GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GATase_4 - Glutamine amidotransferases class-II
Pfam: PF13230 (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: CL0052
Length: 271
Sequences: 2744
Seq/Len: 10.13
HH_delta: 0.148 (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
184_A226_V0.887155.365
39_A46_P0.46882.835
52_P86_V0.465522.815
39_A104_L0.454252.747
249_R252_E0.451732.732
226_V248_F0.42672.580
140_Q161_E0.422742.557
39_A48_V0.409672.477
140_Q165_E0.409372.476
51_S88_L0.406992.461
5_L18_S0.402782.436
120_D165_E0.376482.277
154_E157_E0.370572.241
35_G91_C0.340092.057
133_A166_I0.329891.995
161_E164_K0.323921.959
120_D139_D0.322211.949
241_P244_S0.304521.842
183_F247_V0.286111.730
157_E160_R0.284831.722
248_F253_V0.279581.691
6_G182_L0.27641.672
35_G52_P0.273261.653
184_A246_L0.265781.607
181_R247_V0.263061.591
199_F232_T0.262641.588
8_S73_L0.261231.580
2_C108_N0.259341.568
140_Q143_D0.258571.564
246_L253_V0.257461.557
75_L106_A0.257251.556
133_A174_F0.24931.508
184_A238_E0.24021.453
227_A232_T0.237591.437
181_R249_R0.235761.426
73_L177_S0.234441.418
40_W47_R0.234321.417
159_L183_F0.233731.413
40_W74_F0.229481.388
41_Y73_L0.228841.384
163_A185_H0.22821.380
238_E244_S0.225951.366
126_G131_E0.225521.364
226_V246_L0.223781.353
240_V246_L0.223611.352
94_F128_T0.222751.347
230_P236_D0.220661.334
137_L162_L0.214181.295
9_S223_A0.212581.286
106_A175_L0.211981.282
136_L166_I0.210731.274
20_T61_L0.204481.237
49_F68_K0.203181.229
40_W71_S0.202121.222
224_V237_W0.201831.221
71_S74_F0.201591.219
57_N60_N0.200181.211
140_Q158_A0.197561.195
3_R78_V0.196611.189
83_Q110_T0.192041.161
158_A162_L0.19161.159
17_F20_T0.190611.153
118_L124_P0.190551.152
183_F245_L0.190331.151
107_H130_S0.189871.148
54_P58_S0.189761.148
94_F126_G0.189011.143
41_Y44_G0.188841.142
137_L159_L0.188151.138
160_R164_K0.187241.132
143_D161_E0.186621.129
137_L183_F0.183721.111
82_T110_T0.18091.094
105_F130_S0.177031.071
95_S102_R0.17671.069
89_E127_T0.176441.067
124_P135_C0.176441.067
224_V253_V0.17571.063
36_W78_V0.173831.051
4_L175_L0.173041.046
239_P246_L0.172591.044
116_D165_E0.17191.040
5_L225_V0.171561.038
42_D47_R0.17121.035
128_T131_E0.171151.035
22_F25_R0.17051.031
36_W53_R0.169831.027
3_R36_W0.169731.026
89_E125_V0.165030.998
42_D45_G0.164610.995
79_R82_T0.164220.993
162_L166_I0.163990.992
1_M4_L0.163770.990
175_L182_L0.163640.990
140_Q162_L0.163540.989
18_S225_V0.163360.988
114_F118_L0.163210.987
157_E161_E0.1620.980
48_V95_S0.161530.977
59_P62_R0.161410.976
88_L91_C0.161360.976
46_P104_L0.161030.974
122_Y142_R0.160860.973
35_G134_F0.157930.955
117_I166_I0.157730.954
111_I166_I0.157450.952
79_R108_N0.15580.942
77_H92_H0.155070.938
113_G117_I0.154010.931
90_N128_T0.153790.930
187_Y244_S0.153590.929
5_L76_A0.153160.926
6_G175_L0.152530.922
178_D181_R0.152470.922
40_W69_I0.152140.920
83_Q114_F0.1510.913
187_Y243_G0.150360.909
41_Y141_L0.150260.909
96_R126_G0.149930.907
141_L154_E0.149180.902
79_R84_G0.148160.896
161_E165_E0.148080.896
119_D123_Q0.147570.892
41_Y177_S0.146690.887
52_P91_C0.145910.882
4_L106_A0.145730.881
169_Y172_L0.145710.881
62_R251_G0.145270.879
120_D142_R0.144520.874
105_F134_F0.144150.872
219_P222_R0.143630.869
154_E160_R0.143550.868
95_S125_V0.14280.864
9_S13_T0.142530.862
18_S227_A0.142460.862
73_L182_L0.142280.860
81_A86_V0.142150.860
2_C79_R0.142110.859
76_A229_E0.141560.856
141_L158_A0.141490.856
112_P167_N0.140750.851
2_C82_T0.14030.848
142_R164_K0.140170.848
15_I74_F0.140020.847
46_P102_R0.139940.846
126_G135_C0.139320.843
52_P87_S0.13890.840
10_N221_D0.138770.839
23_A26_G0.138680.839
139_D143_D0.138650.838
55_A78_V0.138450.837
176_L183_F0.137990.834
111_I133_A0.137630.832
157_E250_D0.136930.828
220_D223_A0.136340.825
103_W176_L0.135340.818
84_G110_T0.135110.817
184_A248_F0.134750.815
154_E158_A0.134120.811
22_F26_G0.133890.810
107_H129_D0.133840.809
249_R253_V0.133780.809
38_I56_W0.133670.808
108_N129_D0.133450.807
79_R129_D0.132790.803
130_S134_F0.132710.803
185_H245_L0.132710.803
6_G76_A0.132330.800
103_W179_G0.132330.800
142_R250_D0.13120.793
82_T108_N0.130810.791
96_R135_C0.130030.786
12_P18_S0.130010.786
156_F181_R0.129790.785
47_R68_K0.129770.785
55_A76_A0.129410.783
78_V94_F0.129350.782
156_F160_R0.129330.782
92_H128_T0.128760.779
118_L131_E0.127770.773
23_A80_A0.127370.770
130_S139_D0.127240.769
132_H136_L0.126450.765
182_L248_F0.126340.764
2_C6_G0.125390.758
134_F138_L0.125370.758
224_V227_A0.125320.758
128_T223_A0.125260.758
39_A91_C0.124140.751
116_D120_D0.124140.751
24_A80_A0.122770.742
76_A231_L0.122670.742
91_C158_A0.122670.742
96_R134_F0.122580.741
23_A113_G0.122350.740
224_V248_F0.122140.739
86_V91_C0.121920.737
159_L245_L0.121910.737
2_C84_G0.121810.737
9_S128_T0.121670.736
48_V125_V0.121630.736
82_T107_H0.121190.733
125_V131_E0.121070.732
90_N131_E0.120490.729
229_E242_P0.120310.728
25_R113_G0.119990.726
90_N127_T0.119930.725
47_R70_R0.11970.724
18_S26_G0.119670.724
85_A89_E0.119510.723
143_D154_E0.119310.722
79_R107_H0.119290.721
24_A92_H0.118460.716
18_S25_R0.117670.712
131_E135_C0.117470.710
57_N61_L0.117430.710
52_P81_A0.11740.710
121_R132_H0.11710.708
19_L23_A0.117070.708
92_H234_D0.116940.707
102_R138_L0.116730.706
83_Q128_T0.116530.705
18_S21_S0.11640.704
122_Y232_T0.116380.704
23_A92_H0.115860.701
35_G138_L0.115540.699
80_A92_H0.115360.698
35_G86_V0.11530.697
116_D167_N0.115020.696
101_R130_S0.115010.696
135_C173_N0.114920.695
225_V231_L0.114740.694
233_D236_D0.114380.692
101_R138_L0.114230.691
56_W61_L0.114150.690
101_R178_D0.113850.689
142_R161_E0.113840.688
187_Y242_P0.113750.688
6_G184_A0.112880.683
10_N72_R0.112880.683
23_A110_T0.112510.680
42_D70_R0.112330.679
86_V112_P0.111970.677
3_R35_G0.111890.677
56_W229_E0.111630.675
181_R239_P0.111130.672
175_L226_V0.110830.670
159_L162_L0.11050.668
121_R124_P0.110320.667
74_F113_G0.110230.667
181_R245_L0.110180.666
77_H108_N0.11010.666
54_P170_G0.109870.664
155_L159_L0.109850.664
95_S138_L0.109610.663
56_W59_P0.109150.660
77_H90_N0.108840.658
118_L121_R0.10860.657
5_L15_I0.108590.657
56_W62_R0.108570.657
102_R161_E0.108320.655
170_G173_N0.10820.654
105_F133_A0.108080.654
134_F177_S0.108060.653
25_R117_I0.108010.653
44_G62_R0.107760.652
155_L180_E0.107680.651
142_R177_S0.107530.650
3_R22_F0.107490.650
102_R179_G0.107320.649
170_G187_Y0.107120.648
96_R102_R0.107090.648
121_R169_Y0.106830.646
187_Y229_E0.106680.645
23_A53_R0.106620.645
76_A234_D0.106310.643
176_L245_L0.106310.643
124_P162_L0.106250.643
13_T17_F0.106140.642
22_F117_I0.106040.641
40_W46_P0.105980.641
102_R177_S0.105950.641
133_A172_L0.105520.638
156_F248_F0.10550.638
34_D83_Q0.105440.638
41_Y178_D0.105410.637
124_P132_H0.105240.636
115_E167_N0.104840.634
10_N250_D0.104010.629
42_D46_P0.103990.629
141_L157_E0.103930.629
94_F141_L0.103620.627
199_F235_E0.103610.627
84_G108_N0.103590.626
226_V229_E0.103550.626
70_R180_E0.10350.626
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
1te5A0.94831000.148
3mdnA0.87821000.309
1ecfA0.8931000.432
1ao0A0.8451000.433
2bplA0.82661000.461
1xffA0.81921000.469
1ea0A0.87451000.584
1ofdA0.85981000.589
1ct9A0.704899.90.609
1q15A0.653199.80.709

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