GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
OTCace - Aspartateornithine carbamoyltransferase AspOrn binding domain
Pfam: PF00185 (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: 158
Sequences: 3821
Seq/Len: 24.18
HH_delta: 0.019 (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
104_E131_E1.630914.175
4_K29_E1.569084.016
4_K31_V1.310473.354
116_F128_V1.189533.045
6_A74_A1.188733.043
68_E109_R1.169452.993
115_I139_V1.058492.709
75_D111_K1.042282.668
66_D69_E0.974872.495
117_M139_V0.898262.299
36_E65_D0.791672.026
104_E108_E0.790652.024
33_I70_A0.779021.994
123_N126_E0.760371.946
23_L30_V0.7431.902
105_E108_E0.734531.880
76_V115_I0.72341.852
29_E60_K0.712981.825
19_L78_Y0.704241.803
68_E106_L0.698221.787
29_E62_T0.683631.750
31_V64_T0.679721.740
78_Y143_Q0.667071.708
64_T69_E0.653691.673
107_M114_A0.623131.595
71_L77_V0.619331.585
40_Y96_K0.619311.585
114_A137_R0.610841.564
37_G41_P0.601531.540
79_T102_V0.59181.515
110_A114_A0.571061.462
6_A33_I0.569711.458
77_V102_V0.563111.441
41_P65_D0.555631.422
149_H152_M0.549411.406
92_K96_K0.540371.383
145_E149_H0.527131.349
83_Q90_R0.519491.330
3_L76_V0.511641.310
31_V62_T0.500771.282
72_K109_R0.494081.265
22_L26_F0.489011.252
135_S138_S0.481961.234
107_M137_R0.475411.217
142_E145_E0.474631.215
91_F95_E0.470631.205
64_T70_A0.470261.204
133_D140_Y0.465751.192
130_D134_D0.456811.169
102_V116_F0.454991.165
8_V71_L0.452711.159
104_E135_S0.452451.158
73_G111_K0.452161.157
101_Q129_S0.446351.143
124_R134_D0.444721.138
69_E72_K0.442621.133
122_A133_D0.43281.108
6_A31_V0.432141.106
125_G130_D0.424261.086
37_G96_K0.418311.071
11_G34_A0.413491.058
107_M116_F0.413231.058
124_R133_D0.412381.056
67_I106_L0.410331.050
68_E105_E0.409851.049
5_I23_L0.407121.042
20_I32_L0.396281.014
36_E41_P0.394361.009
23_L28_M0.382680.980
78_Y81_R0.379640.972
103_T129_S0.374570.959
33_I64_T0.374340.958
34_A41_P0.374060.957
90_R94_L0.371990.952
19_L23_L0.370550.949
105_E109_R0.369930.947
96_K99_P0.368180.942
8_V106_L0.367340.940
17_H46_V0.364820.934
47_L63_I0.364420.933
31_V73_G0.36370.931
95_E98_K0.360450.923
98_K101_Q0.359020.919
71_L106_L0.35810.917
4_K73_G0.357330.915
153_A157_L0.354610.908
15_V19_L0.349840.895
77_V114_A0.348440.892
70_A74_A0.348410.892
33_I67_I0.344080.881
154_L158_L0.334760.857
31_V74_A0.33390.855
148_L152_M0.332840.852
71_L109_R0.330960.847
107_M132_V0.323940.829
68_E72_K0.323190.827
91_F94_L0.322160.825
4_K74_A0.321790.824
139_V142_E0.319170.817
8_V79_T0.318670.816
107_M110_A0.316580.810
33_I74_A0.315310.807
40_Y97_F0.313520.803
16_A32_L0.312540.800
133_D141_F0.310050.794
116_F132_V0.306010.783
81_R90_R0.304680.780
7_Y13_N0.302710.775
132_V135_S0.301590.772
120_L141_F0.297620.762
88_K91_F0.29470.754
15_V78_Y0.293370.751
109_R112_P0.293270.751
142_E146_N0.290290.743
108_E137_R0.289590.741
5_I19_L0.28610.732
103_T106_L0.28420.727
104_E137_R0.281390.720
130_D133_D0.281260.720
79_T82_W0.279990.717
14_R80_D0.279020.714
122_A128_V0.276420.708
94_L126_E0.276220.707
102_V128_V0.275980.706
81_R123_N0.275730.706
77_V107_M0.27570.706
107_M128_V0.274560.703
2_G29_E0.273150.699
22_L28_M0.272410.697
5_I78_Y0.271960.696
76_V117_M0.270390.692
151_R154_L0.270390.692
13_N80_D0.269150.689
27_G60_K0.268340.687
42_P63_I0.267940.686
8_V77_V0.26630.682
147_R151_R0.265080.679
92_K95_E0.264310.677
150_V154_L0.263030.673
3_L75_D0.26270.672
145_E148_L0.261670.670
78_Y117_M0.25890.663
21_E25_K0.254460.651
104_E129_S0.253590.649
113_D137_R0.252810.647
125_G131_E0.252140.645
7_Y15_V0.251810.645
104_E107_M0.251250.643
88_K94_L0.250610.641
65_D100_Y0.246130.630
17_H21_E0.245360.628
34_A65_D0.245010.627
8_V99_P0.243150.622
120_L144_A0.241640.619
82_W91_F0.239820.614
20_I47_L0.238990.612
135_S140_Y0.238590.611
102_V106_L0.238490.610
124_R130_D0.237250.607
82_W94_L0.2360.604
62_T73_G0.235640.603
144_A149_H0.235120.602
41_P63_I0.234470.600
2_G115_I0.234450.600
2_G27_G0.232450.595
93_R96_K0.231740.593
125_G133_D0.229270.587
94_L98_K0.228850.586
20_I42_P0.228690.585
133_D138_S0.227760.583
64_T67_I0.227160.581
89_E93_R0.226790.581
14_R119_P0.226510.580
77_V116_F0.226140.579
42_P47_L0.224750.575
133_D151_R0.222590.570
129_S132_V0.222280.569
15_V80_D0.219310.561
7_Y78_Y0.217380.556
8_V33_I0.214540.549
11_G17_H0.212790.545
21_E46_V0.211230.541
72_K111_K0.21110.540
81_R122_A0.210890.540
89_E92_K0.21040.539
110_A137_R0.210280.538
11_G41_P0.209280.536
122_A141_F0.208310.533
106_L109_R0.207830.532
24_A59_G0.206070.527
6_A70_A0.205790.527
80_D83_Q0.205460.526
5_I117_M0.20530.526
32_L61_I0.204690.524
124_R151_R0.204170.523
14_R81_R0.203510.521
37_G40_Y0.202750.519
10_D18_S0.20150.516
128_V133_D0.200890.514
37_G97_F0.200520.513
16_A20_I0.199940.512
82_W99_P0.198990.509
67_I70_A0.198850.509
81_R89_E0.197670.506
14_R151_R0.196350.503
47_L61_I0.196230.502
66_D72_K0.196030.502
83_Q89_E0.195090.499
19_L22_L0.194830.499
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
4ep1A0.9811000.019
1vlvA0.98731000.019
3gd5A0.9811000.024
2i6uA0.98731000.025
3grfA11000.026
1pvvA0.9811000.027
3tpfA0.9811000.029
2w37A0.98731000.029
1duvG0.98731000.03
1dxhA0.98731000.03

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