GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ChlI - Subunit ChlI of Mg-chelatase
Pfam: PF13541 (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: CL0329
Length: 121
Sequences: 4242
Seq/Len: 35.06
HH_delta: 0.057 (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_I115_V1.124213.653
3_V68_A1.052143.419
81_D113_K1.02363.326
82_T114_R0.951883.093
32_A35_N0.914462.972
67_I84_F0.891242.896
84_F116_I0.801122.603
97_V100_I0.768262.496
86_G118_P0.741012.408
66_A88_L0.736462.393
5_I72_A0.69222.249
83_V112_F0.684162.223
20_T23_K0.642772.089
100_I117_V0.578891.881
106_E109_K0.55031.788
79_P114_R0.546461.776
85_I103_R0.534691.737
82_T116_I0.526491.711
100_I104_I0.515641.676
4_D35_N0.498561.620
67_I78_I0.492371.600
89_G95_R0.474191.541
63_L94_I0.44941.460
107_A115_V0.438441.425
11_S44_D0.430681.399
3_V72_A0.428951.394
85_I100_I0.425261.382
10_P44_D0.420071.365
14_I26_R0.414181.346
5_I43_Q0.396741.289
49_L65_I0.393741.279
29_V66_A0.392271.275
83_V107_A0.386581.256
81_D114_R0.376041.222
7_R43_Q0.372211.209
86_G94_I0.368521.198
17_L21_A0.367321.194
23_K26_R0.36491.186
29_V32_A0.362811.179
104_I108_K0.353421.148
9_L41_P0.336651.094
18_P49_L0.327951.066
30_R45_I0.325181.057
24_E56_K0.324721.055
4_D34_K0.324171.053
60_A103_R0.322981.050
47_V65_I0.321331.044
33_L70_L0.321191.044
71_S77_P0.317071.030
13_N27_E0.313561.019
16_G24_E0.31161.013
106_E110_L0.309731.006
85_I97_V0.30811.001
58_G103_R0.306070.995
97_V121_N0.305350.992
5_I73_F0.304820.991
83_V115_V0.30330.986
96_P121_N0.294750.958
31_S34_K0.293940.955
80_E93_E0.29290.952
45_I69_I0.29110.946
100_I121_N0.288960.939
71_S78_I0.288770.938
96_P120_A0.285980.929
87_E90_L0.285650.928
89_G93_E0.281730.915
102_P105_I0.278930.906
17_L20_T0.275550.895
62_D87_E0.271820.883
71_S76_I0.270190.878
23_K27_E0.269440.876
15_V18_P0.266020.864
40_F73_F0.26420.859
101_L105_I0.263020.855
63_L66_A0.26180.851
99_G102_P0.25640.833
84_F118_P0.254980.829
4_D31_S0.253970.825
27_E30_R0.253950.825
52_A87_E0.250570.814
16_G19_D0.248760.808
53_D57_E0.245710.798
52_A59_P0.24410.793
43_Q73_F0.241490.785
18_P21_A0.238860.776
64_A67_I0.237180.771
57_E61_F0.236290.768
9_L44_D0.234710.763
83_V106_E0.234710.763
12_F30_R0.232870.757
29_V35_N0.23190.754
26_R47_V0.231140.751
25_S29_V0.229040.744
30_R34_K0.227690.740
37_G41_P0.227450.739
70_L74_G0.227120.738
79_P82_T0.225750.734
6_S31_S0.225290.732
113_K116_I0.225040.731
57_E98_P0.224440.729
33_L36_S0.224160.728
26_R64_A0.224080.728
3_V64_A0.223080.725
4_D69_I0.222960.725
85_I115_V0.220290.716
50_A102_P0.220020.715
48_N87_E0.218770.711
104_I117_V0.218170.709
71_S79_P0.218150.709
86_G92_G0.217390.706
70_L108_K0.217130.706
105_I108_K0.217050.705
114_R118_P0.216260.703
12_F26_R0.213990.695
53_D59_P0.213930.695
85_I96_P0.213430.694
61_F98_P0.213280.693
22_V49_L0.212790.691
58_G99_G0.212640.691
16_G21_A0.211370.687
20_T55_K0.210920.685
87_E95_R0.209470.681
6_S13_N0.209130.680
77_P80_E0.208660.678
39_P42_N0.208390.677
63_L90_L0.207130.673
28_R32_A0.207090.673
61_F85_I0.20610.670
5_I93_E0.205210.667
10_P42_N0.204970.666
12_F47_V0.203780.662
23_K53_D0.201110.654
16_G56_K0.200890.653
31_S35_N0.200320.651
39_P75_Q0.199540.648
103_R106_E0.197750.643
35_N121_N0.197310.641
49_L90_L0.196240.638
27_E66_A0.196070.637
85_I106_E0.195530.635
65_I87_E0.19540.635
71_S103_R0.194280.631
59_P62_D0.194190.631
15_V22_V0.193760.630
29_V33_L0.193450.629
64_A84_F0.193210.628
96_P99_G0.192590.626
102_P121_N0.192580.626
59_P83_V0.192280.625
117_V121_N0.190770.620
38_F70_L0.188530.613
6_S34_K0.187670.610
50_A95_R0.186850.607
28_R49_L0.184910.601
22_V28_R0.184660.600
85_I98_P0.184140.598
33_L40_F0.183990.598
6_S17_L0.18350.596
12_F45_I0.183390.596
16_G46_T0.182150.592
6_S43_Q0.181980.591
118_P121_N0.181630.590
6_S46_T0.181470.590
11_S41_P0.180860.588
33_L53_D0.180720.587
11_S14_I0.180560.587
15_V21_A0.179880.585
16_G25_S0.179870.584
60_A117_V0.179810.584
56_K99_G0.179560.583
46_T94_I0.177680.577
26_R65_I0.17710.575
5_I75_Q0.176990.575
40_F101_L0.176830.575
58_G85_I0.176110.572
48_N65_I0.17590.572
80_E114_R0.175630.571
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
1rreA11000.057
3m6aA11000.064
2x36A11000.076
1z0wA11000.091
3k1jA11000.105
1xhkA0.97521000.117
4fwgA0.975299.80.341
2pnlA0.942196.50.817
2gefA0.9174960.825
3j3aQ0.917476.40.884

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