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Prasanth Kumar

ID: 1499886867 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 101 (101)
Sequences: 587 (431.3)
Seq/Len: 5.812
Nf(neff/√len): 42.9

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: 5.812).

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
34_I63_M3.1991.00
20_V34_I2.7891.00
32_M68_M2.4871.00
18_V90_I2.3761.00
8_Y15_R2.3721.00
32_M97_M2.1351.00
51_Y66_T1.9421.00
55_H60_S1.8371.00
19_D31_R1.7141.00
2_Q99_W1.6921.00
8_Y17_F1.6090.99
2_Q22_S1.5440.99
39_A60_S1.4650.99
21_Q30_R1.4420.99
54_V83_L1.4400.98
28_P66_T1.3830.98
1_M4_K1.3820.98
8_Y16_L1.3630.98
86_R89_D1.3580.98
34_I65_T1.3400.97
4_K82_D1.3080.97
2_Q67_D1.3000.97
33_V76_I1.2980.97
47_S51_Y1.2760.96
18_V54_V1.2640.96
37_A43_S1.2620.96
64_M67_D1.2380.95
54_V63_M1.2260.95
14_Y101_I1.2250.95
20_V94_I1.2160.95
2_Q8_Y1.2150.94
32_M94_I1.2000.94
2_Q91_K1.1260.91
1_M19_D1.1140.90
56_I80_V1.1030.90
12_S45_K1.0980.90
2_Q14_Y1.0940.89
31_R73_V1.0890.89
88_N92_N1.0740.88
96_L100_G1.0740.88
7_T45_K1.0630.87
51_Y62_R1.0570.87
91_K98_F1.0500.87
46_V62_R1.0440.86
75_V79_E1.0380.86
36_L52_P1.0360.86
17_F71_V1.0260.85
5_V81_A1.0200.84
49_E96_L1.0180.84
7_T57_G1.0150.84
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  
3vubA111000.056Contact Map
2kmtA211000.061Contact Map
4mzmA40.960498.60.628Contact Map
1ub4A20.910998.60.632Contact Map
1m1fA20.930798.60.635Contact Map
4mdxA20.960498.50.644Contact Map
4h63H10.30693.90.925Contact Map
4eu9A20.33663.40.927Contact Map
3fx7A20.316830.929Contact Map
3swyA30.20792.80.93Contact 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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