GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
AMP-binding - AMP-binding enzyme
Pfam: PF00501 (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: CL0378
Length: 417
Sequences: 31752
Seq/Len: 76.14
HH_delta: 0.115 (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
157_P174_V2.403243.701
362_I396_G2.122263.269
91_Q162_F2.115613.258
342_E365_R1.964973.026
32_R68_R1.897822.923
43_V71_A1.860322.865
376_D379_L1.832252.822
50_A94_P1.831742.821
397_R405_Y1.811432.790
47_D95_K1.738432.677
176_T371_S1.649322.540
28_Y68_R1.621822.498
361_E391_R1.564742.410
93_G375_N1.556312.397
344_K353_P1.534112.363
12_I21_S1.528362.354
347_D352_E1.525622.350
48_R74_V1.479162.278
346_V363_V1.446132.227
8_Y11_R1.434042.209
241_E245_R1.404212.163
15_I224_T1.393132.146
62_A98_I1.382062.129
91_Q376_D1.3822.128
2_E28_Y1.377772.122
30_R61_V1.373792.116
198_R224_T1.37182.113
66_C71_A1.370232.110
363_V391_R1.347992.076
28_Y32_R1.32732.044
37_A41_L1.3242.039
379_L382_E1.310612.018
359_P395_L1.310582.018
87_H169_K1.296511.997
377_P381_A1.293921.993
333_S405_Y1.283481.977
4_Q8_Y1.275261.964
197_D280_R1.249591.925
399_D405_Y1.245291.918
34_L61_V1.244361.916
344_K363_V1.228631.892
10_D25_K1.223751.885
291_P295_R1.221491.881
45_K156_D1.208341.861
39_R69_A1.176741.812
398_L404_L1.171971.805
25_K29_E1.170981.803
95_K122_S1.169081.801
378_E382_E1.168641.800
44_K47_D1.166351.796
86_R90_R1.143751.762
399_D403_Y1.11461.717
16_D57_I1.108741.708
197_D249_T1.091751.681
50_A76_L1.089351.678
397_R407_L1.081431.666
3_R7_R1.065991.642
15_I21_S1.06251.636
226_V248_P1.056811.628
345_I396_G1.055711.626
67_L158_A1.047261.613
23_T26_Q1.046621.612
32_R36_A1.043561.607
253_A258_L1.043111.607
31_V68_R1.042191.605
22_L61_V1.036441.596
49_V66_C1.030731.587
247_K278_S1.022791.575
396_G406_I1.019031.569
153_S156_D1.018891.569
60_V215_L1.01631.565
176_T179_N1.003351.545
295_R299_K0.99471.532
9_P25_K0.983971.515
359_P407_L0.976921.505
15_I246_Y0.974981.502
92_S162_F0.973241.499
49_V71_A0.967061.489
312_S390_Y0.963091.483
43_V49_V0.959641.478
13_A27_L0.956131.473
46_G156_D0.954891.471
157_P371_S0.953331.468
356_P398_L0.951011.465
162_F172_G0.946981.458
330_K401_D0.944581.455
48_R374_Y0.943691.453
349_N352_E0.939951.448
347_D354_L0.930311.433
65_A69_A0.929321.431
50_A89_L0.921281.419
4_Q7_R0.917951.414
385_I391_R0.913491.407
12_I15_I0.912321.405
34_L65_A0.90861.399
174_V372_G0.90771.398
5_A28_Y0.900341.387
160_I374_Y0.900061.386
343_V364_I0.892981.375
218_A223_A0.890391.371
200_L248_P0.88811.368
188_A221_S0.885881.364
179_N316_G0.883171.360
284_S289_L0.880741.356
238_S241_E0.879681.355
155_D178_R0.877481.351
258_L282_V0.876421.350
348_P410_S0.872771.344
91_Q375_N0.861921.327
12_I224_T0.860391.325
355_P358_E0.857971.321
383_A390_Y0.856431.319
395_L410_S0.850081.309
22_L57_I0.847031.305
365_R389_W0.846851.304
29_E33_K0.84621.303
243_I278_S0.845921.303
364_I392_T0.843671.299
27_L64_L0.838841.292
359_P397_R0.838531.291
89_L94_P0.838431.291
370_F384_F0.836131.288
256_S287_E0.829621.278
362_I406_I0.824641.270
26_Q29_E0.823711.269
319_A364_I0.817851.260
163_T173_V0.810081.248
198_R226_V0.808011.244
34_L98_I0.804491.239
30_R33_K0.803891.238
72_I157_P0.803481.237
244_S274_K0.803031.237
174_V374_Y0.8011.234
41_L123_S0.800881.233
21_S246_Y0.79991.232
43_V47_D0.796621.227
90_R169_K0.794151.223
74_V92_S0.793891.223
361_E410_S0.793471.222
175_L179_N0.791951.220
337_P343_V0.790191.217
179_N369_V0.78931.216
51_I62_A0.788211.214
197_D250_I0.787151.212
336_K403_Y0.782941.206
43_V96_V0.78221.205
31_V65_A0.776141.195
366_G369_V0.776021.195
344_K389_W0.772981.190
91_Q169_K0.771821.189
64_L219_L0.771461.188
290_P293_L0.771141.188
242_L246_Y0.770581.187
198_R248_P0.769221.185
46_G371_S0.767841.183
330_K403_Y0.765921.180
2_E68_R0.764361.177
87_H91_Q0.762871.175
209_F252_F0.76131.172
48_R72_I0.760041.171
77_D206_S0.756621.165
228_P242_L0.752111.158
13_A24_Y0.75121.157
160_I172_G0.749561.154
251_L279_L0.745111.148
22_L30_R0.736571.134
12_I23_T0.729271.123
27_L61_V0.729131.123
289_L294_L0.723741.115
263_Q296_R0.718881.107
395_L408_G0.717371.105
341_V368_N0.714361.100
161_L313_T0.713911.100
178_R367_P0.712131.097
296_R300_A0.706341.088
48_R160_I0.705051.086
320_T343_V0.703741.084
76_L85_L0.703491.083
35_A68_R0.702441.082
154_P178_R0.696061.072
297_L301_F0.69561.071
16_D20_R0.69011.063
343_V404_L0.68911.061
59_F205_L0.687641.059
135_K139_K0.684771.055
34_L62_A0.682611.051
52_L85_L0.676951.043
37_A40_K0.675141.040
380_T384_F0.674721.039
198_R249_T0.67271.036
57_I61_V0.66661.027
87_H162_F0.665721.025
174_V371_S0.665421.025
27_L31_V0.664581.024
354_L358_E0.663781.022
226_V246_Y0.663091.021
54_P104_D0.660131.017
334_V406_I0.658711.014
362_I404_L0.65831.014
203_L209_F0.656391.011
22_L27_L0.655781.010
199_I218_A0.654521.008
30_R58_E0.650911.002
38_L98_I0.650131.001
48_R93_G0.649411.000
204_P207_H0.648960.999
82_E86_R0.64840.999
81_S84_E0.644580.993
35_A69_A0.642840.990
80_L88_I0.641870.989
254_V257_M0.640060.986
250_I281_T0.639760.985
63_F211_L0.631910.973
262_L296_R0.631360.972
343_V362_I0.63050.971
158_A177_H0.629990.970
259_E293_L0.628490.968
218_A225_L0.628150.967
378_E381_A0.627440.966
173_V370_F0.626320.965
38_L66_C0.624640.962
20_R30_R0.623960.961
226_V242_L0.62380.961
379_L383_A0.619970.955
345_I404_L0.614240.946
50_A97_I0.613990.946
96_V123_S0.613920.946
296_R299_K0.612190.943
47_D71_A0.610550.940
320_T404_L0.610510.940
182_A367_P0.60970.939
63_F73_P0.609540.939
53_L56_S0.607250.935
83_D86_R0.605110.932
345_I354_L0.604340.931
315_T390_Y0.604270.931
5_A9_P0.604090.930
66_C73_P0.602830.928
11_R224_T0.601510.926
125_I129_R0.60040.925
330_K399_D0.60030.925
19_G245_R0.598540.922
363_V385_I0.598090.921
28_Y31_V0.597950.921
155_D176_T0.597920.921
244_S275_D0.596640.919
15_I226_V0.596040.918
357_G400_E0.585640.902
232_D238_S0.585040.901
363_V389_W0.584950.901
36_A39_R0.58420.900
157_P176_T0.582830.898
2_E32_R0.581930.896
51_I73_P0.579020.892
34_L38_L0.573740.884
347_D358_E0.571530.880
140_S143_L0.569920.878
191_E339_P0.569060.876
322_R403_Y0.568270.875
61_V65_A0.568040.875
16_D19_G0.567380.874
333_S403_Y0.567320.874
305_P323_P0.567010.873
14_L57_I0.565480.871
237_E241_E0.56520.870
376_D380_T0.564730.870
346_V353_P0.564590.870
197_D223_A0.563050.867
82_E110_K0.562210.866
58_E61_V0.560660.863
184_A220_F0.55990.862
14_L60_V0.558970.861
200_L228_P0.558110.860
60_V227_L0.557530.859
39_R44_K0.55680.858
50_A74_V0.555290.855
41_L96_V0.551630.850
292_D296_R0.547930.844
175_L316_G0.546970.842
384_F391_R0.546680.842
182_A340_G0.545950.841
104_D107_P0.54590.841
63_F67_L0.544840.839
202_F257_M0.544240.838
258_L297_L0.543040.836
198_R247_K0.541630.834
391_R410_S0.541320.834
209_F285_G0.539120.830
208_I312_S0.538740.830
53_L127_L0.537520.828
231_F257_M0.534860.824
108_L112_K0.533060.821
30_R57_I0.532920.821
82_E113_S0.531010.818
43_V69_A0.530110.816
351_G363_V0.528970.815
38_L96_V0.527120.812
26_Q30_R0.526030.810
62_A66_C0.523840.807
208_I317_S0.521540.803
27_L60_V0.521090.803
87_H90_R0.521040.802
53_L98_I0.519610.800
380_T383_A0.518810.799
237_E264_S0.51870.799
53_L59_F0.517260.797
35_A65_A0.514480.792
3_R6_Q0.514450.792
158_A180_L0.510970.787
10_D23_T0.510370.786
18_E229_S0.51020.786
106_E109_K0.510060.786
20_R57_I0.509670.785
238_S242_L0.507070.781
396_G404_L0.5070.781
183_Q317_S0.505350.778
139_K143_L0.505270.778
308_N332_G0.503740.776
354_L357_G0.501190.772
74_V94_P0.501120.772
342_E389_W0.500090.770
31_V35_A0.500040.770
87_H376_D0.499240.769
229_S232_D0.495930.764
83_D87_H0.495460.763
44_K95_K0.4950.762
91_Q374_Y0.489940.755
281_T307_I0.487220.750
83_D169_K0.486830.750
175_L370_F0.486550.749
66_C69_A0.486050.749
283_I309_L0.485620.748
315_T369_V0.484530.746
167_T171_K0.484220.746
20_R58_E0.48290.744
52_L97_I0.482870.744
315_T364_I0.481790.742
279_L282_V0.480990.741
49_V96_V0.480840.741
159_F175_L0.47980.739
348_P361_E0.47680.734
408_G411_D0.476460.734
24_Y223_A0.476330.734
73_P211_L0.474960.731
15_I198_R0.473840.730
258_L284_S0.473210.729
289_L306_I0.472640.728
34_L37_A0.472290.727
31_V34_L0.47170.726
165_G171_K0.471240.726
139_K142_S0.470960.725
364_I369_V0.470840.725
310_Y319_A0.469810.724
63_F216_L0.468910.722
322_R333_S0.467410.720
164_S171_K0.466440.718
88_I172_G0.466030.718
343_V396_G0.4650.716
136_E139_K0.464180.715
249_T280_R0.46150.711
243_I248_P0.461360.711
33_K36_A0.461230.710
74_V162_F0.460850.710
252_F309_L0.46060.709
123_S127_L0.456980.704
292_D295_R0.456220.703
44_K71_A0.455950.702
50_A92_S0.455370.701
72_I160_I0.45440.700
42_G71_A0.454120.699
93_G374_Y0.453370.698
107_P110_K0.450910.694
408_G412_D0.45090.694
134_K137_A0.448530.691
33_K37_A0.448240.690
255_P287_E0.447760.690
213_S252_F0.447740.690
396_G407_L0.446560.688
244_S277_S0.445860.687
14_L225_L0.445710.686
345_I398_L0.445440.686
159_F211_L0.445190.686
91_Q172_G0.44410.684
21_S224_T0.442980.682
377_P380_T0.442760.682
356_P400_E0.442620.682
345_I362_I0.440960.679
251_L282_V0.440130.678
8_Y25_K0.439920.678
315_T319_A0.439830.677
110_K114_I0.438050.675
241_E274_K0.43750.674
72_I374_Y0.436460.672
385_I389_W0.436220.672
243_I251_L0.435930.671
244_S278_S0.434910.670
231_F239_L0.434670.669
51_I59_F0.432910.667
6_Q9_P0.432390.666
338_L341_V0.431520.665
285_G309_L0.430910.664
202_F254_V0.430650.663
237_E274_K0.430360.663
282_V297_L0.430050.662
22_L26_Q0.429670.662
53_L62_A0.429070.661
125_I128_D0.429030.661
63_F215_L0.428390.660
87_H92_S0.427910.659
200_L243_I0.427870.659
179_N371_S0.425650.656
12_I198_R0.425320.655
268_K300_A0.425120.655
166_T171_K0.425060.655
155_D371_S0.424320.654
183_Q316_G0.423240.652
284_S308_N0.423060.652
110_K113_S0.422430.651
344_K365_R0.422170.650
164_S170_P0.420910.648
228_P239_L0.419590.646
96_V125_I0.418220.644
74_V88_I0.417050.642
201_S214_A0.416620.642
160_I174_V0.416480.641
136_E140_S0.415750.640
239_L257_M0.415350.640
252_F318_I0.4130.636
105_S128_D0.412880.636
259_E296_R0.411340.634
8_Y222_G0.410050.632
19_G246_Y0.409940.631
137_A140_S0.408920.630
14_L22_L0.40850.629
259_E290_P0.408310.629
63_F159_F0.407610.628
376_D382_E0.407430.627
72_I75_P0.406630.626
2_E6_Q0.406050.625
312_S315_T0.404810.623
109_K113_S0.404410.623
309_L318_I0.40360.622
203_L252_F0.403560.622
295_R298_R0.400940.617
64_L216_L0.400640.617
183_Q213_S0.40.616
294_L308_N0.39950.615
48_R94_P0.399170.615
122_S126_I0.399080.615
178_R182_A0.398560.614
369_V390_Y0.398080.613
312_S392_T0.397830.613
214_A252_F0.397820.613
200_L242_L0.397530.612
199_I250_I0.396320.610
209_F283_I0.395780.610
12_I16_D0.395530.609
37_A138_L0.395060.608
241_E244_S0.394640.608
237_E266_E0.39390.607
209_F309_L0.39330.606
224_T246_Y0.392220.604
156_D177_H0.392150.604
284_S306_I0.391790.603
183_Q187_L0.391570.603
159_F180_L0.391450.603
4_Q222_G0.389070.599
183_Q318_I0.388540.598
77_D80_L0.38770.597
242_L245_R0.387690.597
232_D237_E0.387620.597
48_R375_N0.387370.597
36_A40_K0.387310.597
214_A218_A0.387010.596
288_P406_I0.386580.595
372_G377_P0.386530.595
184_A216_L0.384510.592
264_S267_E0.384440.592
308_N334_V0.382580.589
243_I247_K0.382490.589
195_L250_I0.382190.589
274_K277_S0.381780.588
384_F390_Y0.380180.586
219_L225_L0.379370.584
49_V98_I0.378890.584
318_I321_I0.378020.582
333_S399_D0.377830.582
31_V64_L0.377590.582
209_F286_G0.376570.580
76_L89_L0.37630.580
75_P161_L0.376170.579
124_I128_D0.37570.579
168_G171_K0.375560.578
134_K139_K0.374950.577
47_D96_V0.374620.577
341_V366_G0.374130.576
363_V410_S0.373940.576
201_S210_G0.373640.575
24_Y219_L0.373370.575
210_G214_A0.373230.575
281_T305_P0.372920.574
209_F213_S0.372540.574
370_F383_A0.372340.573
140_S144_S0.372130.573
289_L308_N0.371820.573
71_A96_V0.371490.572
373_Y380_T0.37110.572
46_G71_A0.370450.571
88_I162_F0.369930.570
111_L114_I0.368910.568
208_I313_T0.368540.568
239_L243_I0.367630.566
311_G314_E0.367320.566
185_R220_F0.36720.566
347_D351_G0.367160.565
165_G409_R0.366850.565
275_D278_S0.36660.565
51_I66_C0.36640.564
262_L293_L0.365910.564
240_L261_L0.365740.563
213_S318_I0.365580.563
40_K141_A0.365540.563
109_K112_K0.365480.563
345_I360_G0.365470.563
199_I223_A0.36520.562
12_I246_Y0.364380.561
11_R24_Y0.363530.560
6_Q28_Y0.36290.559
164_S409_R0.361970.557
394_D409_R0.361830.557
165_G170_P0.360350.555
357_G397_R0.360030.554
15_I19_G0.358230.552
370_F390_Y0.358190.552
358_E397_R0.358140.552
346_V389_W0.358050.551
297_L306_I0.357570.551
334_V396_G0.357370.550
365_R388_G0.356660.549
252_F285_G0.356460.549
175_L208_I0.356330.549
123_S126_I0.356130.548
312_S316_G0.354470.546
337_P341_V0.354350.546
284_S297_L0.353920.545
205_L227_L0.353350.544
256_S259_E0.35310.544
293_L296_R0.353080.544
259_E263_Q0.352270.543
183_Q186_A0.351760.542
188_A217_A0.351360.541
112_K115_F0.350460.540
201_S225_L0.349670.539
239_L253_A0.349550.538
73_P159_F0.348060.536
353_P398_L0.347740.536
240_L243_I0.347710.536
182_A368_N0.347680.535
24_Y28_Y0.347170.535
184_A188_A0.347090.535
171_K409_R0.346840.534
32_R39_R0.346630.534
298_R305_P0.345430.532
163_T171_K0.344990.531
45_K70_G0.344970.531
92_S172_G0.344660.531
204_P210_G0.344310.530
359_P410_S0.344140.530
253_A257_M0.343690.529
66_C96_V0.34340.529
211_L216_L0.34340.529
200_L239_L0.342930.528
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
3ni2A0.96641000.115
3vnrA0.93761000.115
3tsyA0.96881000.115
3rixA0.96641000.118
2vsqA0.93531000.126
1mdbA0.9641000.129
3o83A0.96641000.13
3g7sA0.96881000.134
4fuqA0.95441000.134
2d1sA0.9641000.136

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