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beps_core_with 4 iterations

ID: 1507630006 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 123 (123)
Sequences: 168 (115)
Seq/Len: 1.366
Nf(neff/√len): 10.4

HHblits Results: (2016_02)
Sequences per length for each position, BEFORE the coverage/gap filter was applied

Legend: Dots above the red line, indicates positions where there is > 5 sequences per length (if visible, green bar = 20 seq/len). Point of this graphic is to give you an idea if resubmitting a sub-portion of your sequence might help increase the overall Seq/Len (which after applying the coverage filter is at: 1.366).

Sequences per length for each position, AFTER the coverage/gap filter was applied
Legend: If visible, the positions blocked in grey are regions that have > 75% gaps and were automatically trimmed and excluded in the GREMLIN analysis.

Trim query Generate MSA using: Filter MSA GREMLIN
Start: End: E-value: Iterations: Coverage: Remove gaps: Prior:

GREMLIN Results:
Residue pairs sorted by coevolution strength:

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] covarying residues with sequence seperation > 3. The i and j are positions as given in the input sequence.

ij Scaled score Prob
84_H92_R1.9780.97
81_N91_G1.9390.97
70_N117_E1.9310.97
58_K72_E1.8740.96
84_H87_R1.8340.95
65_T77_F1.7810.94
81_N94_Q1.7690.94
81_N92_R1.7310.93
88_E92_R1.7240.93
8_A12_R1.6260.90
87_R92_R1.6200.90
64_L105_A1.5430.86
28_E31_R1.5300.86
73_A107_H1.5270.86
6_E107_H1.5200.85
91_G95_R1.5040.84
81_N119_M1.4630.82
100_N103_K1.4440.81
51_L76_L1.4020.78
20_D44_I1.3830.77
44_I49_Q1.3570.75
29_M123_S1.3290.73
84_H88_E1.3280.73
38_F84_H1.3160.72
70_N110_N1.3090.71
2_K62_Q1.2990.70
115_T118_R1.2790.69
50_R53_Q1.2710.68
63_G106_G1.2710.68
38_F91_G1.2390.65
5_F115_T1.2360.65
8_A89_G1.2260.64
61_L105_A1.2160.63
97_F105_A1.2000.61
28_E103_K1.1820.60
3_N60_N1.1720.59
31_R123_S1.1580.57
5_F18_F1.1450.56
7_W12_R1.1310.55
12_R89_G1.1270.54
66_R107_H1.1130.53
19_A33_G1.1120.53
117_E123_S1.0930.51
38_F85_P1.0830.50
31_R34_W1.0770.49
91_G119_M1.0640.48
81_N123_S1.0560.47
74_I117_E1.0540.47
1_F69_F1.0520.47
93_T97_F1.0510.47
51_L83_L1.0500.47
14_I79_S1.0460.46
94_Q118_R1.0430.46
41_G122_A1.0350.45
46_E93_T1.0350.45
100_N110_N1.0350.45
50_R80_L1.0210.44
9_G86_F1.0200.44
54_T57_E1.0170.43
15_P23_T1.0140.43
92_R95_R1.0120.43
Legend: Only predictions with Scaled Score > 1 are listed. For all 3L/2 predictions, click on one of the links below.
Prob = P(contact | scaled_score, seq/len).
Scaled Score = (raw_score/average(raw_scores)).
NEW Features
HHsearch Results: (06Aug15)
GREMLIN results overlayed on top 10 PDB hits:
Legend: Blue filled circles are GREMLIN results (Scaled Score > 1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 HHsearch results which uses the overall probability and per-position alignment confidence. Inter oligomeric contacts in the pdb are in shades of red.
PDB M Cov P(%) HHΔ  
4n67A1199.90.506Contact Map
4npsA10.918799.90.507Contact Map
2jk8A2199.90.509Contact Map
4py3A10099.90.511Contact Map
4m16A1199.90.516Contact Map
3zc7A10.87899.90.559Contact Map
3shgA10.87899.90.58Contact Map
3se5A40.788699.60.669Contact Map
2f6sA20.788699.60.675Contact Map
3zlmA10.788699.60.685Contact Map
M = number of chains, if homo-oligomer
Cov = coverage of hit
P(%) = probability

Sequence Conservation (Image Generated using WebLogo v3)
Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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