GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Aminotran_3 - Aminotransferase class-III
Pfam: PF00202 (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: 339
Sequences: 28223
Seq/Len: 83.25
HH_delta: 0.157 (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
42_A46_N3.206744.768
204_R208_R2.370963.525
67_K291_E2.077173.089
301_R305_L1.935252.878
39_E43_E1.834392.728
38_A42_A1.729572.572
288_A291_E1.704982.535
259_G264_M1.625122.416
297_D300_E1.623222.414
307_E311_E1.612352.397
82_A88_A1.557692.316
35_P39_E1.527962.272
202_E205_E1.498282.228
78_R261_E1.480372.201
110_K146_V1.468612.184
197_P201_R1.422712.115
310_R314_R1.419442.111
36_E292_I1.413972.102
36_E295_E1.344752.000
205_E209_E1.335221.985
312_G315_E1.333261.982
67_K287_L1.320261.963
228_K234_H1.310811.949
34_H292_I1.299721.933
308_R312_G1.299421.932
39_E42_A1.294471.925
36_E288_A1.291681.921
167_E209_E1.290751.919
67_K294_E1.28631.913
201_R205_E1.28291.908
66_E70_E1.281551.906
63_E287_L1.279741.903
115_E149_P1.225251.822
110_K177_E1.203051.789
198_E201_R1.193021.774
41_I285_A1.190871.771
153_P202_E1.162621.729
40_A288_A1.15731.721
305_L308_R1.141331.697
303_R307_E1.138771.693
43_E47_K1.121491.668
207_C214_L1.111091.652
206_L210_H1.1091.649
110_K144_G1.097771.632
254_I286_A1.096631.631
79_V258_L1.094281.627
207_C212_I1.089561.620
167_E171_A1.081881.609
168_E172_A1.077771.603
62_A66_E1.072321.594
63_E291_E1.067371.587
204_R214_L1.0651.584
287_L291_E1.059651.576
311_E315_E1.059321.575
38_A46_N1.056991.572
77_D261_E1.054291.568
67_K70_E1.050591.562
41_I45_A1.034071.538
300_E304_E1.032761.536
59_P63_E1.027791.528
196_P199_Y1.008681.500
304_E308_R1.006611.497
90_E94_K0.997851.484
167_E202_E0.987791.469
43_E288_A0.949071.411
261_E265_E0.948241.410
82_A255_S0.940321.398
180_A215_I0.936831.393
92_A215_I0.927231.379
301_R304_E0.923321.373
36_E39_E0.923231.373
198_E202_E0.908881.351
64_L286_A0.904411.345
288_A292_I0.902321.342
115_E147_F0.901081.340
311_E314_R0.889761.323
38_A45_A0.873981.300
183_V203_L0.868611.292
204_R207_C0.866961.289
300_E303_R0.859771.278
170_I209_E0.850361.264
149_P155_A0.8451.256
279_N282_S0.843741.255
306_G310_R0.841871.252
292_I296_E0.839121.248
308_R311_E0.83241.238
89_V243_T0.826621.229
151_P199_Y0.806071.199
82_A257_V0.804861.197
302_V306_G0.80291.194
40_A43_E0.797231.185
83_N87_E0.792431.178
244_F256_A0.774241.151
114_F199_Y0.770661.146
205_E208_R0.765941.139
43_E46_N0.76241.134
309_L312_G0.761941.133
109_R177_E0.756251.124
257_V267_F0.752471.119
233_E236_G0.749931.115
35_P38_A0.748961.114
70_E294_E0.74791.112
110_K178_I0.742361.104
33_N38_A0.740711.101
183_V200_L0.737341.096
72_F258_L0.734911.093
97_R143_P0.733481.091
167_E210_H0.730421.086
39_E46_N0.730161.086
206_L212_I0.730121.086
181_V212_I0.729431.085
68_L256_A0.729281.084
312_G316_L0.728651.083
187_Q190_G0.726831.081
112_L178_I0.725961.079
185_P188_G0.724541.077
69_A79_V0.722721.075
63_E66_E0.72221.074
181_V207_C0.720621.072
42_A45_A0.719611.070
166_L203_L0.715381.064
67_K71_L0.715281.064
58_H62_A0.704351.047
170_I173_L0.701661.043
292_I295_E0.690331.026
213_L263_I0.689391.025
113_A147_F0.687811.023
41_I281_L0.686191.020
228_K303_R0.68471.018
182_I215_I0.683421.016
208_R238_D0.681281.013
229_F233_E0.679391.010
152_D155_A0.675951.005
75_G261_E0.669080.995
151_P154_A0.66720.992
40_A44_Q0.664380.988
61_A65_A0.661850.984
199_Y202_E0.651810.969
265_E269_P0.650860.968
111_I180_A0.647670.963
305_L309_L0.646340.961
202_E206_L0.640.952
85_G219_V0.63880.950
59_P287_L0.635930.946
63_E67_K0.635350.945
284_A287_L0.634420.943
306_G309_L0.6330.941
96_A213_L0.632850.941
299_L303_R0.632610.941
304_E307_E0.625920.931
78_R265_E0.623570.927
78_R264_M0.620860.923
65_A76_L0.620850.923
298_L301_R0.619550.921
252_L282_S0.615230.915
171_A210_H0.61430.913
138_F143_P0.61380.913
151_P196_P0.610520.908
284_A288_A0.610250.907
175_A178_I0.610130.907
65_A81_F0.60930.906
201_R237_V0.607570.903
174_N177_E0.607550.903
208_R240_D0.601550.894
302_V305_L0.597750.889
64_L81_F0.595930.886
112_L148_V0.595010.885
216_A232_S0.586910.873
148_V169_L0.584060.868
113_A145_V0.583790.868
169_L172_A0.582490.866
149_P152_D0.581740.865
238_D260_S0.580830.864
93_L97_R0.579270.861
95_L267_F0.579050.861
174_N178_I0.578530.860
66_E69_A0.570440.848
109_R144_G0.569010.846
110_K175_A0.568620.846
271_S275_T0.566410.842
244_F258_L0.564590.840
188_G191_G0.561270.835
91_A257_V0.561020.834
198_E235_Y0.557920.830
203_L214_L0.557890.830
58_H61_A0.557610.829
64_L287_L0.5570.828
169_L173_L0.555750.826
249_G254_I0.552230.821
35_P46_N0.546870.813
298_L302_V0.546570.813
81_F283_C0.546150.812
71_L229_F0.545940.812
37_I289_T0.542960.807
80_F264_M0.54040.804
110_K113_A0.539990.803
206_L209_E0.539720.803
167_E206_L0.539630.802
235_Y238_D0.537750.800
186_I189_E0.535610.796
307_E310_R0.534870.795
55_G61_A0.534430.795
71_L294_E0.532110.791
65_A79_V0.530020.788
87_E275_T0.526870.783
106_T109_R0.525640.782
232_S237_V0.524090.779
218_E221_T0.522610.777
250_G289_T0.521090.775
297_D301_R0.519570.773
88_A257_V0.519260.772
201_R236_G0.518350.771
195_P202_E0.516760.768
167_E205_E0.515630.767
168_E171_A0.514540.765
57_T284_A0.513940.764
183_V187_Q0.513820.764
89_V182_I0.513230.763
83_N279_N0.512810.763
228_K233_E0.512070.761
76_L258_L0.511780.761
110_K174_N0.509830.758
242_V256_A0.507650.755
109_R179_A0.507310.754
36_E40_A0.507240.754
285_A288_A0.506970.754
254_I283_C0.506640.753
75_G78_R0.505250.751
64_L256_A0.505180.751
262_E265_E0.500390.744
296_E300_E0.495210.736
293_L299_L0.493520.734
62_A76_L0.491920.731
266_A269_P0.489290.728
68_L258_L0.48910.727
199_Y203_L0.486240.723
140_P143_P0.485810.722
207_C210_H0.484890.721
181_V203_L0.481280.716
211_G240_D0.48080.715
93_L111_I0.480130.714
260_S263_I0.478780.712
34_H296_E0.477440.710
188_G220_Q0.476910.709
254_I278_G0.476350.708
195_P199_Y0.475950.708
170_I210_H0.474990.706
155_A169_L0.474850.706
259_G263_I0.473540.704
201_R235_Y0.470860.700
216_A237_V0.469240.698
37_I285_A0.468540.697
283_C287_L0.467580.695
265_E268_Q0.466830.694
114_F148_V0.466690.694
195_P200_L0.466460.694
233_E238_D0.466280.693
224_G227_G0.466280.693
84_S87_E0.465550.692
309_L313_L0.46450.691
274_S277_G0.463820.690
94_K270_G0.46220.687
108_R177_E0.462090.687
178_I212_I0.460340.684
245_G255_S0.458960.682
79_V256_A0.457850.681
40_A285_A0.457680.681
296_E299_L0.454380.676
66_E291_E0.453620.675
232_S242_V0.453420.674
44_Q284_A0.452620.673
86_S120_G0.451980.672
291_E295_E0.451830.672
273_G276_F0.45140.671
30_L289_T0.449380.668
60_E63_E0.448510.667
140_P144_G0.447820.666
204_R237_V0.446990.665
44_Q47_K0.446950.665
219_V243_T0.444670.661
195_P198_E0.444040.660
299_L302_V0.443880.660
95_L270_G0.441570.657
150_F195_P0.441280.656
60_E287_L0.440360.655
184_E188_G0.440320.655
71_L290_L0.43860.652
60_E283_C0.436560.649
201_R234_H0.435860.648
280_P284_A0.435340.647
96_A180_A0.434050.645
230_F244_F0.432960.644
183_V214_L0.43250.643
223_F248_L0.429390.638
44_Q285_A0.429010.638
236_G240_D0.428910.638
197_P235_Y0.425380.633
200_L216_A0.424790.632
248_L256_A0.424670.631
89_V215_I0.424640.631
97_R111_I0.424080.631
30_L292_I0.423250.629
185_P200_L0.422950.629
179_A215_I0.422840.629
84_S253_P0.421370.627
59_P62_A0.420940.626
62_A65_A0.420770.626
28_V31_G0.420740.626
37_I288_A0.417740.621
93_L182_I0.416920.620
223_F293_L0.41630.619
303_R306_G0.415870.618
236_G239_P0.415750.618
171_A212_I0.41560.618
36_E291_E0.415570.618
84_S255_S0.414420.616
264_M268_Q0.414070.616
49_N252_L0.41250.613
60_E64_L0.412030.613
64_L283_C0.410420.610
148_V155_A0.409390.609
82_A91_A0.409310.609
179_A183_V0.409280.609
170_I206_L0.408990.608
138_F141_L0.408510.607
138_F142_Y0.407810.606
171_A174_N0.407010.605
185_P216_A0.406620.605
92_A242_V0.406320.604
233_E237_V0.405630.603
197_P234_H0.404860.602
244_F286_A0.404760.602
268_Q271_S0.404150.601
80_F267_F0.402420.598
61_A283_C0.40230.598
114_F150_F0.401630.597
55_G268_Q0.398790.593
208_R239_P0.398410.592
114_F195_P0.396910.590
93_L138_F0.396890.590
69_A72_F0.39630.589
47_K284_A0.394320.586
71_L222_G0.392320.583
245_G276_F0.391880.583
114_F203_L0.391170.582
80_F257_V0.391050.581
37_I250_G0.390160.580
70_E291_E0.389990.580
113_A182_I0.389920.580
82_A271_S0.389430.579
67_K290_L0.38780.577
65_A69_A0.387230.576
28_V250_G0.386890.575
231_A235_Y0.385470.573
262_E266_A0.38510.573
293_L298_L0.384030.571
232_S235_Y0.383890.571
224_G299_L0.382750.569
203_L207_C0.381590.567
153_P199_Y0.378760.563
40_A291_E0.378630.563
139_G144_G0.377760.562
51_V56_F0.377250.561
272_H276_F0.37670.560
69_A76_L0.375470.558
112_L169_L0.373090.555
275_T278_G0.371960.553
90_E274_S0.371850.553
110_K176_D0.370090.550
183_V216_A0.369810.550
234_H237_V0.367750.547
167_E170_I0.36730.546
234_H303_R0.36670.545
203_L212_I0.366510.545
52_S57_T0.366170.544
155_A168_E0.363840.541
251_G254_I0.362560.539
96_A215_I0.362280.539
92_A267_F0.361690.538
59_P291_E0.36150.538
208_R237_V0.361430.537
200_L235_Y0.361020.537
94_K141_L0.360950.537
282_S285_A0.360260.536
45_A285_A0.360240.536
146_V169_L0.359840.535
58_H76_L0.35950.535
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
4ffcA0.98231000.157
4a6rA11000.159
3i5tA0.99711000.16
3gjuA11000.16
4atqA0.98231000.16
3hmuA0.99411000.166
3oksA0.98231000.167
3dodA0.99411000.171
3i4jA0.99411000.173
3n5mA0.99121000.189

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