GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Alliinase_C - Allinase
Pfam: PF04864 (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: CL0061
Length: 363
Sequences: 39459
Seq/Len: 108.7
HH_delta: 0.208 (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
324_A361_K2.736283.708
270_K353_D2.663123.609
266_E349_D2.340223.171
51_Q241_K2.099222.844
354_Q358_R2.098882.844
270_K349_D2.077962.816
348_R351_D1.984522.689
274_A356_L1.912122.591
265_R269_E1.893732.566
131_K160_G1.714822.324
238_K241_K1.70112.305
72_G78_L1.669622.262
270_K274_A1.622462.198
274_A277_A1.610782.183
129_N132_N1.519992.060
320_V323_E1.507552.043
278_S360_S1.469511.991
98_S119_R1.455981.973
324_A358_R1.45071.966
354_Q357_E1.427891.935
282_S308_K1.423421.929
68_Y211_E1.417711.921
158_L163_G1.395211.891
277_A360_S1.38741.880
98_S135_N1.385371.877
98_S137_S1.365581.850
269_E273_A1.357741.840
129_N133_S1.354741.836
51_Q237_L1.345581.823
67_R211_E1.341281.817
259_F263_T1.331911.805
268_W272_R1.318441.786
47_E237_L1.31571.783
131_K157_V1.314611.781
156_A160_G1.30671.771
208_V214_A1.300141.762
272_R276_S1.297071.758
274_A353_D1.28061.735
263_T267_R1.278311.732
349_D353_D1.274141.726
274_A278_S1.26031.708
98_S121_Y1.255041.701
50_R54_R1.250361.694
98_S138_P1.228181.664
97_A139_Y1.226821.662
262_S266_E1.226241.662
157_V161_S1.221781.656
319_A323_E1.210861.641
238_K242_V1.203791.631
320_V324_A1.196881.622
190_F205_W1.186311.607
274_A360_S1.184041.604
258_H262_S1.180831.600
273_A277_A1.170381.586
326_I358_R1.162781.576
51_Q54_R1.157721.569
69_I207_L1.141831.547
145_S172_Y1.140471.545
140_I166_I1.122111.520
169_L188_M1.114571.510
255_D258_H1.108481.502
326_I355_L1.102351.494
158_L165_V1.097061.487
131_K161_S1.092011.480
87_S118_S1.089871.477
259_F262_S1.087561.474
274_A357_E1.085341.471
46_P50_R1.079111.462
82_A187_I1.07881.462
357_E361_K1.074991.457
103_A124_A1.073491.455
263_T266_E1.069481.449
100_V138_P1.065871.444
237_L241_K1.065481.444
73_T77_Q1.064281.442
127_A157_V1.060831.437
80_N84_Y1.060821.437
316_D320_V1.049721.422
50_R66_G1.042251.412
128_S132_N1.021761.384
343_L355_L1.020861.383
82_A166_I1.014751.375
353_D357_E1.010781.370
126_D129_N1.003121.359
124_A129_N0.996641.350
270_K273_A0.993591.346
315_E319_A0.988971.340
47_E241_K0.982231.331
166_I189_L0.97521.321
320_V362_L0.96641.309
53_R66_G0.964831.307
273_A276_S0.964251.307
211_E215_K0.959441.300
282_S310_E0.955971.295
351_D354_Q0.950241.288
141_E158_L0.943541.278
75_S189_L0.936811.269
266_E270_K0.934121.266
266_E353_D0.926561.255
263_T349_D0.915971.241
307_L343_L0.900011.220
319_A322_R0.879391.192
318_Y322_R0.878041.190
134_D163_G0.87771.189
47_E51_Q0.873931.184
162_S185_H0.870531.180
179_I182_P0.863331.170
270_K356_L0.857551.162
170_A191_T0.850961.153
56_H207_L0.850141.152
99_V113_T0.841221.140
53_R69_I0.830431.125
229_S232_S0.83041.125
127_A131_K0.82441.117
128_S131_K0.814361.103
203_F236_A0.814141.103
131_K135_N0.813561.102
272_R305_A0.810281.098
258_H261_Y0.806851.093
192_L205_W0.804331.090
97_A137_S0.803651.089
326_I354_Q0.802491.087
159_N184_D0.800551.085
178_P181_A0.798941.083
350_D353_D0.796881.080
159_N186_D0.796611.079
103_A122_K0.793661.075
142_L166_I0.785211.064
79_F108_S0.782481.060
356_L360_S0.779661.056
262_S265_R0.779091.056
350_D354_Q0.776411.052
319_A362_L0.773731.048
313_E316_D0.770871.045
100_V133_S0.770671.044
49_E53_R0.770461.044
324_A362_L0.769711.043
99_V140_I0.766291.038
156_A159_N0.765841.038
267_R349_D0.76561.037
175_H181_A0.762461.033
158_L161_S0.759491.029
88_P97_A0.758231.027
358_R361_K0.756991.026
79_F166_I0.753061.020
72_G204_G0.749631.016
141_E163_G0.745441.010
78_L189_L0.74531.010
157_V163_G0.735440.997
157_V160_G0.733720.994
134_D157_V0.733430.994
261_Y265_R0.726850.985
256_I260_G0.725970.984
134_D138_P0.725040.982
328_T341_V0.724460.982
270_K352_F0.719070.974
49_E71_F0.716110.970
167_H185_H0.715990.970
159_N185_H0.714940.969
110_P114_D0.710840.963
272_R283_L0.708650.960
192_L236_A0.70760.959
164_K213_V0.69760.945
308_K340_Y0.697090.945
72_G206_A0.696380.944
177_T180_T0.696080.943
50_R53_R0.695810.943
111_E114_D0.692880.939
257_F260_G0.687460.932
135_N161_S0.683850.927
83_L113_T0.680210.922
266_E269_E0.67950.921
347_K352_F0.676510.917
267_R270_K0.674140.913
278_S356_L0.670970.909
357_E360_S0.670240.908
134_D161_S0.669540.907
47_E50_R0.668980.906
135_N138_P0.668970.906
75_S170_A0.664630.901
52_I71_F0.663170.899
306_W340_Y0.661730.897
308_K339_R0.659080.893
51_Q55_L0.65670.890
316_D319_A0.654480.887
185_H188_M0.649040.879
284_Q308_K0.647220.877
52_I205_W0.640990.869
321_L328_T0.637610.864
48_L71_F0.635960.862
355_L359_L0.632090.856
260_G264_M0.632030.856
260_G263_T0.630620.854
83_L142_L0.627020.850
45_S234_L0.626840.849
234_L238_K0.624310.846
264_M267_R0.618520.838
221_M225_T0.613940.832
177_T181_A0.613310.831
355_L358_R0.613110.831
315_E318_Y0.611310.828
48_L237_L0.604590.819
121_Y133_S0.60230.816
187_I213_V0.601850.816
68_Y214_A0.598410.811
276_S283_L0.595630.807
206_A217_M0.594250.805
271_L274_A0.593220.804
271_L305_A0.592710.803
267_R352_F0.591580.802
158_L162_S0.590690.800
86_L140_I0.589230.798
317_C320_V0.587080.795
164_K187_I0.586780.795
235_R238_K0.584590.792
321_L358_R0.584210.792
127_A130_F0.577860.783
143_V165_V0.57370.777
186_D210_D0.571470.774
65_D211_E0.571030.774
79_F191_T0.570180.773
58_V65_D0.568120.770
215_K219_K0.567620.769
271_L356_L0.566540.768
273_A353_D0.566320.767
269_E272_R0.563980.764
230_R233_Q0.562530.762
159_N165_V0.561630.761
48_L236_A0.561250.760
85_A217_M0.56120.760
46_P49_E0.557690.756
86_L164_K0.556070.753
223_L226_I0.554020.751
48_L51_Q0.55370.750
256_I259_F0.552930.749
264_M268_W0.552630.749
68_Y215_K0.550420.746
113_T120_L0.549630.745
271_L352_F0.544680.738
214_A218_T0.54360.737
278_S357_E0.542460.735
271_L355_L0.541810.734
84_Y116_F0.541710.734
54_R58_V0.541580.734
113_T118_S0.539140.731
358_R362_L0.538110.729
72_G81_A0.537750.729
328_T343_L0.534840.725
317_C341_V0.530670.719
83_L99_V0.530240.718
146_P301_S0.529280.717
54_R241_K0.529130.717
57_R179_I0.528750.716
210_D213_V0.52750.715
87_S99_V0.526530.713
347_K351_D0.524030.710
216_K219_K0.522060.707
270_K357_E0.520420.705
105_Y110_P0.520030.705
125_G130_F0.517910.702
45_S49_E0.517880.702
313_E338_S0.516310.700
56_H205_W0.515270.698
314_D330_S0.514530.697
144_T148_N0.511910.694
123_W133_S0.510620.692
123_W130_F0.509530.690
212_E215_K0.507960.688
147_N150_D0.506890.687
102_A143_V0.503490.682
271_L343_L0.502750.681
221_M228_V0.501660.680
84_Y220_Y0.500040.678
215_K218_T0.499750.677
75_S191_T0.498850.676
314_D318_Y0.498470.675
101_A113_T0.493830.669
267_R271_L0.493710.669
77_Q225_T0.48790.661
73_T229_S0.486920.660
143_V167_H0.486570.659
171_Y342_R0.486450.659
227_G230_R0.486280.659
87_S97_A0.485760.658
196_T346_L0.485760.658
65_D68_Y0.48550.658
78_L206_A0.484690.657
321_L362_L0.484420.656
265_R268_W0.484410.656
77_Q221_M0.483990.656
280_R283_L0.481750.653
255_D259_F0.481280.652
130_F134_D0.480950.652
223_L227_G0.480260.651
353_D356_L0.479840.650
318_Y330_S0.47970.650
232_S235_R0.479690.650
69_I72_G0.478660.649
169_L172_Y0.477730.647
271_L275_V0.477350.647
54_R57_R0.476870.646
68_Y183_A0.47630.645
352_F355_L0.475980.645
280_R310_E0.47570.645
230_R234_L0.474970.644
225_T228_V0.474850.643
138_P163_G0.473730.642
112_Q116_F0.473470.642
143_V147_N0.473190.641
101_A122_K0.471890.639
317_C328_T0.468630.635
306_W331_G0.46570.631
234_L237_L0.463940.629
124_A133_S0.463570.628
47_E234_L0.463260.628
354_Q361_K0.4630.627
187_I206_A0.46180.626
83_L112_Q0.461310.625
176_Y180_T0.459690.623
201_S232_S0.459670.623
271_L345_M0.458110.621
83_L116_F0.457650.620
109_Y113_T0.457610.620
208_V211_E0.457610.620
314_D332_V0.45650.619
74_G204_G0.455220.617
276_S285_K0.455020.617
100_V123_W0.453540.615
178_P182_P0.453290.614
257_F261_Y0.452980.614
175_H178_P0.452480.613
136_P161_S0.451580.612
168_D194_K0.449480.609
89_N117_D0.449160.609
84_Y115_F0.447790.607
176_Y179_I0.447220.606
82_A189_L0.447130.606
322_R327_I0.447050.606
130_F141_E0.444940.603
101_A120_L0.441150.598
104_P154_R0.44040.597
132_N135_N0.43990.596
278_S281_F0.439430.595
131_K134_D0.439210.595
107_S111_E0.437820.593
48_L52_I0.437660.593
224_N227_G0.435880.591
189_L206_A0.435390.590
82_A86_L0.433280.587
262_S349_D0.432130.586
75_S78_L0.428940.581
272_R285_K0.428560.581
203_F233_Q0.428510.581
143_V146_P0.42810.580
101_A142_L0.427210.579
131_K156_A0.424070.575
117_D120_L0.424020.575
317_C321_L0.423310.574
51_Q240_L0.422730.573
228_V232_S0.422050.572
222_E227_G0.421530.571
144_T154_R0.420520.570
156_A184_D0.419380.568
85_A220_Y0.419040.568
49_E69_I0.415980.564
76_T108_S0.415570.563
343_L359_L0.414740.562
304_F344_S0.413370.560
112_Q115_F0.413080.560
46_P66_G0.41250.559
87_S140_I0.412430.559
102_A147_N0.412090.558
100_V130_F0.411350.557
110_P122_K0.409360.555
231_D235_R0.409010.554
192_L196_T0.408740.554
145_S169_L0.408390.553
239_I242_V0.406590.551
232_S236_A0.406460.551
233_Q237_L0.406090.550
145_S188_M0.405740.550
100_V141_E0.403770.547
56_H190_F0.403530.547
167_H188_M0.403050.546
321_L326_I0.402920.546
70_V214_A0.402310.545
79_F142_L0.399990.542
193_S202_R0.399630.541
192_L207_L0.399410.541
275_V281_F0.399020.541
106_Y109_Y0.395930.536
272_R275_V0.395770.536
187_I208_V0.395750.536
179_I183_A0.395540.536
331_G342_R0.394490.535
175_H180_T0.394470.535
284_Q306_W0.394370.534
159_N162_S0.394020.534
317_C362_L0.39390.534
79_F189_L0.390880.530
203_F228_V0.389430.528
196_T205_W0.389050.527
159_N163_G0.387530.525
144_T147_N0.387450.525
71_F233_Q0.386390.524
307_L340_Y0.384430.521
56_H188_M0.384360.521
276_S282_S0.384260.521
321_L359_L0.384240.521
89_N97_A0.38330.519
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
3bwnA0.95321000.208
1b5pA0.88981000.226
4fl0A0.89531000.226
2hoxA0.96421000.226
3b46A0.90361000.229
2z61A0.88981000.235
3fvsA0.91741000.236
3nraA0.89811000.244
3aowA0.90361000.244
3g0tA0.92011000.248

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