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scEMC6

ID: 1504851534 Query Sequence

Download Alignment
We filter this alignment to remove positions that have > 75% gaps before running GREMLIN.
Length: 108 (105)
Sequences: 368 (261.4)
Seq/Len: 3.505
Nf(neff/√len): 25.5

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: 3.505).

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
31_S60_I2.0981.00
98_M101_T1.9921.00
96_F100_W1.9501.00
50_F93_I1.9241.00
52_W96_F1.7660.99
102_F106_L1.7540.99
97_V101_T1.6630.99
12_N17_V1.5940.98
101_T104_Y1.5800.98
44_I50_F1.5400.97
95_G101_T1.4800.96
43_Q98_M1.3460.93
102_F108_G1.3420.93
53_F69_C1.3380.93
95_G99_A1.3030.92
28_Q64_Y1.2790.91
98_M105_A1.2690.90
51_I58_N1.2670.90
69_C73_P1.2560.90
67_W71_L1.2520.89
100_W104_Y1.2390.89
28_Q95_G1.2370.89
19_D23_R1.2300.88
15_A22_K1.2230.88
22_K87_E1.2120.87
28_Q61_N1.2080.87
75_K97_V1.1960.86
102_F107_I1.1760.85
95_G106_L1.1680.84
104_Y107_I1.1490.83
68_I92_E1.1460.83
54_L75_K1.1450.83
95_G98_M1.1420.83
83_D97_V1.1410.82
72_Q76_F1.1390.82
43_Q91_R1.1190.81
96_F101_T1.1170.81
24_L107_I1.1000.79
32_A48_H1.0970.79
49_G76_F1.0950.79
7_V13_A1.0940.79
9_T14_T1.0900.78
99_A102_F1.0800.77
45_E104_Y1.0780.77
18_V87_E1.0730.77
20_N36_G1.0720.77
105_A108_G1.0550.75
19_D42_L1.0460.74
38_V96_F1.0430.74
27_V30_S1.0340.73
59_L89_F1.0330.73
60_I88_S1.0330.73
95_G100_W1.0270.72
33_L99_A1.0210.72
29_D98_M1.0160.71
98_M108_G1.0140.71
41_F46_S1.0140.71
22_K69_C1.0130.71
39_A43_Q1.0110.71
31_S90_F1.0100.70
54_L93_I1.0090.70
16_N32_A1.0080.70
21_K45_E1.0000.69
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  
4ev6A50.675914.30.914Contact Map
4djkA20.74079.80.92Contact Map
4i0uA100.65747.90.924Contact Map
2l2tA20.40746.10.928Contact Map
2ww8A10.36113.60.935Contact Map
4ycsA60.398130.938Contact Map
3l1lA10.77782.80.939Contact Map
4xnjA102.60.94Contact Map
4u4vA102.50.94Contact Map
2gfpA20.62042.50.94Contact 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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