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4V1J

ID: 1513368391 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 142 (136)
Sequences: 718 (447.9)
Seq/Len: 5.279
Nf(neff/√len): 38.4

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: 5.279).

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
99_C135_C3.1141.00
15_A70_M2.6491.00
7_T10_A1.9791.00
3_M6_Y1.9491.00
99_C132_P1.7651.00
133_S136_R1.5860.99
16_I86_L1.5800.99
132_P135_C1.5550.99
101_Q131_L1.5510.99
77_N80_K1.5240.99
87_W100_G1.5050.99
29_Y35_E1.4930.99
8_A130_H1.4780.98
121_A124_K1.4650.98
20_E23_K1.4520.98
65_V87_W1.4210.98
14_E18_L1.3680.97
29_Y33_H1.3670.97
18_L53_G1.3560.97
126_I131_L1.3490.97
5_D129_K1.3420.97
19_A68_A1.3170.96
116_T121_A1.3090.96
18_L70_M1.3070.96
110_A122_N1.3060.96
118_A122_N1.3040.96
12_V126_I1.3040.96
115_V118_A1.3010.96
14_E55_Y1.2860.96
5_D9_R1.2830.95
79_I82_K1.2680.95
118_A121_A1.2490.95
117_A120_A1.2440.94
26_V47_T1.2380.94
21_G24_S1.2340.94
15_A56_V1.2330.94
13_S17_L1.2140.93
107_K121_A1.2040.93
17_L20_E1.2020.93
2_P9_R1.1910.93
64_G97_W1.1900.93
3_M10_A1.1860.92
109_K121_A1.1760.92
114_D118_A1.1680.92
22_Q45_V1.1670.92
29_Y39_N1.1670.92
61_V64_G1.1620.91
116_T119_A1.1570.91
40_N43_A1.1430.90
57_K71_A1.1410.90
66_V88_A1.1330.90
108_A121_A1.1180.89
36_W66_V1.1160.89
71_A74_N1.1100.89
17_L22_Q1.1040.88
14_E17_L1.1030.88
110_A118_A1.0960.88
55_Y93_G1.0950.88
115_V120_A1.0930.88
11_Q53_G1.0700.86
82_K127_D1.0700.86
64_G88_A1.0660.86
117_A121_A1.0630.86
54_K75_V1.0580.85
114_D117_A1.0490.85
60_E69_Q1.0470.84
7_T129_K1.0360.84
84_L125_K1.0320.83
35_E80_K1.0290.83
106_D121_A1.0190.82
110_A116_T1.0130.82
109_K123_G1.0130.82
29_Y37_P1.0120.82
28_E32_N1.0100.81
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  
3jyzA10.901499.90.239Contact Map
1qveA20.816999.90.28Contact Map
1x6zA10.746599.80.339Contact Map
3sojA20.732499.80.388Contact Map
2hi2A10.957799.70.428Contact Map
3sokA20.802899.60.483Contact Map
1oqwA20.774699.50.53Contact Map
4noaA10.746598.20.706Contact Map
2m3kA10.767694.40.814Contact Map
3g20A20.690181.70.856Contact 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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