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ID: 1499258957 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 53 (53)
Sequences: 825 (745.8)
Seq/Len: 15.566
Nf(neff/√len): 102.4

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: 15.566).

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
39_T42_E2.5251.00
39_T53_A2.1371.00
8_V44_K1.7941.00
14_L31_N1.7691.00
12_V26_S1.6921.00
2_R14_L1.6641.00
11_I18_F1.6151.00
42_E53_A1.5891.00
2_R24_D1.4611.00
17_I44_K1.4040.99
12_V15_Q1.3240.99
5_E15_Q1.3070.99
8_V12_V1.2230.98
9_S30_T1.2090.98
2_R41_T1.1810.98
26_S30_T1.1760.98
20_E24_D1.1670.97
31_N46_G1.1290.97
47_N53_A1.1240.97
13_N21_K1.1140.96
1_V35_D1.1090.96
18_F22_V1.0820.96
21_K24_D1.0650.95
6_V43_V1.0620.95
19_T46_G1.0490.94
40_Q43_V1.0440.94
7_R11_I1.0400.94
40_Q48_K1.0290.94
24_D40_Q1.0250.93
24_D53_A1.0220.93
7_R31_N1.0180.93
1_V38_S1.0140.93
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  
2m8rA1197.80.442Contact Map
2xheB10.811397.80.451Contact Map
1jthB2197.80.452Contact Map
5buzC2097.80.452Contact Map
3c98B10.886897.70.46Contact Map
1gl2B1197.60.467Contact Map
2npsB1197.50.475Contact Map
4jehB10.867997.50.482Contact Map
1sfcB3197.40.489Contact Map
1n7sB1197.40.491Contact 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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