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V2EDE3

ID: 1514007978 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 84 (84)
Sequences: 204 (75.9)
Seq/Len: 2.429
Nf(neff/√len): 8.3

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: 2.429).

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
26_V29_A2.8701.00
3_A7_L1.8730.99
43_A78_V1.8140.98
10_Y16_G1.7610.98
71_A76_Q1.6130.96
19_L41_F1.5940.96
4_V8_Q1.5940.96
70_Q73_V1.5840.96
4_V73_V1.4730.93
25_S29_A1.4600.92
56_I59_C1.3890.90
60_C63_C1.3700.89
52_L60_C1.3650.89
42_H45_L1.3500.88
40_H46_E1.3360.87
63_C66_H1.3150.86
9_T48_T1.3120.86
11_S17_Y1.2600.83
22_D65_R1.2470.82
75_A83_K1.2320.81
48_T51_E1.2250.80
29_A48_T1.1400.73
13_D48_T1.1380.73
5_K81_V1.1380.73
14_T22_D1.1360.73
25_S78_V1.1330.72
9_T13_D1.1300.72
13_D17_Y1.1000.69
38_R44_R1.0860.68
54_Q64_P1.0650.65
2_L6_Y1.0640.65
73_V84_P1.0580.65
75_A82_Q1.0570.65
29_A37_R1.0510.64
69_D74_E1.0490.64
58_C61_P1.0460.63
78_V83_K1.0460.63
7_L69_D1.0450.63
47_G54_Q1.0380.62
10_Y14_T1.0350.62
62_H65_R1.0280.61
68_M81_V1.0250.61
59_C70_Q1.0230.61
8_Q68_M1.0220.61
31_N37_R1.0210.61
15_L27_I1.0130.60
60_C66_H1.0050.59
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  
2wnfA10.333312.20.942Contact Map
3czuB10.55956.40.949Contact Map
2p9xA40.39295.80.95Contact Map
3heiB80.55955.80.95Contact Map
4g0dW40.16675.70.95Contact Map
2xocA20.17865.60.95Contact Map
3ucaA20.34524.60.952Contact Map
1m45B10.27384.40.952Contact Map
4rbnA403.80.954Contact Map
1i1qB10.35713.80.954Contact 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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