GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mec-17 - Touch receptor neuron protein Mec-17
Pfam: PF05301 (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: CL0257
Length: 120
Sequences: 4662
Seq/Len: 38.85
HH_delta: 0.315 (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
24_L71_M1.0832.842
8_L20_V1.075482.822
72_L101_L1.002872.631
91_L95_L0.876252.299
10_K20_V0.869532.281
96_K103_R0.807892.120
11_D17_K0.7992.096
21_I58_R0.797312.092
22_G54_V0.783672.056
9_L63_Y0.781742.051
70_H73_Q0.754491.980
24_L67_L0.71551.877
103_R106_P0.646971.697
88_S91_L0.632331.659
65_K98_H0.594831.561
9_L67_L0.574821.508
26_V71_M0.562791.477
58_R61_R0.548331.439
64_G94_F0.547361.436
10_K18_G0.540661.419
19_A55_H0.539021.414
19_A57_S0.535321.405
7_Y70_H0.505861.327
65_K99_Y0.501641.316
65_K69_D0.500021.312
92_L96_K0.489091.283
7_Y74_E0.485721.274
93_S96_K0.482151.265
54_V63_Y0.47371.243
70_H74_E0.464931.220
72_L99_Y0.452231.187
26_V75_E0.449521.179
11_D58_R0.437351.147
68_F99_Y0.436161.144
66_R70_H0.432531.135
6_L25_K0.432131.134
19_A58_R0.429591.127
9_L22_G0.428281.124
91_L94_F0.421681.106
11_D21_I0.420641.104
88_S92_L0.418551.098
92_L103_R0.406071.065
23_F53_Y0.404661.062
63_Y66_R0.404261.061
94_F99_Y0.403941.060
62_G65_K0.397581.043
69_D72_L0.39281.031
56_E59_Q0.389741.023
3_D28_Y0.389541.022
83_A86_R0.372810.978
29_K42_E0.371610.975
80_H83_A0.370660.973
98_H101_L0.368670.967
9_L54_V0.361550.949
68_F95_L0.360560.946
78_S82_L0.349160.916
22_G67_L0.3450.905
78_S104_Y0.341640.896
25_K53_Y0.340810.894
55_H58_R0.33960.891
72_L76_N0.335260.880
73_Q76_N0.333440.875
104_Y108_S0.330520.867
105_I108_S0.329240.864
29_K38_G0.322710.847
54_V59_Q0.313870.824
81_Q86_R0.311850.818
75_E79_P0.303410.796
81_Q84_I0.302490.794
11_D61_R0.299910.787
85_D92_L0.298780.784
9_L66_R0.298540.783
10_K17_K0.291940.766
11_D19_A0.290880.763
65_K93_S0.28090.737
53_Y94_F0.272330.715
54_V64_G0.271280.712
89_P93_S0.26830.704
7_Y24_L0.266560.699
86_R89_P0.263150.690
95_L101_L0.252570.663
79_P86_R0.249190.654
43_I68_F0.249020.653
5_V74_E0.244880.643
21_I63_Y0.240510.631
24_L68_F0.237080.622
78_S81_Q0.234510.615
81_Q95_L0.23440.615
86_R92_L0.232590.610
60_R64_G0.232570.610
92_L95_L0.232460.610
26_V41_R0.231950.609
23_F41_R0.231760.608
54_V67_L0.230110.604
80_H84_I0.229120.601
22_G63_Y0.2290.601
78_S84_I0.224850.590
6_L23_F0.224270.588
69_D73_Q0.222830.585
53_Y84_I0.222070.583
81_Q88_S0.219140.575
69_D99_Y0.219070.575
38_G76_N0.218380.573
66_R69_D0.217930.572
101_L105_I0.216840.569
18_G73_Q0.215230.565
39_Q78_S0.212640.558
24_L70_H0.212010.556
65_K94_F0.211660.555
39_Q42_E0.210220.552
64_G95_L0.209790.550
4_Q7_Y0.209510.550
24_L85_D0.207160.544
41_R75_E0.200510.526
23_F84_I0.198670.521
21_I71_M0.19840.521
87_P92_L0.198320.520
18_G102_Q0.197670.519
60_R90_K0.196820.516
99_Y103_R0.196190.515
94_F98_H0.194680.511
20_V67_L0.194470.510
9_L21_I0.191710.503
3_D6_L0.191290.502
20_V23_F0.190860.501
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
4e2aA0.883399.10.315
4b5oA0.991799.10.316
4gs4A0.991799.10.317
1tiqA0.87599.10.328
4hkfA0.991799.10.337
3gy9A0.8599.10.338
4h6uA0.991799.10.339
2dxqA0.82599.10.341
2zpaA0.95990.353
2q04A0.9167990.356

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