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test-gremlin-vh3

ID: 1502208276 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 108 (102)
Sequences: 6842 (3866.1)
Seq/Len: 67.078
Nf(neff/√len): 382.8

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: 67.078).

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
12_V86_L3.2601.00
13_Q16_G2.7791.00
39_Q45_L2.3071.00
49_S70_I2.2511.00
62_D65_K2.1041.00
68_F83_M2.0111.00
12_V16_G2.0011.00
38_R92_A1.8911.00
24_A34_M1.8711.00
48_V68_F1.8311.00
19_R82_Q1.7521.00
19_R80_Y1.7201.00
38_R46_E1.7131.00
23_A78_T1.6751.00
37_V47_W1.6141.00
36_W81_L1.5951.00
12_V18_L1.5251.00
50_A59_Y1.4521.00
35_S47_W1.4501.00
94_Y97_A1.4271.00
40_A43_K1.4251.00
90_D94_Y1.4070.99
34_M79_L1.3770.99
10_G18_L1.3570.99
24_A29_F1.3340.99
33_A50_A1.3310.99
47_W61_A1.3210.99
60_Y66_G1.2900.99
35_S97_A1.2870.99
43_K46_E1.2850.99
33_A52_S1.2640.99
61_A64_V1.2610.99
35_S50_A1.2300.98
5_V8_G1.2110.98
73_D76_K1.2070.98
48_V64_V1.2020.98
54_S57_S1.1670.97
35_S99_G1.1440.97
60_Y64_V1.1420.97
67_R90_D1.1210.97
2_V5_V1.1080.96
51_I59_Y1.0980.96
51_I79_L1.0910.96
53_G56_G1.0780.95
22_C38_R1.0750.95
7_S10_G1.0720.95
59_Y65_K1.0390.94
60_Y63_S1.0340.94
3_Q6_E1.0340.94
6_E9_G1.0250.93
66_G85_S1.0020.92
15_G22_C1.0010.92
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  
4ut7H10.990799.70.208Contact Map
4pfeA2099.70.21Contact Map
1dqtA40.944499.70.241Contact Map
4qo1A10.990799.70.259Contact Map
2vyrE8199.70.263Contact Map
1yjdC10.96399.70.263Contact Map
3k3qA1199.70.265Contact Map
3qycA20.990799.70.269Contact Map
4qgyA2199.70.272Contact Map
1jtpA2199.60.276Contact 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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