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4nn2

ID: 1501760704 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 50% gaps before running GREMLIN.
Length: 124 (120)
Sequences: 716 (689.3)
Seq/Len: 5.967
Nf(neff/√len): 62.9

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: 5.967).

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 > 50% 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
71_M93_T3.0981.00
71_M84_G2.6451.00
32_H35_C2.5641.00
95_H98_C2.4601.00
119_C122_H2.4021.00
68_G82_T2.2621.00
19_G22_H2.2301.00
84_G93_T2.1451.00
73_C76_C2.1011.00
73_C95_H1.8461.00
33_Y44_Q1.8151.00
7_F31_A1.7131.00
90_C98_C1.7021.00
94_Y117_L1.6491.00
85_C98_C1.5750.99
76_C95_H1.5730.99
73_C98_C1.5650.99
85_C95_H1.5580.99
25_N28_K1.5320.99
75_L104_A1.5290.99
96_Y99_G1.5090.99
76_C85_C1.4980.99
34_K96_Y1.4460.99
39_S81_A1.4280.98
73_C85_C1.4230.98
90_C95_H1.4140.98
5_C35_C1.3950.98
85_C90_C1.3550.98
84_G91_V1.3230.97
30_A33_Y1.3210.97
41_G68_G1.3100.97
65_I68_G1.2930.97
5_C32_H1.2920.97
76_C98_C1.2860.97
73_C80_G1.2260.95
64_E69_K1.1830.94
39_S96_Y1.1740.93
94_Y102_D1.1650.93
3_P12_E1.1420.92
4_K9_H1.1160.91
80_G95_H1.1100.91
39_S82_T1.1050.90
82_T96_Y1.1010.90
38_F83_I1.0970.90
65_I69_K1.0590.88
67_R84_G1.0320.86
39_S68_G1.0070.84
73_C90_C1.0000.83
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  
4nn2A211000.05Contact Map
2lq6A10.508199.10.546Contact Map
4lk9A10.822694.80.785Contact Map
4gneA10.717793.80.794Contact Map
3v43A10.8226920.807Contact Map
2kwjA10.814590.20.815Contact Map
2ysmA10.766184.80.831Contact Map
2g6qA10.395282.40.835Contact Map
1wewA10.5484820.836Contact Map
4cosA10.37980.70.838Contact 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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