GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Aconitase_C - Aconitase C-terminal domain
Pfam: PF00694 (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: CL0364
Length: 131
Sequences: 2810
Seq/Len: 21.45
HH_delta: 0.053 (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
82_E108_E0.788832.829
83_N86_C0.764362.742
43_F46_W0.668132.397
97_L123_L0.619232.221
41_I44_D0.619112.221
23_Q46_W0.591282.121
67_P70_K0.588352.110
46_W59_K0.545971.958
7_I75_D0.526141.887
25_I29_F0.512231.837
20_D23_Q0.510721.832
118_L125_P0.494011.772
60_P68_R0.473051.697
60_P65_N0.467281.676
118_L123_L0.459051.647
80_G107_A0.444681.595
39_G47_R0.435291.561
75_D103_R0.43351.555
37_G40_N0.429061.539
17_S20_D0.428351.536
60_P64_L0.423821.520
94_A111_A0.41661.494
79_V107_A0.414251.486
11_A14_D0.408621.466
13_P69_Y0.405761.455
17_S108_E0.400521.437
82_E130_E0.39911.432
17_S82_E0.397941.427
119_I125_P0.397691.426
77_L104_A0.390411.400
9_G75_D0.382951.374
15_F80_G0.379671.362
114_F118_L0.379431.361
68_R73_G0.375031.345
98_K123_L0.357471.282
84_F114_F0.352591.265
26_P29_F0.350231.256
43_F47_R0.346981.245
17_S80_G0.34671.244
98_K121_N0.344971.237
70_K73_G0.344561.236
30_L92_H0.343761.233
29_F41_I0.343271.231
29_F44_D0.342811.230
31_G92_H0.327071.173
61_D64_L0.325281.167
28_M45_D0.322381.156
32_T38_L0.320061.148
20_D86_C0.318171.141
35_N99_D0.313231.124
32_T41_I0.311691.118
94_A121_N0.302211.084
35_N95_W0.295551.060
108_E130_E0.288671.035
43_F59_K0.287111.030
30_L99_D0.284981.022
40_N48_Y0.275290.987
66_A70_K0.275070.987
94_A123_L0.271280.973
27_A45_D0.27050.970
7_I104_A0.269410.966
25_I96_A0.263780.946
88_S117_N0.263040.944
36_T96_A0.262580.942
10_V73_G0.261560.938
12_V74_G0.256660.921
25_I32_T0.253710.910
106_I128_F0.250680.899
28_M44_D0.25030.898
10_V69_Y0.249610.895
32_T96_A0.249450.895
16_N23_Q0.247850.889
115_R119_I0.247850.889
79_V106_I0.246890.886
38_L42_L0.246130.883
11_A78_V0.244610.877
113_I117_N0.243640.874
63_Y67_P0.243330.873
44_D48_Y0.239310.858
16_N19_I0.234510.841
21_T24_I0.233540.838
7_I11_A0.23020.826
121_N124_L0.229560.823
11_A74_G0.229250.822
95_W99_D0.229150.822
59_K70_K0.228160.818
76_I104_A0.226290.812
16_N40_N0.224610.806
68_R129_P0.223050.800
119_I129_P0.222290.797
86_C97_L0.222180.797
10_V15_F0.219160.786
38_L41_I0.219060.786
115_R125_P0.219050.786
26_P89_S0.218740.785
23_Q125_P0.217710.781
20_D30_L0.216340.776
62_F65_N0.20910.750
47_R61_D0.208450.748
107_A110_F0.20830.747
48_Y65_N0.207030.743
92_H111_A0.204210.732
25_I92_H0.20330.729
27_A121_N0.203220.729
92_H95_W0.202280.726
41_I48_Y0.200740.720
42_L100_L0.200110.718
30_L33_F0.199770.717
30_L34_A0.199730.716
32_T35_N0.198950.714
77_L102_I0.196980.707
95_W121_N0.196190.704
84_F97_L0.195840.702
38_L102_I0.195760.702
79_V118_L0.195740.702
63_Y66_A0.195720.702
18_N34_A0.195640.702
24_I43_F0.195590.702
61_D66_A0.192980.692
42_L97_L0.192610.691
16_N122_G0.192430.690
90_R113_I0.192280.690
33_F95_W0.191990.689
107_A127_E0.191870.688
70_K130_E0.191030.685
41_I79_V0.190780.684
98_K130_E0.190760.684
34_A99_D0.189490.680
27_A44_D0.189420.679
115_R127_E0.189270.679
29_F67_P0.188910.678
32_T37_G0.188890.678
25_I42_L0.188350.676
73_G101_G0.188240.675
93_A113_I0.18810.675
88_S93_A0.186440.669
63_Y68_R0.184370.661
17_S107_A0.184060.660
31_G35_N0.184020.660
79_V105_V0.183560.658
95_W100_L0.183130.657
16_N120_N0.1820.653
18_N83_N0.18090.649
40_N44_D0.180490.647
42_L96_A0.180460.647
83_N109_S0.180170.646
38_L47_R0.179330.643
98_K103_R0.178280.639
10_V68_R0.178210.639
41_I108_E0.177440.636
13_P63_Y0.176160.632
64_L67_P0.176040.631
76_I102_I0.175410.629
88_S113_I0.174970.628
89_S117_N0.173770.623
37_G84_F0.173410.622
27_A92_H0.173020.621
106_I127_E0.172690.619
35_N92_H0.171980.617
106_I126_L0.171690.616
77_L97_L0.17130.614
80_G128_F0.171190.614
80_G118_L0.16830.604
90_R93_A0.167850.602
96_A100_L0.167680.601
8_K75_D0.167430.601
8_K130_E0.166870.599
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
3q3wA0.96181000.053
3h5jA0.90081000.11
2hcuA0.95421000.116
3vbaA0.83971000.187
2b3yA11000.192
2pkpA0.82441000.192
1v7lA0.81681000.212
1l5jA0.90081000.24
1c96A11000.267
1ryiA0.534429.20.935

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