GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
CPSase_L_chain - Carbamoyl-phosphate synthase L chain N-terminal domain
Pfam: PF00289 (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: 110
Sequences: 42129
Seq/Len: 382.99
HH_delta: 0.21 (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
10_R30_A2.893352.887
6_L75_A2.762852.757
4_K27_E2.39622.391
29_V75_A2.063312.059
4_K29_V2.027482.023
62_N65_A1.860241.856
65_A68_D1.749531.746
5_V26_I1.730031.727
67_I97_D1.716561.713
7_I18_I1.702971.700
67_I98_A1.618571.615
63_I67_I1.60811.605
71_R98_A1.59431.591
5_V21_L1.587931.585
17_I79_H1.557291.554
20_A23_E1.553021.550
67_I94_A1.535311.532
6_L31_V1.528491.525
3_K76_D1.482361.479
94_A98_A1.475361.472
20_A24_L1.474351.471
68_D72_K1.453071.450
31_V51_E1.417511.415
89_A93_E1.405321.402
95_C102_F1.365971.363
21_L28_T1.342011.339
67_I71_R1.338531.336
4_K76_D1.324181.321
18_I30_A1.323281.321
34_N37_T1.29921.297
78_I95_C1.295461.293
94_A97_D1.196041.194
80_P88_N1.186261.184
52_P61_L1.184131.182
51_E65_A1.151411.149
93_E97_D1.134211.132
19_R23_E1.133371.131
5_V77_A1.129241.127
17_I81_G1.118971.117
8_A80_P1.099411.097
16_R19_R1.085971.084
29_V49_Y1.078121.076
63_I90_E1.077911.076
38_V42_V1.076191.074
29_V47_E1.075771.074
64_E68_D1.057681.056
68_D71_R1.02631.024
12_E16_R1.02271.021
86_S90_E1.017571.015
3_K26_I1.011311.009
93_E96_E0.998270.996
72_K75_A0.990640.989
70_A75_A0.982830.981
8_A91_F0.979630.978
40_T43_D0.977310.975
63_I94_A0.974290.972
65_A69_I0.966360.964
27_E47_E0.965650.964
35_P38_V0.96560.964
35_P39_S0.958640.957
90_E94_A0.957050.955
37_T40_T0.954250.952
16_R20_A0.926810.925
63_I93_E0.925570.924
95_C99_G0.92440.923
35_P50_F0.916210.914
22_R46_D0.90480.903
78_I100_I0.90070.899
86_S89_A0.886070.884
8_A78_I0.869450.868
87_E90_E0.86710.865
34_N50_F0.862250.860
15_V19_R0.858620.857
95_C100_I0.854060.852
36_D39_S0.846820.845
18_I28_T0.844660.843
29_V72_K0.836280.835
32_N37_T0.833370.832
64_E67_I0.830690.829
91_F95_C0.816030.814
84_F87_E0.778330.777
4_K75_A0.77770.776
15_V40_T0.773070.771
66_I70_A0.760840.759
17_I21_L0.74380.742
39_S43_D0.741240.740
78_I91_F0.736410.735
80_P91_F0.731160.730
40_T44_M0.727580.726
60_Y87_E0.726580.725
32_N48_A0.718850.717
10_R18_I0.717260.716
8_A60_Y0.710750.709
39_S42_V0.705420.704
5_V79_H0.700880.699
52_P60_Y0.698110.697
18_I22_R0.693650.692
70_A78_I0.68720.686
12_E80_P0.685120.684
82_Y87_E0.685050.684
33_S52_P0.675220.674
47_E50_F0.674140.673
3_K27_E0.673710.672
95_C98_A0.666610.665
22_R28_T0.665470.664
7_I21_L0.663660.662
11_G14_A0.661910.661
4_K26_I0.661470.660
32_N38_V0.660960.660
49_Y52_P0.659660.658
15_V44_M0.654570.653
25_G28_T0.653170.652
8_A31_V0.652790.651
85_L89_A0.652550.651
21_L26_I0.646650.645
92_A102_F0.642030.641
64_E94_A0.640690.639
8_A82_Y0.636660.635
49_Y69_I0.627390.626
30_A48_A0.619650.618
90_E93_E0.618740.617
69_I72_K0.615380.614
19_R44_M0.601920.601
67_I70_A0.599310.598
11_G15_V0.598740.598
12_E15_V0.589320.588
80_P84_F0.587740.587
13_I17_I0.586170.585
49_Y72_K0.586150.585
70_A95_C0.585150.584
6_L70_A0.578740.578
19_R22_R0.575330.574
80_P102_F0.57390.573
21_L79_H0.572660.571
88_N92_A0.570130.569
62_N68_D0.567050.566
21_L25_G0.566170.565
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
3u9tA199.20.21
3n6rA199.20.214
3va7A199.20.216
3ouzA199.20.219
2w70A199.10.239
1ulzA0.990999.10.245
3hblA199.10.25
2vpqA0.9909990.278
2dzdA1990.282
3glkA1990.285

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