GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GARS_A - Phosphoribosylglycinamide synthetase ATP-grasp (A) domain
Pfam: PF01071 (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: CL0179
Length: 194
Sequences: 17495
Seq/Len: 90.18
HH_delta: 0.072 (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
19_K87_E2.164323.269
34_E60_R1.930182.915
59_D62_E1.876422.834
30_L64_L1.661862.510
139_T142_L1.603462.422
152_E156_K1.542592.330
7_K86_E1.472982.225
38_Y60_R1.456172.199
10_M182_V1.418082.142
25_D28_E1.377962.081
148_E153_P1.355472.047
140_D144_E1.345232.032
56_I88_F1.317771.990
21_K35_E1.289331.947
4_S22_V1.2881.945
2_S46_D1.276461.928
144_E148_E1.171151.769
60_R64_L1.127841.703
90_E177_E1.127641.703
142_L145_E1.115841.685
5_F8_E1.098721.660
8_E12_R1.091281.648
174_M183_L1.07261.620
4_S8_E1.058761.599
42_V56_I1.051331.588
8_E11_K1.020931.542
58_D62_E1.020661.542
6_A10_M1.006471.520
144_E147_I1.005961.519
64_L68_R1.000061.510
32_Y36_Q0.988161.493
32_Y35_E0.972341.469
175_L180_P0.954461.442
145_E148_E0.941981.423
142_L175_L0.940671.421
30_L60_R0.940571.421
42_V88_F0.925641.398
31_E35_E0.912821.379
26_Y30_L0.909731.374
102_G166_R0.896421.354
143_L147_I0.896061.353
46_D82_K0.885861.338
101_D104_N0.885711.338
33_L38_Y0.875891.323
42_V54_V0.87111.316
96_L146_I0.864031.305
20_Y86_E0.863031.304
176_T179_G0.858421.297
26_Y68_R0.843761.274
4_S46_D0.842861.273
100_T105_F0.83941.268
9_F13_Y0.829491.253
30_L34_E0.828431.251
21_K32_Y0.822431.242
148_E152_E0.821851.241
28_E31_E0.820121.239
87_E181_K0.813141.228
171_A185_F0.807131.219
89_L181_K0.8051.216
55_V69_E0.799671.208
11_K19_K0.793311.198
71_F81_S0.791811.196
7_K17_T0.790861.195
176_T181_K0.777521.174
58_D90_E0.776651.173
15_I182_V0.769291.162
19_K35_E0.766341.157
24_T82_K0.758931.146
98_A151_L0.757381.144
40_Y85_I0.756651.143
16_P181_K0.741761.120
38_Y59_D0.741131.119
67_L71_F0.738861.116
24_T28_E0.733781.108
11_K17_T0.722051.091
16_P150_I0.709181.071
31_E34_E0.707671.069
141_E145_E0.703241.062
65_E69_E0.697491.053
99_L168_V0.697321.053
23_F32_Y0.694851.050
147_I152_E0.694371.049
26_Y64_L0.69421.049
10_M157_G0.693511.047
140_D143_L0.690561.043
98_A169_L0.689681.042
9_F12_R0.686931.038
33_L40_Y0.686431.037
12_R157_G0.679741.027
153_P156_K0.677191.023
10_M154_T0.66991.012
94_V175_L0.668391.010
57_A66_A0.668221.009
27_E30_L0.667261.008
150_I173_L0.665441.005
38_Y63_A0.652310.985
29_A67_L0.648290.979
13_Y157_G0.641280.969
36_Q40_Y0.635920.960
27_E31_E0.635160.959
68_R72_V0.634990.959
69_E72_V0.634850.959
8_E20_Y0.628510.949
28_E32_Y0.621950.939
22_V82_K0.618730.935
65_E68_R0.616770.932
29_A63_A0.616450.931
5_F9_F0.615730.930
47_G80_G0.611980.924
43_I85_I0.611450.924
138_I142_L0.608370.919
168_V189_F0.601560.909
145_E179_G0.601330.908
114_H117_L0.600770.907
43_I83_V0.600210.907
155_L169_L0.600150.906
33_L63_A0.596840.901
19_K36_Q0.584970.884
40_Y57_A0.579740.876
91_G177_E0.576380.871
92_E112_Q0.574240.867
90_E176_T0.56620.855
26_Y71_F0.559040.844
87_E176_T0.552850.835
4_S84_V0.552270.834
11_K20_Y0.551280.833
55_V66_A0.551180.833
55_V70_I0.55010.831
93_E172_G0.547960.828
141_E144_E0.540220.816
44_K86_E0.538340.813
96_L110_P0.537630.812
154_T157_G0.535430.809
71_F83_V0.528530.798
107_P147_I0.526640.795
46_D84_V0.521630.788
18_A89_L0.519510.785
18_A87_E0.517660.782
34_E64_L0.511910.773
89_L176_T0.50790.767
183_L186_N0.503730.761
93_E97_F0.50060.756
145_E150_I0.498240.753
148_E156_K0.49780.752
132_Y136_P0.495620.749
145_E180_P0.491910.743
97_F170_Y0.491650.743
23_F29_A0.490890.741
92_E175_L0.490470.741
146_I180_P0.487890.737
18_A181_K0.487770.737
2_S47_G0.487530.736
4_S82_K0.484420.732
61_E65_E0.482090.728
89_L183_L0.478460.723
43_I57_A0.477940.722
153_P157_G0.476830.720
98_A171_A0.476640.720
2_S5_F0.476590.720
9_F157_G0.476570.720
151_L173_L0.475640.718
109_P133_S0.471430.712
165_Y169_L0.462140.698
70_I83_V0.46040.695
96_L173_L0.460260.695
105_F152_E0.457080.690
26_Y67_L0.455490.688
154_T158_L0.448460.677
39_P57_A0.448140.677
96_L147_I0.447870.676
66_A70_I0.446650.675
61_E64_L0.446250.674
62_E65_E0.445210.672
173_L180_P0.444880.672
43_I66_A0.439410.664
150_I180_P0.435960.658
17_T20_Y0.435160.657
135_V138_I0.434450.656
57_A63_A0.433870.655
33_L37_G0.433560.655
108_L111_A0.432010.653
96_L151_L0.43120.651
168_V172_G0.421380.636
3_K6_A0.421090.636
171_A182_V0.420270.635
10_M185_F0.413260.624
168_V188_R0.413010.624
151_L155_L0.412640.623
88_F174_M0.412290.623
150_I154_T0.411460.621
113_D116_R0.410080.619
4_S20_Y0.409290.618
99_L108_L0.408930.618
175_L179_G0.408590.617
6_A182_V0.407810.616
3_K54_V0.406630.614
95_S98_A0.405970.613
6_A186_N0.39940.603
21_K31_E0.39930.603
150_I153_P0.39680.599
97_F188_R0.395430.597
104_N152_E0.393850.595
62_E66_A0.393750.595
94_V146_I0.392050.592
37_G87_E0.391790.592
55_V65_E0.391770.592
51_G170_Y0.391480.591
39_P56_I0.388150.586
112_Q135_V0.387740.586
110_P113_D0.387610.585
169_L172_G0.387440.585
95_S111_A0.387220.585
154_T185_F0.38710.585
104_N156_K0.386120.583
29_A32_Y0.385120.582
93_E170_Y0.378950.572
139_T175_L0.377830.571
21_K24_T0.376980.569
170_Y188_R0.376390.569
33_L60_R0.374520.566
15_I150_I0.374460.566
153_P180_P0.372390.562
3_K186_N0.369530.558
8_E22_V0.368630.557
94_V138_I0.367780.555
3_K44_K0.367760.555
94_V135_V0.367420.555
30_L33_L0.36670.554
151_L171_A0.366640.554
139_T179_G0.365630.552
142_L180_P0.365510.552
141_E148_E0.364930.551
11_K21_K0.361650.546
104_N108_L0.360840.545
3_K45_A0.355680.537
19_K181_K0.355020.536
184_E188_R0.354590.536
145_E153_P0.353380.534
27_E64_L0.353040.533
113_D117_L0.352590.533
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
3lp8A0.99481000.072
3mjfA0.99481000.079
2yw2A0.99481000.099
2yrxA0.98971000.101
2qk4A0.99481000.104
2xclA0.99481000.104
1vkzA0.97941000.105
2ip4A0.96391000.119
3votA0.92271000.173
1a9xA0.917599.90.187

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