Y0.47070.614
74_A78_Y0.470680.614
171_Y174_A0.468520.611
223_C227_P0.468280.611
245_Y252_A0.467680.610
114_A154_A0.466180.608
162_A177_I0.464210.606
216_R252_A0.463430.604
75_A79_E0.4630.604
182_A198_Y0.462940.604
261_D265_R0.462160.603
138_Y164_L0.461160.602
216_R245_Y0.459960.600
61_A64_C0.459610.600
243_E246_E0.458670.598
117_L144_L0.458320.598
80_E83_N0.458170.598
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
1qqeA0.99651000.006
3sf4A0.946899.90.144
4a1sA0.946899.90.161
3sf4A0.939799.90.165
4a1sA0.939799.90.172
4jhrA0.900799.90.172
3ro2A0.911399.90.175
1w3bA0.84499.90.182
2ifuA0.96199.90.183
1w3bA0.88399.90.185

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