GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DegT_DnrJ_EryC1 - DegTDnrJEryC1StrS aminotransferase family
Pfam: PF01041 (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: 24440
Seq/Len: 67.33
HH_delta: 0.185 (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
107_E138_K1.984653.375
128_D131_A1.858463.160
133_R137_R1.636032.782
105_A108_K1.531782.605
67_E88_E1.518742.583
252_R256_A1.508152.565
133_R143_L1.411042.400
247_R251_Q1.408412.395
105_A109_A1.403522.387
67_E90_V1.368542.327
251_Q255_E1.340432.279
67_E111_T1.338062.275
33_E237_K1.309112.226
291_D294_E1.303432.217
256_A259_G1.235672.101
32_K36_E1.232372.096
103_P135_I1.230132.092
130_D134_A1.227492.087
131_A134_A1.197922.037
134_A138_K1.197442.036
245_R249_N1.184642.015
102_D105_A1.162191.976
107_E135_I1.149421.955
107_E139_H1.145921.949
67_E114_T1.143661.945
46_V52_A1.142511.943
136_A141_I1.141811.942
33_E233_L1.131621.924
103_P131_A1.122891.910
254_R280_F1.120061.905
72_A93_D1.115641.897
66_D115_K1.109241.886
136_A143_L1.099431.870
298_A301_A1.096131.864
67_E113_K1.091461.856
244_A248_E1.071081.821
245_R248_E1.069521.819
110_I135_I1.062231.806
93_D105_A1.047341.781
95_D98_T1.040151.769
297_E301_A1.023751.741
298_A302_R0.988121.680
42_Y190_P0.986251.677
92_V109_A0.986091.677
117_I136_A0.984081.673
47_S51_S0.974251.657
29_E33_E0.947921.612
34_F184_A0.937371.594
254_R258_A0.936551.593
190_P194_E0.929691.581
241_E244_A0.914081.554
135_I139_H0.913171.553
116_A144_I0.909721.547
53_L77_A0.90271.535
294_E298_A0.899021.529
187_T193_A0.88171.499
33_E36_E0.879241.495
56_A166_I0.867221.475
137_R165_D0.862721.467
28_E32_K0.860671.464
107_E131_A0.858911.461
111_T114_T0.856971.457
104_E108_K0.845391.438
90_V109_A0.839071.427
60_L142_P0.835721.421
299_L306_T0.829681.411
147_A167_A0.828311.409
255_E259_G0.821031.396
72_A91_F0.817361.390
95_D102_D0.812411.382
66_D113_K0.80731.373
226_E229_A0.804051.367
106_L132_I0.801561.363
296_V306_T0.794111.350
104_E107_E0.793481.349
185_V196_A0.785541.336
243_I247_R0.784471.334
250_A254_R0.782651.331
248_E252_R0.775421.319
110_I141_I0.773781.316
264_K285_P0.768441.307
252_R255_E0.760081.293
264_K283_R0.754511.283
240_D244_A0.752441.280
104_E131_A0.751331.278
69_I109_A0.739841.258
229_A232_G0.737391.254
107_E111_T0.734571.249
225_S228_Q0.732931.246
119_V132_I0.728771.239
294_E297_E0.726521.235
171_F184_A0.72261.229
37_Y240_D0.717961.221
62_L87_A0.714791.216
100_N128_D0.714471.215
54_H58_R0.712721.212
244_A247_R0.708671.205
26_Y29_E0.704471.198
297_E300_R0.702841.195
38_F186_V0.702331.194
130_D162_S0.699071.189
121_H150_A0.697991.187
240_D243_I0.696251.184
266_P283_R0.696161.184
52_A168_I0.686811.168
293_D297_E0.685651.166
255_E258_A0.685491.166
82_I87_A0.684291.164
53_L144_I0.67821.153
56_A144_I0.676781.151
41_K190_P0.676161.150
26_Y233_L0.672971.144
248_E251_Q0.668511.137
68_V82_I0.661221.124
256_A260_I0.658941.121
49_G168_I0.652531.110
64_P86_G0.646131.099
46_V55_L0.641551.091
41_K188_N0.641071.090
238_R241_E0.638341.086
144_I168_I0.637381.084
32_K35_A0.63611.082
25_P29_E0.634251.079
134_A137_R0.629361.070
130_D156_K0.629281.070
136_A139_H0.619791.054
63_G66_D0.619591.054
95_D100_N0.616551.048
148_A170_S0.615961.047
106_L117_I0.61281.042
44_V193_A0.608391.035
43_A186_V0.608091.034
106_L135_I0.607831.034
35_A43_A0.607751.033
136_A140_G0.604431.028
61_G87_A0.598031.017
117_I141_I0.59711.015
111_T139_H0.596611.015
58_R199_L0.59491.012
31_E35_A0.590921.005
135_I141_I0.590441.004
249_N252_R0.585150.995
169_F186_V0.582150.990
70_V82_I0.58170.989
242_I245_R0.580690.987
49_G148_A0.577710.982
69_I92_V0.577610.982
69_I114_T0.575310.978
43_A48_S0.573850.976
242_I246_R0.570630.970
118_L144_I0.569740.969
110_I139_H0.56970.969
230_A234_A0.568880.967
92_V105_A0.567120.964
296_V308_P0.56440.960
57_L82_I0.558170.949
58_R85_A0.557610.948
110_I114_T0.556720.947
29_E32_K0.554660.943
228_Q232_G0.554410.943
95_D105_A0.549670.935
178_T181_E0.548990.934
54_H84_W0.547850.932
253_Y256_A0.545080.927
142_P165_D0.543020.923
88_E111_T0.534280.909
129_M145_E0.532950.906
55_L196_A0.532650.906
121_H129_M0.531370.904
80_S83_L0.530770.903
169_F184_A0.529690.901
135_I138_K0.525810.894
108_K112_P0.525730.894
76_P80_S0.522940.889
43_A184_A0.522070.888
222_F225_S0.521120.886
126_P160_V0.520460.885
33_E232_G0.520420.885
300_R305_E0.518850.882
107_E134_A0.518540.882
101_I106_L0.516560.878
241_E245_R0.514690.875
258_A265_P0.514570.875
193_A197_R0.51410.874
254_R265_P0.514040.874
126_P154_R0.512550.872
27_V31_E0.510240.868
179_T232_G0.510030.867
262_G285_P0.505220.859
53_L168_I0.503140.856
82_I89_P0.502860.855
226_E230_A0.499580.850
119_V143_L0.498790.848
103_P107_E0.498460.848
147_A150_A0.497730.846
234_A237_K0.491790.836
29_E233_L0.491070.835
253_Y257_L0.487170.828
228_Q231_I0.486590.827
58_R201_N0.486070.827
90_V111_T0.4860.826
249_N253_Y0.483410.822
52_A185_V0.47790.813
92_V101_I0.476950.811
103_P128_D0.476120.810
60_L166_I0.475550.809
260_I263_I0.474450.807
28_E31_E0.473770.806
34_F45_A0.469040.798
66_D87_A0.468490.797
60_L116_A0.46710.794
295_L298_A0.465590.792
37_Y151_F0.464880.791
295_L299_L0.464540.790
33_E37_Y0.464290.790
70_V91_F0.464290.790
57_L118_L0.463870.789
292_R308_P0.463450.788
276_S279_R0.462130.786
42_Y193_A0.461510.785
119_V129_M0.460980.784
238_R242_I0.459820.782
79_A91_F0.456830.777
191_E194_E0.456750.777
65_G88_E0.456280.776
166_I187_T0.454480.773
103_P106_L0.452560.770
246_R249_N0.45140.768
234_A238_R0.450230.766
65_G115_K0.446240.759
79_A83_L0.446220.759
73_Y127_A0.445970.758
117_I132_I0.444290.756
231_I234_A0.444140.755
55_L199_L0.443130.754
51_S200_R0.441290.750
131_A135_I0.440660.749
106_L110_I0.439560.747
63_G87_A0.438840.746
43_A46_V0.43790.745
69_I106_L0.437470.744
296_V300_R0.437190.743
179_T182_G0.436620.742
116_A142_P0.430570.732
54_H222_F0.430170.732
299_L304_I0.429470.730
254_R268_I0.428760.729
122_L149_Q0.427650.727
133_R136_A0.426770.726
166_I192_L0.425180.723
30_F45_A0.42280.719
194_E198_A0.419560.713
69_I117_I0.41940.713
158_R162_S0.416720.709
284_L295_L0.412690.702
157_G162_S0.41240.701
133_R165_D0.412240.701
39_G161_G0.410760.699
278_Y281_P0.40840.694
34_F43_A0.408070.694
251_Q254_R0.406610.691
164_G167_A0.406550.691
112_P139_H0.404810.688
56_A168_I0.404420.688
137_R140_G0.40420.687
39_G157_G0.403670.686
34_F151_F0.4030.685
132_I143_L0.402930.685
31_E45_A0.400660.681
115_K142_P0.397840.677
46_V185_V0.397380.676
224_M229_A0.396730.675
54_H81_A0.396240.674
114_T141_I0.394820.671
166_I185_V0.391270.665
59_A196_A0.391260.665
70_V89_P0.390080.663
43_A49_G0.389970.663
98_T268_I0.388640.661
142_P192_L0.388370.660
227_L231_I0.388120.660
80_S202_H0.387570.659
36_E40_V0.387530.659
188_N191_E0.385880.656
100_N127_A0.385210.655
36_E234_A0.383580.652
68_V116_A0.382930.651
166_I170_S0.378380.643
69_I90_V0.375320.638
71_P92_V0.374240.636
224_M227_L0.373140.635
155_Y240_D0.373130.635
70_V79_A0.372810.634
133_R163_F0.372010.633
175_K178_T0.370270.630
176_I243_I0.370080.629
35_A38_F0.369930.629
137_R143_L0.368710.627
49_G53_L0.368610.627
121_H164_G0.366310.623
63_G115_K0.364920.621
30_F34_F0.364380.620
36_E39_G0.363890.619
83_L89_P0.36380.619
227_L230_A0.362920.617
77_A81_A0.360870.614
133_R164_G0.360570.613
151_F176_I0.358250.609
121_H147_A0.35790.609
130_D155_Y0.3560.605
38_F184_A0.354370.603
127_A132_I0.353050.600
231_I235_Q0.352660.600
226_E232_G0.352510.599
149_Q175_K0.351320.597
30_F33_E0.351040.597
71_P119_V0.349720.595
221_N226_E0.348040.592
42_Y188_N0.34240.582
62_L66_D0.341610.581
56_A185_V0.34050.579
60_L144_I0.337660.574
292_R310_Y0.337330.574
87_A115_K0.337250.574
266_P281_P0.336910.573
92_V106_L0.335810.571
247_R250_A0.335360.570
44_V196_A0.335320.570
187_T190_P0.335070.570
129_M143_L0.334820.569
90_V114_T0.334720.569
239_L243_I0.334680.569
81_A85_A0.334140.568
239_L242_I0.333740.568
29_E228_Q0.332630.566
187_T196_A0.332220.565
50_T77_A0.330890.563
223_R226_E0.330690.562
103_P132_I0.330210.562
129_M133_R0.329680.561
145_E167_A0.329370.560
93_D109_A0.328870.559
50_T54_H0.327350.557
35_A40_V0.327040.556
176_I278_Y0.325030.553
38_F151_F0.324350.552
221_N224_M0.323950.551
30_F232_G0.323790.551
160_V163_F0.32350.550
54_H202_H0.322470.548
37_Y150_A0.321860.547
108_K111_T0.318650.542
293_D296_V0.317020.539
224_M228_Q0.31630.538
223_R227_L0.316240.538
49_G52_A0.315030.536
201_N204_R0.314630.535
100_N125_N0.314220.534
232_G235_Q0.31420.534
251_Q268_I0.312620.532
102_D131_A0.311840.530
83_L91_F0.311450.530
155_Y243_I0.310690.528
264_K282_I0.309960.527
101_I127_A0.309870.527
109_A114_T0.308840.525
33_E234_A0.308810.525
58_R84_W0.308680.525
293_D308_P0.307050.522
70_V74_T0.306730.522
52_A170_S0.306720.522
53_L118_L0.305690.520
121_H145_E0.304080.517
78_T81_A0.302950.515
101_I128_D0.302030.514
56_A60_L0.301280.512
224_M230_A0.300880.512
62_L85_A0.300630.511
34_F169_F0.300560.511
27_V45_A0.300390.511
38_F43_A0.30.510
187_T192_L0.299390.509
165_D175_K0.299320.509
78_T120_V0.299110.509
26_Y30_F0.298730.508
99_L283_R0.296830.505
167_A186_V0.296360.504
40_V186_V0.296350.504
31_E43_A0.295790.503
237_K241_E0.295620.503
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
3ju7A0.96691000.185
3frkA0.96141000.201
3nytA0.95321000.203
3dr4A0.97521000.21
3uwcA0.95871000.246
3b8xA0.98621000.248
2c81A0.99171000.248
1b9hA0.9891000.25
3bb8A0.99451000.25
1mdoA0.98071000.264

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