GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Amidohydro_2 - Amidohydrolase
Pfam: PF04909 (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: CL0034
Length: 273
Sequences: 3760
Seq/Len: 13.77
HH_delta: 0.244 (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
260_E265_D0.795014.183
255_S258_E0.77984.103
225_D261_K0.779664.102
119_D161_R0.749533.944
127_E164_D0.639523.365
89_E92_R0.616413.243
91_E125_A0.597933.146
125_A128_E0.56952.996
94_L131_L0.52862.781
59_D92_R0.506462.665
74_G99_F0.466852.456
264_Y268_R0.463312.438
216_R220_D0.461622.429
75_F101_G0.414482.181
224_P258_E0.410752.161
261_K265_D0.400512.107
124_E128_E0.400332.106
119_D162_F0.396542.086
136_H232_D0.396382.085
228_L266_N0.393312.069
224_P261_K0.382182.011
127_E162_F0.379541.997
130_G272_G0.3751.973
90_L122_I0.374321.969
130_G166_R0.373151.963
88_E91_E0.345431.817
124_E162_F0.342941.804
63_E67_K0.33961.787
91_E128_E0.339421.786
121_P124_E0.336161.769
261_K269_R0.333971.757
260_E264_Y0.325771.714
159_L167_I0.325261.711
125_A129_L0.324241.706
258_E261_K0.318821.677
92_R96_E0.311771.640
102_V126_A0.309521.628
168_I270_L0.307751.619
76_A93_A0.304251.601
228_L270_L0.301061.584
256_E259_R0.297591.566
126_A133_V0.29681.562
91_E129_L0.295391.554
94_L129_L0.292881.541
157_E160_E0.290391.528
261_K266_N0.277651.461
219_V258_E0.275821.451
217_R221_E0.272411.433
119_D124_E0.270341.422
87_V125_A0.270161.421
256_E260_E0.269291.417
166_R269_R0.26651.402
65_A74_G0.26371.387
265_D269_R0.262751.382
170_A195_D0.260531.371
166_R270_L0.260331.370
92_R97_L0.25621.348
75_F271_Y0.255921.346
225_D269_R0.255411.344
60_W63_E0.253461.334
127_E130_G0.250051.316
226_R269_R0.245021.289
264_Y267_A0.241731.272
257_E261_K0.241381.270
85_D88_E0.240971.268
111_F117_R0.234951.236
55_R59_D0.23481.235
124_E127_E0.228161.200
217_R220_D0.226821.193
265_D268_R0.225671.187
123_F158_L0.225441.186
62_V97_L0.224191.180
132_P270_L0.223831.178
90_L129_L0.22371.177
127_E165_L0.22341.175
62_V99_F0.223351.175
73_I100_R0.222011.168
255_S259_R0.221111.163
268_R272_G0.219631.156
90_L126_A0.218291.149
130_G164_D0.217791.146
193_Y270_L0.217191.143
65_A99_F0.21691.141
62_V66_A0.216761.140
224_P262_I0.216031.137
193_Y269_R0.21351.123
123_F162_F0.2121.115
87_V91_E0.211971.115
219_V224_P0.21041.107
172_L218_A0.207431.091
168_I228_L0.207291.091
55_R89_E0.204211.074
83_P87_V0.202571.066
193_Y226_R0.202341.065
76_A99_F0.20231.064
103_K170_A0.201181.058
212_R216_R0.199921.052
63_E66_A0.197471.039
101_G134_L0.196141.032
171_H232_D0.196061.032
134_L170_A0.195651.029
157_E161_R0.190191.001
132_P168_I0.187950.989
90_L102_V0.187160.985
39_M44_V0.186960.984
259_R263_L0.184190.969
78_I86_A0.183370.965
243_E246_W0.182010.958
156_E185_L0.181450.955
266_N269_R0.181170.953
168_I271_Y0.181120.953
33_E36_L0.180980.952
93_A97_L0.18080.951
87_V121_P0.180530.950
184_R187_D0.180510.950
223_G258_E0.176040.926
31_S34_D0.175750.925
257_E265_D0.175270.922
166_R226_R0.174630.919
243_E247_E0.173020.910
114_D157_E0.171320.901
170_A230_G0.171220.901
78_I122_I0.170860.899
123_F133_V0.170530.897
59_D89_E0.169930.894
32_P36_L0.169610.892
89_E93_A0.169260.891
84_E88_E0.1690.889
78_I102_V0.168820.888
116_P119_D0.168690.888
103_K195_D0.1680.884
241_P244_Y0.167920.883
59_D63_E0.166180.874
93_A99_F0.165320.870
242_Y246_W0.163250.859
61_L74_G0.163190.859
180_E183_L0.162150.853
220_D255_S0.161570.850
90_L94_L0.161040.847
123_F165_L0.160970.847
83_P86_A0.16060.845
180_E184_R0.159920.841
178_W181_E0.159290.838
104_L133_V0.15880.836
90_L125_A0.158740.835
214_F217_R0.158420.834
156_E188_R0.15690.826
214_F218_A0.156810.825
103_K134_L0.156130.821
181_E184_R0.155730.819
26_D264_Y0.155030.816
58_N89_E0.154530.813
228_L267_A0.153020.805
150_A169_L0.152770.804
178_W182_A0.152390.802
229_F245_I0.151960.800
219_V227_I0.150970.794
134_L271_Y0.150180.790
194_V197_S0.150150.790
34_D37_V0.149760.788
27_R73_I0.1490.784
73_I271_Y0.148880.783
171_H235_H0.148320.780
102_V133_V0.148240.780
169_L182_A0.147780.778
64_L68_H0.145790.767
190_P193_Y0.145470.765
30_A34_D0.144320.759
237_D241_P0.143690.756
121_P125_A0.143310.754
122_I126_A0.143260.754
90_L131_L0.142510.750
126_A165_L0.142430.749
29_L35_L0.142170.748
111_F118_L0.141390.744
219_V223_G0.140980.742
159_L192_V0.139980.736
52_A55_R0.139630.735
134_L197_S0.139190.732
46_G49_E0.138870.731
36_L68_H0.138380.728
51_Q85_D0.138020.726
194_V218_A0.137130.721
59_D62_V0.136950.721
155_L169_L0.136770.720
102_V131_L0.136750.719
59_D97_L0.136190.717
69_P72_F0.13590.715
267_A271_Y0.135350.712
51_Q55_R0.134540.708
160_E188_R0.134290.707
229_F263_L0.13370.703
75_F134_L0.133510.702
156_E184_R0.132780.699
266_N270_L0.13210.695
76_A80_P0.131620.692
169_L174_G0.131350.691
122_I133_V0.130110.685
160_E184_R0.12960.682
106_P113_P0.129390.681
33_E37_V0.129250.680
44_V48_D0.129230.680
94_L125_A0.128950.678
132_P165_L0.128860.678
59_D96_E0.128750.677
220_D258_E0.128710.677
242_Y245_I0.127990.673
88_E92_R0.127150.669
112_D148_D0.127150.669
88_E125_A0.127150.669
30_A72_F0.126250.664
39_M47_A0.126210.664
66_A98_G0.126170.664
132_P166_R0.125780.662
68_H72_F0.125770.662
103_K171_H0.125480.660
181_E185_L0.125290.659
62_V76_A0.125040.658
60_W64_L0.124520.655
105_H134_L0.124240.654
119_D123_F0.124210.654
127_E163_P0.124150.653
181_E190_P0.123410.649
118_L123_F0.123380.649
134_L195_D0.123070.648
261_K264_Y0.123040.647
82_D85_D0.122960.647
186_L194_V0.122850.646
150_A178_W0.122590.645
156_E160_E0.122340.644
26_D29_L0.122050.642
193_Y266_N0.121940.642
106_P111_F0.121260.638
170_A232_D0.12070.635
55_R92_R0.120140.632
216_R249_Y0.12010.632
103_K232_D0.119940.631
103_K152_P0.119450.628
192_V198_G0.119440.628
196_L227_I0.119350.628
213_P220_D0.11920.627
28_Q34_D0.119120.627
258_E262_I0.119040.626
27_R30_A0.11860.624
254_L258_E0.11850.623
191_N197_S0.117990.621
57_F77_A0.117980.621
84_E117_R0.117890.620
63_E97_L0.117520.618
196_L229_F0.117490.618
169_L270_L0.117210.617
58_N61_L0.1170.616
148_D213_P0.116950.615
219_V262_I0.116640.614
86_A122_I0.116620.614
153_E158_L0.11660.613
167_I191_N0.116380.612
219_V254_L0.11620.611
132_P271_Y0.116150.611
56_G59_D0.115520.608
168_I267_A0.115120.606
98_G128_E0.115080.605
191_N195_D0.115030.605
50_V53_S0.114680.603
148_D151_D0.114320.601
44_V47_A0.114320.601
153_E159_L0.113930.599
181_E269_R0.113810.599
47_A72_F0.113670.598
192_V196_L0.113660.598
220_D223_G0.113640.598
159_L191_N0.113230.596
75_F168_I0.112730.593
247_E250_F0.112630.593
96_E256_E0.112530.592
254_L259_R0.112010.589
180_E214_F0.11170.588
215_L219_V0.111670.588
87_V92_R0.111640.587
244_Y263_L0.111580.587
87_V128_E0.111580.587
99_F131_L0.111350.586
136_H174_G0.111170.585
121_P163_P0.109770.578
26_D30_A0.109490.576
35_L236_P0.109320.575
35_L39_M0.107870.568
210_F215_L0.10780.567
56_G61_L0.107680.567
179_W183_L0.107630.566
91_E94_L0.107310.565
36_L39_M0.106760.562
124_E129_L0.106720.561
104_L126_A0.106580.561
210_F230_G0.106540.561
153_E157_E0.106470.560
228_L271_Y0.106450.560
31_S171_H0.106320.559
171_H192_V0.105990.558
96_E164_D0.105480.555
103_K136_H0.105320.554
133_V236_P0.105290.554
74_G169_L0.105250.554
216_R258_E0.105180.553
35_L38_D0.104870.552
39_M71_R0.10480.551
48_D51_Q0.104660.551
67_K70_D0.104380.549
232_D235_H0.104370.549
198_G236_P0.104370.549
109_G112_D0.104040.547
115_D118_L0.103830.546
83_P89_E0.10350.545
114_D152_P0.103070.542
173_G234_P0.102980.542
244_Y247_E0.102970.542
213_P217_R0.102890.541
91_E96_E0.102870.541
230_G237_D0.102690.540
73_I76_A0.102580.540
255_S262_I0.102470.539
113_P123_F0.102450.539
94_L98_G0.102380.539
135_I199_I0.102320.538
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
3ij6A0.95241000.244
4do7A0.94141000.245
4d9aA0.91581000.254
3nurA0.94511000.257
3irsA0.94141000.267
4l5pA0.94511000.268
4infA0.94511000.27
2f6kA0.95971000.273
2dvtA0.94511000.279
2wm1A0.94871000.281

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