GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Mg_chelatase_2 - Magnesium chelatase subunit ChlI
Pfam: PF13335 (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: CL0023
Length: 96
Sequences: 1674
Seq/Len: 17.44
HH_delta: 0.681 (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
81_S88_H1.12063.706
3_E11_R0.924413.057
23_Y32_L0.907533.002
44_S47_A0.879352.908
4_S7_E0.869922.877
3_E8_I0.764632.529
8_I11_R0.724512.396
79_E88_H0.629872.083
81_S85_T0.624182.064
38_R66_H0.610922.021
15_A78_L0.601051.988
47_A89_I0.567521.877
9_R13_E0.54881.815
27_K36_E0.530631.755
54_A93_L0.52991.753
33_P36_E0.525521.738
41_C84_I0.500961.657
17_E20_R0.495441.639
7_E10_E0.468021.548
50_L90_A0.463461.533
34_G66_H0.458651.517
14_A80_G0.455031.505
37_L70_R0.413741.368
6_A10_E0.405891.342
91_E95_Y0.403811.336
43_L47_A0.40251.331
61_S64_G0.393031.300
21_E24_G0.392411.298
79_E87_E0.390551.292
48_K52_E0.387881.283
14_A18_R0.379391.255
85_T88_H0.36731.215
47_A50_L0.349861.157
16_R20_R0.348811.154
16_R28_C0.347491.149
27_K31_Q0.34641.146
75_I91_E0.337411.116
44_S85_T0.33391.104
50_L86_R0.326651.080
60_L93_L0.326061.078
43_L48_K0.325051.075
52_E56_E0.321251.062
73_R84_I0.318711.054
45_S49_K0.311971.032
13_E17_E0.31061.027
68_I93_L0.307791.018
62_A65_Y0.305131.009
32_L36_E0.297320.983
10_E13_E0.294620.974
47_A86_R0.288480.954
61_S94_S0.288240.953
28_C31_Q0.280350.927
42_P83_R0.279120.923
17_E21_E0.277920.919
46_E86_R0.277760.919
50_L53_Q0.277550.918
10_E14_A0.274670.908
55_A65_Y0.270870.896
60_L68_I0.270070.893
14_A17_E0.268980.890
49_K53_Q0.268380.888
55_A64_G0.266930.883
19_Q29_N0.264420.875
18_R82_E0.25890.856
35_E39_K0.258170.854
64_G96_R0.244140.807
37_L41_C0.243380.805
50_L89_I0.240720.796
5_S8_I0.238370.788
44_S83_R0.232930.770
42_P48_K0.231060.764
60_L64_G0.229340.759
12_V15_A0.221450.732
50_L54_A0.219990.728
86_R90_A0.219990.728
44_S86_R0.219070.725
35_E75_I0.210710.697
64_G67_R0.209890.694
32_L40_Y0.209080.692
34_G37_L0.206410.683
62_A93_L0.205320.679
18_R80_G0.204460.676
71_V95_Y0.204010.675
22_R77_D0.20340.673
53_Q56_E0.203290.672
31_Q65_Y0.202580.670
73_R76_A0.20250.670
5_S12_V0.202460.670
23_Y40_Y0.201740.667
32_L41_C0.201650.667
6_A14_A0.201370.666
27_K32_L0.201190.665
13_E55_A0.20010.662
10_E45_S0.199590.660
38_R94_S0.199380.659
66_H70_R0.199050.658
39_K87_E0.198070.655
11_R78_L0.195050.645
81_S87_E0.193340.639
37_L40_Y0.192780.638
48_K55_A0.192170.636
49_K52_E0.191830.634
14_A21_E0.188580.624
54_A58_L0.188290.623
53_Q57_K0.186660.617
7_E87_E0.182720.604
14_A83_R0.18240.603
54_A68_I0.181260.599
13_E20_R0.179310.593
51_L61_S0.178440.590
4_S44_S0.17820.589
32_L70_R0.176620.584
65_Y68_I0.17630.583
81_S84_I0.17620.583
40_Y84_I0.176140.583
20_R27_K0.175870.582
76_A88_H0.175810.581
50_L91_E0.17340.573
29_N32_L0.172150.569
18_R73_R0.171890.569
35_E42_P0.171870.568
20_R28_C0.171260.566
45_S48_K0.169890.562
28_C70_R0.169820.562
16_R23_Y0.169560.561
58_L95_Y0.169520.561
23_Y66_H0.169330.560
48_K84_I0.168790.558
4_S86_R0.1680.556
19_Q73_R0.165950.549
11_R62_A0.165270.547
11_R15_A0.164520.544
19_Q65_Y0.164270.543
16_R30_A0.16390.542
66_H71_V0.162480.537
41_C47_A0.161820.535
23_Y95_Y0.161730.535
73_R91_E0.161330.534
6_A9_R0.161160.533
52_E65_Y0.159840.529
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
3f9vA0.916798.30.681
2r44A0.979297.60.739
1g8pA197.40.75
3f8tA0.916796.40.79
4fdgB0.791796.10.798
3k1jA0.958394.20.822
3nbxX0.968892.40.833
2c9oA0.854277.10.866
1f6vA0.8229570.882
3mn2A0.833348.40.888
If you are interested in a protein containing this domain,
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