GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
GTPase_Cys_C - Catalytic cysteine-containing C-terminus of GTPase MnmE
Pfam: PF12631 (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: 73
Sequences: 1599
Seq/Len: 21.9
HH_delta: 0.113 (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
16_Q20_Q0.647482.320
22_L26_E0.60372.163
67_N71_N0.600892.153
11_N14_Q0.589732.113
20_Q51_S0.589172.111
30_E34_N0.563592.019
24_H44_D0.544311.950
64_I68_I0.517041.852
24_H47_E0.501241.796
17_L51_S0.457491.639
16_Q19_E0.456371.635
27_D44_D0.452831.622
20_Q54_E0.430631.543
31_A44_D0.429611.539
51_S54_E0.398271.427
23_E26_E0.388071.390
15_R19_E0.381241.366
29_L33_E0.379641.360
53_G59_V0.375611.346
26_E30_E0.370341.327
12_A16_Q0.368241.319
23_E27_D0.368111.319
39_D43_E0.367841.318
28_A41_V0.360121.290
24_H27_D0.352391.262
15_R64_I0.345331.237
26_E29_L0.344771.235
25_L48_A0.342991.229
27_D30_E0.341811.225
53_G58_E0.339761.217
10_T14_Q0.331761.189
10_T15_R0.322331.155
20_Q23_E0.321131.150
22_L29_L0.312471.119
19_E22_L0.300351.076
9_L18_L0.278880.999
49_L64_I0.278510.998
49_L53_G0.275820.988
43_E47_E0.275520.987
30_E33_E0.269620.966
26_E34_N0.263830.945
60_V65_L0.263070.942
12_A15_R0.261080.935
49_L56_T0.258930.928
27_D47_E0.252680.905
46_R68_I0.249580.894
47_E50_E0.248070.889
48_A51_S0.244810.877
40_L43_E0.236670.848
12_A19_E0.231830.831
62_E66_D0.228080.817
37_P41_V0.228050.817
11_N71_N0.226790.812
22_L25_L0.226170.810
50_E59_V0.223660.801
13_R21_A0.215080.771
54_E60_V0.215020.770
66_D70_S0.214380.768
8_I59_V0.214350.768
31_A41_V0.212810.762
29_L35_G0.211140.756
28_A39_D0.209550.751
43_E46_R0.209440.750
50_E53_G0.209080.749
59_V63_D0.207610.744
33_E36_L0.206550.740
42_A68_I0.20440.732
17_L40_L0.203190.728
13_R18_L0.20170.723
20_Q33_E0.201110.720
17_L21_A0.199180.714
46_R65_L0.198460.711
28_A31_A0.198120.710
54_E67_N0.191780.687
11_N43_E0.191140.685
24_H48_A0.189530.679
14_Q68_I0.189280.678
15_R25_L0.189240.678
19_E23_E0.186270.667
40_L63_D0.184990.663
23_E51_S0.183910.659
20_Q30_E0.183540.658
69_F73_C0.181440.650
13_R57_G0.180830.648
57_G62_E0.180220.646
53_G63_D0.180180.645
31_A36_L0.179940.645
59_V65_L0.176690.633
17_L54_E0.176510.632
61_T66_D0.175710.629
18_L42_A0.173340.621
26_E36_L0.172550.618
34_N48_A0.172010.616
18_L22_L0.171580.615
36_L40_L0.171490.614
46_R57_G0.170620.611
56_T63_D0.170.609
24_H52_L0.169040.606
21_A52_L0.166990.598
49_L66_D0.165870.594
39_D44_D0.165840.594
17_L49_L0.164650.590
15_R55_I0.163550.586
24_H51_S0.162270.581
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
3gehA199.60.113
3geeA199.60.117
1xzpA199.50.151
2wwwA0.9726980.562
2lv7A0.945233.10.844
3nsoA0.821930.10.848
2i7aA0.972627.90.85
1k2hA0.808225.50.852
1qxpA0.931519.50.86
1qlsA0.86319.40.86

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