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ID: 1517351559 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 57 (56)
Sequences: 527 (444)
Seq/Len: 9.411
Nf(neff/√len): 59.3

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: 9.411).

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_R51_I2.5031.00
12_A16_S2.2781.00
9_A15_V1.9881.00
10_D14_L1.9361.00
25_Q34_G1.8281.00
25_Q35_R1.7841.00
4_R8_V1.7661.00
10_D15_V1.7491.00
16_S21_L1.6331.00
27_V33_D1.6281.00
43_T46_D1.6241.00
16_S22_L1.6081.00
14_L44_P1.5111.00
23_T26_Q1.4991.00
15_V19_T1.4721.00
47_I51_I1.4611.00
11_R52_A1.4391.00
6_Q15_V1.4080.99
28_K31_Q1.3870.99
3_T6_Q1.3670.99
27_V32_R1.3250.99
17_A24_G1.2890.99
8_V12_A1.2420.98
46_D50_A1.2370.98
39_Y42_M1.2350.98
50_A54_V1.1900.98
47_I50_A1.0350.93
7_L10_D1.0290.93
48_K52_A1.0050.92
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  
1hywA1199.10.061Contact Map
2y7cA117.30.817Contact Map
3mq9A816.20.823Contact Map
2xr1A215.30.829Contact Map
3af5A10.929850.83Contact Map
2p17A1030.848Contact Map
1tksA20.89472.80.85Contact Map
3rx6A10.78952.60.853Contact Map
1vpyA10.87722.60.853Contact Map
1vpqA10.85962.50.854Contact 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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