GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SnoaL_2 - SnoaL-like domain
Pfam: PF12680 (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: CL0051
Length: 102
Sequences: 10335
Seq/Len: 101.32
HH_delta: -0.054 (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
12_D15_A1.832793.098
17_A40_R1.749382.957
24_A39_I1.642742.777
71_W88_G1.576312.665
21_A100_V1.379082.331
22_P36_R1.365872.309
14_D40_R1.196462.023
94_F99_I1.166291.972
95_E100_V1.116831.888
35_G38_A1.108651.874
6_E10_A1.102571.864
58_H72_T1.062671.796
20_F24_A1.031961.745
17_A36_R1.027061.736
15_A18_A1.022821.729
40_R44_E1.007141.703
71_W90_S0.963521.629
74_T85_S0.962431.627
7_A15_A0.953141.611
68_V91_V0.895511.514
25_V34_R0.889731.504
13_L17_A0.868681.469
66_R93_R0.858241.451
3_R19_L0.852461.441
56_E74_T0.805951.362
72_T85_S0.78391.325
37_E40_R0.781881.322
37_E41_E0.781541.321
59_D70_E0.777651.315
14_D17_A0.775321.311
36_R40_R0.764071.292
11_G47_F0.760421.285
5_F9_N0.755881.278
3_R15_A0.746931.263
13_L44_E0.744651.259
95_E98_K0.742641.255
72_T87_R0.734741.242
20_F39_I0.705631.193
93_R100_V0.704361.191
56_E72_T0.694331.174
41_E45_E0.683471.155
41_E44_E0.663141.121
54_R74_T0.662261.120
3_R6_E0.660571.117
3_R18_A0.654811.107
6_E9_N0.64721.094
73_V88_G0.639861.082
62_A67_V0.636061.075
3_R7_A0.631481.068
65_D93_R0.62891.063
33_L38_A0.617461.044
61_F68_V0.612731.036
14_D18_A0.605811.024
74_T83_P0.605091.023
66_R91_V0.577840.977
39_I43_F0.577220.976
65_D95_E0.576520.975
60_I69_V0.573350.969
9_N55_F0.567490.959
7_A19_L0.566710.958
27_H32_T0.559960.947
67_V94_F0.555510.939
21_A95_E0.550750.931
7_A12_D0.54590.923
44_E48_E0.540040.913
73_V86_F0.539280.912
10_A15_A0.531510.899
7_A18_A0.516270.873
70_E89_C0.506690.857
38_A41_E0.504590.853
69_V92_F0.502640.850
26_F39_I0.497140.840
45_E48_E0.495020.837
24_A36_R0.491920.832
68_V89_C0.47470.802
60_I67_V0.474580.802
17_A37_E0.463720.784
5_F90_S0.460750.779
35_G39_I0.459960.778
4_F19_L0.450950.762
75_G86_F0.450270.761
63_D66_R0.441780.747
13_L40_R0.440870.745
92_F99_I0.438850.742
70_E87_R0.42950.726
4_F8_W0.423680.716
4_F20_F0.415870.703
23_D35_G0.414290.700
57_I69_V0.406230.687
23_D95_E0.401750.679
71_W75_G0.401750.679
13_L16_I0.399480.675
8_W16_I0.398290.673
61_F66_R0.397920.673
5_F57_I0.397250.672
22_P98_K0.3960.669
34_R38_A0.386220.653
5_F8_W0.383440.648
25_V32_T0.382280.646
36_R98_K0.381980.646
7_A10_A0.381050.644
13_L47_F0.372710.630
28_D90_S0.372490.630
26_F92_F0.358140.605
21_A98_K0.357250.604
54_R57_I0.356680.603
16_I19_L0.355180.600
42_F46_F0.354690.600
27_H31_G0.351820.595
14_D44_E0.350910.593
16_I20_F0.348950.590
23_D100_V0.348920.590
21_A24_A0.345260.584
59_D66_R0.345120.583
24_A35_G0.344550.582
45_E49_S0.339690.574
16_I43_F0.339570.574
20_F26_F0.3370.570
58_H70_E0.334840.566
33_L42_F0.333370.564
7_A16_I0.331890.561
57_I60_I0.329210.557
4_F16_I0.328530.555
55_F71_W0.322080.544
26_F30_G0.318990.539
4_F99_I0.317920.537
26_F90_S0.317910.537
4_F90_S0.317330.536
6_E15_A0.316270.535
65_D94_F0.316140.534
75_G84_I0.315940.534
21_A96_D0.314270.531
26_F43_F0.312170.528
9_N54_R0.309690.524
12_D18_A0.307670.520
18_A98_K0.306290.518
75_G90_S0.306060.517
8_W43_F0.301290.509
42_F45_E0.299990.507
28_D42_F0.298210.504
8_W28_D0.295590.500
28_D31_G0.294340.498
22_P37_E0.294040.497
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
4h3uA199.5-0.054
3dm8A199.40.002
3fgyA199.40.028
3ebtA0.990299.40.032
3k0zA0.980499.40.034
2gexA199.40.035
2f99A199.40.041
3ec9A199.40.042
3grdA199.40.044
2geyA0.990299.40.044

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