GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GATase_3 - CobBCobQ-like glutamine amidotransferase domain
Pfam: PF07685 (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: CL0014
Length: 158
Sequences: 8849
Seq/Len: 56.01
HH_delta: 0.227 (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
55_L144_V1.531543.429
38_A43_G1.451843.251
52_Y146_G1.076292.410
58_S81_D1.02462.294
56_G116_T0.998012.235
139_Y142_G0.990982.219
49_C150_H0.922122.065
39_A45_I0.911562.041
56_G137_A0.910522.039
139_Y143_N0.844141.890
137_A146_G0.84171.885
32_K36_R0.839081.879
33_E36_R0.817541.831
35_I54_Y0.806521.806
10_G44_P0.764281.711
55_L146_G0.753021.686
123_P140_Q0.728191.631
123_P138_I0.726771.627
57_E79_P0.699491.566
33_E37_E0.697591.562
125_F138_I0.681831.527
42_G142_G0.67781.518
124_P134_F0.67591.513
11_I43_G0.667851.495
52_Y116_T0.646041.447
114_G148_Y0.6371.426
11_I38_A0.630361.412
32_K57_E0.623591.396
60_I81_D0.617661.383
32_K58_S0.617561.383
49_C112_H0.615581.378
21_F57_E0.610911.368
39_A144_V0.608841.363
12_Y46_Y0.604521.354
126_F136_G0.595941.334
73_P113_Y0.585951.312
49_C53_Q0.584261.308
34_A37_E0.562011.258
124_P127_K0.558181.250
47_A51_G0.53881.206
52_Y137_A0.534121.196
37_E41_A0.532151.192
39_A77_L0.53071.188
36_R58_S0.527971.182
36_R40_E0.527411.181
15_G49_C0.523891.173
138_I145_L0.518411.161
20_L72_Y0.518161.160
11_I45_I0.499791.119
40_E142_G0.496321.111
57_E76_G0.495431.109
79_P105_E0.495121.109
31_L34_A0.488941.095
122_E139_Y0.485861.088
39_A59_I0.483951.084
48_E147_T0.474741.063
103_G106_V0.474421.062
79_P119_I0.472151.057
16_G50_G0.471871.057
46_Y147_T0.462471.036
37_E40_E0.442310.990
34_A38_A0.43870.982
18_P21_F0.435710.976
118_G127_K0.435040.974
17_Y20_L0.434710.973
35_I45_I0.433370.970
59_I144_V0.429550.962
13_L45_I0.429320.961
59_I139_Y0.426190.954
46_Y145_L0.426130.954
38_A45_I0.423960.949
30_G33_E0.417570.935
16_G111_F0.41520.930
115_R133_G0.411360.921
13_L35_I0.410360.919
18_P22_A0.402740.902
36_R39_A0.400010.896
78_L109_H0.398070.891
56_G80_I0.394830.884
45_I144_V0.392550.879
119_I122_E0.392210.878
89_A92_Y0.391740.877
112_H148_Y0.391270.876
48_E53_Q0.38530.863
121_G139_Y0.381750.855
30_G34_A0.378540.848
110_E135_D0.375520.841
53_Q112_H0.373850.837
42_G143_N0.373750.837
116_T148_Y0.373060.835
108_G149_L0.372610.834
120_P140_Q0.369960.828
121_G140_Q0.367640.823
44_P143_N0.362420.812
19_E22_A0.360720.808
121_G141_K0.360280.807
38_A41_A0.357450.800
8_A43_G0.357440.800
13_L31_L0.3570.799
66_D115_R0.356870.799
46_Y152_H0.356220.798
53_Q148_Y0.353860.792
15_G150_H0.351660.787
87_E90_L0.351470.787
50_G110_E0.348460.780
77_L109_H0.347920.779
112_H150_H0.343050.768
106_V149_L0.342740.767
52_Y56_G0.341910.766
53_Q114_G0.334180.748
148_Y152_H0.332370.744
109_H153_F0.329740.738
87_E92_Y0.329250.737
125_F145_L0.329110.737
80_I116_T0.325690.729
73_P78_L0.324970.728
8_A11_I0.324770.727
19_E114_G0.321360.720
31_L54_Y0.31740.711
16_G153_F0.312650.700
32_K75_L0.312420.700
14_P17_Y0.311550.698
45_I55_L0.311190.697
53_Q150_H0.309610.693
53_Q146_G0.308290.690
116_T137_A0.307910.689
127_K130_G0.307380.688
59_I122_E0.303760.680
23_L54_Y0.302290.677
11_I34_A0.300810.674
66_D72_Y0.30040.673
127_K132_G0.30010.672
33_E40_E0.300070.672
32_K54_Y0.299040.670
125_F136_G0.29810.668
72_Y131_G0.294970.660
39_A55_L0.289310.648
17_Y50_G0.287980.645
148_Y151_G0.28460.637
66_D73_P0.284090.636
125_F135_D0.283510.635
13_L51_G0.281890.631
81_D105_E0.281680.631
127_K133_G0.281620.631
147_T151_G0.280340.628
13_L17_Y0.280280.628
122_E137_A0.280170.627
16_G20_L0.279210.625
60_I67_A0.277460.621
21_F24_E0.275660.617
17_Y111_F0.274820.615
128_V133_G0.271740.608
50_G54_Y0.271320.608
78_L110_E0.27120.607
47_A55_L0.269530.604
88_K92_Y0.269230.603
49_C148_Y0.264590.592
51_G112_H0.2640.591
23_L32_K0.263940.591
15_G153_F0.263330.590
52_Y148_Y0.26220.587
58_S73_P0.260230.583
14_P18_P0.259850.582
57_E81_D0.258880.580
7_D43_G0.25860.579
76_G79_P0.257840.577
19_E59_I0.257830.577
89_A123_P0.2560.573
37_E42_G0.252780.566
87_E138_I0.24840.556
125_F128_V0.247980.555
104_E141_K0.247410.554
74_G114_G0.247340.554
14_P111_F0.247210.554
118_G128_V0.246610.552
119_I134_F0.245980.551
81_D128_V0.245320.549
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
3m3pA0.892499.90.227
3l7nA0.905199.90.232
1o1yA0.898799.90.26
3uowA0.949499.90.262
2ywbA0.860899.90.271
3tqiA0.917799.90.276
1gpmA0.917799.90.277
2vxoA0.860899.80.306
3r75A0.892499.80.31
2a9vA0.867199.80.31

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