GREMLIN.BAKERLAB.org
Powered by OPENSEQ.org
1403tk1

ID: 1500560722 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 95 (89)
Sequences: 650 (459.9)
Seq/Len: 7.303
Nf(neff/√len): 48.7

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: 7.303).

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
3_L82_V4.0061.00
27_V43_A2.0881.00
54_W82_V2.0211.00
58_V62_S1.9301.00
25_L78_V1.8681.00
42_V56_L1.8051.00
27_V57_L1.6991.00
15_R21_H1.6871.00
42_V75_D1.5921.00
48_G53_E1.5491.00
47_I81_I1.4810.99
43_A78_V1.4590.99
3_L10_I1.4520.99
22_D44_I1.4520.99
58_V77_C1.4230.99
2_K29_M1.3700.99
49_A81_I1.3650.99
63_A75_D1.3110.98
6_V27_V1.3060.98
5_V54_W1.2920.98
18_G73_P1.2630.97
47_I78_V1.2140.96
28_E40_C1.1880.96
41_A76_L1.1830.96
29_M41_A1.1670.95
30_I54_W1.1490.95
50_G53_E1.1430.94
18_G21_H1.1270.94
61_S64_R1.1240.94
11_V44_I1.1220.94
59_S76_L1.1130.93
4_A41_A1.1050.93
7_T40_C1.0910.93
28_E38_G1.0660.91
2_K59_S1.0660.91
12_C80_G1.0570.91
65_Q71_T1.0490.90
53_E58_V1.0440.90
8_G50_G1.0440.90
5_V27_V1.0340.90
23_K49_A1.0250.89
30_I37_D1.0200.89
9_Q51_T1.0140.88
23_K50_G1.0140.88
11_V14_V1.0110.88
54_W85_V1.0050.88
53_E81_I1.0030.88
65_Q70_E1.0010.87
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  
2qw7A1011000.019Contact Map
4n8fA511000.021Contact Map
4jw0B511000.022Contact Map
2hd3A1211000.024Contact Map
4i7aA50.91581000.081Contact Map
2rcfA50.86321000.135Contact Map
4umwA10.82119.50.919Contact Map
3j09A20.83167.70.922Contact Map
4w23L10.86327.40.923Contact Map
3r4rA20.452670.923Contact 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.

Page generated in 0.0112 seconds.