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2bg9

ID: 1499447851 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 91 (91)
Sequences: 1125 (752.8)
Seq/Len: 12.363
Nf(neff/√len): 78.9

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: 12.363).

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
1_P5_V2.4641.00
38_S41_L2.1111.00
22_V36_S1.7691.00
87_N91_R1.6341.00
77_S80_I1.6151.00
25_L35_L1.5771.00
66_K77_S1.5521.00
2_L6_V1.4501.00
82_T86_I1.4181.00
72_M76_I1.4030.99
78_S82_T1.3880.99
53_L56_S1.3850.99
38_S49_V1.3710.99
4_F11_P1.3550.99
81_V85_V1.3530.99
67_Y71_T1.3450.99
23_F26_P1.3340.99
5_V9_I1.3200.99
34_T38_S1.2830.99
83_V87_N1.2620.99
8_V11_P1.2540.99
32_K74_F1.2240.98
43_L49_V1.2230.98
75_V79_I1.2100.98
31_E41_L1.2100.98
40_L43_L1.1740.98
82_T90_H1.1680.97
8_V13_L1.1630.97
27_T65_G1.1520.97
72_M78_S1.1310.97
5_V14_L1.1280.97
34_T41_L1.1230.97
6_V10_I1.1150.96
31_E34_T1.1100.96
17_F24_Y1.1070.96
16_S21_L1.0990.96
84_V87_N1.0890.96
73_I91_R1.0830.96
66_K69_L1.0760.95
55_P58_S1.0580.95
25_L33_M1.0430.94
43_L75_V1.0400.94
82_T88_T1.0350.94
20_V24_Y1.0350.94
68_M75_V1.0300.94
77_S81_V1.0200.93
51_V54_I1.0190.93
12_C22_V1.0130.93
7_N23_F1.0120.93
78_S85_V1.0060.93
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  
1oedC1199.7-0.049Contact Map
4aq5C1199.7-0.043Contact Map
1oedB1199.7-0.038Contact Map
1oedA2199.7-0.036Contact Map
4aq5B1199.7-0.034Contact Map
4aq5E1199.7-0.032Contact Map
1oedE1199.7-0.029Contact Map
4aq5A2199.7-0.026Contact Map
4pirA50.95699.70.002Contact Map
2bg9C1199.70.02Contact 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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