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parp1- try22

ID: 1518002194 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 106 (79)
Sequences: 5108 (3179.4)
Seq/Len: 64.658
Nf(neff/√len): 357.7

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: 64.658).

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
26_I31_G4.0101.00
69_S72_F3.1601.00
11_T26_I3.1091.00
7_M41_S2.6041.00
57_M61_K2.5631.00
20_D23_K2.2661.00
9_I42_L2.1631.00
42_L68_V2.1451.00
58_E62_E1.9791.00
24_A28_K1.9541.00
2_K5_S1.9331.00
10_L40_A1.8381.00
23_K27_E1.8211.00
25_M29_L1.8141.00
8_K34_T1.8011.00
45_S67_V1.7671.00
17_R74_Q1.7451.00
8_K32_K1.7391.00
68_V76_V1.7041.00
58_E61_K1.6801.00
11_T22_V1.6411.00
25_M28_K1.5361.00
15_L22_V1.4541.00
49_E53_M1.4531.00
68_V72_F1.4461.00
59_E63_A1.4321.00
25_M77_S1.4151.00
71_D75_D1.3350.99
23_K35_G1.3140.99
55_K59_E1.2910.99
72_F75_D1.2530.99
16_S47_K1.1550.97
9_I26_I1.1520.97
3_P29_L1.1400.97
11_T73_L1.1200.96
59_E62_E1.1160.96
34_T38_N1.1160.96
23_K33_L1.1070.96
22_V73_L1.0990.96
11_T44_I1.0880.96
26_I73_L1.0750.95
34_T40_A1.0370.94
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  
2cokA10.981199.70.235Contact Map
2k6gA10.735899.60.331Contact Map
1dgsA2099.60.332Contact Map
2owoA1099.60.335Contact Map
1l7bA10.801999.60.34Contact Map
2ebuA10.858599.50.347Contact Map
4xpzA10.811399.30.42Contact Map
3ef1A10.811399.30.421Contact Map
4q66A40.726499.30.422Contact Map
4yg8A10.924599.30.424Contact 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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