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sh3_2

ID: 1513268967 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 71 (63)
Sequences: 8847 (4938.4)
Seq/Len: 140.429
Nf(neff/√len): 622.2

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: 140.429).

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
13_A20_S3.3541.00
43_C52_V2.9101.00
42_L49_Q2.8171.00
10_D22_R2.7711.00
7_A21_F2.7401.00
28_T44_S2.3881.00
31_E42_L2.3801.00
3_V32_R2.3511.00
52_V57_L2.2341.00
25_D45_L2.1111.00
44_S49_Q2.0841.00
4_L26_I2.0591.00
4_L28_T1.9011.00
5_A59_I1.8561.00
6_K58_K1.7841.00
41_W54_G1.6521.00
21_F27_M1.6411.00
22_R25_D1.5971.00
3_V59_I1.5821.00
6_K60_L1.5041.00
8_L58_K1.4841.00
27_M43_C1.4361.00
10_D23_K1.4181.00
26_I60_L1.3800.99
5_A57_L1.3670.99
5_A29_V1.3160.99
6_K26_I1.3140.99
50_G53_P1.2800.99
45_L48_R1.1430.97
53_P56_R1.0830.96
32_R59_I1.0670.95
30_L44_S1.0600.95
39_G54_G1.0520.95
12_V20_S1.0230.93
19_L43_C1.0060.93
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  
4n78F1099.30Contact Map
4mt7A1099.20.009Contact Map
2pz1A10.845199.20.019Contact Map
2dvjA10.957799.20.029Contact Map
4igzA10.957799.20.04Contact Map
2dybA20.957799.20.042Contact Map
4bneA2099.20.048Contact Map
3jv3A20.957799.20.049Contact Map
1ug1A10.985999.20.05Contact Map
3pvlA10.901499.20.052Contact 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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