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PilE co-evolution

ID: 1513364842 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 149 (146)
Sequences: 215 (186.2)
Seq/Len: 1.473
Nf(neff/√len): 15.4

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: 1.473).

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
62_G66_R3.1581.00
54_E139_K2.5951.00
54_E120_A2.3010.99
31_I45_Y1.9140.97
4_D9_L1.8970.97
31_I36_I1.8800.97
35_G39_A1.6790.93
22_F26_E1.6420.92
25_I29_V1.6370.91
61_V124_G1.6090.90
31_I38_A1.6060.90
3_T6_K1.6030.90
32_I35_G1.5580.88
24_L41_A1.5530.88
54_E122_F1.5150.87
6_K16_Q1.5100.86
62_G65_N1.5080.86
1_M6_K1.4840.85
51_K58_R1.4650.84
36_I45_Y1.4580.84
27_L41_A1.4550.83
23_T26_E1.4520.83
8_K11_Q1.4490.83
24_L37_L1.4470.83
9_L12_H1.3960.80
10_L18_K1.3710.78
54_E96_Y1.3710.78
55_S137_F1.3700.78
26_E37_L1.3080.73
45_Y49_V1.2970.72
53_R66_R1.2790.71
24_L27_L1.2550.69
66_R69_Q1.2510.68
14_I17_H1.2370.67
120_A139_K1.2070.64
112_A121_E1.1920.63
21_G26_E1.1810.62
27_L30_V1.1800.62
140_G143_P1.1780.62
61_V64_M1.1770.62
4_D7_A1.1660.60
3_T9_L1.1500.59
2_K20_E1.1490.59
21_G24_L1.1460.58
5_L15_D1.1420.58
108_E112_A1.1380.58
36_I49_V1.1370.58
95_Y122_F1.1260.56
3_T7_A1.1260.56
57_A96_Y1.1260.56
27_L34_I1.1200.56
4_D12_H1.1190.56
7_A12_H1.1150.55
3_T11_Q1.1020.54
86_Q137_F1.1020.54
5_L18_K1.0990.54
62_G73_L1.0820.52
36_I39_A1.0710.51
72_Y131_G1.0690.51
39_A48_Q1.0670.50
23_T29_V1.0580.49
50_N72_Y1.0580.49
23_T37_L1.0520.49
21_G27_L1.0510.49
56_E89_V1.0490.49
8_K12_H1.0450.48
79_A86_Q1.0260.46
7_A18_K1.0220.46
100_T109_S1.0210.46
26_E41_A1.0210.46
13_L38_A1.0160.45
114_V121_E1.0130.45
64_M72_Y1.0070.44
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  
2hi2A10.832299.50.691Contact Map
3sokA20.845699.40.703Contact Map
1oqwA20.852399.30.713Contact Map
2m7gA10.409499.30.723Contact Map
3g20A20.69898.40.799Contact Map
2m3kA10.657797.10.848Contact Map
4noaA10.664496.30.861Contact Map
4d40A2094.50.878Contact Map
2kepA10.637679.90.907Contact Map
3gn9A30.630979.30.908Contact 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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