GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
LIP - Secretory lipase
Pfam: PF03583 (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: CL0028
Length: 290
Sequences: 15572
Seq/Len: 53.7
HH_delta: 0.21 (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
74_A105_G1.977075.320
228_T259_P1.415283.808
75_L85_A1.278533.440
72_R104_V1.055592.840
256_V273_D1.048942.822
258_Y273_D1.03312.780
89_A106_A0.907212.441
228_T257_R0.878142.363
74_A278_L0.877332.361
223_L277_W0.869392.339
254_E280_D0.819482.205
25_R275_L0.817412.199
33_D38_G0.808592.176
110_G230_D0.803362.162
242_V253_V0.784012.110
82_G111_P0.771462.076
35_E54_A0.719221.935
273_D276_A0.709941.910
239_D257_R0.688961.854
106_A222_V0.688171.852
226_Q238_T0.685381.844
86_L108_A0.679511.828
242_V255_Y0.676521.820
272_P276_A0.667871.797
108_A111_P0.664661.788
54_A57_A0.662191.782
239_D243_A0.650881.751
74_A104_V0.650021.749
85_A106_A0.633691.705
223_L256_V0.621251.672
226_Q255_Y0.618611.665
258_Y261_G0.617171.661
235_P257_R0.616181.658
35_E57_A0.605561.629
74_A107_A0.593491.597
107_A223_L0.591991.593
240_A244_K0.576251.551
27_Y279_D0.572721.541
222_V245_W0.570691.536
226_Q257_R0.566211.524
20_A24_A0.564141.518
21_A25_R0.561791.512
77_G82_G0.549891.480
79_S263_H0.549141.478
76_W109_G0.546331.470
25_R279_D0.538171.448
34_Y84_A0.535271.440
276_A280_D0.534531.438
23_L29_V0.534151.437
239_D255_Y0.533751.436
228_T260_G0.523041.407
77_G85_A0.516711.390
235_P239_D0.516111.389
73_V103_L0.514391.384
223_L254_E0.5111.375
88_A92_A0.510521.374
63_P99_L0.50871.369
214_G217_T0.505081.359
62_P73_V0.5031.353
19_L23_L0.494671.331
107_A274_A0.494231.330
57_A61_L0.483521.301
61_L64_K0.482041.297
87_W90_E0.480411.293
21_A271_A0.47881.288
236_A239_D0.478271.287
76_W107_A0.470381.266
56_R91_L0.468641.261
109_G270_S0.45731.230
226_Q235_P0.455221.225
105_G221_P0.448011.205
27_Y74_A0.445031.197
77_G81_G0.444751.197
224_I242_V0.440321.185
18_F271_A0.439591.183
27_Y278_L0.439491.183
229_A260_G0.439141.182
261_G265_G0.439131.182
19_L31_A0.438721.180
254_E273_D0.436961.176
53_D56_R0.436411.174
21_A24_A0.43431.169
50_A54_A0.429951.157
78_Y264_L0.420211.131
107_A278_L0.418261.125
75_L103_L0.416811.122
34_Y80_Q0.415641.118
237_D240_A0.413821.113
23_L26_G0.409711.102
225_Y258_Y0.408041.098
18_F22_W0.406271.093
106_A220_V0.405251.090
239_D242_V0.405191.090
19_L29_V0.404531.088
230_D263_H0.403991.087
92_A97_P0.403811.087
240_A243_A0.402671.083
224_I255_Y0.402581.083
108_A224_I0.400581.078
87_W91_L0.392381.056
59_R63_P0.390371.050
34_Y37_L0.389361.048
50_A53_D0.388891.046
215_D218_P0.386481.040
54_A59_R0.384321.034
75_L88_A0.382291.029
56_R60_N0.381371.026
52_L91_L0.381221.026
270_S274_A0.380941.025
275_L279_D0.380441.024
79_S264_L0.377111.015
86_L241_L0.372781.003
54_A61_L0.372131.001
218_P245_W0.36930.994
105_G277_W0.368280.991
225_Y270_S0.367560.989
78_Y110_G0.367240.988
50_A57_A0.36710.988
241_L245_W0.3630.977
203_R206_A0.357630.962
79_S110_G0.355160.956
230_D233_V0.355050.955
224_I253_V0.35320.950
80_Q84_A0.350880.944
245_W253_V0.350670.944
78_Y109_G0.349660.941
162_D165_R0.348980.939
271_A274_A0.345930.931
223_L273_D0.345150.929
224_I238_T0.344360.927
176_Y179_Q0.343080.923
105_G108_A0.342150.921
109_G225_Y0.341340.918
81_G85_A0.341130.918
228_T235_P0.34050.916
276_A279_D0.339960.915
60_N63_P0.33690.907
47_E54_A0.33690.907
85_A89_A0.335230.902
104_V107_A0.33490.901
219_T251_A0.332460.895
105_G223_L0.332210.894
224_I241_L0.332110.894
238_T253_V0.330730.890
270_S277_W0.329830.887
225_Y265_G0.328930.885
56_R92_A0.327670.882
177_A180_D0.325950.877
26_G29_V0.32490.874
40_P43_N0.323940.872
262_G265_G0.323480.870
75_L106_A0.322830.869
92_A98_E0.319450.860
21_A275_L0.318740.858
218_P221_P0.318120.856
57_A60_N0.318030.856
55_V88_A0.316750.852
112_P233_V0.31560.849
56_R59_R0.31410.845
90_E214_G0.312550.841
47_E50_A0.311770.839
261_G269_A0.311630.839
204_A208_N0.30880.831
17_P20_A0.308650.830
33_D39_T0.305010.821
83_Q112_P0.304420.819
59_R88_A0.302670.814
226_Q233_V0.301580.811
30_V61_L0.301070.810
114_D240_A0.299190.805
238_T242_V0.295880.796
216_W244_K0.295460.795
26_G275_L0.295380.795
227_G261_G0.295180.794
78_Y266_A0.294490.792
20_A23_L0.293570.790
35_E50_A0.293390.789
227_G257_R0.292660.787
92_A99_L0.291920.785
203_R207_E0.291320.784
99_L103_L0.288750.777
103_L220_V0.287270.773
109_G274_A0.287190.773
271_A277_W0.287140.773
60_N64_K0.284890.767
51_V54_A0.284220.765
227_G265_G0.28420.765
58_A61_L0.283630.763
200_A203_R0.283050.762
264_L267_A0.282480.760
254_E257_R0.282020.759
112_P115_L0.281650.758
48_A54_A0.28120.757
235_P255_Y0.279590.752
89_A220_V0.27870.750
261_G268_F0.278180.749
49_Y53_D0.277230.746
90_E217_T0.276380.744
49_Y52_L0.275570.741
82_G233_V0.275080.740
169_L172_I0.273170.735
37_L80_Q0.272870.734
45_R48_A0.272490.733
58_A62_P0.272150.732
52_L56_R0.27080.729
107_A225_Y0.267820.721
53_D57_A0.267470.720
271_A275_L0.265230.714
32_P58_A0.263750.710
71_S104_V0.261680.704
42_L45_R0.261190.703
233_V238_T0.260580.701
168_C171_D0.260420.701
103_L106_A0.260240.700
27_Y275_L0.259590.698
207_E210_L0.259390.698
82_G110_G0.259330.698
171_D178_F0.258820.696
202_R205_L0.257950.694
110_G227_G0.257350.692
158_R161_L0.255880.689
163_D166_T0.255440.687
234_P237_D0.254980.686
167_R172_I0.254790.686
22_W275_L0.253380.682
159_A162_D0.253160.681
167_R171_D0.252510.679
54_A62_P0.251420.677
224_I245_W0.249210.671
109_G266_A0.248570.669
80_Q83_Q0.247410.666
98_E103_L0.246770.664
178_F181_L0.246220.663
49_Y91_L0.245320.660
73_V104_V0.244080.657
25_R272_P0.244010.657
59_R98_E0.243620.656
204_A207_E0.243480.655
238_T255_Y0.24250.653
222_V253_V0.241910.651
55_V59_R0.241890.651
22_W26_G0.241390.650
82_G108_A0.241370.649
22_W274_A0.24060.647
237_D241_L0.240560.647
22_W29_V0.240470.647
131_V135_L0.24030.647
160_L163_D0.240280.647
52_L58_A0.240120.646
110_G226_Q0.239940.646
59_R62_P0.239140.643
34_Y78_Y0.239110.643
270_S273_D0.237340.639
86_L245_W0.236560.637
89_A218_P0.236410.636
86_L106_A0.235590.634
254_E276_A0.234980.632
30_V58_A0.23440.631
238_T241_L0.234020.630
31_A37_L0.232810.626
21_A272_P0.23280.626
200_A204_A0.231530.623
28_A71_S0.230720.621
59_R73_V0.229810.618
74_A78_Y0.229580.618
54_A58_A0.229520.618
86_L113_A0.229340.617
225_Y256_V0.229080.616
28_A31_A0.228920.616
194_D202_R0.227990.613
273_D277_W0.227640.613
43_N47_E0.227360.612
53_D60_N0.227170.611
42_L47_E0.227060.611
253_V256_V0.225430.607
107_A277_W0.223980.603
88_A103_L0.222460.599
258_Y265_G0.22240.598
165_R169_L0.222230.598
158_R162_D0.221850.597
105_G278_L0.221460.596
164_A167_R0.221130.595
275_L278_L0.220940.594
62_P88_A0.220820.594
254_E277_W0.220430.593
168_C176_Y0.219510.591
129_G132_P0.218750.589
86_L111_P0.218280.587
221_P252_D0.21820.587
52_L57_A0.215650.580
202_R206_A0.215060.579
136_L139_A0.214870.578
22_W27_Y0.214260.577
130_L134_A0.214220.576
162_D166_T0.213550.575
58_A88_A0.213390.574
32_P37_L0.212520.572
166_T169_L0.212210.571
113_A232_V0.211020.568
167_R170_A0.21060.567
168_C172_I0.210460.566
218_P222_V0.210140.565
223_L226_Q0.209880.565
266_A270_S0.209780.564
127_F130_L0.209130.563
59_R99_L0.208820.562
113_A241_L0.208550.561
80_Q112_P0.208130.560
114_D117_A0.20780.559
83_Q111_P0.20660.556
54_A63_P0.206010.554
51_V55_V0.205240.552
76_W274_A0.204950.551
82_G89_A0.204930.551
136_L143_P0.204760.551
232_V262_G0.203840.548
229_A261_G0.20360.548
81_G263_H0.201650.543
227_G259_P0.201390.542
256_V276_A0.201140.541
88_A91_L0.200930.541
165_R168_C0.200840.540
272_P275_L0.199850.538
163_D167_R0.199730.537
63_P73_V0.199180.536
22_W76_W0.199040.536
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
3v48A0.848399.90.21
3w04A0.824199.90.214
1b6gA0.862199.90.219
3fobA0.841499.90.221
1brtA0.848399.90.223
3i28A0.920799.90.225
3nwoA0.999.90.226
3w06A0.851799.90.228
2xt0A0.841499.90.23
3afiE0.999.90.234

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