GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
chey

ID: 1504721032 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 102 (98)
Sequences: 200024 (137397)
Seq/Len: 2041.061
Nf(neff/√len): 13879.2

Jackhmmer Results: (2016_04)
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: 2041.061).

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
11_A28_W3.0881.00
15_Q28_W2.8021.00
11_A30_D2.7801.00
4_V35_T2.3311.00
27_V46_F2.1731.00
36_R66_L2.1481.00
33_A57_D2.0261.00
54_H80_D2.0241.00
58_G66_L1.9471.00
32_L58_G1.8531.00
29_A38_H1.8451.00
40_E70_H1.8431.00
76_V94_V1.7751.00
51_L63_V1.7711.00
27_V38_H1.7371.00
64_V74_A1.6741.00
31_S57_D1.6701.00
27_V44_H1.6691.00
65_D92_K1.6261.00
30_D34_Q1.5381.00
53_L61_G1.5121.00
66_L70_H1.4691.00
68_L95_L1.4121.00
15_Q19_Q1.3770.99
38_H44_H1.3290.99
80_D85_M1.3260.99
39_L67_V1.3240.99
32_L63_V1.3030.99
31_S34_Q1.2950.99
61_G89_L1.2890.99
33_A58_G1.2870.99
38_H41_Q1.2520.99
58_G62_E1.2450.98
49_A72_L1.2170.98
38_H46_F1.2170.98
88_Q92_K1.2040.98
2_L29_A1.1890.98
83_V87_T1.1840.98
59_P62_E1.1760.98
87_T91_K1.1500.97
66_L69_Q1.1330.97
8_K30_D1.1060.96
3_L14_L1.0960.96
36_R63_V1.0940.96
76_V89_L1.0890.96
6_D52_D1.0730.95
82_Q85_M1.0590.95
61_G88_Q1.0540.95
64_V94_V1.0020.92
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  
3breA20.980499.80.059Contact Map
4g97A10.95199.80.061Contact Map
3n0rA10.95199.80.064Contact Map
1w25A20.970699.80.065Contact Map
3eq2A20.970699.80.082Contact Map
3dzdA20.970699.80.091Contact Map
4l4uA10.970699.80.107Contact Map
2vycA100.970699.80.113Contact Map
3lufA20.970699.70.123Contact Map
3rqiA10.960899.70.125Contact 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.

Page generated in 0.2951 seconds.