GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Aminotran_4 - Aminotransferase class IV
Pfam: PF01063 (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. )
Length: 231
Sequences: 4660
Seq/Len: 20.17
HH_delta: 0.107 (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
152_T183_E1.076913.994
153_L175_A0.938883.482
185_R191_D0.925513.433
8_E24_R0.87873.259
11_R24_R0.767652.847
152_T181_P0.739292.742
164_P169_Q0.726532.695
33_E37_A0.68522.541
140_G143_S0.676912.511
154_Y185_R0.634872.355
144_N165_G0.615942.285
23_S26_E0.612732.273
5_E169_Q0.608532.257
29_E33_E0.607242.252
136_N186_P0.585172.170
14_A50_V0.573392.127
178_L226_R0.568332.108
10_L50_V0.560052.077
169_Q173_E0.546712.028
178_L230_A0.542782.013
149_K196_D0.520881.932
33_E36_E0.515961.914
172_L182_V0.515761.913
4_D28_R0.513761.906
198_V210_V0.511821.898
15_R21_P0.507771.883
225_R229_E0.505841.876
146_F201_T0.500231.855
2_F170_L0.485071.799
8_E12_R0.46561.727
5_E173_E0.442591.642
153_L180_I0.439311.629
3_L7_L0.428011.588
226_R230_A0.426351.581
155_T168_R0.425781.579
168_R184_E0.419241.555
109_R113_V0.413811.535
148_V223_I0.412891.531
146_F199_F0.412281.529
145_I198_V0.410821.524
110_L113_V0.402481.493
171_L201_T0.39711.473
173_E177_E0.396131.469
28_R32_Q0.395861.468
140_G200_L0.394341.463
13_S104_H0.393991.461
12_R15_R0.392191.455
136_N188_T0.38771.438
147_F195_A0.381221.414
132_D136_N0.377631.401
187_I191_D0.376541.397
147_F187_I0.369661.371
4_D8_E0.368181.366
154_Y183_E0.367271.362
119_A123_K0.367091.362
89_R212_S0.365371.355
198_V213_I0.361721.342
127_E140_G0.359091.332
29_E32_Q0.355361.318
12_R164_P0.351341.303
147_F198_V0.350571.300
25_E29_E0.349581.297
3_L28_R0.344051.276
132_D161_G0.343281.273
30_I67_P0.342621.271
221_G224_T0.333771.238
148_V197_E0.330531.226
41_Q44_G0.330071.224
168_R172_L0.32681.212
197_E221_G0.324421.203
154_Y187_I0.323921.201
49_T107_T0.322951.198
147_F154_Y0.321011.191
226_R229_E0.316891.175
202_N205_R0.314641.167
157_P186_P0.312421.159
5_E8_E0.310161.150
146_F155_T0.311.150
129_L145_I0.307891.142
127_E141_S0.306221.136
7_L28_R0.303821.127
148_V153_L0.302961.124
84_G87_G0.301871.120
19_G50_V0.301731.119
137_V147_F0.301371.118
200_L210_V0.30111.117
2_F5_E0.300291.114
188_T191_D0.300111.113
197_E224_T0.298851.108
11_R20_L0.298741.108
109_R112_N0.29781.105
5_E166_I0.296521.100
32_Q36_E0.293841.090
176_K181_P0.293411.088
127_E143_S0.291441.081
180_I223_I0.29091.079
175_A180_I0.289851.075
157_P185_R0.289251.073
195_A198_V0.287731.067
160_S186_P0.286581.063
153_L199_F0.28261.048
11_R15_R0.282581.048
146_F172_L0.280611.041
125_A214_D0.279511.037
72_I76_R0.277161.028
31_I46_I0.276921.027
110_L114_L0.276211.024
5_E170_L0.275281.021
165_G168_R0.275031.020
7_L27_L0.271371.007
7_L31_I0.271031.005
51_T107_T0.270031.002
149_K194_Q0.268820.997
8_E11_R0.26810.994
134_D186_P0.266870.990
146_F168_R0.266360.988
111_A114_L0.265830.986
71_S74_P0.26570.986
149_K154_Y0.265380.984
156_P187_I0.262940.975
138_T162_I0.262330.973
158_L168_R0.261330.969
131_L189_L0.261190.969
108_N113_V0.260770.967
177_E230_A0.260340.966
26_E29_E0.259160.961
176_K184_E0.258970.961
131_L137_V0.258680.959
4_D25_E0.257160.954
193_Q216_R0.256860.953
73_A76_R0.25620.950
167_T203_S0.254850.945
29_E36_E0.253520.940
175_A227_L0.253190.939
151_G181_P0.2530.938
173_E176_K0.251560.933
212_S215_G0.24960.926
157_P184_E0.248880.923
16_A104_H0.248720.923
118_R122_E0.247460.918
89_R92_S0.247410.918
119_A122_E0.247270.917
71_S75_P0.246150.913
34_L38_N0.244420.907
190_D194_Q0.242470.899
91_A94_P0.242170.898
225_R228_Q0.241440.896
14_A20_L0.240770.893
212_S219_G0.239730.889
7_L11_R0.23970.889
144_N201_T0.2380.883
3_L31_I0.237310.880
212_S217_S0.236970.879
222_P226_R0.235990.875
16_A103_R0.235490.873
92_S95_L0.232860.864
120_A124_G0.232220.861
180_I226_R0.231460.859
123_K214_D0.230590.855
117_L121_R0.230580.855
34_L37_A0.227950.845
205_R208_R0.227070.842
91_A95_L0.226180.839
1_F170_L0.224580.833
165_G201_T0.224550.833
149_K195_A0.223850.830
19_G65_S0.223330.828
45_Y204_L0.222880.827
24_R28_R0.221450.821
12_R16_A0.221330.821
80_P85_S0.221280.821
192_L198_V0.221070.820
175_A182_V0.220820.819
174_L178_L0.220060.816
80_P84_G0.219480.814
129_L192_L0.21870.811
222_P225_R0.217140.805
25_E28_R0.216650.804
4_D24_R0.216370.803
69_P72_I0.214610.796
143_S200_L0.214560.796
151_G180_I0.21390.793
87_G90_R0.211190.783
11_R27_L0.211080.783
158_L184_E0.211040.783
135_G190_D0.210510.781
7_L24_R0.209930.779
9_R163_L0.209520.777
155_T184_E0.209280.776
116_A128_A0.208890.775
83_V123_K0.208580.774
155_T172_L0.208480.773
116_A119_A0.208420.773
22_F30_I0.206990.768
215_G218_F0.205820.763
129_L198_V0.205460.762
11_R21_P0.205140.761
71_S76_R0.204870.760
8_E169_Q0.204660.759
172_L184_E0.204470.758
35_L44_G0.201340.747
105_K139_E0.20110.746
2_F166_I0.199930.742
174_L230_A0.199480.740
12_R103_R0.199460.740
148_V151_G0.198380.736
197_E209_P0.196860.730
221_G225_R0.196360.728
145_I156_P0.195240.724
136_N160_S0.193710.718
22_F26_E0.193690.718
60_S63_E0.192670.715
80_P83_V0.192180.713
87_G91_A0.191850.712
171_L207_I0.191070.709
17_L104_H0.190920.708
120_A123_K0.190140.705
116_A130_L0.189460.703
44_G75_P0.189340.702
126_D208_R0.188820.700
171_L227_L0.188490.699
135_G189_L0.188250.698
81_P212_S0.185720.689
45_Y48_I0.185490.688
47_R107_T0.185430.688
90_R95_L0.185090.687
87_G92_S0.184880.686
76_R79_P0.184350.684
139_E163_L0.184050.683
150_D196_D0.182110.675
30_I33_E0.182040.675
148_V221_G0.181830.674
34_L71_S0.180560.670
144_N168_R0.180090.668
69_P73_A0.178710.663
140_G146_F0.178340.661
148_V199_F0.177930.660
214_D217_S0.177740.659
58_G61_P0.17770.659
193_Q196_D0.177670.659
167_T201_T0.176470.655
130_L162_I0.176380.654
149_K191_D0.17620.654
26_E30_I0.17540.651
159_D186_P0.175320.650
151_G196_D0.175050.649
107_T111_A0.174890.649
174_L227_L0.174380.647
102_P138_T0.174080.646
189_L192_L0.1740.645
82_L94_P0.173810.645
187_I195_A0.173810.645
154_Y191_D0.173390.643
199_F224_T0.173030.642
199_F207_I0.172840.641
189_L193_Q0.172420.640
126_D142_T0.172280.639
164_P184_E0.171510.636
193_Q214_D0.171270.635
30_I71_S0.171170.635
117_L142_T0.171140.635
47_R61_P0.170590.633
148_V224_T0.170440.632
156_P162_I0.170010.631
116_A141_S0.169910.630
142_T205_R0.169540.629
167_T202_N0.1690.627
120_A125_A0.16890.626
70_F73_A0.168510.625
15_R19_G0.168090.623
105_K163_L0.167860.623
175_A178_L0.166340.617
218_F221_G0.166240.617
155_T158_L0.166210.616
188_T195_A0.166010.616
166_I170_L0.165690.615
144_N155_T0.165490.614
155_T165_G0.165120.612
9_R105_K0.164570.610
146_F171_L0.164490.610
108_N112_N0.164450.610
49_T68_P0.164150.609
172_L176_K0.164130.609
192_L213_I0.163540.607
78_P81_P0.162920.604
2_F167_T0.162060.601
128_A141_S0.162030.601
207_I227_L0.162020.601
73_A77_R0.161960.601
87_G94_P0.161920.601
59_G109_R0.161270.598
79_P82_L0.161020.597
11_R22_F0.160950.597
214_D218_F0.160380.595
106_T110_L0.159980.593
117_L141_S0.159920.593
167_T199_F0.159780.593
72_I75_P0.159540.592
201_T207_I0.159180.590
63_E66_A0.159090.590
88_V92_S0.1590.590
137_V145_I0.158970.590
10_L22_F0.158660.588
101_L104_H0.157680.585
176_K182_V0.157670.585
36_E39_P0.1570.582
9_R139_E0.156960.582
120_A128_A0.156580.581
85_S91_A0.155630.577
106_T112_N0.155330.576
174_L177_E0.1550.575
55_G58_G0.154690.574
135_G188_T0.154480.573
170_L174_L0.154470.573
179_G226_R0.154350.572
47_R59_G0.154140.572
123_K215_G0.154070.571
148_V180_I0.153840.571
32_Q35_L0.153820.571
224_T228_Q0.153490.569
224_T227_L0.153440.569
1_F203_S0.1530.567
60_S64_N0.152870.567
11_R14_A0.15280.567
12_R169_Q0.15260.566
71_S77_R0.152420.565
223_I226_R0.15190.563
45_Y57_L0.151080.560
57_L61_P0.151010.560
137_V210_V0.150510.558
131_L138_T0.150010.556
137_V191_D0.149470.554
223_I230_A0.149440.554
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
2xpfA0.97841000.107
1i2kA0.97841000.113
3daaA0.9741000.121
1iyeA0.9871000.122
3u0gA0.97841000.124
3lulA0.94811000.125
2eiyA0.98271000.132
3snoA0.95241000.134
4jxuA0.98271000.137
4dqnA0.97841000.145

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