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1aba

ID: 1501248399 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 87 (77)
Sequences: 6645 (3471.6)
Seq/Len: 86.299
Nf(neff/√len): 395.6

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: 86.299).

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
79_F83_R3.4961.00
25_T31_F2.5681.00
4_V68_V2.0031.00
67_Q75_H1.9521.00
1_M71_P1.9191.00
20_A68_V1.8931.00
22_R26_V1.8681.00
62_G67_Q1.8671.00
20_A82_L1.8261.00
6_G33_F1.8211.00
3_K34_I1.8071.00
12_H35_N1.7871.00
19_N83_R1.7871.00
9_S33_F1.7761.00
19_N79_F1.5761.00
27_K86_F1.5711.00
35_N38_P1.5621.00
21_K33_F1.5001.00
20_A79_F1.4841.00
6_G21_K1.4731.00
62_G75_H1.4481.00
23_L27_K1.4141.00
68_V82_L1.3990.99
16_P79_F1.3780.99
23_L83_R1.3540.99
50_E54_K1.3510.99
2_F70_A1.3450.99
69_F75_H1.3070.99
3_K54_K1.2910.99
23_L79_F1.2780.99
2_F29_Q1.2760.99
42_V50_E1.2270.98
4_V24_L1.1770.98
50_E53_T1.1700.97
81_Q84_E1.1330.97
7_Y13_K1.1310.97
18_D22_R1.1170.96
78_G81_Q1.1110.96
51_L65_M1.1100.96
52_L63_L1.0780.95
3_K32_E1.0710.95
7_Y65_M1.0710.95
51_L55_L1.0650.95
21_K25_T1.0550.95
49_A53_T1.0500.94
23_L86_F1.0400.94
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  
1u6tA10.827699.50.064Contact Map
2jadA10.827699.50.077Contact Map
2ct6A10.827699.40.136Contact Map
2wciA20.873699.40.141Contact Map
1t1vA20.827699.30.165Contact Map
2wulA40.873699.30.191Contact Map
3ipzA10.873699.20.205Contact Map
1wikA10.873699.20.207Contact Map
3gx8A10.873699.20.211Contact Map
2yanA20.873699.20.212Contact 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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