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Protein2

ID: 1515742939 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 93 (83)
Sequences: 998 (314.7)
Seq/Len: 12.024
Nf(neff/√len): 34.5

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: 12.024).

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
83_Y87_H2.1851.00
27_S79_V2.0271.00
45_V49_N1.8991.00
37_R46_V1.8361.00
55_Y63_C1.7061.00
83_Y89_H1.6241.00
46_V54_S1.6131.00
39_R43_Q1.5371.00
56_Y66_R1.5141.00
56_Y63_C1.4961.00
55_Y58_C1.3980.99
58_C63_C1.3810.99
59_T66_R1.3630.99
37_R49_N1.3610.99
22_V48_G1.3520.99
43_Q59_T1.2830.99
75_D83_Y1.2800.99
55_Y65_V1.2680.99
72_A78_A1.2490.99
48_G52_P1.2010.98
14_K31_I1.1900.98
25_T32_L1.1860.98
57_K91_V1.1620.97
75_D78_A1.1220.97
37_R54_S1.1130.96
35_G85_G1.1030.96
61_I68_H1.0950.96
55_Y59_T1.0940.96
52_P65_V1.0920.96
44_K47_K1.0880.96
13_S16_V1.0840.96
22_V28_D1.0770.95
24_Q62_G1.0710.95
36_Y91_V1.0640.95
13_S93_A1.0610.95
23_V48_G1.0510.94
63_C69_V1.0460.94
50_P60_T1.0430.94
85_G89_H1.0310.94
55_Y67_K1.0310.94
34_D40_K1.0220.93
72_A77_R1.0100.93
13_S31_I1.0040.93
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  
2aydA10.80651000.17Contact Map
1wj2A10.76341000.194Contact Map
2rprA10.774283.80.877Contact Map
3ax1A10.946213.60.928Contact Map
4nm6A10.67747.10.936Contact Map
3i84A20.75276.10.938Contact Map
4lmgA40.84955.90.939Contact Map
2pbzA30.74194.30.943Contact Map
4n1iA10.46243.90.944Contact Map
4criA20.58063.70.944Contact 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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