GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DALR_1 - DALR anticodon binding domain
Pfam: PF05746 (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: CL0258
Length: 119
Sequences: 3377
Seq/Len: 28.38
HH_delta: 0.003 (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
65_L107_G1.280774.003
41_Q71_A0.922732.884
8_I97_L0.810212.532
9_S101_R0.775232.423
41_Q44_R0.75982.375
32_E79_V0.714492.233
57_E60_K0.694982.172
5_Y105_K0.65162.037
45_F106_N0.638161.995
34_E78_N0.635181.985
72_F97_L0.604761.890
102_Q106_N0.576321.801
80_R83_D0.570881.784
35_E93_R0.546291.707
5_Y9_S0.510391.595
44_R47_D0.506921.584
36_R40_K0.506521.583
46_P99_A0.505251.579
75_F79_V0.489291.529
8_I101_R0.487431.524
4_A73_N0.478691.496
41_Q67_E0.464831.453
5_Y101_R0.464371.451
81_I97_L0.463931.450
86_E89_R0.457431.430
98_K102_Q0.452391.414
33_E37_E0.446891.397
52_A61_L0.432541.352
101_R105_K0.427881.337
51_K55_D0.417111.304
74_S78_N0.416111.301
69_A73_N0.413091.291
10_S13_R0.412361.289
37_E71_A0.408591.277
45_F64_Y0.398581.246
32_E35_E0.388441.214
75_F81_I0.387861.212
37_E74_S0.385481.205
83_D89_R0.380031.188
39_L43_A0.377661.180
84_E89_R0.377281.179
49_L110_L0.376121.176
80_R84_E0.376111.176
11_I97_L0.375851.175
11_I81_I0.373991.169
98_K101_R0.370661.159
64_Y68_L0.36771.149
63_D66_Y0.362991.135
30_L92_N0.36071.127
75_F96_L0.359491.124
66_Y70_Q0.357371.117
50_E54_K0.355791.112
51_K54_K0.348651.090
42_L100_V0.341931.069
42_L103_V0.330071.032
59_H63_D0.325311.017
86_E91_N0.320871.003
53_A61_L0.316010.988
14_K18_S0.314530.983
45_F107_G0.312030.975
49_L53_A0.301120.941
72_F76_Y0.299460.936
15_A94_L0.292710.915
33_E36_R0.292370.914
103_V106_N0.291470.911
4_A70_Q0.286140.894
99_A102_Q0.278170.869
2_Q5_Y0.274250.857
79_V93_R0.274040.857
3_Y6_A0.267820.837
87_E91_N0.267460.836
75_F100_V0.262040.819
16_E20_I0.261150.816
48_V64_Y0.261040.816
88_I93_R0.260430.814
48_V51_K0.259030.810
3_Y73_N0.257130.804
34_E74_S0.253020.791
51_K60_K0.252310.789
106_N109_D0.251870.787
85_D88_I0.251580.786
55_D60_K0.24950.780
4_A69_A0.247920.775
14_K17_E0.247640.774
95_A99_A0.24560.768
6_A10_S0.245380.767
8_I72_F0.244940.766
44_R67_E0.24350.761
35_E38_L0.242480.758
75_F97_L0.237070.741
5_Y104_L0.234370.733
40_K44_R0.234370.733
12_L98_K0.233680.730
6_A9_S0.232560.727
3_Y76_Y0.232390.726
52_A58_P0.230960.722
82_L94_L0.229480.717
47_D51_K0.229180.716
53_A56_L0.229030.716
4_A104_L0.227430.711
49_L61_L0.226950.709
11_I75_F0.226850.709
8_I100_V0.226480.708
73_N77_D0.225350.704
68_L100_V0.22310.697
25_D28_F0.222260.695
48_V60_K0.222090.694
5_Y12_L0.22170.693
66_Y83_D0.22120.691
38_L75_F0.220620.690
76_Y81_I0.220250.688
59_H70_Q0.219530.686
16_E19_G0.215990.675
12_L94_L0.215670.674
9_S13_R0.214950.672
38_L100_V0.213360.667
103_V107_G0.213180.666
52_A64_Y0.212220.663
85_D89_R0.21060.658
32_E78_N0.209150.654
24_Y88_I0.208910.653
35_E96_L0.208810.653
76_Y82_L0.20780.650
35_E79_V0.207770.649
16_E21_N0.20770.649
35_E67_E0.207080.647
67_E70_Q0.205290.642
93_R96_L0.204960.641
42_L99_A0.204040.638
95_A98_K0.203610.636
34_E79_V0.203470.636
15_A82_L0.203070.635
43_A46_P0.201250.629
61_L106_N0.198670.621
20_I24_Y0.194480.608
39_L92_N0.193110.604
61_L107_G0.191230.598
11_I82_L0.190380.595
30_L36_R0.188560.589
58_P61_L0.188190.588
35_E88_I0.188130.588
40_K60_K0.187870.587
99_A103_V0.187620.586
44_R48_V0.185340.579
15_A110_L0.184930.578
64_Y67_E0.182880.572
61_L64_Y0.181440.567
67_E71_A0.18130.567
69_A108_L0.180880.565
17_E20_I0.180540.564
2_Q10_S0.178960.559
18_S89_R0.178220.557
66_Y77_D0.1780.556
79_V97_L0.176770.553
36_R63_D0.176350.551
49_L103_V0.176140.551
21_N24_Y0.174230.545
75_F93_R0.173550.542
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
1f7uA0.991699.90.003
2zueA0.991699.90.083
3fnrA0.95899.90.13
1iq0A0.949699.90.147
4dlpA0.932897.80.7
3h99A0.91697.70.706
3kflA0.949697.40.728
3u1fA0.949697.20.741
2csxA0.91696.40.771
2x1lA0.991695.40.791

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